Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011943.1 Kokia drynarioides strain JFW-HI SEQ_126941, 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: 322276
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 263 characters in sequence are not A, C, G, or T
Found at i:17 original size:2 final size:2
Alignment explanation
Indices: 12--50 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2 AAAAAAAAAA
12 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 A
51 ATTTTATAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9139 original size:3 final size:3
Alignment explanation
Indices: 9133--9163 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
9123 GAAAAAGATA
9133 AAT AAT AAT AAT AAT AAT AAAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
9164 TTATCAGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:19327 original size:23 final size:25
Alignment explanation
Indices: 19301--19353 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
19291 TGAATAAAAC
19301 TAAATTTAAAT-ATA-TAAATACAT
1 TAAATTTAAATAATATTAAATACAT
*
19324 TAAA--TAAATAATATTAAATATAT
1 TAAATTTAAATAATATTAAATACAT
19347 TACAATT
1 TA-AATT
19354 ATTTATCATT
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
21 5 0.21
22 3 0.12
23 14 0.58
24 2 0.08
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.40
Consensus pattern (25 bp):
TAAATTTAAATAATATTAAATACAT
Found at i:22759 original size:2 final size:2
Alignment explanation
Indices: 22694--22740 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
22684 CCTGGCAAGG
* *
22694 TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA TA TA GA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
22736 TA TA T
1 TA TA T
22741 CTAAAGTTCT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:26944 original size:41 final size:40
Alignment explanation
Indices: 26883--26976 Score: 143
Period size: 41 Copynumber: 2.3 Consensus size: 40
26873 ATGATATTTA
26883 TTTTAAATTATCTTTTAAATTTCAAAATATTTTAATTGTAT
1 TTTTAAATTAT-TTTTAAATTTCAAAATATTTTAATTGTAT
* *
26924 TTTTAAATTATTTTTCAAATTTTAAAATATTTTAATTTTAT
1 TTTTAAATTATTTTT-AAATTTCAAAATATTTTAATTGTAT
*
26965 TTTAAAATTATT
1 TTTTAAATTATT
26977 GATGTTATAT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
40 4 0.08
41 45 0.92
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (40 bp):
TTTTAAATTATTTTTAAATTTCAAAATATTTTAATTGTAT
Found at i:37178 original size:13 final size:13
Alignment explanation
Indices: 37160--37188 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
37150 ACTATCATCT
37160 TTTGCATGAACTC
1 TTTGCATGAACTC
37173 TTTGCATGAACTC
1 TTTGCATGAACTC
37186 TTT
1 TTT
37189 CTTAGACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.21, C:0.21, G:0.14, T:0.45
Consensus pattern (13 bp):
TTTGCATGAACTC
Found at i:49837 original size:81 final size:81
Alignment explanation
Indices: 49723--49876 Score: 308
Period size: 81 Copynumber: 1.9 Consensus size: 81
49713 TACGATTTAA
49723 TTGGTTGAGAGTGAGAGAGACGACACCAATATTTATTTTTGTATTTATTTATTTTACCATTTGAG
1 TTGGTTGAGAGTGAGAGAGACGACACCAATATTTATTTTTGTATTTATTTATTTTACCATTTGAG
49788 TTGTTTTTTTTTTTTT
66 TTGTTTTTTTTTTTTT
49804 TTGGTTGAGAGTGAGAGAGACGACACCAATATTTATTTTTGTATTTATTTATTTTACCATTTGAG
1 TTGGTTGAGAGTGAGAGAGACGACACCAATATTTATTTTTGTATTTATTTATTTTACCATTTGAG
49869 TTGTTTTT
66 TTGTTTTT
49877 NNNNNNTTTG
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 73 1.00
ACGTcount: A:0.23, C:0.08, G:0.18, T:0.51
Consensus pattern (81 bp):
TTGGTTGAGAGTGAGAGAGACGACACCAATATTTATTTTTGTATTTATTTATTTTACCATTTGAG
TTGTTTTTTTTTTTTT
Found at i:51797 original size:23 final size:22
Alignment explanation
Indices: 51771--51873 Score: 116
Period size: 23 Copynumber: 4.5 Consensus size: 22
51761 ACATTAGCGC
* * *
51771 GCTTACTGTTCAGCATTGTGTGT
1 GCTTACTGTT-TGCACTGTGTAT
*
51794 GCTTACTGTTTTGCAATGTGTAT
1 GCTTACTG-TTTGCACTGTGTAT
51817 GCTTACTGATTTGCACTGTGTAT
1 GCTTACTG-TTTGCACTGTGTAT
*
51840 GCTTACTGATTTGCACTGTGTGT
1 GCTTACTG-TTTGCACTGTGTAT
*
51863 ACTTACTGTTT
1 GCTTACTGTTT
51874 CCCCAACACT
