Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011814.1 Kokia drynarioides strain JFW-HI SEQ_126809, whole genome shotgun sequence
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: 89926
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:38 original size:12 final size:12
Alignment explanation
Indices: 23--48 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
13 TTACAATATT
23 TATTATTATTAA
1 TATTATTATTAA
35 TATTATTATTAA
1 TATTATTATTAA
47 TA
1 TA
49 ACCATTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TATTATTATTAA
Found at i:802 original size:17 final size:17
Alignment explanation
Indices: 758--856 Score: 108
Period size: 17 Copynumber: 5.7 Consensus size: 17
748 TTAATTTTAT
* *
758 AATAATTTTAAATTTGAA
1 AATAAATTTAAACTT-AA
*
776 AATGAATTTAAACTTAA
1 AATAAATTTAAACTTAA
* *
793 ATTAAATTTAAAATTAA
1 AATAAATTTAAACTTAA
*
810 AATAAATTTAAATTCTAA
1 AATAAATTTAAACT-TAA
* *
828 AACAAATTTAATCTTAA
1 AATAAATTTAAACTTAA
845 AATAAATTTAAA
1 AATAAATTTAAA
857 ATGAGTTTGA
Statistics
Matches: 67, Mismatches: 13, Indels: 3
0.81 0.16 0.04
Matches are distributed among these distances:
17 41 0.61
18 26 0.39
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (17 bp):
AATAAATTTAAACTTAA
Found at i:803 original size:35 final size:35
Alignment explanation
Indices: 764--856 Score: 109
Period size: 35 Copynumber: 2.7 Consensus size: 35
754 TTATAATAAT
* **
764 TTTAAATTTGAAAATGAATTTAAACT-TAAATTAAA
1 TTTAAATTT-AAAATAAATTTAAACTCTAAAACAAA
* *
799 TTTAAAATTAAAATAAATTTAAATTCTAAAACAAA
1 TTTAAATTTAAAATAAATTTAAACTCTAAAACAAA
834 TTT-AATCTTAAAATAAATTTAAA
1 TTTAAAT-TTAAAATAAATTTAAA
857 ATGAGTTTGA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
34 16 0.32
35 34 0.68
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (35 bp):
TTTAAATTTAAAATAAATTTAAACTCTAAAACAAA
Found at i:814 original size:52 final size:52
Alignment explanation
Indices: 758--858 Score: 141
Period size: 52 Copynumber: 1.9 Consensus size: 52
748 TTAATTTTAT
* ** *
758 AATAATTTTAAATT-TGAAAATGAATTTAAACTTAAATTAAATTTAAAATTAA
1 AATAAATTTAAATTCT-AAAACAAATTTAAACTTAAAATAAATTTAAAATTAA
*
810 AATAAATTTAAATTCTAAAACAAATTTAATCTTAAAATAAATTTAAAAT
1 AATAAATTTAAATTCTAAAACAAATTTAAACTTAAAATAAATTTAAAAT
859 GAGTTTGAGC
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
52 42 0.98
53 1 0.02
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (52 bp):
AATAAATTTAAATTCTAAAACAAATTTAAACTTAAAATAAATTTAAAATTAA
Found at i:1963 original size:20 final size:20
Alignment explanation
Indices: 1940--1983 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1930 AGCATACTTG
1940 TATCGGTAAAACTGAAGTTA
1 TATCGGTAAAACTGAAGTTA
* * *
1960 TATCGGTAGAAGTGAAGTTC
1 TATCGGTAAAACTGAAGTTA
1980 TATC
1 TATC
1984 AATAGAAGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (20 bp):
TATCGGTAAAACTGAAGTTA
Found at i:1989 original size:20 final size:20
Alignment explanation
Indices: 1952--1992 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1942 TCGGTAAAAC
**
1952 TGAAGTTATATCGGTAGAAG
1 TGAAGTTATATCAATAGAAG
*
1972 TGAAGTTCTATCAATAGAAG
1 TGAAGTTATATCAATAGAAG
1992 T
1 T
1993 CCTAGGGTAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.07, G:0.24, T:0.32
Consensus pattern (20 bp):
TGAAGTTATATCAATAGAAG
Found at i:5861 original size:19 final size:19
Alignment explanation
Indices: 5819--5871 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 19
5809 ATTATATATT
5819 AAAATTCAAAATAAAATTACA
1 AAAATT-AAAA-AAAATTACA
* *
5840 AAAATTAAAAATAATTATA
1 AAAATTAAAAAAAATTACA
5859 AAAATATAAAAAA
1 AAAAT-TAAAAAA
5872 TTAAATTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 12 0.43
20 10 0.36
21 6 0.21
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.25
Consensus pattern (19 bp):
AAAATTAAAAAAAATTACA
Found at i:8895 original size:24 final size:26
Alignment explanation
Indices: 8868--8915 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
8858 AGAGAAATGT
8868 AAATG-TGATATATGA-A-ATTATGAG
1 AAATGATGA-ATATGAGAGATTATGAG
8892 AAATGATGAATATGAGAGATTATG
1 AAATGATGAATATGAGAGATTATG
8916 CCCATGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (26 bp):
AAATGATGAATATGAGAGATTATGAG
Found at i:9017 original size:23 final size:23
Alignment explanation
Indices: 8978--9123 Score: 101
Period size: 23 Copynumber: 6.5 Consensus size: 23
8968 ACGCTAGTGC
*
8978 GCTTACTGTTCAT-CACTATGTGT
1 GCTTACTGTT-TTGCACTATGTGT
*
9001 GCTTACTGTTTTGCACT-TCATGT
1 GCTTACTGTTTTGCACTAT-GTGT
*
9024 GCTTACTGTTTCGCACCTCA--TGT
1 GCTTACTGTTTTGCA-CT-ATGTGT
* *
9047 GCCTACTGATTTGCACTATGTGT
1 GCTTACTGTTTTGCACTATGTGT
*
9070 G-TCTACTG-ATTGCAC--TGTGT
1 GCT-TACTGTTTTGCACTATGTGT
* **
