Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013841.1 Kokia drynarioides strain JFW-HI SEQ_128869, 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: 108778
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 98 characters in sequence are not A, C, G, or T
Found at i:2707 original size:2 final size:2
Alignment explanation
Indices: 2700--2734 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2690 GTACCGTTCG
2700 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
2735 CATAATTCCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:10815 original size:58 final size:57
Alignment explanation
Indices: 10684--10850 Score: 165
Period size: 58 Copynumber: 2.9 Consensus size: 57
10674 TTGATTTAAT
* * * * * ***
10684 ATTTGGTACATGAACTTGACATTTTTTTCCTAATTTGGTACCTAAATTTTTTTTTGTCC
1 ATTTGGTACTTAAACTTGACACTTTTTT--TAATTTGGTACTTAAACTTTTTGGGGTCC
* * *
10743 A-TTGATACTCAAACTTGACACTTTTTTTAAGTTGGTACTTAAACTTTTTGGGGTCC
1 ATTTGGTACTTAAACTTGACACTTTTTTTAATTTGGTACTTAAACTTTTTGGGGTCC
* * *
10799 AATTTGGTACTTAAACTTGACGCTTTTTCTTAATTTGATACTTAATCTTTTT
1 -ATTTGGTACTTAAACTTGACACTTTTT-TTAATTTGGTACTTAAACTTTTT
10851 TAATATTAAT
Statistics
Matches: 88, Mismatches: 17, Indels: 6
0.79 0.15 0.05
Matches are distributed among these distances:
56 23 0.26
57 1 0.01
58 43 0.49
59 21 0.24
ACGTcount: A:0.24, C:0.15, G:0.13, T:0.49
Consensus pattern (57 bp):
ATTTGGTACTTAAACTTGACACTTTTTTTAATTTGGTACTTAAACTTTTTGGGGTCC
Found at i:11095 original size:61 final size:59
Alignment explanation
Indices: 11009--11122 Score: 167
Period size: 58 Copynumber: 1.9 Consensus size: 59
10999 AATTGAAACT
*
11009 AAAAAAAGCTTAGGTACCAAATTAGGAAAAAAAAATGCCAAGTTTAGGTATCAAATTGGGTC
1 AAAAAAAGATTAGGTACCAAATTAGG---AAAAAATGCCAAGTTTAGGTATCAAATTGGGTC
* *
11071 AAAAAAA-ATTAGGTGCCAAATTAGGAAAAAATGTCAAGTTTAGGTATCAAAT
1 AAAAAAAGATTAGGTACCAAATTAGGAAAAAATGCCAAGTTTAGGTATCAAAT
11123 ATTGTATTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
58 26 0.53
61 16 0.33
62 7 0.14
ACGTcount: A:0.48, C:0.10, G:0.18, T:0.24
Consensus pattern (59 bp):
AAAAAAAGATTAGGTACCAAATTAGGAAAAAATGCCAAGTTTAGGTATCAAATTGGGTC
Found at i:11602 original size:22 final size:21
Alignment explanation
Indices: 11551--11609 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
11541 ATATATTTGG
11551 TATAAAAA-AATATTAATTTTA
1 TATAAAAATAA-ATTAATTTTA
* * *
11572 CATACAAATAAATTTATTTATA
1 TATAAAAATAAATTAATTT-TA
11594 TATAAAAATAAATTAA
1 TATAAAAATAAATTAA
11610 CAAATATTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
21 13 0.43
22 17 0.57
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (21 bp):
TATAAAAATAAATTAATTTTA
Found at i:13051 original size:96 final size:96
Alignment explanation
Indices: 12887--13088 Score: 395
Period size: 96 Copynumber: 2.1 Consensus size: 96
12877 ATGGCTAAAA
*
12887 GAAGAAAGGCAAGGTGGTTACAAGTGGAATTTTCTTCCCAATCGCATGGAAATAGATAAGGGCAA
1 GAAGAAGGGCAAGGTGGTTACAAGTGGAATTTTCTTCCCAATCGCATGGAAATAGATAAGGGCAA
12952 AAGAGATACAGGCTGTAACTTTGCTGATTAT
66 AAGAGATACAGGCTGTAACTTTGCTGATTAT
12983 GAAGAAGGGCAAGGTGGTTACAAGTGGAATTTTCTTCCCAATCGCATGGAAATAGATAAGGGCAA
1 GAAGAAGGGCAAGGTGGTTACAAGTGGAATTTTCTTCCCAATCGCATGGAAATAGATAAGGGCAA
13048 AAGAGATACAGGCTGTAACTTTGCTGATTAT
66 AAGAGATACAGGCTGTAACTTTGCTGATTAT
13079 GAAGAAGGGC
1 GAAGAAGGGC
13089 CGTTAAAGAG
Statistics
Matches: 105, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 105 1.00
ACGTcount: A:0.35, C:0.13, G:0.28, T:0.24
Consensus pattern (96 bp):
GAAGAAGGGCAAGGTGGTTACAAGTGGAATTTTCTTCCCAATCGCATGGAAATAGATAAGGGCAA
AAGAGATACAGGCTGTAACTTTGCTGATTAT
Found at i:24096 original size:18 final size:19
Alignment explanation
Indices: 24067--24118 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
24057 CTAAGTATCA
* *
24067 AAAAACTATGAGGGACATT
1 AAAAATTATGAGGGACATC
* *
24086 AAAAATT-TGAGAG-TATC
1 AAAAATTATGAGGGACATC
24103 AAAAATTATGAGGGAC
1 AAAAATTATGAGGGAC
24119 TATCCATATT
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
17 9 0.36
18 10 0.40
19 6 0.24
ACGTcount: A:0.48, C:0.08, G:0.21, T:0.23
Consensus pattern (19 bp):
AAAAATTATGAGGGACATC
Found at i:25824 original size:19 final size:20
Alignment explanation
Indices: 25802--25869 Score: 70
Period size: 19 Copynumber: 3.5 Consensus size: 20
25792 ATTGAATAAG
25802 TACAAAAAAAA-CATGAGAA
1 TACAAAAAAAATCATGAGAA
* *
25821 TACAAAAAAATTATTATG-GAT
1 TACAAAAAAA--ATCATGAGAA
*
25842 TACAAAAAAAATGA-GAGAA
1 TACAAAAAAAATCATGAGAA
25861 TACAAAAAA
1 TACAAAAAA
25870 TTATGAGGGA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
18 1 0.02
19 24 0.59
21 13 0.32
22 3 0.07
ACGTcount: A:0.65, C:0.07, G:0.10, T:0.18
Consensus pattern (20 bp):
TACAAAAAAAATCATGAGAA
Found at i:25846 original size:40 final size:39
Alignment explanation
Indices: 25802--25890 Score: 117
Period size: 39 Copynumber: 2.3 Consensus size: 39
25792 ATTGAATAAG
* *
25802 TACAAAAAAAA-CATGAGAATACAAAAAAATTATTATGGAT
1 TACAAAAAAAATCA-GAGAATAC-AAAAAATTATGAGGGAT
*
25842 TACAAAAAAAATGAGAGAATACAAAAAATTATGAGGGAT
1 TACAAAAAAAATCAGAGAATACAAAAAATTATGAGGGAT
*
25881 TACCAAAAAA
1 TACAAAAAAA