Statistics
Matches: 72, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
22 3 0.04
23 67 0.93
24 2 0.03
ACGTcount: A:0.16, C:0.17, G:0.22, T:0.46
Consensus pattern (22 bp):
GCTTACTGTTTGCACTGTGTAT
Found at i:52706 original size:17 final size:18
Alignment explanation
Indices: 52684--52717 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
52674 CTTCACCCTT
52684 AAATATATATA-TATTTA
1 AAATATATATATTATTTA
52701 AAATATATATATTATTT
1 AAATATATATATTATTT
52718 TGTAATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AAATATATATATTATTTA
Found at i:52708 original size:15 final size:16
Alignment explanation
Indices: 52682--52713 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
52672 ACCTTCACCC
52682 TTAAATATATATATAT
1 TTAAATATATATATAT
52698 TTAAA-ATATATATAT
1 TTAAATATATATATAT
52713 T
1 T
52714 ATTTTGTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAAATATATATATAT
Found at i:55827 original size:23 final size:24
Alignment explanation
Indices: 55768--55830 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
55758 TAATGTATAA
55768 AAATTAATTTTTAATAATAAAAAT
1 AAATTAATTTTTAATAATAAAAAT
* *
55792 AAATAAATATTTTAATAA-AAAATT
1 AAATTAAT-TTTTAATAATAAAAAT
* *
55816 TAATTTATTTTTAAT
1 AAATTAATTTTTAAT
55831 TGATTAATTG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
23 7 0.21
24 17 0.52
25 9 0.27
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
AAATTAATTTTTAATAATAAAAAT
Found at i:62438 original size:13 final size:13
Alignment explanation
Indices: 62420--62444 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
62410 TTATTAATTA
62420 ATGAATGTTATAC
1 ATGAATGTTATAC
62433 ATGAATGTTATA
1 ATGAATGTTATA
62445 ATGTACATTC
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:0.40, C:0.04, G:0.16, T:0.40
Consensus pattern (13 bp):
ATGAATGTTATAC
Found at i:62981 original size:24 final size:24
Alignment explanation
Indices: 62936--62988 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
62926 AAAATTATAA
* *
62936 ATAAAAAAGTATTCAAAAAACAAT
1 ATAAAAAAGTATTAAAAAAACAAC
*
62960 ATAAAAAATTA-TAAAAACAACAAC
1 ATAAAAAAGTATTAAAAA-AACAAC
62984 ATAAA
1 ATAAA
62989 GTATGCATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 5 0.20
24 20 0.80
ACGTcount: A:0.70, C:0.09, G:0.02, T:0.19
Consensus pattern (24 bp):
ATAAAAAAGTATTAAAAAAACAAC
Found at i:71855 original size:60 final size:60
Alignment explanation
Indices: 71779--71923 Score: 152
Period size: 60 Copynumber: 2.4 Consensus size: 60
71769 GGGCCTGAAC
* *
71779 TTTTTTTGGTTCAAGTTAATCCCTGAACTTGACAATTGTTGCCACATTG-AGGCTTGAAATT
1 TTTTTTTTG-TCAAGTTAATCCCTGAACTAGACAATTGTTGCCAC-TTGTAGGCTTGAAATT
* * * * *
71840 TTTTTTTTGTCAAGTTAA-CCCTTGAAGTAGGCAATTGTTTCCACTTGTTGGCTTGAACTT
1 TTTTTTTTGTCAAGTTAATCCC-TGAACTAGACAATTGTTGCCACTTGTAGGCTTGAAATT
* * *
71900 TTTTATTTCT-AAGTTAGTCCCTGA
1 TTTTTTTTGTCAAGTTAATCCCTGA
71924 TATTTCCTTT
Statistics
Matches: 71, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
59 15 0.21
60 48 0.68
61 8 0.11
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44
Consensus pattern (60 bp):
TTTTTTTTGTCAAGTTAATCCCTGAACTAGACAATTGTTGCCACTTGTAGGCTTGAAATT
Found at i:80736 original size:12 final size:12
Alignment explanation
Indices: 80704--80749 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
80694 TCCCATCATT
*
80704 ATCATCATCATG
1 ATCATCACCATG
*
80716 ATCACCACCATG
1 ATCATCACCATG
*
80728 ATCATCACCATC
1 ATCATCACCATG
*
80740 ACCATCACCA
1 ATCATCACCA
80750 CCACCGTCAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.35, C:0.39, G:0.04, T:0.22
Consensus pattern (12 bp):
ATCATCACCATG
Found at i:82165 original size:17 final size:17
Alignment explanation
Indices: 82143--82175 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
82133 GGATTTAGTA
82143 TTTTTTATGATAAATAT
1 TTTTTTATGATAAATAT
*
82160 TTTTTTTTGATAAATA
1 TTTTTTATGATAAATA
82176 AAAAGGCTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (17 bp):
TTTTTTATGATAAATAT
Found at i:94937 original size:17 final size:17
Alignment explanation