9090 GCCTACTGGATTGCACTATGTGT
1 GCTTACTGTTTTGCACTATGTGT
*
9113 GCTTATTGTTT
1 GCTTACTGTTT
9124 CCCCAGCACT
Statistics
Matches: 98, Mismatches: 13, Indels: 24
0.73 0.10 0.18
Matches are distributed among these distances:
20 11 0.11
21 8 0.08
22 10 0.10
23 67 0.68
24 2 0.02
ACGTcount: A:0.15, C:0.22, G:0.21, T:0.42
Consensus pattern (23 bp):
GCTTACTGTTTTGCACTATGTGT
Found at i:9103 original size:21 final size:20
Alignment explanation
Indices: 9044--9111 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 20
9034 TCGCACCTCA
9044 TGTGCCTACTGATTTGCACTATG
1 TGTGCCTACTGA-TTGCAC--TG
*
9067 TGTGTCTACTGATTGCACTG
1 TGTGCCTACTGATTGCACTG
*
9087 TGTGCCTACTGGATTGCACTA
1 TGTGCCTACT-GATTGCACTG
9108 TGTG
1 TGTG
9112 TGCTTATTGT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
20 11 0.27
21 13 0.32
22 6 0.15
23 11 0.27
ACGTcount: A:0.16, C:0.21, G:0.25, T:0.38
Consensus pattern (20 bp):
TGTGCCTACTGATTGCACTG
Found at i:18513 original size:15 final size:14
Alignment explanation
Indices: 18493--18526 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
18483 AATAAAATTA
*
18493 TTTATATTTATTTAT
1 TTTATAATT-TTTAT
18508 TTTATAATTTTTAT
1 TTTATAATTTTTAT
18522 TTTAT
1 TTTAT
18527 TTTGTATACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTATAATTTTTAT
Found at i:18725 original size:37 final size:37
Alignment explanation
Indices: 18684--18760 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
18674 TCATTTTAGA
*
18684 TTTAAC-TT-TTAAATGATTTTTATTAATTTTTAAAAAT
1 TTTAACTTTATTAAAT-ATTTTTA-TAAATTTTAAAAAT
* *
18721 TTTAACTTTATTTAATATTTTTATAAATTTTAATAAT
1 TTTAACTTTATTAAATATTTTTATAAATTTTAAAAAT
18758 TTT
1 TTT
18761 TTACAAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
37 21 0.60
38 9 0.26
39 5 0.14
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (37 bp):
TTTAACTTTATTAAATATTTTTATAAATTTTAAAAAT
Found at i:31437 original size:22 final size:21
Alignment explanation
Indices: 31395--31451 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
31385 CATTTAAAAA
* * *
31395 TAATTAAAATTTAAGTTATAT
1 TAATTAAAAATTATGTAATAT
31416 TAATTAAAAATTATGCTAATAT
1 TAATTAAAAATTATG-TAATAT
31438 TAAATT-AAAATTAT
1 T-AATTAAAAATTAT
31452 TATTGAATAG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 13 0.42
22 14 0.45
23 4 0.13
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.44
Consensus pattern (21 bp):
TAATTAAAAATTATGTAATAT
Found at i:31717 original size:12 final size:12
Alignment explanation
Indices: 31700--31745 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
31690 TTGTAAAAAA
31700 TATTTTAATTAT
1 TATTTTAATTAT
* *
31712 TATTTTATTTTT
1 TATTTTAATTAT
*
31724 TATTATAA-T-T
1 TATTTTAATTAT
31734 TATTTTAATTAT
1 TATTTTAATTAT
31746 ATTCAATAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
10 8 0.30
11 2 0.07
12 17 0.63
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TATTTTAATTAT
Found at i:31722 original size:17 final size:18
Alignment explanation
Indices: 31700--31745 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
31690 TTGTAAAAAA
31700 TATTTTAATTATTAT-TT
1 TATTTTAATTATTATATT
31717 TATTTT--TTATTATAATT
1 TATTTTAATTATTAT-ATT
31734 TATTTTAATTAT
1 TATTTTAATTAT
31746 ATTCAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 7 0.28
17 14 0.56
19 4 0.16
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TATTTTAATTATTATATT
Found at i:31728 original size:15 final size:16
Alignment explanation
Indices: 31708--31748 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
31698 AATATTTTAA
31708 TTATTAT-TTTATTTT
1 TTATTATATTTATTTT
31723 TTATTATAATTTA-TTT
1 TTATTAT-ATTTATTTT
*
31739 TAATTATATT
1 TTATTATATT
31749 CAATAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 10 0.43
16 9 0.39
17 4 0.17
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTATTATATTTATTTT
Found at i:31728 original size:18 final size:17
Alignment explanation
Indices: 31702--31746 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
31692 GTAAAAAATA
*
31702 TTTTAATTATTATTTTAT
1 TTTTAATTA-TAATTTAT
*
31720 TTTTTATTATAATTTA-
1 TTTTAATTATAATTTAT
31736 TTTTAATTATA
1 TTTTAATTATA
31747 TTCAATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 10 0.42
17 6 0.25
18 8 0.33
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTTAATTATAATTTAT
Found at i:35881 original size:50 final size:50
Alignment explanation
Indices: 35801--35899 Score: 189
Period size: 50 Copynumber: 2.0 Consensus size: 50
35791 CTTCACTTGA
35801 TCTTGATCATCAAGTAACTAATTTTCGCATAGAATTGACTCTGCATCTAT
1 TCTTGATCATCAAGTAACTAATTTTCGCATAGAATTGACTCTGCATCTAT
*
35851 TCTTGATCATCAAGTAACTAATTTTTGCATAGAATTGACTCTGCATCTA