25891 TGTAAGAGTA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
39 24 0.55
40 19 0.43
41 1 0.02
ACGTcount: A:0.61, C:0.08, G:0.12, T:0.19
Consensus pattern (39 bp):
TACAAAAAAAATCAGAGAATACAAAAAATTATGAGGGAT
Found at i:25875 original size:20 final size:20
Alignment explanation
Indices: 25816--25891 Score: 66
Period size: 20 Copynumber: 3.8 Consensus size: 20
25806 AAAAAAACAT
*
25816 GAGAATACAAAAAAATTATTA
1 GAGAATAC-AAAAAATTATGA
* *
25837 TG-GATTACAAAAAA-AATGA
1 -GAGAATACAAAAAATTATGA
25856 GAGAATACAAAAAATTATGA
1 GAGAATACAAAAAATTATGA
* *
25876 GGGATTACCAAAAAAT
1 GAGAATA-CAAAAAAT
25892 GTAAGAGTAC
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
18 1 0.02
19 14 0.32
20 15 0.34
21 13 0.30
22 1 0.02
ACGTcount: A:0.58, C:0.07, G:0.14, T:0.21
Consensus pattern (20 bp):
GAGAATACAAAAAATTATGA
Found at i:25906 original size:39 final size:39
Alignment explanation
Indices: 25802--25911 Score: 118
Period size: 38 Copynumber: 2.8 Consensus size: 39
25792 ATTGAATAAG
* * *
25802 TACAAAAAAAA-CATGAGAATACAAAAAAATTATTATGGAT
1 TACAAAAAAAATGA-GAGAATAC-AAAAAATTATGAGGGAT
25842 TACAAAAAAAATGAGAGAATACAAAAAATTATGAGGGAT
1 TACAAAAAAAATGAGAGAATACAAAAAATTATGAGGGAT
* * *
25881 TAC-CAAAAAATGTA-AGAGTACCAAAAATTAT
1 TACAAAAAAAATG-AGAGAATACAAAAAATTAT
25912 TTATGGATTG
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
38 23 0.37
39 19 0.31
40 19 0.31
41 1 0.02
ACGTcount: A:0.58, C:0.08, G:0.13, T:0.21
Consensus pattern (39 bp):
TACAAAAAAAATGAGAGAATACAAAAAATTATGAGGGAT
Found at i:25920 original size:39 final size:38
Alignment explanation
Indices: 25816--25926 Score: 125
Period size: 39 Copynumber: 2.8 Consensus size: 38
25806 AAAAAAACAT
*
25816 GAGAATACAAAAAAATTATTATGGATTACAAAAAAAATGA
1 GAGAATAC-AAAAAATTATTATGGATTAC-CAAAAAATGA
* *
25856 GAGAATACAAAAAATTATGAGGGATTACCAAAAAATGTA
1 GAGAATACAAAAAATTATTATGGATTACCAAAAAATG-A
* * *
25895 -AGAGTACCAAAAATTATTTATGGATTGCCAAA
1 GAGAATACAAAAAATTA-TTATGGATTACCAAA
25927 TATTGTTTTG
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
38 22 0.36
39 31 0.51
40 8 0.13
ACGTcount: A:0.53, C:0.08, G:0.15, T:0.23
Consensus pattern (38 bp):
GAGAATACAAAAAATTATTATGGATTACCAAAAAATGA
Found at i:29666 original size:20 final size:21
Alignment explanation
Indices: 29641--29679 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
29631 TGCATTTTTA
*
29641 GCATTTT-TAACTTAGTGACT
1 GCATTTTCTAACTCAGTGACT
29661 GCATTTTCTAACTCAGTGA
1 GCATTTTCTAACTCAGTGA
29680 TGCTTGGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (21 bp):
GCATTTTCTAACTCAGTGACT
Found at i:34651 original size:18 final size:18
Alignment explanation
Indices: 34628--34663 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
34618 AAGTAAGTTT
34628 ACTTATAGACTTACCTTA
1 ACTTATAGACTTACCTTA
34646 ACTTATAGACTTACCTTA
1 ACTTATAGACTTACCTTA
34664 CTTTTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.39
Consensus pattern (18 bp):
ACTTATAGACTTACCTTA
Found at i:34779 original size:26 final size:25
Alignment explanation
Indices: 34750--34830 Score: 65
Period size: 26 Copynumber: 3.2 Consensus size: 25
34740 ATCGAATTAA
34750 GTAAACACATATATAAGCTGACAAGC
1 GTAAA-ACATATATAAGCTGACAAGC
** * ** *
34776 GT-AAATGTGTGCAAGCTGGCAAGC
1 GTAAAACATATATAAGCTGACAAGC
* *
34800 GTAAATGCATATATAAGCTGAGAAGC
1 GTAAA-ACATATATAAGCTGACAAGC
34826 GTAAA
1 GTAAA
34831 TGTGTGCAAG
Statistics
Matches: 39, Mismatches: 14, Indels: 4
0.68 0.25 0.07
Matches are distributed among these distances:
24 16 0.41
25 4 0.10
26 19 0.49
ACGTcount: A:0.41, C:0.15, G:0.23, T:0.21
Consensus pattern (25 bp):
GTAAAACATATATAAGCTGACAAGC
Found at i:34792 original size:24 final size:24
Alignment explanation
Indices: 34764--34843 Score: 97
Period size: 24 Copynumber: 3.2 Consensus size: 24
34754 ACACATATAT
34764 AAGCTGACAAGCGTAAATGTGTGC
1 AAGCTGACAAGCGTAAATGTGTGC
* * **
34788 AAGCTGGCAAGCGTAAATGCATATAT
1 AAGCTGACAAGCGTAAATG--TGTGC
*
34814 AAGCTGAGAAGCGTAAATGTGTGC
1 AAGCTGACAAGCGTAAATGTGTGC
34838 AAGCTG
1 AAGCTG
34844 GCGAGCATAA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
24 26 0.58
26 19 0.42
ACGTcount: A:0.35, C:0.15, G:0.29, T:0.21
Consensus pattern (24 bp):
AAGCTGACAAGCGTAAATGTGTGC
Found at i:34811 original size:50 final size:50
Alignment explanation
Indices: 34751--34871 Score: 188
Period size: 50 Copynumber: 2.4 Consensus size: 50
34741 TCGAATTAAG
*
34751 TAAACACATATATAAGCTGACAAGCGTAAATGTGTGCAAGCTGGCAAGCG
1 TAAACACATATATAAGCTGACAAGCGTAAATGTGTGCAAGCTGGCAAGCA
** * *
34801 TAAATGCATATATAAGCTGAGAAGCGTAAATGTGTGCAAGCTGGCGAGCA
1 TAAACACATATATAAGCTGACAAGCGTAAATGTGTGCAAGCTGGCAAGCA
*
34851 TAAACACATATATAAACTGAC
1 TAAACACATATATAAGCTGAC
34872 GAACGCATAT
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 62 1.00
ACGTcount: A:0.40, C:0.17, G:0.22, T:0.21
Consensus pattern (50 bp):
TAAACACATATATAAGCTGACAAGCGTAAATGTGTGCAAGCTGGCAAGCA
Found at i:34854 original size:24 final size:24
Alignment explanation
Indices: 34764--34854 Score: 94
Period size: 24 Copynumber: 3.7 Consensus size: 24
34754 ACACATATAT
*
34764 AAGCTGACAAGCGTAAATGTGTGC
1 AAGCTGGCAAGCGTAAATGTGTGC
* **