Indices: 94917--94956 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
94907 TAAGGTAATC
*
94917 ATAAAATAATAATTTTA
1 ATAAAATAATAATTTAA
**
94934 ATAACCTAATAATTTAA
1 ATAAAATAATAATTTAA
94951 ATAAAA
1 ATAAAA
94957 ATTTTCGAAT
Statistics
Matches: 18, Mismatches: 5, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (17 bp):
ATAAAATAATAATTTAA
Found at i:103139 original size:23 final size:21
Alignment explanation
Indices: 103113--103157 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 21
103103 TAAATTAAAA
*
103113 TTATATTTTTTATTAGATTATAT
1 TTATATTTATTATTA-ATT-TAT
103136 TTATATTTATTATTAATTTAT
1 TTATATTTATTATTAATTTAT
103157 T
1 T
103158 GCACGATCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.19
22 3 0.14
23 14 0.67
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
TTATATTTATTATTAATTTAT
Found at i:105112 original size:3 final size:3
Alignment explanation
Indices: 105104--105128 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
105094 TCACGAGGGG
105104 GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT G
105129 CTCTCTGCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:118580 original size:2 final size:2
Alignment explanation
Indices: 118569--118598 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
118559 ATACACACAC
118569 TA TA TGA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA T
118599 CACAATTTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:119343 original size:17 final size:17
Alignment explanation
Indices: 119301--119343 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
119291 TGATGGATAT
119301 TAATTT-ATTGTACTAA
1 TAATTTAATTGTACTAA
* **
119317 TCATCAAATTGTACTAA
1 TAATTTAATTGTACTAA
119334 TAATTTAATT
1 TAATTTAATT
119344 ATATTATAGC
Statistics
Matches: 20, Mismatches: 6, Indels: 1
0.74 0.22 0.04
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.47
Consensus pattern (17 bp):
TAATTTAATTGTACTAA
Found at i:120087 original size:19 final size:19
Alignment explanation
Indices: 120042--120087 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
120032 AAAAAAATAT
* *
120042 TTTTTAA-AATTTTTATGC
1 TTTTTAATAATTTTAATGA
120060 TTTTGTAATAATTTTAATGA
1 TTTT-TAATAATTTTAATGA
120080 TTTTTAAT
1 TTTTTAAT
120088 TTTTAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 4 0.17
19 7 0.29
20 13 0.54
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.61
Consensus pattern (19 bp):
TTTTTAATAATTTTAATGA
Found at i:123894 original size:18 final size:18
Alignment explanation
Indices: 123871--123913 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
123861 GTTCAAGGTG
123871 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
123889 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
123907 TAATTAA
1 TAATTAA
123914 AAACCTATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:136621 original size:61 final size:61
Alignment explanation
Indices: 136551--136682 Score: 237
Period size: 61 Copynumber: 2.1 Consensus size: 61
136541 ATGACAATGC
*
136551 ATTATTTAACCATTGGAATATTGATAAAAATTGTATTAATAGTTAAATTGTATTTTATCTT
1 ATTATTTAACCATTGGAATATTGATAAAAATTGTATTAATAGGTAAATTGTATTTTATCTT
136612 ATTATTTAACCATTGGAATATTGATAAAAATTGTATTAATAGGTAAATTGTATTTTATCTT
1 ATTATTTAACCATTGGAATATTGATAAAAATTGTATTAATAGGTAAATTGTATTTTATCTT
*
136673 TTCTATTTAA
1 AT-TATTTAA
136683 AAAATAATAA
Statistics
Matches: 68, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
61 61 0.90
62 7 0.10
ACGTcount: A:0.37, C:0.05, G:0.10, T:0.48
Consensus pattern (61 bp):
ATTATTTAACCATTGGAATATTGATAAAAATTGTATTAATAGGTAAATTGTATTTTATCTT
Found at i:157671 original size:12 final size:12
Alignment explanation
Indices: 157654--157678 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
157644 CCTGTTTGTT
157654 GTAGATATTGAA
1 GTAGATATTGAA
157666 GTAGATATTGAA
1 GTAGATATTGAA
157678 G
1 G
157679 AGGTACCACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.28, T:0.32
Consensus pattern (12 bp):
GTAGATATTGAA
Found at i:161716 original size:31 final size:31
Alignment explanation