1 TCTTGATCATCAAGTAACTAATTTTCGCATAGAATTGACTCTGCATCTA
35900 ATGATTCACG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.38
Consensus pattern (50 bp):
TCTTGATCATCAAGTAACTAATTTTCGCATAGAATTGACTCTGCATCTAT
Found at i:47244 original size:36 final size:36
Alignment explanation
Indices: 47192--47271 Score: 133
Period size: 36 Copynumber: 2.2 Consensus size: 36
47182 CGACTTAAAC
*
47192 TCAAATCACACTTGAGATAATCAACATTTTTAATCA
1 TCAAATCACACCTGAGATAATCAACATTTTTAATCA
*
47228 TCAAATCACACCTGAGATAGTCAACATTTTTAATCA
1 TCAAATCACACCTGAGATAATCAACATTTTTAATCA
*
47264 TCAGATCA
1 TCAAATCA
47272 TCACATAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.40, C:0.21, G:0.07, T:0.31
Consensus pattern (36 bp):
TCAAATCACACCTGAGATAATCAACATTTTTAATCA
Found at i:48425 original size:17 final size:18
Alignment explanation
Indices: 48393--48432 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
48383 TTTGACAATG
*
48393 TTTTCATCTCAAAAAAAA
1 TTTTTATCTCAAAAAAAA
*
48411 TTTTTATCT-AAAAAATA
1 TTTTTATCTCAAAAAAAA
48428 TTTTT
1 TTTTT
48433 GAAAAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.47
Consensus pattern (18 bp):
TTTTTATCTCAAAAAAAA
Found at i:60017 original size:92 final size:92
Alignment explanation
Indices: 59860--60041 Score: 346
Period size: 92 Copynumber: 2.0 Consensus size: 92
59850 TTGAAAGTGG
*
59860 ACCACTTTCTCCGCCGCTGGACTTGCTACATAGAGGCAATAAGCATGTGCTCATTACATATTAGC
1 ACCACTTCCTCCGCCGCTGGACTTGCTACATAGAGGCAATAAGCATGTGCTCATTACATATTAGC
59925 CACGTTGTAGAATTTGAGATAAGATTA
66 CACGTTGTAGAATTTGAGATAAGATTA
*
59952 ACCACTTCCTCCGCCGCTGGACTTGCTACATAGAGGCAATAAGCATGTGCTCATTGCATATTAGC
1 ACCACTTCCTCCGCCGCTGGACTTGCTACATAGAGGCAATAAGCATGTGCTCATTACATATTAGC
60017 CACGTTGTAGAATTTGAGATAAGAT
66 CACGTTGTAGAATTTGAGATAAGAT
60042 ACTTTAATCG
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
92 88 1.00
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.29
Consensus pattern (92 bp):
ACCACTTCCTCCGCCGCTGGACTTGCTACATAGAGGCAATAAGCATGTGCTCATTACATATTAGC
CACGTTGTAGAATTTGAGATAAGATTA
Found at i:63645 original size:25 final size:24
Alignment explanation
Indices: 63610--63657 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
63600 TATGTTTTTA
63610 TTTTTCAAAATAAATTTTTAATTT
1 TTTTTCAAAATAAATTTTTAATTT
*
63634 TTTTTCACAAATAAGTTTTTAATT
1 TTTTTCA-AAATAAATTTTTAATT
63658 ATTAAAAAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.56
Consensus pattern (24 bp):
TTTTTCAAAATAAATTTTTAATTT
Found at i:64138 original size:26 final size:27
Alignment explanation
Indices: 64109--64191 Score: 73
Period size: 27 Copynumber: 3.0 Consensus size: 27
64099 TTATTTTATT
*
64109 ATATACAACAAATTTAAAAATA-TATA
1 ATATACAACAAATTTAAAAATATTAAA
*
64135 ATATATCAA-ATATACTTAAAAATATTAAA
1 ATATA-CAACA-A-ATTTAAAAATATTAAA
* *
64164 AAATA-AACAAATTTAAAATAAATTAAA
1 ATATACAACAAATTTAAAA-ATATTAAA
64191 A
1 A
64192 ATTCTTTATA
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
26 13 0.28
27 15 0.33
28 11 0.24
29 7 0.15
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (27 bp):
ATATACAACAAATTTAAAAATATTAAA
Found at i:64139 original size:28 final size:27
Alignment explanation
Indices: 64108--64181 Score: 73
Period size: 28 Copynumber: 2.7 Consensus size: 27
64098 ATTATTTTAT
64108 TATATACAACAAATTTAAAAATATATAA
1 TATATACAACAAATTTAAAAATAT-TAA
*
64136 TATAT-CAA-ATATACTTAAAAATATTAA
1 TATATACAACA-A-ATTTAAAAATATTAA
* *
64163 AAAATA-AACAAATTTAAAA
1 TATATACAACAAATTTAAAA
64182 TAAATTAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
26 8 0.21
27 13 0.34
28 17 0.45
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (27 bp):
TATATACAACAAATTTAAAAATATTAA
Found at i:64347 original size:12 final size:12
Alignment explanation
Indices: 64326--64413 Score: 78
Period size: 12 Copynumber: 7.7 Consensus size: 12
64316 ACATCCAAAT
64326 AACAAAAATAGC
1 AACAAAAATAGC
*
64338 AACCAAAATAGC
1 AACAAAAATAGC
*
64350 AGCAAAACA-A-C
1 AACAAAA-ATAGC
64361 AAC-AAAA-A-C
1 AACAAAAATAGC
64370 AACAAAAATAGC
1 AACAAAAATAGC
* *
64382 AACAAAAACAAC
1 AACAAAAATAGC
**
64394 AACAAAAATAAT
1 AACAAAAATAGC
64406 AACAAAAA
1 AACAAAAA
64414 CAACACCAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
9 6 0.09
10 7 0.11
11 4 0.06
12 46 0.72
13 1 0.02
ACGTcount: A:0.70, C:0.19, G:0.05, T:0.06
Consensus pattern (12 bp):
AACAAAAATAGC
Found at i:64362 original size:32 final size:33
Alignment explanation
Indices: 64337--64401 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
64327 ACAAAAATAG
* *
64337 CAACCAAAATAGCAGC-AAAACAACAACAAAAA
1 CAACAAAAATAGCAACAAAAACAACAACAAAAA
64369 CAACAAAAATAGCAACAAAAACAACAACAAAAA
1 CAACAAAAATAGCAACAAAAACAACAACAAAAA
64402 TAATAACAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 14 0.47