34788 AAGCTGGCAAGCGTAAATGCATATAT
1 AAGCTGGCAAGCGTAAATG--TGTGC
34814 AAGCTGAG-AAGCGTAAATGTGTGC
1 AAGCTG-GCAAGCGTAAATGTGTGC
* *
34838 AAGCTGGCGAGCATAAA
1 AAGCTGGCAAGCGTAAA
34855 CACATATATA
Statistics
Matches: 54, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
23 1 0.02
24 33 0.61
26 19 0.35
27 1 0.02
ACGTcount: A:0.36, C:0.15, G:0.29, T:0.20
Consensus pattern (24 bp):
AAGCTGGCAAGCGTAAATGTGTGC
Found at i:41573 original size:28 final size:25
Alignment explanation
Indices: 41523--41574 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
41513 GTCAATAAAT
*
41523 AATTTAAAAATTATAAAATATTCAA
1 AATTTAAAAAATATAAAATATTCAA
41548 AATTTCAAAAAATATATAAATAATTCA
1 AATTT-AAAAAATATA-AAAT-ATTCA
41575 TAAAAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 5 0.22
26 9 0.39
27 4 0.17
28 5 0.22
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.35
Consensus pattern (25 bp):
AATTTAAAAAATATAAAATATTCAA
Found at i:43638 original size:22 final size:23
Alignment explanation
Indices: 43613--43656 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
43603 AAGAAAGTTA
43613 AAATAACAT-AAAA-GAAAAAATT
1 AAATAAC-TCAAAATGAAAAAATT
*
43635 AAATTACTCAAAATGAAAAAAT
1 AAATAACTCAAAATGAAAAAAT
43657 ATAGGGACCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 1 0.05
22 10 0.53
23 8 0.42
ACGTcount: A:0.68, C:0.07, G:0.05, T:0.20
Consensus pattern (23 bp):
AAATAACTCAAAATGAAAAAATT
Found at i:44321 original size:46 final size:46
Alignment explanation
Indices: 44211--44305 Score: 129
Period size: 46 Copynumber: 2.1 Consensus size: 46
44201 AATAATACAA
* * * *
44211 ATACAATCATGGCACAGATATAGTTACAAATACAATCATGCAACAG
1 ATACAATCACGTCACAGATACAATTACAAATACAATCATGCAACAG
*
44257 ATACAGTCACGTCACAGATACAATTACAAATACAATCATGTC-ACAG
1 ATACAATCACGTCACAGATACAATTACAAATACAATCATG-CAACAG
44303 ATA
1 ATA
44306 TAATACAGTT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
46 42 0.98
47 1 0.02
ACGTcount: A:0.45, C:0.21, G:0.12, T:0.22
Consensus pattern (46 bp):
ATACAATCACGTCACAGATACAATTACAAATACAATCATGCAACAG
Found at i:44365 original size:52 final size:52
Alignment explanation
Indices: 44300--44415 Score: 133
Period size: 52 Copynumber: 2.2 Consensus size: 52
44290 AATCATGTCA
* * * * *
44300 CAGATATAATACAGTTACAGATGCAGACATAATATAAATACAGTTACAGATG
1 CAGACATAATACAGATACAGATACAGACACAATACAAATACAGTTACAGATG
* ** *
44352 CAGACATAATACAGATACAGTTACAGATGCAATACAGATACAGTTACAGATG
1 CAGACATAATACAGATACAGATACAGACACAATACAAATACAGTTACAGATG
* *
44404 CAAACATGATAC
1 CAGACATAATAC
44416 CCCCATTCGT
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.46, C:0.16, G:0.16, T:0.22
Consensus pattern (52 bp):
CAGACATAATACAGATACAGATACAGACACAATACAAATACAGTTACAGATG
Found at i:44369 original size:6 final size:6
Alignment explanation
Indices: 44337--44402 Score: 55
Period size: 6 Copynumber: 11.3 Consensus size: 6
44327 CATAATATAA
* * * * * *
44337 ATACAG TTACAG ATGCAG ACATA- ATACAG ATACAG TTACAG ATGCA-
1 ATACAG ATACAG ATACAG ATACAG ATACAG ATACAG ATACAG ATACAG
*
44383 ATACAG ATACAG TTACAG AT
1 ATACAG ATACAG ATACAG AT
44403 GCAAACATGA
Statistics
Matches: 44, Mismatches: 14, Indels: 4
0.71 0.23 0.06
Matches are distributed among these distances:
5 7 0.16
6 37 0.84
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.23
Consensus pattern (6 bp):
ATACAG
Found at i:44378 original size:23 final size:23
Alignment explanation
Indices: 44336--44401 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 23
44326 ACATAATATA
* * * *
44336 AATACAGTTACAGATGCAGACAT
1 AATACAGATACAGTTACAGACAC
**
44359 AATACAGATACAGTTACAGATGC
1 AATACAGATACAGTTACAGACAC
44382 AATACAGATACAGTTACAGA
1 AATACAGATACAGTTACAGA
44402 TGCAAACATG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.45, C:0.17, G:0.17, T:0.21
Consensus pattern (23 bp):
AATACAGATACAGTTACAGACAC
Found at i:44392 original size:29 final size:29
Alignment explanation
Indices: 44308--44415 Score: 138
Period size: 29 Copynumber: 3.9 Consensus size: 29
44298 CACAGATATA
* *
44308 ATACAGTTACAGATGCAGACATAATATAA
1 ATACAGTTACAGATGCAGACATAATACAG
44337 ATACAGTTACAGATGCAGACATAATACAG
1 ATACAGTTACAGATGCAGACATAATACAG
44366 ATACAGTTACAGAT---G-C--AATACAG
1 ATACAGTTACAGATGCAGACATAATACAG
* *
44389 ATACAGTTACAGATGCAAACATGATAC
1 ATACAGTTACAGATGCAGACATAATAC
44416 CCCCATTCGT
Statistics
Matches: 69, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
23 21 0.30
25 1 0.01
26 1 0.01
27 1 0.01
29 45 0.65
ACGTcount: A:0.45, C:0.17, G:0.16, T:0.22
Consensus pattern (29 bp):
ATACAGTTACAGATGCAGACATAATACAG
Found at i:44402 original size:23 final size:23
Alignment explanation
Indices: 44359--44415 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
44349 ATGCAGACAT
44359 AATACAGATACAGTTACAGATGC
1 AATACAGATACAGTTACAGATGC
44382 AATACAGATACAGTTACAGATGC
1 AATACAGATACAGTTACAGATGC
44405 AA-ACATGATAC
1 AATACA-GATAC
44416 CCCCATTCGT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 3 0.09
23 30 0.91
ACGTcount: A:0.46, C:0.18, G:0.16, T:0.21
Consensus pattern (23 bp):
AATACAGATACAGTTACAGATGC
Found at i:44618 original size:130 final size:130