Indices: 161680--161744 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
161670 GAATGAAAAT
161680 TTTAATACA-AAATAATTAATTTA-TTATTTGA
1 TTTAATACATAAA-AATTAATTTATTTATTT-A
* *
161711 TTTAATATATAAAAATTTATTTATTTATTTA
1 TTTAATACATAAAAATTAATTTATTTATTTA
161742 TTT
1 TTT
161745 GAGTAAATAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 21 0.70
32 9 0.30
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (31 bp):
TTTAATACATAAAAATTAATTTATTTATTTA
Found at i:173448 original size:27 final size:27
Alignment explanation
Indices: 173395--173460 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
173385 ATTAACCATT
* *
173395 TTATTAAAAATT--TCATTCATTTTTA
1 TTATTTAAAATTAATCATTCATTTCTA
173420 TTATTTAAAATTAATCATTCATTTCTA
1 TTATTTAAAATTAATCATTCATTTCTA
*
173447 TTATTTAAAGTTAA
1 TTATTTAAAATTAA
173461 CCTATATACG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
25 11 0.31
27 25 0.69
ACGTcount: A:0.38, C:0.08, G:0.02, T:0.53
Consensus pattern (27 bp):
TTATTTAAAATTAATCATTCATTTCTA
Found at i:216574 original size:21 final size:21
Alignment explanation
Indices: 216548--216587 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
216538 CATTTGATAA
*
216548 CATTTTAGGTTCTTGTTTTCT
1 CATTTTAAGTTCTTGTTTTCT
*
216569 CATTTTAATTTCTTGTTTT
1 CATTTTAAGTTCTTGTTTT
216588 AATAATTTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.12, C:0.12, G:0.10, T:0.65
Consensus pattern (21 bp):
CATTTTAAGTTCTTGTTTTCT
Found at i:222747 original size:24 final size:24
Alignment explanation
Indices: 222720--222767 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
222710 AAGCCAAACC
222720 CAATGTCATAACACATCAAAGTCT
1 CAATGTCATAACACATCAAAGTCT
222744 CAATGTCATAACACATCAAAGTCT
1 CAATGTCATAACACATCAAAGTCT
222768 TAATAGCATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.25, G:0.08, T:0.25
Consensus pattern (24 bp):
CAATGTCATAACACATCAAAGTCT
Found at i:225785 original size:24 final size:24
Alignment explanation
Indices: 225758--225804 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
225748 ATTATATAAG
225758 AGCAATTGAATTTCTACTAAAATT
1 AGCAATTGAATTTCTACTAAAATT
*
225782 AGCAATTGACTTTCTACTAAAAT
1 AGCAATTGAATTTCTACTAAAAT
225805 CTTATTGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.36
Consensus pattern (24 bp):
AGCAATTGAATTTCTACTAAAATT
Found at i:242572 original size:12 final size:12
Alignment explanation
Indices: 242555--242579 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
242545 TTTAAATCAC
242555 GATTATTTGAAA
1 GATTATTTGAAA
242567 GATTATTTGAAA
1 GATTATTTGAAA
242579 G
1 G
242580 GTCTAGTGCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (12 bp):
GATTATTTGAAA
Found at i:247036 original size:46 final size:46
Alignment explanation
Indices: 246983--247121 Score: 260
Period size: 46 Copynumber: 3.0 Consensus size: 46
246973 TCACAATGTG
*
246983 AGAAATAAATCTACTAAAATTCAATTTAAGAGAAAACTGCACATTA
1 AGAAATAAATCTACTAAAATTCAATTTAAGAGAAAATTGCACATTA
247029 AGAAATAAATCTACTAAAATTCAATTTAAGAGAAAATTGCACATTA
1 AGAAATAAATCTACTAAAATTCAATTTAAGAGAAAATTGCACATTA
*
247075 AGAAATAAATCTACTAATATTCAATTTAAGAGAAAATTGCACATTA
1 AGAAATAAATCTACTAAAATTCAATTTAAGAGAAAATTGCACATTA
247121 A
1 A
247122 TCATCCCTAA
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 91 1.00
ACGTcount: A:0.52, C:0.12, G:0.09, T:0.28
Consensus pattern (46 bp):
AGAAATAAATCTACTAAAATTCAATTTAAGAGAAAATTGCACATTA
Found at i:250215 original size:17 final size:18
Alignment explanation
Indices: 250193--250231 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
250183 TTGGCATTAT
*
250193 TTTTTAT-TCAAAAGTGC
1 TTTTTATGTCAAAAGTAC
*
250210 TTTTTATGTTAAAAGTAC
1 TTTTTATGTCAAAAGTAC
250228 TTTT
1 TTTT
250232 AAAAAACACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.54
Consensus pattern (18 bp):
TTTTTATGTCAAAAGTAC
Found at i:253507 original size:3 final size:3
Alignment explanation
Indices: 253501--253525 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
253491 AGCTGCTGAT
253501 GCG GCG GCG GCG GCG GCG GCG GCG G
1 GCG GCG GCG GCG GCG GCG GCG GCG G
