Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015342.1 Kokia drynarioides strain JFW-HI SEQ_130389, 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: 128256
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 672 characters in sequence are not A, C, G, or T
Found at i:9198 original size:27 final size:30
Alignment explanation
Indices: 9168--9231 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
9158 AAATAAACTA
9168 TTTTCTT-TCAT-AAGATAGTGGATGATGT
1 TTTTCTTATCATAAAGATAGTGGATGATGT
* *
9196 TTTTTTTATTATAAAGATAGTGGATGATGT
1 TTTTCTTATCATAAAGATAGTGGATGATGT
*
9226 TATTCT
1 TTTTCT
9232 CTACTACTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 6 0.20
29 3 0.10
30 21 0.70
ACGTcount: A:0.27, C:0.05, G:0.19, T:0.50
Consensus pattern (30 bp):
TTTTCTTATCATAAAGATAGTGGATGATGT
Found at i:9270 original size:14 final size:15
Alignment explanation
Indices: 9245--9285 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
9235 CTACTATGGC
*
9245 TAATAATAATTAAAG
1 TAATATTAATTAAAG
9260 TAA-ATTAATT-AAG
1 TAATATTAATTAAAG
*
9273 TAATGTTAATTAA
1 TAATATTAATTAA
9286 GATTTAATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 6 0.27
14 12 0.55
15 4 0.18
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (15 bp):
TAATATTAATTAAAG
Found at i:11289 original size:6 final size:6
Alignment explanation
Indices: 11275--11307 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
11265 TAATTTGTTG
*
11275 AAATCT AAATTT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAA
11308 CTATCTTGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (6 bp):
AAATCT
Found at i:12079 original size:23 final size:23
Alignment explanation
Indices: 12048--12092 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
12038 CTCTTCATGT
* * *
12048 TTTAGGGTTTTTAGGAGTTTTTA
1 TTTAAGGTTTGTAAGAGTTTTTA
12071 TTTAAGGTTTGTAAGAGTTTTT
1 TTTAAGGTTTGTAAGAGTTTTT
12093 GGAGTTTTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.24, T:0.56
Consensus pattern (23 bp):
TTTAAGGTTTGTAAGAGTTTTTA
Found at i:12181 original size:17 final size:18
Alignment explanation
Indices: 12148--12187 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
12138 TTTTAATTTT
* *
12148 TTTATTTTTTATATAATC
1 TTTATATTTTATATAATA
12166 TTTATATTTT-TATAATA
1 TTTATATTTTATATAATA
12183 TTTAT
1 TTTAT
12188 GGTTAGTGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTATATTTTATATAATA
Found at i:18287 original size:15 final size:17
Alignment explanation
Indices: 18267--18298 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
18257 AAAATAAATT
18267 AAAATTA-AA-ATTAAA
1 AAAATTATAATATTAAA
18282 AAAATTATAATATTAAA
1 AAAATTATAATATTAAA
18299 TATTTAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 2 0.13
17 6 0.40
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAATTATAATATTAAA
Found at i:18296 original size:23 final size:22
Alignment explanation
Indices: 18255--18308 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
18245 TTAAGTTTGT
18255 TTAAAATAAATTAAAATTAAAA
1 TTAAAATAAATTAAAATTAAAA
18277 TTAAAA-AAATTATAATATTAAATA
1 TTAAAATAAATTA-AA-ATTAAA-A
*
18301 TTTAAATA
1 TTAAAATA
18309 TTGAAAAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 6 0.22
22 8 0.30
23 6 0.22
24 6 0.22
25 1 0.04
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
TTAAAATAAATTAAAATTAAAA
Found at i:19694 original size:30 final size:30
Alignment explanation
Indices: 19634--19701 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
19624 CACCACTAAT
*
19634 CATTTTCCGTTACAGACATAACAGAGCTAC
1 CATTTTCCGTTACAGACATAACAGAACTAC
* * *
19664 CATTTTCCGTTTCAGACTTAATTA-AACTAC
1 CATTTTCCGTTACAGACATAA-CAGAACTAC
19694 CATTTTCC
1 CATTTTCC
19702 ATCCCCCTCC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 32 0.97
31 1 0.03
ACGTcount: A:0.29, C:0.26, G:0.09, T:0.35
Consensus pattern (30 bp):