33 16 0.53
ACGTcount: A:0.69, C:0.23, G:0.05, T:0.03
Consensus pattern (33 bp):
CAACAAAAATAGCAACAAAAACAACAACAAAAA
Found at i:64394 original size:24 final size:24
Alignment explanation
Indices: 64355--64424 Score: 97
Period size: 24 Copynumber: 2.9 Consensus size: 24
64345 ATAGCAGCAA
64355 AACAACAACAAA-AACAACAAAAAT
1 AACAACAA-AAACAACAACAAAAAT
*
64379 AGCAACAAAAACAACAACAAAAAT
1 AACAACAAAAACAACAACAAAAAT
* *
64403 AATAACAAAAACAACACCAAAA
1 AACAACAAAAACAACAACAAAA
64425 CAATAAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 3 0.07
24 38 0.93
ACGTcount: A:0.73, C:0.21, G:0.01, T:0.04
Consensus pattern (24 bp):
AACAACAAAAACAACAACAAAAAT
Found at i:64423 original size:12 final size:12
Alignment explanation
Indices: 64355--64424 Score: 79
Period size: 12 Copynumber: 5.8 Consensus size: 12
64345 ATAGCAGCAA
64355 AACAACAACAAA-
1 AACAACAA-AAAC
*
64367 AACAACAAAAAT
1 AACAACAAAAAC
*
64379 AGCAACAAAAAC
1 AACAACAAAAAC
*
64391 AACAACAAAAAT
1 AACAACAAAAAC
*
64403 AATAACAAAAAC
1 AACAACAAAAAC
*
64415 AACACCAAAA
1 AACAACAAAA
64425 CAATAAAAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
11 3 0.06
12 46 0.94
ACGTcount: A:0.73, C:0.21, G:0.01, T:0.04
Consensus pattern (12 bp):
AACAACAAAAAC
Found at i:64433 original size:21 final size:21
Alignment explanation
Indices: 64385--64510 Score: 87
Period size: 21 Copynumber: 5.9 Consensus size: 21
64375 AAATAGCAAC
* *
64385 AAAAACAACAACAAAAATAATAA
1 AAAAACAAC-ACCAAAACAAT-A
64408 CAAAAACAACACCAAAACAATA
1 -AAAAACAACACCAAAACAATA
* *
64430 AAAAA-AGGCACCAAAACAGT-
1 AAAAACA-ACACCAAAACAATA
* *
64450 AAAAACAACATCAAAACAACA
1 AAAAACAACACCAAAACAATA
* * *
64471 ACAAAA-AAAACCAAAATAGTA
1 A-AAAACAACACCAAAACAATA
* *
64492 AAAAGCAGCACCAAAACAA
1 AAAAACAACACCAAAACAA
64511 CAATATAATT
Statistics
Matches: 79, Mismatches: 18, Indels: 13
0.72 0.16 0.12
Matches are distributed among these distances:
20 18 0.23
21 38 0.48
22 5 0.06
23 9 0.11
24 9 0.11
ACGTcount: A:0.69, C:0.21, G:0.05, T:0.06
Consensus pattern (21 bp):
AAAAACAACACCAAAACAATA
Found at i:64454 original size:41 final size:41
Alignment explanation
Indices: 64409--64513 Score: 131
Period size: 41 Copynumber: 2.5 Consensus size: 41
64399 AAATAATAAC
* **
64409 AAAAACAACACCAAAACAATAA-AAAAAGGCACCAAAACAGT
1 AAAAACAACACCAAAACAACAACAAAAA-AAACCAAAACAGT
* *
64450 AAAAACAACATCAAAACAACAACAAAAAAAACCAAAATAGT
1 AAAAACAACACCAAAACAACAACAAAAAAAACCAAAACAGT
*
64491 AAAAAGCAGCACCAAAACAACAA
1 AAAAA-CAACACCAAAACAACAA
64514 TATAATTTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
41 35 0.64
42 20 0.36
ACGTcount: A:0.68, C:0.22, G:0.06, T:0.05
Consensus pattern (41 bp):
AAAAACAACACCAAAACAACAACAAAAAAAACCAAAACAGT
Found at i:64464 original size:20 final size:20
Alignment explanation
Indices: 64409--64510 Score: 89
Period size: 21 Copynumber: 5.0 Consensus size: 20
64399 AAATAATAAC
64409 AAAAACAACACCAAAACAAT
1 AAAAACAACACCAAAACAAT
*
64429 AAAAA-AAGGCACCAAAACAGT
1 AAAAACAA--CACCAAAACAAT
* *
64450 AAAAACAACATCAAAACAAC
1 AAAAACAACACCAAAACAAT
* * * *
64470 AACAAAAAAAACCAAAATAGT
1 AA-AAACAACACCAAAACAAT
*
64491 AAAAAGCAGCACCAAAACAA
1 AAAAA-CAACACCAAAACAA
64511 CAATATAATT
Statistics
Matches: 62, Mismatches: 15, Indels: 9
0.72 0.17 0.10
Matches are distributed among these distances:
19 2 0.03
20 19 0.31
21 39 0.63
22 2 0.03
ACGTcount: A:0.68, C:0.22, G:0.06, T:0.05
Consensus pattern (20 bp):
AAAAACAACACCAAAACAAT
Found at i:64495 original size:62 final size:65
Alignment explanation
Indices: 64385--64509 Score: 159
Period size: 62 Copynumber: 2.0 Consensus size: 65
64375 AAATAGCAAC
* *
64385 AAAAACAACAACAAAAATAATAACAAAAACAACACCAAAACAATAAAAA-AAGGCACCAAAACAG
1 AAAAACAACAACAAAAACAACAACAAAAACAACACCAAAACAATAAAAAGAA-GCACCAAAACAG
64449 T
65 T
* * * *
64450 AAAAACAACATC-AAAACAACAACAAAAA-AA-ACCAAAATAGTAAAAAGCAGCACCAAAACA
1 AAAAACAACAACAAAAACAACAACAAAAACAACACCAAAACAATAAAAAGAAGCACCAAAACA
64510 ACAATATAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
62 25 0.47
63 3 0.06
64 14 0.26
65 11 0.21
ACGTcount: A:0.69, C:0.21, G:0.05, T:0.06
Consensus pattern (65 bp):
AAAAACAACAACAAAAACAACAACAAAAACAACACCAAAACAATAAAAAGAAGCACCAAAACAGT
Found at i:67054 original size:15 final size:15
Alignment explanation
Indices: 67036--67072 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
67026 TTTTATTGAT
67036 ATCCTTTCGGATGAC
1 ATCCTTTCGGATGAC
67051 ATCCTTTCGGATGAC
1 ATCCTTTCGGATGAC
67066 ATCCTTT
1 ATCCTTT
67073 TCAACATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.19, C:0.27, G:0.16, T:0.38
Consensus pattern (15 bp):
ATCCTTTCGGATGAC
Found at i:67096 original size:40 final size:40