253526 TTGCAGCTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.68, T:0.00
Consensus pattern (3 bp):
GCG
Found at i:254492 original size:30 final size:32
Alignment explanation
Indices: 254456--254516 Score: 99
Period size: 30 Copynumber: 1.9 Consensus size: 32
254446 TCAGCTGATG
254456 AAAAAAAATAAAA-TTA-AATAATTGAGTGGC
1 AAAAAAAATAAAATTTATAATAATTGAGTGGC
254486 AAAAAAAATAAAATTTATTAATAATTGAGTG
1 AAAAAAAATAAAATTTA-TAATAATTGAGTG
254517 ATCATACAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
30 13 0.46
31 3 0.11
33 12 0.43
ACGTcount: A:0.59, C:0.02, G:0.11, T:0.28
Consensus pattern (32 bp):
AAAAAAAATAAAATTTATAATAATTGAGTGGC
Found at i:261159 original size:89 final size:89
Alignment explanation
Indices: 261008--261232 Score: 423
Period size: 89 Copynumber: 2.5 Consensus size: 89
260998 AATATGATAT
* * *
261008 AAAATGACTTTACTCTTCATCATTCCATTGAAAGGAACATTCCATTCTCATTATAATGTAGTTTT
1 AAAATAACTTCACTCTTCATCATTCCATTGAAAGGAACATTCCATTCTCACTATAATGTAGTTTT
261073 ATTACTTGAAAATTTAAAATATAG
66 ATTACTTGAAAATTTAAAATATAG
261097 AAAATAACTTCACTCTTCATCATTCCATTGAAAGGAACATTCCATTCTCACTATAATGTAGTTTT
1 AAAATAACTTCACTCTTCATCATTCCATTGAAAGGAACATTCCATTCTCACTATAATGTAGTTTT
261162 ATTACTTGAAAATTTAAAATATAG
66 ATTACTTGAAAATTTAAAATATAG
261186 AAAATAACTTCACTCTTCATCATTCCATTGAAAGGAACATTCCATTC
1 AAAATAACTTCACTCTTCATCATTCCATTGAAAGGAACATTCCATTC
261233 CATAACTAAG
Statistics
Matches: 133, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 133 1.00
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (89 bp):
AAAATAACTTCACTCTTCATCATTCCATTGAAAGGAACATTCCATTCTCACTATAATGTAGTTTT
ATTACTTGAAAATTTAAAATATAG
Found at i:275695 original size:14 final size:12
Alignment explanation
Indices: 275662--275691 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
275652 AGTTTTAACC
275662 TTTATAATGTAT
1 TTTATAATGTAT
275674 TTTATAATGTAT
1 TTTATAATGTAT
275686 TTTATA
1 TTTATA
275692 TAATATTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (12 bp):
TTTATAATGTAT
Found at i:276984 original size:210 final size:209
Alignment explanation
Indices: 276622--277035 Score: 765
Period size: 210 Copynumber: 2.0 Consensus size: 209
276612 AAATTCTTTT
** * *
276622 GTTAATCAGGTACATACCTGACATCTGAGAGTGTACTAATCGTCTCATCGTGCATTCTAATTTTA
1 GTTAATCAAATACATACCTAACATCTGAGAGTGTACTAATCGTCTCATCGTGCATCCTAATTTTA
*
276687 ACAGTATCAATACCGTTTACCTTACTAGATGAATTGTTTCTCATGCACACAACTCCACCTTCAAC
66 ACAGTATCAATACCGATTACCTTACTAGATGAATTGTTTCTCATGCACACAACTCCACCTTCAAC
276752 TGAACAATATGTGGAGAATCACTTTCTATTGGGACATATGTGGAAAGAACATATTGAATCTAGGA
131 TGAACAATATGTGGAGAATCACTTTCTATTGGGACATATGTGGAAAGAACATATT-AATCTAGGA
276817 TGCACTCAGATGTTC
195 TGCACTCAGATGTTC
276832 GTTAATCAAATACATACCTAACATCTGAGAGTGTACTAATCGTCTCATCGTGCATCCTAATTTTA
1 GTTAATCAAATACATACCTAACATCTGAGAGTGTACTAATCGTCTCATCGTGCATCCTAATTTTA
276897 ACAGTATCAATACCGATTACCTTACTAGATGAATTGTTTCTCATGCACACAACTCCACCTTCAAC
66 ACAGTATCAATACCGATTACCTTACTAGATGAATTGTTTCTCATGCACACAACTCCACCTTCAAC
*
276962 TGAACGATATGTGGAGAATCACTTTCTATTGGGACATATGTGGAAAGAACATATTAATCTAGGAT
131 TGAACAATATGTGGAGAATCACTTTCTATTGGGACATATGTGGAAAGAACATATTAATCTAGGAT
277027 GCACTCAGA
196 GCACTCAGA
277036 CGTAAGTTTG
Statistics
Matches: 198, Mismatches: 6, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
209 19 0.10
210 179 0.90
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (209 bp):
GTTAATCAAATACATACCTAACATCTGAGAGTGTACTAATCGTCTCATCGTGCATCCTAATTTTA
ACAGTATCAATACCGATTACCTTACTAGATGAATTGTTTCTCATGCACACAACTCCACCTTCAAC
TGAACAATATGTGGAGAATCACTTTCTATTGGGACATATGTGGAAAGAACATATTAATCTAGGAT
GCACTCAGATGTTC
Found at i:285162 original size:108 final size:109
Alignment explanation
Indices: 285033--285258 Score: 436
Period size: 108 Copynumber: 2.1 Consensus size: 109
285023 GCATAATTAA
285033 TTAAAATATAGTAATAAAATTTAAAATATTTTGAAAATACTTAAATAATACCTATTAATGTTAGC
1 TTAAAATATAGTAATAAAATTTAAAATATTTTGAAAATACTTAAATAATACCTATTAATGTTAGC
285098 TCCAAAATTAGGAGTTGAAAGTAAATGACATAACGATAGATA-G
66 TCCAAAATTAGGAGTTGAAAGTAAATGACATAACGATAGATAGG
285141 TTAAAATATAGTAATAAAATTTAAAATATTTTGAAAATACTTAAATAATACCTATTAATGTTAGC