CATTTTCCGTTACAGACATAACAGAACTAC
Found at i:21617 original size:132 final size:132
Alignment explanation
Indices: 21380--21642 Score: 463
Period size: 132 Copynumber: 2.0 Consensus size: 132
21370 TATGTAATAA
* *
21380 AAAATAATTATTGATGACTTTTTTGTTATTTTTAAAAAATTGAGTGATTAAATTAAAATTTAAAT
1 AAAATAATTACTGATGACTGTTTTGTTATTTTTAAAAAATTGAGTGATTAAATTAAAATTTAAAT
*
21445 GACTGTTTTCTCCACTACAAAGTTAAGTGAATATCAATACAATTTACCCCATCTTTTACTTGCAT
66 GACTGTTTTCTCCACTACAAAGTTAAGTGAATATCAATACAATTCACCCCATCTTTTACTTGCAT
21510 TG
131 TG
* *
21512 AAAATAATTACTGATGACTGTTTTGTTATTTTTTAAAAATTGAGTGGTTAAATTAAAATTTAAAT
1 AAAATAATTACTGATGACTGTTTTGTTATTTTTAAAAAATTGAGTGATTAAATTAAAATTTAAAT
* *
21577 GACTGTTTTCTCCACTACAAAGTTAAGTGAATATTAATACAATTCACCCCATTTTTTACTTGCAT
66 GACTGTTTTCTCCACTACAAAGTTAAGTGAATATCAATACAATTCACCCCATCTTTTACTTGCAT
21642 T
131 T
21643 TTTTTTTAAA
Statistics
Matches: 124, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
132 124 1.00
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (132 bp):
AAAATAATTACTGATGACTGTTTTGTTATTTTTAAAAAATTGAGTGATTAAATTAAAATTTAAAT
GACTGTTTTCTCCACTACAAAGTTAAGTGAATATCAATACAATTCACCCCATCTTTTACTTGCAT
TG
Found at i:28687 original size:2 final size:2
Alignment explanation
Indices: 28682--28716 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
28672 ATATATCTTT
*
28682 TA TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28717 TAAATATTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:28693 original size:8 final size:8
Alignment explanation
Indices: 28657--28712 Score: 53
Period size: 8 Copynumber: 7.2 Consensus size: 8
28647 GATATGATTC
28657 ATTTA-AT
1 ATTTATAT
*
28664 ATTTATAA
1 ATTTATAT
* *
28672 ATATATCT
1 ATTTATAT
28680 -TTTATAT
1 ATTTATAT
28687 ATTTATAT
1 ATTTATAT
*
28695 ATATATAT
1 ATTTATAT
*
28703 ATATATAT
1 ATTTATAT
28711 AT
1 AT
28713 ATATTAAATA
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
7 10 0.25
8 30 0.75
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (8 bp):
ATTTATAT
Found at i:46386 original size:78 final size:78
Alignment explanation
Indices: 46257--46412 Score: 312
Period size: 78 Copynumber: 2.0 Consensus size: 78
46247 TGAAGGTATA
46257 GATAGCACTGGAAAGCTTTTGTAACTCTTCCTACTATAATAAAAGAAAGGGTAAATTATACCAAC
1 GATAGCACTGGAAAGCTTTTGTAACTCTTCCTACTATAATAAAAGAAAGGGTAAATTATACCAAC
46322 AATCACTCTAGTT
66 AATCACTCTAGTT
46335 GATAGCACTGGAAAGCTTTTGTAACTCTTCCTACTATAATAAAAGAAAGGGTAAATTATACCAAC
1 GATAGCACTGGAAAGCTTTTGTAACTCTTCCTACTATAATAAAAGAAAGGGTAAATTATACCAAC
46400 AATCACTCTAGTT
66 AATCACTCTAGTT
46413 TCAATTCAAT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.29
Consensus pattern (78 bp):
GATAGCACTGGAAAGCTTTTGTAACTCTTCCTACTATAATAAAAGAAAGGGTAAATTATACCAAC
AATCACTCTAGTT
Found at i:50745 original size:10 final size:11
Alignment explanation
Indices: 50721--50753 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
50711 TTTTCCAAAG
50721 ACAGACAGACA
1 ACAGACAGACA
50732 ACAGACAG-CA
1 ACAGACAGACA
50742 ACAGACAAGACA
1 ACAGAC-AGACA
50754 GTCCACCAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 8 0.40
11 10 0.50
12 2 0.10
ACGTcount: A:0.55, C:0.27, G:0.18, T:0.00
Consensus pattern (11 bp):
ACAGACAGACA
Found at i:53647 original size:5 final size:6
Alignment explanation
Indices: 53618--53648 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
53608 TTTAATATAA
53618 AAAAGG AAAAGG AAAAGG AAAAGG -AAAGG AA
1 AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG AA
53649 TCGCTTTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (6 bp):
AAAAGG
Found at i:55556 original size:8 final size:8
Alignment explanation
Indices: 55543--55570 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
55533 AATATAATGG
55543 AAAAAAAT
1 AAAAAAAT
55551 AAAAAAAT
1 AAAAAAAT
55559 AAAAAAAT
1 AAAAAAAT
55567 AAAA
1 AAAA