Alignment explanation
Indices: 44385--44646 Score: 515
Period size: 130 Copynumber: 2.0 Consensus size: 130
44375 CAGATGCAAT
44385 ACAGATACAGTTACAGATGCAAACATGATACCCCCATTCGTTATACACCATCTTCGTCCAACCCC
1 ACAGATACAGTTACAGATGCAAACATGATACCCCCATTCGTTATACACCATCTTCGTCCAACCCC
44450 TCTCCATTATCCATCCCTACACTCCAGAAGGTGTTGGTATGGCACGTCGCAGTGTTTACAGTGTC
66 TCTCCATTATCCATCCCTACACTCCAGAAGGTGTTGGTATGGCACGTCGCAGTGTTTACAGTGTC
*
44515 ACAGATACAGTTACAGATGCAAACATGATACCCCCATTCGTTATACACCATTTTCGTCCAACCCC
1 ACAGATACAGTTACAGATGCAAACATGATACCCCCATTCGTTATACACCATCTTCGTCCAACCCC
44580 TCTCCATTATCCATCCCTACACTCCAGAAGGTGTTGGTATGGCACGTCGCAGTGTTTACAGTGTC
66 TCTCCATTATCCATCCCTACACTCCAGAAGGTGTTGGTATGGCACGTCGCAGTGTTTACAGTGTC
44645 AC
1 AC
44647 TGTCAGTTCA
Statistics
Matches: 131, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
130 131 1.00
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.27
Consensus pattern (130 bp):
ACAGATACAGTTACAGATGCAAACATGATACCCCCATTCGTTATACACCATCTTCGTCCAACCCC
TCTCCATTATCCATCCCTACACTCCAGAAGGTGTTGGTATGGCACGTCGCAGTGTTTACAGTGTC
Found at i:44737 original size:40 final size:40
Alignment explanation
Indices: 44628--44738 Score: 143
Period size: 40 Copynumber: 2.8 Consensus size: 40
44618 ATGGCACGTC
* *
44628 GCAGTGTTTACAGTGTCACTGTCAGTTCAATTATAATCTT
1 GCAGTGTTTACAGTGTCACTGCCAGTTCAGTTATAATCTT
* * *
44668 GCAATGTTTACAGTGTCACTACTAGTTCAGTTGA-AATCTT
1 GCAGTGTTTACAGTGTCACTGCCAGTTCAGTT-ATAATCTT
* *
44708 GCAGTGTTTATAGTGTCACTGCCAATTCAGT
1 GCAGTGTTTACAGTGTCACTGCCAGTTCAGT
44739 AAATATTCTC
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
40 59 0.98
41 1 0.02
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (40 bp):
GCAGTGTTTACAGTGTCACTGCCAGTTCAGTTATAATCTT
Found at i:45462 original size:42 final size:43
Alignment explanation
Indices: 45404--45515 Score: 156
Period size: 42 Copynumber: 2.6 Consensus size: 43
45394 CCCGTGTGCC
45404 ACACACACCCTGACACATGCCCGTGTGCC-CCTAAACAATATA-
1 ACACACACCCTGACACATGCCCGTGTGCCTCC-AAACAATATAG
* * *
45446 ACACACACCCTAACACATGCCCGTGTGCCTCCAAATAGTATAG
1 ACACACACCCTGACACATGCCCGTGTGCCTCCAAACAATATAG
**
45489 ACACACACCCTGACACACCCCCGTGTG
1 ACACACACCCTGACACATGCCCGTGTG
45516 TCAGCCCACG
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
42 36 0.58
43 26 0.42
ACGTcount: A:0.31, C:0.39, G:0.13, T:0.16
Consensus pattern (43 bp):
ACACACACCCTGACACATGCCCGTGTGCCTCCAAACAATATAG
Found at i:47240 original size:22 final size:22
Alignment explanation
Indices: 47192--47240 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
47182 TAATTGAATT
* *
47192 TAAATTTTTAAATTCGAAATAA
1 TAAAATTTTAAATTCCAAATAA
*
47214 AAAAATTTTAAATTTCCAAA-AA
1 TAAAATTTTAAA-TTCCAAATAA
47236 TAAAA
1 TAAAA
47241 GTACAAAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.35
Consensus pattern (22 bp):
TAAAATTTTAAATTCCAAATAA
Found at i:51350 original size:68 final size:68
Alignment explanation
Indices: 51266--51406 Score: 264
Period size: 68 Copynumber: 2.1 Consensus size: 68
51256 AATTTTAGTA
51266 AAAGAATTAAATTCAAATGAAAATCCTGAAATTTAGGATGAAATGTTGATTTGGCTTTAAACTAT
1 AAAGAATTAAATTCAAATGAAAATCCTGAAATTTAGGATGAAATGTTGATTTGGCTTTAAACTAT
51331 TAG
66 TAG
* *
51334 AAAGAATTAAATTCAAATGAAAATGCTGAAATTTAGGATGAAATGTTGATTTGGTTTTAAACTAT
1 AAAGAATTAAATTCAAATGAAAATCCTGAAATTTAGGATGAAATGTTGATTTGGCTTTAAACTAT
51399 TAG
66 TAG
51402 AAAGA
1 AAAGA
51407 GATACTATTC
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 71 1.00
ACGTcount: A:0.44, C:0.06, G:0.17, T:0.33
Consensus pattern (68 bp):
AAAGAATTAAATTCAAATGAAAATCCTGAAATTTAGGATGAAATGTTGATTTGGCTTTAAACTAT
TAG
Found at i:57882 original size:11 final size:11
Alignment explanation
Indices: 57849--57882 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
57839 TTATATAGTT
*
57849 TGGGTTTTAAT
1 TGGGTTTTAAA
57860 TGGGTTTGTAAA
1 TGGGTTT-TAAA
57872 TGGGTTTTAAA
1 TGGGTTTTAAA
57883 GGGACATTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.47
Consensus pattern (11 bp):
TGGGTTTTAAA
Found at i:58513 original size:114 final size:114
Alignment explanation
Indices: 58306--58846 Score: 733
Period size: 114 Copynumber: 4.7 Consensus size: 114
58296 ATTCGCTATT
* *
58306 TGTTTTAACCCACTTCTCTGTACCTCACCAGGAAAATGGGATTTGAAGTCTCACTCCACTCCACT
1 TGTTTTGACCCACTTCTCTGTACCTCACCAGGAAGATGGGATTTGAAGTCTCACTCCACTCCACT
* * *
58371 GTATCCTCAGGGACATTGAGCTCGACTTCGTTGTTTTGATTCAACACAT
66 GTATCCTCAGGGACGTTGAGCTCAACTTCGTTGTTTTGATTCAACACAC
* * *
58420 TTTTTTGACCCACTTCTCTGTACCCCACCAGGAAGATGGGATTTGAAGTTTCACTCCACTCCACT
1 TGTTTTGACCCACTTCTCTGTACCTCACCAGGAAGATGGGATTTGAAGTCTCACTCCACTCCACT
* * *
58485 ATATCCTCAGGGACGTTAAACTCAACTTCGTTGTTTTGATTCAACACAC
66 GTATCCTCAGGGACGTTGAGCTCAACTTCGTTGTTTTGATTCAACACAC
* * * *
58534 TATTTTGACCCACTTTTCTGTACCTCACCAGGAAGATGGGATTTGAAGTCTCACTCTACTCCATT
1 TGTTTTGACCCACTTCTCTGTACCTCACCAGGAAGATGGGATTTGAAGTCTCACTCCACTCCACT
* * *
58599 GTATCCTCACGGACGTTGAGCTCAGCTTTGTTGTTTTGATTCAACACAC
66 GTATCCTCAGGGACGTTGAGCTCAACTTCGTTGTTTTGATTCAACACAC
* * * * * *
58648 TGTATTGACCCACTTCTTTATACCTAACTAGGAAGATGGGATTTGAAGTCTCACTCTACTCCACT
1 TGTTTTGACCCACTTCTCTGTACCTCACCAGGAAGATGGGATTTGAAGTCTCACTCCACTCCACT