1 TTAAAATATAGTAATAAAATTTAAAATATTTTGAAAATACTTAAATAATACCTATTAATGTTAGC
285206 TCCAAAATTAGGAGTTGAAAGTAAATGACATAACGATAGATAGG
66 TCCAAAATTAGGAGTTGAAAGTAAATGACATAACGATAGATAGG
285250 TGTAAAATA
1 T-TAAAATA
285259 CAAATTCTTA
Statistics
Matches: 116, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
108 107 0.92
109 2 0.02
110 7 0.06
ACGTcount: A:0.48, C:0.07, G:0.12, T:0.32
Consensus pattern (109 bp):
TTAAAATATAGTAATAAAATTTAAAATATTTTGAAAATACTTAAATAATACCTATTAATGTTAGC
TCCAAAATTAGGAGTTGAAAGTAAATGACATAACGATAGATAGG
Found at i:288633 original size:43 final size:43
Alignment explanation
Indices: 288585--288674 Score: 162
Period size: 43 Copynumber: 2.1 Consensus size: 43
288575 TGGACATATC
288585 CTTAACATCATAATCAAACAAGACACTGATTCATTCATCAACG
1 CTTAACATCATAATCAAACAAGACACTGATTCATTCATCAACG
* *
288628 CTTAACATCATAATCAAACAGGACACTGATTCATTCATCAATG
1 CTTAACATCATAATCAAACAAGACACTGATTCATTCATCAACG
288671 CTTA
1 CTTA
288675 CATACACATG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.40, C:0.24, G:0.08, T:0.28
Consensus pattern (43 bp):
CTTAACATCATAATCAAACAAGACACTGATTCATTCATCAACG
Found at i:298967 original size:29 final size:28
Alignment explanation
Indices: 298926--298992 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 28
298916 TACAAAGTAG
*
298926 TAAATATTAATAAAATGATATTTTTATA
1 TAAATATTAATAAAAAGATATTTTTATA
*
298954 TAAACTATTAATAAAAAGGTATTTTTATA
1 TAAA-TATTAATAAAAAGATATTTTTATA
298983 TAAAATATTA
1 T-AAATATTA
298993 TTACGACTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
28 4 0.11
29 28 0.80
30 3 0.09
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.43
Consensus pattern (28 bp):
TAAATATTAATAAAAAGATATTTTTATA
Found at i:301671 original size:19 final size:18
Alignment explanation
Indices: 301649--301721 Score: 56
Period size: 19 Copynumber: 3.8 Consensus size: 18
301639 TTTTATGAGA
*
301649 TTAATAATTTCTAAAACAT
1 TTAATAA-TTCTAAAAAAT
*
301668 TTAATAACTACTAAAAAAAT
1 TTAATAA-TTCT-AAAAAAT
** *
301688 GAAAAAATTCTAAAAAAT
1 TTAATAATTCTAAAAAAT
*
301706 TAAATAATTCTTAAAA
1 TTAATAATTC-TAAAA
301722 CATTAACGAT
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
18 15 0.35
19 18 0.42
20 10 0.23
ACGTcount: A:0.58, C:0.08, G:0.01, T:0.33
Consensus pattern (18 bp):
TTAATAATTCTAAAAAAT
Found at i:301704 original size:18 final size:19
Alignment explanation
Indices: 301681--301761 Score: 58
Period size: 18 Copynumber: 4.2 Consensus size: 19
301671 ATAACTACTA
301681 AAAAAATGAAAAAATTC-T
1 AAAAAATGAAAAAATTCTT
* *
301699 AAAAAATTAAATAATTCTT
1 AAAAAATGAAAAAATTCTT
* * ** *
301718 AAAACAT-TAACGATCTGTT
1 AAAAAATGAAAAAAT-TCTT
301737 AAAAACATGAAAAAATTACTT
1 AAAAA-ATGAAAAAATT-CTT
301758 AAAA
1 AAAA
301762 TATAAAAGGC
Statistics
Matches: 46, Mismatches: 12, Indels: 7
0.71 0.18 0.11
Matches are distributed among these distances:
18 19 0.41
19 14 0.30
20 3 0.07
21 10 0.22
ACGTcount: A:0.59, C:0.09, G:0.05, T:0.27
Consensus pattern (19 bp):
AAAAAATGAAAAAATTCTT
Found at i:301726 original size:19 final size:19
Alignment explanation
Indices: 301681--301727 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
301671 ATAACTACTA
* *
301681 AAAAAATGAAAAAATTC-T
1 AAAAAATTAAATAATTCTT
301699 AAAAAATTAAATAATTCTT
1 AAAAAATTAAATAATTCTT
*
301718 AAAACATTAA
1 AAAAAATTAA
301728 CGATCTGTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 15 0.60
19 10 0.40
ACGTcount: A:0.64, C:0.06, G:0.02, T:0.28
Consensus pattern (19 bp):
AAAAAATTAAATAATTCTT
Found at i:308883 original size:57 final size:57
Alignment explanation
Indices: 308795--308910 Score: 232
Period size: 57 Copynumber: 2.0 Consensus size: 57
308785 AAAATTCCAA
308795 TTCTTTTATCATGCTCGATCCTTAACTTCAGATTTGATGCGAAATTCATGGGGCGTG
1 TTCTTTTATCATGCTCGATCCTTAACTTCAGATTTGATGCGAAATTCATGGGGCGTG
308852 TTCTTTTATCATGCTCGATCCTTAACTTCAGATTTGATGCGAAATTCATGGGGCGTG
1 TTCTTTTATCATGCTCGATCCTTAACTTCAGATTTGATGCGAAATTCATGGGGCGTG
308909 TT
1 TT
308911 TTGTAGGATG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 59 1.00