55571 TGGAGAAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAAAAAT
Found at i:55869 original size:30 final size:26
Alignment explanation
Indices: 55832--55885 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
55822 AACTTGCAAT
55832 CATTAATTAATTACGATGGACATAAG
1 CATTAATTAATTACGATGGACATAAG
55858 CATTAATTAATTACGATGGACATAAG
1 CATTAATTAATTACGATGGACATAAG
55884 CA
1 CA
55886 ATCACTTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.30
Consensus pattern (26 bp):
CATTAATTAATTACGATGGACATAAG
Found at i:58279 original size:87 final size:84
Alignment explanation
Indices: 58122--58282 Score: 216
Period size: 87 Copynumber: 1.9 Consensus size: 84
58112 TACATGCATA
*
58122 AGGTTGAGTTATTACTCTTAATAAGTTCATATCCCAAGTTGGGTGGTCCTATTGAGACAAACTTA
1 AGGTTGAGTTATTACTCTTAATAAGTTCATATCCAAAGTTGGGTGGTCCTATTGAGACAAACTTA
58187 ATGAATTCATCGATATGAG
66 ATGAATTCATCGATATGAG
* * * **
58206 AGGTTGAGTTTATTACTTTTAATGAA-TTCATATCCTAAAATTTGGGTGGTCCTATTGCGACGGA
1 AGGTTGAG-TTATTACTCTTAAT-AAGTTCATATCC--AAAGTTGGGTGGTCCTATTGAGACAAA
*
58270 CTTGATGAATTCA
62 CTTAATGAATTCA
58283 CCGAACTTAA
Statistics
Matches: 66, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
84 8 0.12
85 22 0.33
86 2 0.03
87 34 0.52
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (84 bp):
AGGTTGAGTTATTACTCTTAATAAGTTCATATCCAAAGTTGGGTGGTCCTATTGAGACAAACTTA
ATGAATTCATCGATATGAG
Found at i:63556 original size:15 final size:15
Alignment explanation
Indices: 63536--63587 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
63526 ACTACAAAAC
63536 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
63551 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
63570 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
63585 ATT
1 ATT
63588 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:63651 original size:16 final size:16
Alignment explanation
Indices: 63620--63656 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
63610 ATGTGAAGAA
63620 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
63636 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
63652 TATTA
1 TATTA
63657 AAATAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:66922 original size:14 final size:14
Alignment explanation
Indices: 66905--66935 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
66895 AGGGTTTAAA
66905 AAATTTATTTAATT
1 AAATTTATTTAATT
66919 AAATTTATTTAATT
1 AAATTTATTTAATT
66933 AAA
1 AAA
66936 GATTTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
AAATTTATTTAATT
Found at i:78762 original size:11 final size:12
Alignment explanation
Indices: 78737--78769 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
78727 CGTTTCGTTG
78737 TTTATTTTTTAA
1 TTTATTTTTTAA
78749 TTTATTTTTT-A
1 TTTATTTTTTAA
78760 TTTAGTTTTT
1 TTTA-TTTTT
78770 CACATGATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (12 bp):
TTTATTTTTTAA
Found at i:80557 original size:20 final size:20
Alignment explanation
Indices: 80534--80576 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
80524 ATATAAATTT
80534 AAAAATTAAAAAAAATAATA
1 AAAAATTAAAAAAAATAATA
* *
80554 AAAAATTAAATAAAATATTA
1 AAAAATTAAAAAAAATAATA
80574 AAA
1 AAA
80577 TGATTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (20 bp):
AAAAATTAAAAAAAATAATA
Found at i:80565 original size:12 final size:12
Alignment explanation
Indices: 80519--80575 Score: 50
Period size: 12 Copynumber: 4.9 Consensus size: 12
80509 GTGATTTGAC
80519 AAAAAATATAAATT
1 AAAAAAT-TAAA-T
*
80533 TAAAAATT-AA-
1 AAAAAATTAAAT
80543 AAAAAA-T-AAT
1 AAAAAATTAAAT
80553 AAAAAATTAAAT
1 AAAAAATTAAAT
*
80565 AAAATATTAAA
1 AAAAAATTAAA
80576 ATGATTTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
9 3 0.08
10 11 0.30
11 1 0.03
12 15 0.41
13 1 0.03
14 6 0.16
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
AAAAAATTAAAT
Found at i:80710 original size:19 final size:19