Alignment explanation
Indices: 67051--67203 Score: 240
Period size: 40 Copynumber: 3.9 Consensus size: 40
67041 TTCGGATGAC
* *
67051 ATCCTTTCG-GATGACATCCTTTTCAACATTTTCATTTGAT
1 ATCCTTTCGAG-TAACATCCTTTTCAACCTTTTCATTTGAT
67091 ATCCTTTCGAGTAACATCCTTTTCAACCTTTTCATTTGAT
1 ATCCTTTCGAGTAACATCCTTTTCAACCTTTTCATTTGAT
67131 ATCCTTTCGAGTAACATCCTTTTCAACCTTTTCATTTGAT
1 ATCCTTTCGAGTAACATCCTTTTCAACCTTTTCATTTGAT
*
67171 ATCCTTTC-AGATAATATCC-TTTCAACCTTTTCA
1 ATCCTTTCGAG-TAACATCCTTTTCAACCTTTTCA
67204 AGAATCCAGT
Statistics
Matches: 108, Mismatches: 3, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
39 16 0.15
40 91 0.84
41 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.07, T:0.44
Consensus pattern (40 bp):
ATCCTTTCGAGTAACATCCTTTTCAACCTTTTCATTTGAT
Found at i:70481 original size:25 final size:24
Alignment explanation
Indices: 70460--70549 Score: 110
Period size: 25 Copynumber: 3.7 Consensus size: 24
70450 TAGGCTCATG
70460 TGAGCTAAAGTTGTCTGGGCTCGTA
1 TGAGCTAAAGTT-TCTGGGCTCGTA
* *** *
70485 AGAGCTAACCATTCTGGGCTCGTG
1 TGAGCTAAAGTTTCTGGGCTCGTA
70509 TGAGCTAAAGTTGTCTGGGCTCGTA
1 TGAGCTAAAGTT-TCTGGGCTCGTA
70534 TGAGCTAAA-TTTCTGG
1 TGAGCTAAAGTTTCTGG
70550 AAGACTCAGT
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
23 5 0.09
24 21 0.39
25 28 0.52
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.31
Consensus pattern (24 bp):
TGAGCTAAAGTTTCTGGGCTCGTA
Found at i:70491 original size:49 final size:49
Alignment explanation
Indices: 70424--70541 Score: 182
Period size: 49 Copynumber: 2.4 Consensus size: 49
70414 AGCTAACCAT
* * *
70424 TCTGGGCTCCTAAAAGCTAGCCATTCTAGGCTCATGTGAGCTAAAGTTG
1 TCTGGGCTCGTAAGAGCTAACCATTCTAGGCTCATGTGAGCTAAAGTTG
* *
70473 TCTGGGCTCGTAAGAGCTAACCATTCTGGGCTCGTGTGAGCTAAAGTTG
1 TCTGGGCTCGTAAGAGCTAACCATTCTAGGCTCATGTGAGCTAAAGTTG
*
70522 TCTGGGCTCGTATGAGCTAA
1 TCTGGGCTCGTAAGAGCTAA
70542 ATTTCTGGAA
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 63 1.00
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (49 bp):
TCTGGGCTCGTAAGAGCTAACCATTCTAGGCTCATGTGAGCTAAAGTTG
Found at i:70506 original size:24 final size:24
Alignment explanation
Indices: 70400--70541 Score: 113
Period size: 24 Copynumber: 5.8 Consensus size: 24
70390 TTAAACTCTA
*
70400 TCTGGGCTCATAAGAGCTAACCAT
1 TCTGGGCTCGTAAGAGCTAACCAT
* * *
70424 TCTGGGCTCCTAAAAGCTAGCCAT
1 TCTGGGCTCGTAAGAGCTAACCAT
* * ** ***
70448 TCTAGGCTCATGTGAGCTAAAGTT
1 TCTGGGCTCGTAAGAGCTAACCAT
70472 GTCTGGGCTCGTAAGAGCTAACCAT
1 -TCTGGGCTCGTAAGAGCTAACCAT
** ***
70497 TCTGGGCTCGTGTGAGCTAAAGTT
1 TCTGGGCTCGTAAGAGCTAACCAT
*
70521 GTCTGGGCTCGTATGAGCTAA
1 -TCTGGGCTCGTAAGAGCTAA
70542 ATTTCTGGAA
Statistics
Matches: 91, Mismatches: 25, Indels: 3
0.76 0.21 0.03
Matches are distributed among these distances:
24 55 0.60
25 36 0.40
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (24 bp):
TCTGGGCTCGTAAGAGCTAACCAT
Found at i:71693 original size:32 final size:32
Alignment explanation
Indices: 71655--71859 Score: 130
Period size: 29 Copynumber: 6.7 Consensus size: 32
71645 CTTATATGGA
*
71655 AACCCCTTCTTGCATGTGGAACCCTATAAGC-
1 AACCCCTTCTTGCATGTGAAACCCTATAAGCG
* * * *
71686 AAGCCC--CTTACATGTGAAACCTTATATGCG
1 AACCCCTTCTTGCATGTGAAACCCTATAAGCG
*
71716 AACCCCTTATTGCATGTGAAACCCTAT-AGACG
1 AACCCCTTCTTGCATGTGAAACCCTATAAG-CG
* * * *
71748 -AGCCC--CTTACATGTGAAACCTTATATA-CA
1 AACCCCTTCTTGCATGTGAAACCCTATA-AGCG
*
71777 AACCCCCTCTTGCATGTGAAA-CCTA-ATAGACG
1 AACCCCTTCTTGCATGTGAAACCCTATA-AG-CG
* * * * *
71809 -A-GCC-TCTTGCATATGAAACCTTATATGTG
1 AACCCCTTCTTGCATGTGAAACCCTATAAGCG
*
71838 AACCCCCTCTTGCATGTGAAAC
1 AACCCCTTCTTGCATGTGAAAC
71860 ATTATATACA
Statistics
Matches: 132, Mismatches: 26, Indels: 31
0.70 0.14 0.16
Matches are distributed among these distances:
29 50 0.38
30 19 0.14
31 18 0.14
32 45 0.34
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (32 bp):
AACCCCTTCTTGCATGTGAAACCCTATAAGCG
Found at i:71856 original size:61 final size:60
Alignment explanation
Indices: 71644--71859 Score: 274
Period size: 61 Copynumber: 3.5 Consensus size: 60
71634 ATGTGCAAGC
* * *
71644 CCTTATATG-GAAACCCCTTCTTGCATGTGGAACCCTATA-AGCAAGCCCCTTACATGTGAAA
1 CCTTATATGCG-AACCCCCTCTTGCATGT-GAAACCTATAGA-CGAGCCCCTTACATGTGAAA
* *
71705 CCTTATATGCGAACCCCTTATTGCATGTGAAACCCTATAGACGAGCCCCTTACATGTGAAA
1 CCTTATATGCGAACCCCCTCTTGCATGTGAAA-CCTATAGACGAGCCCCTTACATGTGAAA
* * * * *
71766 CCTTATATACAAACCCCCTCTTGCATGTGAAACCTAATAGACGAGCCTCTTGCATATGAAA
1 CCTTATATGCGAACCCCCTCTTGCATGTGAAACCT-ATAGACGAGCCCCTTACATGTGAAA
*
71827 CCTTATATGTGAACCCCCTCTTGCATGTGAAAC
1 CCTTATATGCGAACCCCCTCTTGCATGTGAAAC
71860 ATTATATACA
Statistics