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.40
Consensus pattern (57 bp):
TTCTTTTATCATGCTCGATCCTTAACTTCAGATTTGATGCGAAATTCATGGGGCGTG
Found at i:315898 original size:17 final size:17
Alignment explanation
Indices: 315851--315898 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
315841 AATATTTTTT
* *
315851 ATAAAAATCTTTAAAAA
1 ATAAAAAACTTTATAAA
*
315868 ATAAAAAACATTATAAA
1 ATAAAAAACTTTATAAA
315885 ATAAGAAAA-TTTAT
1 ATAA-AAAACTTTAT
315899 TAATATTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 22 0.85
18 4 0.15
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (17 bp):
ATAAAAAACTTTATAAA
Found at i:315940 original size:20 final size:20
Alignment explanation
Indices: 315917--315987 Score: 51
Period size: 20 Copynumber: 3.6 Consensus size: 20
315907 AAATTGATAT
315917 AAATTTAAAAAAATTATAAA
1 AAATTTAAAAAAATTATAAA
***
315937 AAA-TTATAATGTATTAT-AA
1 AAATTTA-AAAAAATTATAAA
* *
315956 AAATAT-AAAAAATT-TAAT
1 AAATTTAAAAAAATTATAAA
315974 AAATTATAAAAAAA
1 AAATT-TAAAAAAA
315988 ATCAAATTAA
Statistics
Matches: 37, Mismatches: 9, Indels: 10
0.66 0.16 0.18
Matches are distributed among these distances:
17 1 0.03
18 10 0.27
19 9 0.24
20 17 0.46
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.32
Consensus pattern (20 bp):
AAATTTAAAAAAATTATAAA
Found at i:315973 original size:27 final size:29
Alignment explanation
Indices: 315906--315985 Score: 94
Period size: 27 Copynumber: 2.8 Consensus size: 29
315896 TATTAATATT
*
315906 AAAATTGAT-ATAAATTTAAAAAAATTATAA
1 AAAATT-ATAATAAA-TTATAAAAATTATAA
**
315936 AAAATTATAATGTATTATAAAAA-TATAA
1 AAAATTATAATAAATTATAAAAATTATAA
315964 AAAATT-TAATAAATTATAAAAA
1 AAAATTATAATAAATTATAAAAA
315986 AAATCAAATT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
27 14 0.32
28 11 0.25
29 10 0.23
30 9 0.20
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.34
Consensus pattern (29 bp):
AAAATTATAATAAATTATAAAAATTATAA
Found at i:316055 original size:10 final size:10
Alignment explanation
Indices: 316040--316127 Score: 58
Period size: 10 Copynumber: 8.9 Consensus size: 10
316030 TTAGAATTCT
*
316040 TAAAAACTAA
1 TAAAAACTTA
*
316050 TAAAAA-TTG
1 TAAAAACTTA
316059 TAAAATACTTA
1 TAAAA-ACTTA
*
316070 TAAAAA-ATA
1 TAAAAACTTA
*
316079 TTAAAA-TTA
1 TAAAAACTTA
*
316088 TATAAACTTA
1 TAAAAACTTA
316098 TAAAAA-TTAAA
1 TAAAAACTT--A
* *
316109 TAAAAAATCA
1 TAAAAACTTA
316119 TAAAAACTT
1 TAAAAACTT
316128 GAATCGAATC
Statistics
Matches: 60, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
9 21 0.35
10 24 0.40
11 14 0.23
12 1 0.02
ACGTcount: A:0.62, C:0.06, G:0.01, T:0.31
Consensus pattern (10 bp):
TAAAAACTTA
Found at i:321284 original size:8 final size:8
Alignment explanation
Indices: 321271--321296 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
321261 TAAATTGTTT
321271 TAATTAAA
1 TAATTAAA
321279 TAATTAAA
1 TAATTAAA
321287 TAATTAAA
1 TAATTAAA
321295 TA
1 TA
321297 TTAGTAGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
TAATTAAA
Found at i:321596 original size:49 final size:49
Alignment explanation
Indices: 321518--321646 Score: 161
Period size: 49 Copynumber: 2.6 Consensus size: 49
321508 TTAAATACTG
* * *
321518 ATACATGTTATATGGTA-TCGATACATATTCATCTAAATCTCTGATATCA
1 ATACCTGTTATATAGTACT-GATACCTATTCATCTAAATCTCTGATATCA
* **
321567 ATACCTGTTATATTGTACTGATACCTATTCATCTAAATCTCTGATATTG
1 ATACCTGTTATATAGTACTGATACCTATTCATCTAAATCTCTGATATCA
* **
321616 ATATCTGTTACGTAGTACTGATACCTATTCA
1 ATACCTGTTATATAGTACTGATACCTATTCA
321647 AAAAGTATCG
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
49 69 0.99
50 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.40
Consensus pattern (49 bp):
ATACCTGTTATATAGTACTGATACCTATTCATCTAAATCTCTGATATCA
Found at i:321983 original size:7 final size:7
Alignment explanation
Indices: 321973--322156 Score: 72
Period size: 7 Copynumber: 25.6 Consensus size: 7
321963 GAGGCTTAAA
321973 GGTTTAG
1 GGTTTAG
*
321980 GGTTTAA
1 GGTTTAG
*
321987 GTTTTAG
1 GGTTTAG
*
321994 GGTTTAAA
1 GGTTT-AG
*
322002 GGTTTAA
1 GGTTTAG
322009 GGTTTAG
1 GGTTTAG