Alignment explanation
Indices: 80688--80724 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
80678 TTTGTAGTCT
* *
80688 TAATTTGGTACTTAAATTA
1 TAATTTGATACCTAAATTA
80707 TAATTTGATACCTAAATT
1 TAATTTGATACCTAAATT
80725 CACGCACGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (19 bp):
TAATTTGATACCTAAATTA
Found at i:81056 original size:20 final size:20
Alignment explanation
Indices: 81022--81061 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
81012 TTATAAATTG
81022 TAAAAAATTCAAAACAATAGA
1 TAAAAAATTCAAAAC-ATAGA
81043 TAAAAAATTC-AAACATAGA
1 TAAAAAATTCAAAACATAGA
81062 AAACAGTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.26
20 4 0.21
21 10 0.53
ACGTcount: A:0.65, C:0.10, G:0.05, T:0.20
Consensus pattern (20 bp):
TAAAAAATTCAAAACATAGA
Found at i:81206 original size:17 final size:17
Alignment explanation
Indices: 81168--81211 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
81158 ATTTTTTTAA
* *
81168 AAAAAGTATATATTTTTT
1 AAAAA-TATATATTTATG
81186 AAAAATATATATTTATG
1 AAAAATATATATTTATG
81203 -AAAATATAT
1 AAAAATATAT
81212 TTAAAATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 9 0.38
17 10 0.42
18 5 0.21
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (17 bp):
AAAAATATATATTTATG
Found at i:90383 original size:29 final size:28
Alignment explanation
Indices: 90351--90409 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 28
90341 AATTTTGATG
**
90351 ATTTAAATTTTGTATTTATCAAATAATGT
1 ATTTAAATTTCATATTT-TCAAATAATGT
* *
90380 ATTTATATTTCATATTTTCAAGTAATGT
1 ATTTAAATTTCATATTTTCAAATAATGT
90408 AT
1 AT
90410 GAAAAAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 12 0.46
29 14 0.54
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.53
Consensus pattern (28 bp):
ATTTAAATTTCATATTTTCAAATAATGT
Found at i:93275 original size:18 final size:18
Alignment explanation
Indices: 93252--93294 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
93242 GTTCAAGTTG
*
93252 TAATTAATTTAAATT-TTT
1 TAATTAA-TTAAATTGATT
93270 TAATTAATTAAATTGATT
1 TAATTAATTAAATTGATT
93288 TAATTAA
1 TAATTAA
93295 AAACTTATTC
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:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAATTGATT
Found at i:93769 original size:20 final size:20
Alignment explanation
Indices: 93729--93769 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
93719 TTATTTTTGT
*
93729 ATTTTCTTATTTGCAGGTGA
1 ATTTTCTTATTTGCAGATGA
* *
93749 ATTTTTTTATTTTCAGATGA
1 ATTTTCTTATTTGCAGATGA
93769 A
1 A
93770 ACCTTAATTG
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:0.24, C:0.07, G:0.15, T:0.54
Consensus pattern (20 bp):
ATTTTCTTATTTGCAGATGA
Found at i:97083 original size:22 final size:25
Alignment explanation
Indices: 97058--97111 Score: 60
Period size: 27 Copynumber: 2.2 Consensus size: 25
97048 GTTTTCTTCA
*
97058 AATGATTTTAA-T-AATAA-AAAAT
1 AATGATTTCAATTAAATAATAAAAT
97080 AATGTTATTTCAATTAAATAATAAAAT
1 AATG--ATTTCAATTAAATAATAAAAT
97107 AATGA
1 AATGA
97112 AAAATAATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
22 4 0.15
24 6 0.23
25 2 0.08
26 5 0.19
27 9 0.35
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.37
Consensus pattern (25 bp):
AATGATTTCAATTAAATAATAAAAT
Found at i:102760 original size:13 final size:13
Alignment explanation
Indices: 102742--102773 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
102732 GTATTAATAC
102742 TTATTAATACTAT
1 TTATTAATACTAT
*
102755 TTATTACTACTAT
1 TTATTAATACTAT
102768 TTATTA
1 TTATTA
102774 TTAACCATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.56
Consensus pattern (13 bp):
TTATTAATACTAT
Found at i:103113 original size:6 final size:6
Alignment explanation
Indices: 103099--103145 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
103089 TTTTAAATCC
* **