* ** * ** * *
58713 GTATCCTTAAAGATGTTGAGCTCGGCTTCATTATTTTGATTCAACACAC
66 GTATCCTCAGGGACGTTGAGCTCAACTTCGTTGTTTTGATTCAACACAC
* * * *
58762 TGTATTGACCCATTTCTCTGTACCTCACC-GAGAAGATGTGATTTGAAGTTTCACTCCACTCCAC
1 TGTTTTGACCCACTTCTCTGTACCTCACCAG-GAAGATGGGATTTGAAGTCTCACTCCACTCCAC
*
58826 TGTATCCTTAGGGACGTTGAG
65 TGTATCCTCAGGGACGTTGAG
58847 TTCTGATTCA
Statistics
Matches: 376, Mismatches: 50, Indels: 2
0.88 0.12 0.00
Matches are distributed among these distances:
113 1 0.00
114 375 1.00
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.34
Consensus pattern (114 bp):
TGTTTTGACCCACTTCTCTGTACCTCACCAGGAAGATGGGATTTGAAGTCTCACTCCACTCCACT
GTATCCTCAGGGACGTTGAGCTCAACTTCGTTGTTTTGATTCAACACAC
Found at i:58919 original size:96 final size:96
Alignment explanation
Indices: 58769--58964 Score: 259
Period size: 96 Copynumber: 2.0 Consensus size: 96
58759 CACTGTATTG
* * * * * * *
58769 ACCCATTTCTCTGTACCTCACCGAGAAGATGTGATTTGAAGTTTCACTCCACTCCACTGTATCCT
1 ACCCACTTCTCAGTACCTCACAGAGAAGATGGGATTTGAAGTCTCACTCCACTCCACTGTAACAT
58834 TAGGGACGTTGAGTTCTGATTCATTATTTTA
66 TAGGGACGTTGAGTTCTGATTCATTATTTTA
* *
58865 ACCCACTTCTCAGTACCTCACTAG-GAAGCTGGGATTTTAAGTCTCACTCCACTCCACTGTAACA
1 ACCCACTTCTCAGTACCTCAC-AGAGAAGATGGGATTTGAAGTCTCACTCCACTCCACTGTAACA
* * * *
58929 TTAGGGACGTTGAGTTTTGCTTCATTGTTTTG
65 TTAGGGACGTTGAGTTCTGATTCATTATTTTA
58961 ACCC
1 ACCC
58965 GACCCACTAC
Statistics
Matches: 86, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
96 85 0.99
97 1 0.01
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.35
Consensus pattern (96 bp):
ACCCACTTCTCAGTACCTCACAGAGAAGATGGGATTTGAAGTCTCACTCCACTCCACTGTAACAT
TAGGGACGTTGAGTTCTGATTCATTATTTTA
Found at i:59490 original size:147 final size:147
Alignment explanation
Indices: 59260--59547 Score: 371
Period size: 147 Copynumber: 2.0 Consensus size: 147
59250 GGGAATAAGA
* * * * * *
59260 TTCGTCGTTGCGGCTTCAATCTTTCCCTTCACATCTCTAAGGTTTAAGTTCCACCGTTGACACTT
1 TTCGTCATAGCGGCTTCAACCTTTCCCTCCACATCTCTAAGGTATAAGGTCCACCGTTGACACTT
* * * * * *
59325 CAACCTTTGCCTCTACATCTCTAGAGTATAAGATTCGTTGTTGTGGCTTCAATATTTCCCTTCAT
66 CAACCTTTCCCTCCACATCTCTAGAGTATAAGATTCGTCGTTGCGGCCTCAACATTTCCCTTCAT
59390 ATCTCTAGGGTCGAAGG
131 ATCTCTAGGGTCGAAGG
* ** *
59407 TTCGTCATAGCGGCTTCAACCTTTCCCTCCACATCTCTAGGGTATAAGGTCTGCCGTT-ACCGCT
1 TTCGTCATAGCGGCTTCAACCTTTCCCTCCACATCTCTAAGGTATAAGGTCCACCGTTGA-CACT
* * * * *
59471 TCAACCTTTCCCTCCACATCTCTAGTGTATATGGTTCGTCGTTGCGGCCTCGACCTTTCCCTTCA
65 TCAACCTTTCCCTCCACATCTCTAGAGTATAAGATTCGTCGTTGCGGCCTCAACATTTCCCTTCA
59536 TATCTCTAGGGT
130 TATCTCTAGGGT
59548 ATATGATTCA
Statistics
Matches: 119, Mismatches: 21, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
146 1 0.01
147 118 0.99
ACGTcount: A:0.18, C:0.29, G:0.17, T:0.36
Consensus pattern (147 bp):
TTCGTCATAGCGGCTTCAACCTTTCCCTCCACATCTCTAAGGTATAAGGTCCACCGTTGACACTT
CAACCTTTCCCTCCACATCTCTAGAGTATAAGATTCGTCGTTGCGGCCTCAACATTTCCCTTCAT
ATCTCTAGGGTCGAAGG
Found at i:59552 original size:49 final size:49
Alignment explanation
Indices: 59254--59550 Score: 267
Period size: 49 Copynumber: 6.1 Consensus size: 49
59244 TCTTCGGGGA
* * * *
59254 ATAAGATTCGTCGTTGCGGCTTCAATCTTTCCCTTCACATCTCTAAGGT
1 ATAAGGTTCGTCGTTGCGGCTTCAACCTTTCCCTCCACATCTCTAGGGT
* ** * * * *
59303 TTAA-GTTCCACCGTTGAC-ACTTCAACCTTTGCCTCTACATCTCTAGAGT
1 ATAAGGTT-CGTCGTTG-CGGCTTCAACCTTTCCCTCCACATCTCTAGGGT
* * * ** * *
59352 ATAAGATTCGTTGTTGTGGCTTCAATATTTCCCTTCATATCTCTAGGGT
1 ATAAGGTTCGTCGTTGCGGCTTCAACCTTTCCCTCCACATCTCTAGGGT
** * *
59401 CGAAGGTTCGTCATAGCGGCTTCAACCTTTCCCTCCACATCTCTAGGGT
1 ATAAGGTTCGTCGTTGCGGCTTCAACCTTTCCCTCCACATCTCTAGGGT
* * * *
59450 ATAAGG-TCTGCCGTTACCGCTTCAACCTTTCCCTCCACATCTCTAGTGT
1 ATAAGGTTC-GTCGTTGCGGCTTCAACCTTTCCCTCCACATCTCTAGGGT
* * * * *
59499 ATATGGTTCGTCGTTGCGGCCTCGACCTTTCCCTTCATATCTCTAGGGT
1 ATAAGGTTCGTCGTTGCGGCTTCAACCTTTCCCTCCACATCTCTAGGGT
59548 ATA
1 ATA
59551 TGATTCAACA
Statistics
Matches: 189, Mismatches: 53, Indels: 12
0.74 0.21 0.05
Matches are distributed among these distances:
48 4 0.02
49 180 0.95
50 5 0.03
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.35
Consensus pattern (49 bp):
ATAAGGTTCGTCGTTGCGGCTTCAACCTTTCCCTCCACATCTCTAGGGT
Found at i:60511 original size:19 final size:19
Alignment explanation
Indices: 60466--60533 Score: 59
Period size: 18 Copynumber: 3.5 Consensus size: 19
60456 AACCTCTTCT
* * *
60466 TTTCTTCTTCCTTCTTTT-
1 TTTCTTTTTTCTTTTTTTC
*
60484 TTTCCTTTTTCTTTTTTTC
1 TTTCTTTTTTCTTTTTTTC
60503 TTTCTTTTTT-TTCTTTTTC
1 TTTCTTTTTTCTT-TTTTTC
60522 TCTTCCTTTTTT
1 T-TT-CTTTTTT
60534 TATTTTTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
18 16 0.39
19 16 0.39
20 2 0.05
21 7 0.17
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTCTTTTTTCTTTTTTTC
Found at i:60514 original size:15 final size:16
Alignment explanation
Indices: 60462--60514 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 16
60452 CCTTAACCTC
* *
60462 TTCTTTTCTT-CTTCC
1 TTCTTTTTTTCCTTCT
60477 TTCTTTTTTTCCTT-T
1 TTCTTTTTTTCCTTCT
*
60492 TTCTTTTTTTCTTTCT
1 TTCTTTTTTTCCTTCT
60508 TT-TTTTT
1 TTCTTTTT