Matches: 138, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
60 6 0.04
61 130 0.94
62 2 0.01
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (60 bp):
CCTTATATGCGAACCCCCTCTTGCATGTGAAACCTATAGACGAGCCCCTTACATGTGAAA
Found at i:71865 original size:32 final size:32
Alignment explanation
Indices: 71644--71877 Score: 177
Period size: 32 Copynumber: 7.6 Consensus size: 32
71634 ATGTGCAAGC
* *
71644 CCTTATATG-GAAACCCCTTCTTGCATGTGGAA
1 CCTTATATGCG-AACCCCCTCTTGCATGTGAAA
* * * *
71676 CCCTATAAGC-AA-GCCC-CTTACATGTGAAA
1 CCTTATATGCGAACCCCCTCTTGCATGTGAAA
* *
71705 CCTTATATGCGAACCCCTTATTGCATGTGAAA
1 CCTTATATGCGAACCCCCTCTTGCATGTGAAA
* * *
71737 CCCTATA-GACG-A-GCCC-CTTACATGTGAAA
1 CCTTATATG-CGAACCCCCTCTTGCATGTGAAA
* *
71766 CCTTATATACAAACCCCCTCTTGCATGTGAAA
1 CCTTATATGCGAACCCCCTCTTGCATGTGAAA
* * *
71798 CCTAATA-GACG-A--GCCTCTTGCATATGAAA
1 CCTTATATG-CGAACCCCCTCTTGCATGTGAAA
*
71827 CCTTATATGTGAACCCCCTCTTGCATGTGAAA
1 CCTTATATGCGAACCCCCTCTTGCATGTGAAA
* * *
71859 CATTATATACAAACCCCCT
1 CCTTATATGCGAACCCCCT
71878 TAGTAAATCA
Statistics
Matches: 153, Mismatches: 35, Indels: 28
0.71 0.16 0.13
Matches are distributed among these distances:
29 59 0.39
30 9 0.06
31 10 0.07
32 75 0.49
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.27
Consensus pattern (32 bp):
CCTTATATGCGAACCCCCTCTTGCATGTGAAA
Found at i:72011 original size:59 final size:58
Alignment explanation
Indices: 71918--72061 Score: 198
Period size: 59 Copynumber: 2.4 Consensus size: 58
71908 TCATGCAAAC
* ** *
71918 CCTACATGATAATATATGTGGACCCTCATGTTTTATGGAATATGATTTAAAATGCGAA
1 CCTACATGATAACATATGTAAACCCTCATGTTTTATGGAATAGGATTTAAAATGCGAA
** *
71976 CTCTACATGATAACATATGTAAACTTTCATGTTTTATGGAATAGGATTTAAGATGCGAA
1 C-CTACATGATAACATATGTAAACCCTCATGTTTTATGGAATAGGATTTAAAATGCGAA
*
72035 CCTTACATGATAACATATGTGAACCCT
1 CC-TACATGATAACATATGTAAACCCT
72062 ATACATATGC
Statistics
Matches: 74, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
58 2 0.03
59 72 0.97
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (58 bp):
CCTACATGATAACATATGTAAACCCTCATGTTTTATGGAATAGGATTTAAAATGCGAA
Found at i:75185 original size:195 final size:194
Alignment explanation
Indices: 74799--75235 Score: 483
Period size: 195 Copynumber: 2.2 Consensus size: 194
74789 ATGTAGGGGA
* * *
74799 GTACCGCATATGTTGCGAGTCCTCGACAGCTCATGTAAGCAGCATCGTGAGTCGAGAAATGAGAA
1 GTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGACTCGAGAAA-GAGAA
* * *
74864 AAGAATCCAAGAATGGATTATAGGCCCTACGATGGTTGAGATTTATGCATAAGTGCATATTCTCC
65 AAGAATCCAAGAATGGATTATAGGCCCTACGATGGTAGAGATCTATGCATAAGTGCATACTCTCC
* * * * *
74929 ACAGGTCGTGTGAGTAGCATCGTTAGGGAACAGTTATATGCACATATACCGTATCGATGGCTGAG
130 ACAGCTCATGTGAGCAGCATCGTTAGGGAACAGTTATATACACATACACCGTATCGATGGCTGAG
* * * *
74994 GTACCGTATATGTTGCGAGTCCTCGACAACTTGTGTGAGCAGCATTGTGACTCGA-AAA-AGAAA
1 GTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGACTCGAGAAAGAGAAA
* * * * * *
75057 TATGGATCCCA-AATGGATTATAGGCCCTATGATGGCTAG-GA-CTATGCTTTA-TGCTTACTCT
66 -A-GAATCCAAGAATGGATTATAGGCCCTACGATGG-TAGAGATCTATGCATAAGTGCATACTCT
* * * *
75118 CGACAGCTCATGTGAGCAGCATCGTTAGGGAGCAGTTTATAGTATAGATAGACACCGTA-CTGAT
128 CCACAGCTCATGTGAGCAGCATCGTTAGGGAACAG-TTATA-TACACAT--ACACCGTATC-GAT
*
75182 GGCTGGG
188 GGCTGAG
* * *
75189 GTACCACATATGTTACAAGTCCTCGACAGCTCGTGTGAGCAGCATCG
1 GTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCG
75236 AGTACTGGTA
Statistics
Matches: 201, Mismatches: 33, Indels: 16
0.80 0.13 0.06
Matches are distributed among these distances:
191 38 0.19
192 17 0.08
193 30 0.15
194 12 0.06
195 104 0.52
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (194 bp):
GTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGACTCGAGAAAGAGAAA
AGAATCCAAGAATGGATTATAGGCCCTACGATGGTAGAGATCTATGCATAAGTGCATACTCTCCA
CAGCTCATGTGAGCAGCATCGTTAGGGAACAGTTATATACACATACACCGTATCGATGGCTGAG
Found at i:75438 original size:18 final size:19
Alignment explanation
Indices: 75405--75440 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
75395 AAAGATGTTA
*
75405 TTGTTGTTTTGTAGATTGT
1 TTGTTGTTTTGAAGATTGT
75424 TTGTTG-TTTGAAGATTG
1 TTGTTGTTTTGAAGATTG
75441 GATCATCTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.14, C:0.00, G:0.28, T:0.58
Consensus pattern (19 bp):
TTGTTGTTTTGAAGATTGT
Found at i:77402 original size:123 final size:122
Alignment explanation
Indices: 77179--77526 Score: 515
Period size: 123 Copynumber: 2.8 Consensus size: 122
77169 AAAAAAAAAA
* *
77179 ATCTCATATTAAAATGGAAATCTATATCTTTAGAGAAATATATGGAAGGTTTATT-AAACATTAT
1 ATCTCATATTAAAAT-GAAA-ATAT-TCTTTAAAGAAATATATGGAAGGTTTATTAAAACATTAT
* *
77243 ATCCTTTCCAAAATGATATTAACTTCCATGTTTTTAATATTCAATTTATTTTTATATAAT