*
322016 GGTTAAG
1 GGTTTAG
* *
322023 TGTTTGG
1 GGTTTAG
322030 GGTTT-G
1 GGTTTAG
*
322036 TGTTTAAG
1 GGTTT-AG
322044 GGTTTAAG
1 GGTTT-AG
*
322052 GG-TTAA
1 GGTTTAG
*
322058 GATTT-G
1 GGTTTAG
322064 AGGTTTAAG
1 -GGTTT-AG
**
322073 GGTAAAG
1 GGTTTAG
322080 GGTTTTAG
1 GG-TTTAG
322088 GTTTGTTTAG
1 G---GTTTAG
*
322098 GGTTTAA
1 GGTTTAG
*
322105 GGTTGAG
1 GGTTTAG
* *
322112 GGTTGAT
1 GGTTTAG
322119 GGTTTAG
1 GGTTTAG
*
322126 GGTTT-T
1 GGTTTAG
*
322132 GGTTTTG
1 GGTTTAG
322139 AGGTTTA-
1 -GGTTTAG
*
322146 AGTTTAG
1 GGTTTAG
322153 GGTT
1 GGTT
322157 AGAGGTTAAT
Statistics
Matches: 131, Mismatches: 32, Indels: 28
0.69 0.17 0.15
Matches are distributed among these distances:
6 17 0.13
7 78 0.60
8 28 0.21
9 1 0.01
10 6 0.05
11 1 0.01
ACGTcount: A:0.20, C:0.00, G:0.36, T:0.44
Consensus pattern (7 bp):
GGTTTAG
Found at i:321984 original size:29 final size:29
Alignment explanation
Indices: 321952--322014 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
321942 ATGGTTCAGT
*
321952 GTTTAAGGCTTGA-GGCTTAAAGGTTTAGG
1 GTTTAA-GCTTGAGGGCTTAAAGGTTTAAG
* * *
321981 GTTTAAGTTTTAGGGTTTAAAGGTTTAAG
1 GTTTAAGCTTGAGGGCTTAAAGGTTTAAG
322010 GTTTA
1 GTTTA
322015 GGGTTAAGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 4 0.14
29 25 0.86
ACGTcount: A:0.25, C:0.03, G:0.30, T:0.41
Consensus pattern (29 bp):
GTTTAAGCTTGAGGGCTTAAAGGTTTAAG
Found at i:321986 original size:15 final size:15
Alignment explanation
Indices: 321968--322014 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
321958 GGCTTGAGGC
321968 TTAAAGGTTTAGGGT
1 TTAAAGGTTTAGGGT
*
321983 TT-AAGTTTTAGGGT
1 TTAAAGGTTTAGGGT
*
321997 TTAAAGGTTTAAGGT
1 TTAAAGGTTTAGGGT
322012 TTA
1 TTA
322015 GGGTTAAGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 13 0.46
15 15 0.54
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.45
Consensus pattern (15 bp):
TTAAAGGTTTAGGGT
Found at i:321994 original size:14 final size:14
Alignment explanation
Indices: 321935--322156 Score: 103
Period size: 14 Copynumber: 15.4 Consensus size: 14
321925 TCGATGCTCG
* *
321935 AGGGTTTATGGTTC
1 AGGGTTTAAGGTTT
* *
321949 AGTGTTTAAGGCTTG
1 AGGGTTTAAGG-TTT
* *
321964 AGGCTTAAAGGTTT
1 AGGGTTTAAGGTTT
*
321978 AGGGTTTAAGTTTT
1 AGGGTTTAAGGTTT
321992 AGGGTTTAAAGGTTT
1 AGGGTTT-AAGGTTT
* * *
322007 AAGGTTTAGGGTTA
1 AGGGTTTAAGGTTT
* **
322021 AGTGTTTGGGGTTT
1 AGGGTTTAAGGTTT
*
322035 -GTGTTTAAGGGTTT
1 AGGGTTTAA-GGTTT
*
322049 AAGGG-TTAAGATTT
1 -AGGGTTTAAGGTTT
**
322063 -GAGGTTTAAGGGTAA
1 AG-GGTTTAA-GGTTT
*
322078 AGGGTTTTAGGTTTGTTT
1 AGGG-TTTAAG---GTTT
*
322096 AGGGTTTAAGGTTG
1 AGGGTTTAAGGTTT
* *
322110 AGGGTTGATGGTTT
1 AGGGTTTAAGGTTT
*
322124 AGGGTTT-TGGTTT
1 AGGGTTTAAGGTTT
*
322137 TGAGGTTTAA-GTTT
1 AG-GGTTTAAGGTTT
322151 AGGGTT
1 AGGGTT
322157 AGAGGTTAAT
Statistics
Matches: 156, Mismatches: 37, Indels: 31
0.70 0.17 0.14
Matches are distributed among these distances:
12 1 0.01
13 19 0.12
14 87 0.56
15 31 0.20
16 7 0.04
17 5 0.03
18 6 0.04
ACGTcount: A:0.20, C:0.01, G:0.36, T:0.43
Consensus pattern (14 bp):
AGGGTTTAAGGTTT
Found at i:322027 original size:29 final size:29
Alignment explanation
Indices: 321968--322027 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
321958 GGCTTGAGGC
* * *
321968 TTAAAGGTTTAGGGTTTAAGTTTTAGGGT
1 TTAAAGGTTTAAGGTTTAAGGTTAAGGGT
* *
321997 TTAAAGGTTTAAGGTTTAGGGTTAAGTGT
1 TTAAAGGTTTAAGGTTTAAGGTTAAGGGT
322026 TT
1 TT
322028 GGGGTTTGTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.45
Consensus pattern (29 bp):
TTAAAGGTTTAAGGTTTAAGGTTAAGGGT
Found at i:322174 original size:18 final size:19
Alignment explanation
Indices: 322138--322181 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
322128 TTTTGGTTTT
*
322138 GAGGTTTAAGTTTAGGGTTA
1 GAGG-TTAAGTTTAAGGTTA
322158 GAGGTTAA-TTTAAGGTTA
1 GAGGTTAAGTTTAAGGTTA
*
322176 GGGGTT
1 GAGGTT
322182 CGTGGTTCGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 14 0.64
19 4 0.18
20 4 0.18
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (19 bp):
GAGGTTAAGTTTAAGGTTA
Done.