60515 CTTTTTCTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 27 0.82
16 6 0.18
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (16 bp):
TTCTTTTTTTCCTTCT
Found at i:60515 original size:21 final size:21
Alignment explanation
Indices: 60489--60543 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
60479 CTTTTTTTCC
*
60489 TTTTTCTTTTTTTCTTTCTTT
1 TTTTTCTTTTTTTCTTCCTTT
*
60510 TTTTTCTTTTTCTCTTCCTTT
1 TTTTTCTTTTTTTCTTCCTTT
60531 TTTTAT-TTTTTTT
1 TTTT-TCTTTTTTT
60544 GGGATGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 29 0.97
22 1 0.03
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.84
Consensus pattern (21 bp):
TTTTTCTTTTTTTCTTCCTTT
Found at i:60521 original size:15 final size:15
Alignment explanation
Indices: 60477--60522 Score: 62
Period size: 13 Copynumber: 3.3 Consensus size: 15
60467 TTCTTCTTCC
*
60477 TTCTTTTTTTCCTTT
1 TTCTTTTTTTTCTTT
60492 TTC-TTTTTTTC--T
1 TTCTTTTTTTTCTTT
60504 TTCTTTTTTTTCTTT
1 TTCTTTTTTTTCTTT
60519 TTCT
1 TTCT
60523 CTTCCTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 4 0.15
13 8 0.30
14 7 0.26
15 8 0.30
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TTCTTTTTTTTCTTT
Found at i:60525 original size:29 final size:28
Alignment explanation
Indices: 60480--60543 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
60470 TTCTTCCTTC
* *
60480 TTTTTTTCCTTTTTCTT-TTTTTCTTTCT
1 TTTTTTTCCTTTTTCTTCCTTTT-TTTAT
*
60508 TTTTTTTCTTTTTCTCTTCCTTTTTTTAT
1 TTTTTTTCCTTTT-TCTTCCTTTTTTTAT
60537 TTTTTTT
1 TTTTTTT
60544 GGGATGAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 12 0.39
29 15 0.48
30 4 0.13
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.83
Consensus pattern (28 bp):
TTTTTTTCCTTTTTCTTCCTTTTTTTAT
Found at i:60539 original size:19 final size:18
Alignment explanation
Indices: 60480--60540 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 18
60470 TTCTTCCTTC
60480 TTTT-TTTCCTTTTTCTTT
1 TTTTCTTTCCTTTTT-TTT
*
60498 TTTTCTTTCTTTTTTTTCT
1 TTTTCTTTCCTTTTTTT-T
60517 TTTTCTCTTCCTTTTTTTAT
1 TTTTCT-TTCCTTTTTTT-T
60537 TTTT
1 TTTT
60541 TTTGGGATGA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
18 6 0.16
19 16 0.43
20 15 0.41
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTCTTTCCTTTTTTTT
Found at i:61405 original size:20 final size:22
Alignment explanation
Indices: 61356--61410 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
61346 TTCATCTTAC
* *
61356 TTTTTCTTTCTTTTCTTTGTTTT
1 TTTTTCGTT-TTTTCTTTGTCTT
61379 TTGTTTC-TTTTTTCTTT-TCTT
1 TT-TTTCGTTTTTTCTTTGTCTT
61400 TTTTTCGTTTT
1 TTTTTCGTTTT
61411 AAGATGCCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
20 4 0.14
21 9 0.31
22 8 0.28
23 4 0.14
24 4 0.14
ACGTcount: A:0.00, C:0.13, G:0.05, T:0.82
Consensus pattern (22 bp):
TTTTTCGTTTTTTCTTTGTCTT
Found at i:69277 original size:21 final size:22
Alignment explanation
Indices: 69237--69281 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
69227 AAATTAGAAG
*
69237 AAAAAATTAGTAGATGAAAGTGA
1 AAAAAATTAGAAGA-GAAAGTGA
69260 AAAAAATTAGAAGA-AAAGTGA
1 AAAAAATTAGAAGAGAAAGTGA
69281 A
1 A
69282 GGAAAGTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.38
23 13 0.62
ACGTcount: A:0.62, C:0.00, G:0.20, T:0.18
Consensus pattern (22 bp):
AAAAAATTAGAAGAGAAAGTGA
Found at i:71208 original size:105 final size:105
Alignment explanation
Indices: 71026--71238 Score: 390
Period size: 105 Copynumber: 2.0 Consensus size: 105
71016 ATCAAAATTG
*
71026 AATGTTACAACATTGACTGAATGTTGCAACATTGGATTTAAATGTCGTAACATTTCTTATGCGCG
1 AATGTTACAACATTGACTGAATGTTGCAACATTGGATTTAAATGTCGTAACATTGCTTATGCGCG
71091 ACCACAATTTCCTACGCCCGTCGATTGTGATTTTAAGATA
66 ACCACAATTTCCTACGCCCGTCGATTGTGATTTTAAGATA
* *
71131 AATGTTGCGACATTGACTGAATGTTGCAACATTGGATTTAAATGTCGTAACATTGCTTATGCGCG
1 AATGTTACAACATTGACTGAATGTTGCAACATTGGATTTAAATGTCGTAACATTGCTTATGCGCG
*
71196 ACCACAATTTCCTACGCTCGTCGATTGTGATTTTAAGATA
66 ACCACAATTTCCTACGCCCGTCGATTGTGATTTTAAGATA
71236 AAT
1 AAT
71239 TAGAGGTCTT
Statistics
Matches: 104, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
105 104 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34
Consensus pattern (105 bp):
AATGTTACAACATTGACTGAATGTTGCAACATTGGATTTAAATGTCGTAACATTGCTTATGCGCG
ACCACAATTTCCTACGCCCGTCGATTGTGATTTTAAGATA
Found at i:72326 original size:30 final size:30
Alignment explanation
Indices: 72290--72370 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 30
72280 CAAAGAATAG
* *
72290 CCACAAAGACTTCCACATATCAGAGTACAA
1 CCACAAAGACTTTCACATATCAGAGAACAA
*
72320 CCACAAA-AGCTTTCACATTTCAGAGAACAA
1 CCACAAAGA-CTTTCACATATCAGAGAACAA
* *
72350 CCATAAAGGCTTTCACATATC
1 CCACAAAGACTTTCACATATC
72371 GGTAACTTAG
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
29 1 0.02
30 42 0.98
ACGTcount: A:0.41, C:0.28, G:0.10, T:0.21
Consensus pattern (30 bp):
CCACAAAGACTTTCACATATCAGAGAACAA
Found at i:75285 original size:21 final size:20
Alignment explanation
Indices: 75260--75313 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
75250 TAGTGTAGAC
75260 TTCTACCGATACAAGTGTCTT-
1 TTCTACCGATACAA--GTCTTA
* *
75281 TTCTACCCAAACAAGTCTTA
1 TTCTACCGATACAAGTCTTA