63 ATCCTTTCCAAAAGGATATTAACTTCCATGTTTTTAATATTCAATTTACTTTTATATAAT
*
77303 ATTTCATATTAAAATGAAAATATTCCTTTAAAGAAATATATGGAAGGTTTATTAAAACATTATAT
1 ATCTCATATTAAAATGAAAATATT-CTTTAAAGAAATATATGGAAGGTTTATTAAAACATTATAT
* * *
77368 CATTTCTAAAAGGATATTAACTTCCATGTTTTTAATATTCAATTTCCTTTTATATAAT
65 CCTTTCCAAAAGGATATTAACTTCCATGTTTTTAATATTCAATTTACTTTTATATAAT
* * *
77426 ATCTCATATTAAAATGGAAATATTTCTTTAAAGAAATATATGGGAGGGTTATTAAAACA-T-TAT
1 ATCTCATATTAAAATGAAAATA-TTCTTTAAAGAAATATATGGAAGGTTTATTAAAACATTATAT
*
77489 CCTTTCCAAAAGGAT-TTAACTTTCATGTTTTTAATATT
65 CCTTTCCAAAAGGATATTAACTTCCATGTTTTTAATATT
77527 TAATGAAATC
Statistics
Matches: 206, Mismatches: 15, Indels: 10
0.89 0.06 0.04
Matches are distributed among these distances:
120 22 0.11
121 17 0.08
122 31 0.15
123 120 0.58
124 16 0.08
ACGTcount: A:0.39, C:0.10, G:0.09, T:0.43
Consensus pattern (122 bp):
ATCTCATATTAAAATGAAAATATTCTTTAAAGAAATATATGGAAGGTTTATTAAAACATTATATC
CTTTCCAAAAGGATATTAACTTCCATGTTTTTAATATTCAATTTACTTTTATATAAT
Found at i:81972 original size:21 final size:21
Alignment explanation
Indices: 81946--81985 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
81936 GTCTAGATAT
*
81946 TTCTACCGATACTTAAATTAG
1 TTCTACCGATACTAAAATTAG
81967 TTCTACCGATACTAAAATT
1 TTCTACCGATACTAAAATT
81986 GACAAGTGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (21 bp):
TTCTACCGATACTAAAATTAG
Found at i:82773 original size:30 final size:31
Alignment explanation
Indices: 82726--82786 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
82716 TGCTAGGCAT
*
82726 ATAGCCCGAAATACACCGGCACGAAGCCTAC
1 ATAGCCCGAAATACACCGACACGAAGCCTAC
* *
82757 ATAGCCTGAAA-ACACCGACATGAAGCCTAC
1 ATAGCCCGAAATACACCGACACGAAGCCTAC
82787 TAGGCACATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 17 0.63
31 10 0.37
ACGTcount: A:0.38, C:0.33, G:0.18, T:0.11
Consensus pattern (31 bp):
ATAGCCCGAAATACACCGACACGAAGCCTAC
Found at i:82813 original size:21 final size:21
Alignment explanation
Indices: 82789--82842 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
82779 AAGCCTACTA
* *
82789 GGCACATAGCTTGAAAACACC
1 GGCACAAAGCCTGAAAACACC
82810 GGCACAAAGCCTGAAAACACC
1 GGCACAAAGCCTGAAAACACC
*
82831 GGCACGAAGCCT
1 GGCACAAAGCCT
82843 ACTAGGCACA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.37, C:0.31, G:0.22, T:0.09
Consensus pattern (21 bp):
GGCACAAAGCCTGAAAACACC
Found at i:82849 original size:58 final size:58
Alignment explanation
Indices: 82759--82879 Score: 197
Period size: 58 Copynumber: 2.1 Consensus size: 58
82749 AAGCCTACAT
* * *
82759 AGCCTGAAAACACCGACATGAAGCCTACTAGGCACATAGCTTGAAAACACCGGCACAA
1 AGCCTGAAAACACCGACACGAAGCCTACTAGGCACATAGCCTGAAAACACCGACACAA
* *
82817 AGCCTGAAAACACCGGCACGAAGCCTACTAGGCACATAGCCTGAAAACATCGACACAA
1 AGCCTGAAAACACCGACACGAAGCCTACTAGGCACATAGCCTGAAAACACCGACACAA
82875 AGCCT
1 AGCCT
82880 ACTAGACACA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.39, C:0.31, G:0.19, T:0.12
Consensus pattern (58 bp):
AGCCTGAAAACACCGACACGAAGCCTACTAGGCACATAGCCTGAAAACACCGACACAA
Found at i:82851 original size:37 final size:37
Alignment explanation
Indices: 82810--82934 Score: 178
Period size: 37 Copynumber: 3.4 Consensus size: 37
82800 TGAAAACACC
82810 GGCACAAAGCCTGAAAACACCGGCACGAAGCCTACTA
1 GGCACAAAGCCTGAAAACACCGGCACGAAGCCTACTA
* * * *
82847 GGCACATAGCCTGAAAACATCGACACAAAGCCTACTA
1 GGCACAAAGCCTGAAAACACCGGCACGAAGCCTACTA
* *
82884 GACACAAAGCCTGAAAACACTGGCACGAAGCCTACTA
1 GGCACAAAGCCTGAAAACACCGGCACGAAGCCTACTA
* *
82921 GGCATAGAGCCTGA
1 GGCACAAAGCCTGA
82935 TATTTAAATG
Statistics
Matches: 75, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 75 1.00
ACGTcount: A:0.38, C:0.30, G:0.21, T:0.11
Consensus pattern (37 bp):
GGCACAAAGCCTGAAAACACCGGCACGAAGCCTACTA
Found at i:82878 original size:21 final size:21
Alignment explanation
Indices: 82789--82879 Score: 75
Period size: 21 Copynumber: 4.6 Consensus size: 21
82779 AAGCCTACTA
* * *
82789 GGCACATAGCTTGAAAACACC
1 GGCACAAAGCCTGAAAACATC
*
82810 GGCACAAAGCCTGAAAACACC
1 GGCACAAAGCCTGAAAACATC
* *
82831 GGCACGAAGCCT----AC-TA
1 GGCACAAAGCCTGAAAACATC
*
82847 GGCACATAGCCTGAAAACATC
1 GGCACAAAGCCTGAAAACATC
*
82868 GACACAAAGCCT
1 GGCACAAAGCCT
82880 ACTAGACACA
Statistics
Matches: 55, Mismatches: 10, Indels: 10
0.73 0.13 0.13
Matches are distributed among these distances:
16 10 0.18
17 2 0.04
20 2 0.04
21 41 0.75
ACGTcount: A:0.38, C:0.31, G:0.20, T:0.11
Consensus pattern (21 bp):
GGCACAAAGCCTGAAAACATC
Found at i:88807 original size:21 final size:21
Alignment explanation
Indices: 88774--88813 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
88764 GTCTAGATAT
* *
88774 TTTTACCGATACTTAAATTAG