75301 CTTCTACCGATAC
1 -TTCTACCGATAC
75314 TAAAAACTCC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
19 5 0.19
21 22 0.81
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (20 bp):
TTCTACCGATACAAGTCTTA
Found at i:78435 original size:27 final size:27
Alignment explanation
Indices: 78397--78485 Score: 160
Period size: 27 Copynumber: 3.3 Consensus size: 27
78387 AATCTAATTT
78397 TGGCTCGAAAGAGCGTTATTCTGATTC
1 TGGCTCGAAAGAGCGTTATTCTGATTC
78424 TGGCTCGAAAGAGCGTTATTCTGATTC
1 TGGCTCGAAAGAGCGTTATTCTGATTC
*
78451 TGGCTCGAAAGAGCATTATTCTGATTC
1 TGGCTCGAAAGAGCGTTATTCTGATTC
78478 TGGGCTCG
1 T-GGCTCG
78486 TGTGAGCTAA
Statistics
Matches: 60, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
27 54 0.90
28 6 0.10
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (27 bp):
TGGCTCGAAAGAGCGTTATTCTGATTC
Found at i:80376 original size:50 final size:50
Alignment explanation
Indices: 80317--80509 Score: 210
Period size: 50 Copynumber: 3.8 Consensus size: 50
80307 AGGTTGAAGT
*
80317 AGTGGCAGTATATCTACAAATCAGTGGTGGCATGTCCACAAAATTATATC
1 AGTGGCAGTATATCTACAAATCAGTGGTGGCTTGTCCACAAAATTATATC
* * ** * * *
80367 AGTGGCAGTATATTTGCAAAGGAGTGGTAGCTTGGCCACAAAAATATATC
1 AGTGGCAGTATATCTACAAATCAGTGGTGGCTTGTCCACAAAATTATATC
* * *
80417 AGTGGCAGTATATCTACAAATTAGTGGTGGCTTGTCCACAATAGTGT-TATT
1 AGTGGCAGTATATCTACAAATCAGTGGTGGCTTGTCCACAA-AAT-TATATC
* * * *
80468 AGTGGCAGT-TGATATGCAAATCAATGGTGCCTTGTCCACAAA
1 AGTGGCAGTAT-ATCTACAAATCAGTGGTGGCTTGTCCACAAA
80510 TGGTGATTCG
Statistics
Matches: 118, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
50 79 0.67
51 38 0.32
52 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (50 bp):
AGTGGCAGTATATCTACAAATCAGTGGTGGCTTGTCCACAAAATTATATC
Found at i:89469 original size:29 final size:29
Alignment explanation
Indices: 89436--89507 Score: 110
Period size: 29 Copynumber: 2.4 Consensus size: 29
89426 TACGCTAGAG
89436 GTGTGTCTCTGTCTGTGCTACATA-TTGTT
1 GTGTGT-TCTGTCTGTGCTACATATTTGTT
*
89465 GTGTGTTTCTATCTGTGCTACATATTTGTT
1 GTGTG-TTCTGTCTGTGCTACATATTTGTT
89495 GTGTGTTCTGTCT
1 GTGTGTTCTGTCT
89508 ATGTTATATG
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 28 0.72
30 11 0.28
ACGTcount: A:0.10, C:0.15, G:0.24, T:0.51
Consensus pattern (29 bp):
GTGTGTTCTGTCTGTGCTACATATTTGTT
Found at i:97978 original size:65 final size:65
Alignment explanation
Indices: 97897--98028 Score: 246
Period size: 65 Copynumber: 2.0 Consensus size: 65
97887 CTGTTAAACT
97897 AAGCCTTATTGGATAATATGTTTTGATATAAAAAATTAAAGTGTTTTTGAATAAAAGCTAAGTGG
1 AAGCCTTATTGGATAATATGTTTTGATATAAAAAATTAAAGTGTTTTTGAATAAAAGCTAAGTGG
* *
97962 AAGCCTTATTGGATAATATGTTTTGATATAACAAATTAAAGTGTTTTTGAATAAAAGCTGAGTGG
1 AAGCCTTATTGGATAATATGTTTTGATATAAAAAATTAAAGTGTTTTTGAATAAAAGCTAAGTGG
98027 AA
1 AA
98029 AAGACTCCAG
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.39, C:0.05, G:0.19, T:0.36
Consensus pattern (65 bp):
AAGCCTTATTGGATAATATGTTTTGATATAAAAAATTAAAGTGTTTTTGAATAAAAGCTAAGTGG
Found at i:101105 original size:20 final size:20
Alignment explanation
Indices: 101077--101130 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
101067 CTCCAGTGAG
*
101077 ACTTCTACCGATAGAACTCC
1 ACTTCTACCGATACAACTCC
*
101097 ACTTATACCGATACAACTCC
1 ACTTCTACCGATACAACTCC
101117 ACTTCTACCGATAC
1 ACTTCTACCGATAC
101131 CTTGAAGAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.31, C:0.35, G:0.07, T:0.26
Consensus pattern (20 bp):
ACTTCTACCGATACAACTCC
Found at i:101341 original size:20 final size:20
Alignment explanation
Indices: 101316--101371 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
101306 CAACTCTAGG
* *
101316 ACTTCTACCGATAGAACTCC
1 ACTTCTACCGATACAACTAC
*
101336 ACTTCTACTGATACAACTAC
1 ACTTCTACCGATACAACTAC
*
101356 AATTCTACCGATACAA
1 ACTTCTACCGATACAA
101372 GTATGCTTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.36, C:0.30, G:0.07, T:0.27
Consensus pattern (20 bp):
ACTTCTACCGATACAACTAC
Found at i:102793 original size:50 final size:50
Alignment explanation
Indices: 102708--102817 Score: 130
Period size: 50 Copynumber: 2.2 Consensus size: 50
102698 AAAGCAAAGG
* * * ** * * *
102708 CAGTATATCTGCAAATCAGTGGTGGCATGTCCACAAAATTATATTAGTGA
1 CAGTATATATGCAAATCAGCGATGGCATGGACACAAAAATATATCAATGA
* *
102758 CAGTATATATGCAAATCAGCGATGGCTTGGACACAAAAATATATCAATGG
1 CAGTATATATGCAAATCAGCGATGGCATGGACACAAAAATATATCAATGA
102808 CAGTATATAT
1 CAGTATATAT
102818 ATACAAATTG
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.28
Consensus pattern (50 bp):
CAGTATATATGCAAATCAGCGATGGCATGGACACAAAAATATATCAATGA
Found at i:104127 original size:23 final size:23
Alignment explanation
Indices: 104097--104171 Score: 107
Period size: 23 Copynumber: 3.3 Consensus size: 23
104087 GAAACAGTAA
104097 GCACACACAGTGCAATCCAATAG
1 GCACACACAGTGCAATCCAATAG
*
104120 GCACACACAGTGCAATCCAGTAG
1 GCACACACAGTGCAATCCAATAG
* *
104143 GCACACATAGCGCAAAT-CAATAG
1 GCACACACAGTGC-AATCCAATAG
104166 GCACAC
1 GCACAC
104172 GAAGTGTGAA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
23 44 0.94
24 3 0.06
ACGTcount: A:0.39, C:0.31, G:0.19, T:0.12
Consensus pattern (23 bp):