1 TTTTACAGATACTAAAATTAG
*
88795 TTTTACAGGTACTAAAATT
1 TTTTACAGATACTAAAATT
88814 GATAGTGAGC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.42
Consensus pattern (21 bp):
TTTTACAGATACTAAAATTAG
Found at i:89619 original size:37 final size:37
Alignment explanation
Indices: 89526--89838 Score: 353
Period size: 37 Copynumber: 8.4 Consensus size: 37
89516 GTTCTTGGAT
* * * *
89526 CACCGGCACAAAGTCTGCTAGGCACATAGCCCGAAATA
1 CACCGGCACAAAGCCTACTAGGCAAATAGCCTGAAA-A
* * * *
89564 TACCAGCACGAAGTCTACTAGGCAAATAGCCTGAAAA
1 CACCGGCACAAAGCCTACTAGGCAAATAGCCTGAAAA
* * *
89601 CATCGGCACGAAGCCTACTAGGCACATAGCCTGAAAA
1 CACCGGCACAAAGCCTACTAGGCAAATAGCCTGAAAA
* * * *
89638 CACCGGCACAAAGCCTCCTAGACACAA-AGCTTGAAAG
1 CACCGGCACAAAGCCTACTAGGCA-AATAGCCTGAAAA
* *
89675 CACCGGCACGAAGCCTACTAGGCACATAGCCTGAAAA
1 CACCGGCACAAAGCCTACTAGGCAAATAGCCTGAAAA
* * * *
89712 CACCGGCACAAAGCCTCCTAGACACAA-AGCATGAAAG
1 CACCGGCACAAAGCCTACTAGGCA-AATAGCCTGAAAA
* *
89749 CACCGGCACGAAGCCTACTAGGCACATAGCCTGAAAA
1 CACCGGCACAAAGCCTACTAGGCAAATAGCCTGAAAA
89786 CACCGGCACAAAGCCTACTAGGCACAA-AGCCTGAAAA
1 CACCGGCACAAAGCCTACTAGGCA-AATAGCCTGAAAA
*
89823 CACCGACACAAAGCCT
1 CACCGGCACAAAGCCT
89839 GATATTTAAA
Statistics
Matches: 231, Mismatches: 39, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
36 2 0.01
37 196 0.85
38 33 0.14
ACGTcount: A:0.37, C:0.32, G:0.20, T:0.11
Consensus pattern (37 bp):
CACCGGCACAAAGCCTACTAGGCAAATAGCCTGAAAA
Found at i:89686 original size:74 final size:74
Alignment explanation
Indices: 89526--89838 Score: 430
Period size: 74 Copynumber: 4.2 Consensus size: 74
89516 GTTCTTGGAT
* * * * * * * * *
89526 CACCGGCACAAAGTCTGCTAGGCACATAGCCCGAAATATACCAGCACGAAGTCTACTAGGCA-AA
1 CACCGGCACGAAGCCTACTAGGCACATAGCCTGAAA-ACACCGGCACAAAGCCTACTAGACACAA
89590 TAGCCTGAAAA
65 -AGCCTGAAAA
* *
89601 CATCGGCACGAAGCCTACTAGGCACATAGCCTGAAAACACCGGCACAAAGCCTCCTAGACACAAA
1 CACCGGCACGAAGCCTACTAGGCACATAGCCTGAAAACACCGGCACAAAGCCTACTAGACACAAA
* *
89666 GCTTGAAAG
66 GCCTGAAAA
*
89675 CACCGGCACGAAGCCTACTAGGCACATAGCCTGAAAACACCGGCACAAAGCCTCCTAGACACAAA
1 CACCGGCACGAAGCCTACTAGGCACATAGCCTGAAAACACCGGCACAAAGCCTACTAGACACAAA
* *
89740 GCATGAAAG
66 GCCTGAAAA
*
89749 CACCGGCACGAAGCCTACTAGGCACATAGCCTGAAAACACCGGCACAAAGCCTACTAGGCACAAA
1 CACCGGCACGAAGCCTACTAGGCACATAGCCTGAAAACACCGGCACAAAGCCTACTAGACACAAA
89814 GCCTGAAAA
66 GCCTGAAAA
* *
89823 CACCGACACAAAGCCT
1 CACCGGCACGAAGCCT
89839 GATATTTAAA
Statistics
Matches: 216, Mismatches: 21, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
74 183 0.85
75 33 0.15
ACGTcount: A:0.37, C:0.32, G:0.20, T:0.11
Consensus pattern (74 bp):
CACCGGCACGAAGCCTACTAGGCACATAGCCTGAAAACACCGGCACAAAGCCTACTAGACACAAA
GCCTGAAAA
Found at i:89763 original size:111 final size:111
Alignment explanation
Indices: 89526--89838 Score: 392
Period size: 111 Copynumber: 2.8 Consensus size: 111
89516 GTTCTTGGAT
* * * * * * * * *
89526 CACCGGCACAAAGTCTGCTAGGCACATAGCCCGAAATATACCAGCACGAAGTCTACTAGGCAAAT
1 CACCGGCACAAAGCCTACTAGACACAAAGCCTGAAA-ACACCGGCACGAAGCCTACTAGGCACAT
* * * * *
89591 AGCCTGAAAACATCGGCACGAAGCCTACTAGGCACATAGCCTGAAAA
65 AGCCTGAAAACACCGGCACAAAGCCTACTAGACACAAAGCATGAAAA
* * *
89638 CACCGGCACAAAGCCTCCTAGACACAAAGCTTGAAAGCACCGGCACGAAGCCTACTAGGCACATA
1 CACCGGCACAAAGCCTACTAGACACAAAGCCTGAAAACACCGGCACGAAGCCTACTAGGCACATA
* *
89703 GCCTGAAAACACCGGCACAAAGCCTCCTAGACACAAAGCATGAAAG
66 GCCTGAAAACACCGGCACAAAGCCTACTAGACACAAAGCATGAAAA
* * * * *
89749 CACCGGCACGAAGCCTACTAGGCACATAGCCTGAAAACACCGGCACAAAGCCTACTAGGCACAAA
1 CACCGGCACAAAGCCTACTAGACACAAAGCCTGAAAACACCGGCACGAAGCCTACTAGGCACATA
*
89814 GCCTGAAAACACCGACACAAAGCCT
66 GCCTGAAAACACCGGCACAAAGCCT
89839 GATATTTAAA
Statistics
Matches: 174, Mismatches: 27, Indels: 1
0.86 0.13 0.00
Matches are distributed among these distances:
111 144 0.83
112 30 0.17
ACGTcount: A:0.37, C:0.32, G:0.20, T:0.11
Consensus pattern (111 bp):
CACCGGCACAAAGCCTACTAGACACAAAGCCTGAAAACACCGGCACGAAGCCTACTAGGCACATA
GCCTGAAAACACCGGCACAAAGCCTACTAGACACAAAGCATGAAAA
Found at i:89793 original size:21 final size:21
Alignment explanation
Indices: 89769--89840 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 21
89759 AAGCCTACTA
*
89769 GGCACATAGCCTGAAAACACC
1 GGCACAAAGCCTGAAAACACC
89790 GGCACAAAGCCT----ACTA--
1 GGCACAAAGCCTGAAAAC-ACC
89806 GGCACAAAGCCTGAAAACACC
1 GGCACAAAGCCTGAAAACACC
*
89827 GACACAAAGCCTGA
1 GGCACAAAGCCTGA
89841 TATTTAAATG
Statistics
Matches: 42, Mismatches: 2, Indels: 14
0.72 0.03 0.24
Matches are distributed among these distances:
16 12 0.29
17 2 0.05
18 1 0.02
19 1 0.02
20 2 0.05
21 24 0.57
ACGTcount: A:0.40, C:0.32, G:0.19, T:0.08
Consensus pattern (21 bp):
GGCACAAAGCCTGAAAACACC
Done.