GCACACACAGTGCAATCCAATAG
Found at i:104147 original size:46 final size:46
Alignment explanation
Indices: 104088--104206 Score: 136
Period size: 46 Copynumber: 2.6 Consensus size: 46
104078 AGTGCTGGGG
104088 AAACAGTAAGCACACACAGTGC-AATCCAATAGGCACAC-ACAGTG-C
1 AAACAGTAAGCACACACAGTGCAAAT-CAATAGGCACACGA-AGTGTC
* * * * *
104133 AATCCAGTAGGCACACATAGCGCAAATCAATAGGCACACGAAGTGTG
1 AA-ACAGTAAGCACACACAGTGCAAATCAATAGGCACACGAAGTGTC
104180 AAACAGTAAGCACACACAGTGCTAAAT
1 AAACAGTAAGCACACACAGTGC-AAAT
104207 ACTAAGCGCG
Statistics
Matches: 60, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
45 2 0.03
46 48 0.80
47 10 0.17
ACGTcount: A:0.42, C:0.25, G:0.19, T:0.13
Consensus pattern (46 bp):
AAACAGTAAGCACACACAGTGCAAATCAATAGGCACACGAAGTGTC
Found at i:104200 original size:23 final size:22
Alignment explanation
Indices: 104088--104201 Score: 86
Period size: 23 Copynumber: 5.0 Consensus size: 22
104078 AGTGCTGGGG
104088 AAACAGTAAGCACACACAGTGC
1 AAACAGTAAGCACACACAGTGC
* * *
104110 AATCCAATAGGCACACACAGTGC
1 AA-ACAGTAAGCACACACAGTGC
* * * *
104133 AATCCAGTAGGCACACATAGCGC
1 AA-ACAGTAAGCACACACAGTGC
* * *
104156 AAATCAATAGGCACACGA-AGTGTG
1 AAA-CAGTAAGCACAC-ACAGTG-C
104180 AAACAGTAAGCACACACAGTGC
1 AAACAGTAAGCACACACAGTGC
104202 TAAATACTAA
Statistics
Matches: 74, Mismatches: 13, Indels: 10
0.76 0.13 0.10
Matches are distributed among these distances:
22 3 0.04
23 67 0.91
24 4 0.05
ACGTcount: A:0.41, C:0.26, G:0.20, T:0.12
Consensus pattern (22 bp):
AAACAGTAAGCACACACAGTGC
Found at i:104314 original size:24 final size:26
Alignment explanation
Indices: 104276--104323 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
104266 TCTACATGGG
104276 CATAATCTCTCATAT-TCATCATTTCT
1 CATAATCTCTCATATATCA-CATTTCT
104302 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
104324 ACATTTCTCT
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:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTCT
Found at i:106442 original size:50 final size:50
Alignment explanation
Indices: 106357--106466 Score: 130
Period size: 50 Copynumber: 2.2 Consensus size: 50
106347 AAAGCAAAGG
* * * ** * * *
106357 CAGTATATCTGCAAATCAGTGGTGGCATGTCCACAAAATTATATTAGTGA
1 CAGTATATATGCAAATCAGCGATGGCATGGACACAAAAATATATCAATGA
* *
106407 CAGTATATATGCAAATCAGCGATGGCTTGGACACAAAAATATATCAATGG
1 CAGTATATATGCAAATCAGCGATGGCATGGACACAAAAATATATCAATGA
106457 CAGTATATAT
1 CAGTATATAT
106467 ATACAAATTG
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.28
Consensus pattern (50 bp):
CAGTATATATGCAAATCAGCGATGGCATGGACACAAAAATATATCAATGA
Found at i:107776 original size:23 final size:23
Alignment explanation
Indices: 107746--107820 Score: 107
Period size: 23 Copynumber: 3.3 Consensus size: 23
107736 GAAACAGTAA
107746 GCACACACAGTGCAATCCAATAG
1 GCACACACAGTGCAATCCAATAG
*
107769 GCACACACAGTGCAATCCAGTAG
1 GCACACACAGTGCAATCCAATAG
* *
107792 GCACACATAGCGCAAAT-CAATAG
1 GCACACACAGTGC-AATCCAATAG
107815 GCACAC
1 GCACAC
107821 GAAGTGTGAA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
23 44 0.94
24 3 0.06
ACGTcount: A:0.39, C:0.31, G:0.19, T:0.12
Consensus pattern (23 bp):
GCACACACAGTGCAATCCAATAG
Found at i:107796 original size:46 final size:46
Alignment explanation
Indices: 107737--107855 Score: 136
Period size: 46 Copynumber: 2.6 Consensus size: 46
107727 AGTGCTGGGG
107737 AAACAGTAAGCACACACAGTGC-AATCCAATAGGCACAC-ACAGTG-C
1 AAACAGTAAGCACACACAGTGCAAAT-CAATAGGCACACGA-AGTGTC
* * * * *
107782 AATCCAGTAGGCACACATAGCGCAAATCAATAGGCACACGAAGTGTG
1 AA-ACAGTAAGCACACACAGTGCAAATCAATAGGCACACGAAGTGTC
107829 AAACAGTAAGCACACACAGTGCTAAAT
1 AAACAGTAAGCACACACAGTGC-AAAT
107856 ACTAAGCGCG
Statistics
Matches: 60, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
45 2 0.03
46 48 0.80
47 10 0.17
ACGTcount: A:0.42, C:0.25, G:0.19, T:0.13
Consensus pattern (46 bp):
AAACAGTAAGCACACACAGTGCAAATCAATAGGCACACGAAGTGTC
Found at i:107849 original size:23 final size:22
Alignment explanation
Indices: 107737--107850 Score: 86
Period size: 23 Copynumber: 5.0 Consensus size: 22
107727 AGTGCTGGGG
107737 AAACAGTAAGCACACACAGTGC
1 AAACAGTAAGCACACACAGTGC
* * *
107759 AATCCAATAGGCACACACAGTGC
1 AA-ACAGTAAGCACACACAGTGC
* * * *
107782 AATCCAGTAGGCACACATAGCGC
1 AA-ACAGTAAGCACACACAGTGC
* * *
107805 AAATCAATAGGCACACGA-AGTGTG
1 AAA-CAGTAAGCACAC-ACAGTG-C
107829 AAACAGTAAGCACACACAGTGC
1 AAACAGTAAGCACACACAGTGC
107851 TAAATACTAA
Statistics
Matches: 74, Mismatches: 13, Indels: 10
0.76 0.13 0.10
Matches are distributed among these distances:
22 3 0.04
23 67 0.91
24 4 0.05
ACGTcount: A:0.41, C:0.26, G:0.20, T:0.12
Consensus pattern (22 bp):
AAACAGTAAGCACACACAGTGC
Found at i:107963 original size:24 final size:26
Alignment explanation
Indices: 107925--107972 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
107915 TCTACATGGG
107925 CATAATCTCTCATAT-TCATCATTTCT
1 CATAATCTCTCATATATCA-CATTTCT
107951 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
107973 ACATTTCTCT
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:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTCT
Done.