103099 ATTTAA ATTTTA A-TTAA ATTTAA ATTTAA A-GCAA ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
103145 A
1 A
103146 AATAAATTTG
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
5 7 0.21
6 26 0.79
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (6 bp):
ATTTAA
Found at i:103119 original size:17 final size:17
Alignment explanation
Indices: 103099--103145 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
103089 TTTTAAATCC
* **
103099 ATTTAAATTTTAATTAA
1 ATTTAAATTTAAAGCAA
103116 ATTTAAATTTAAAGCAA
1 ATTTAAATTTAAAGCAA
103133 ATTTAAATTTAAA
1 ATTTAAATTTAAA
103146 AATAAATTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (17 bp):
ATTTAAATTTAAAGCAA
Found at i:103373 original size:30 final size:31
Alignment explanation
Indices: 103310--103447 Score: 116
Period size: 29 Copynumber: 4.7 Consensus size: 31
103300 TATGTGTCTG
* * *
103310 AAAATTACCA-TTTT-ACCCCCGAA-CTTTC
1 AAAAATACCATTTTTGACCCTCGAACCTTCC
*
103338 AAAAATCCCATTTTTGACCCT-GAACCTTCC
1 AAAAATACCATTTTTGACCCTCGAACCTTCC
*
103368 AAAAATTATCA-TTTT-ACCCTCGAA-CTTCC
1 AAAAA-TACCATTTTTGACCCTCGAACCTTCC
* * *
103397 AAAAATCCCATTTTTGA-CTTCAAACCTTCC
1 AAAAATACCATTTTTGACCCTCGAACCTTCC
*
103427 AAAACTACCA-TTTTG-CCCTCG
1 AAAAATACCATTTTTGACCCTCG
103448 TGCATCCGAA
Statistics
Matches: 87, Mismatches: 14, Indels: 17
0.74 0.12 0.14
Matches are distributed among these distances:
28 11 0.13
29 39 0.45
30 34 0.39
31 3 0.03
ACGTcount: A:0.32, C:0.31, G:0.05, T:0.32
Consensus pattern (31 bp):
AAAAATACCATTTTTGACCCTCGAACCTTCC
Found at i:103423 original size:59 final size:58
Alignment explanation
Indices: 103310--103447 Score: 188
Period size: 59 Copynumber: 2.4 Consensus size: 58
103300 TATGTGTCTG
* * *
103310 AAAATTACCATTTTACCCCCGAACTTTCAAAAATCCCATTTTTGACCCTGAACCTTCC
1 AAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCTAAACCTTCC
* *
103368 AAAAATTATCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA-CTTCAAACCTTCC
1 -AAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCT-AAACCTTCC
* *
103427 AAAACTACCATTTTGCCCTCG
1 AAAATTACCATTTTACCCTCG
103448 TGCATCCGAA
Statistics
Matches: 70, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
58 20 0.29
59 50 0.71
ACGTcount: A:0.32, C:0.31, G:0.05, T:0.32
Consensus pattern (58 bp):
AAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCTAAACCTTCC
Found at i:108936 original size:21 final size:21
Alignment explanation
Indices: 108912--108951 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
108902 TATTTTAAGA
108912 GTATGATCCTTTTAATTTGGG
1 GTATGATCCTTTTAATTTGGG
* * *
108933 GTATTATCTTTTTATTTTG
1 GTATGATCCTTTTAATTTG
108952 TAGGGACTCA
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:0.17, C:0.07, G:0.17, T:0.57
Consensus pattern (21 bp):
GTATGATCCTTTTAATTTGGG
Found at i:109963 original size:16 final size:16
Alignment explanation
Indices: 109942--109972 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
109932 CTATTTTCTA
109942 TTTCTTTTAATTTTAT
1 TTTCTTTTAATTTTAT
*
109958 TTTCTTTTATTTTTA
1 TTTCTTTTAATTTTA
109973 ATTCTATTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTCTTTTAATTTTAT
Found at i:109982 original size:21 final size:22
Alignment explanation
Indices: 109932--109991 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
109922 TTCGACTTCC
*
109932 CTATTTTCTATTT-CTTTTAATT
1 CTATTTTCT-TTTATTTTTAATT
*
109954 TTATTTTCTTTTATTTTTAATT
1 CTATTTTCTTTTATTTTTAATT
109976 CTA-TTTCTTTTATTTT
1 CTATTTTCTTTTATTTT
109992 CCCTCAGATC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 16 0.47
22 18 0.53
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.73
Consensus pattern (22 bp):
CTATTTTCTTTTATTTTTAATT
Found at i:112336 original size:17 final size:18
Alignment explanation
Indices: 112314--112349 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
112304 GCAAGTACAT
112314 AGCTAG-ATGCAACCACA
1 AGCTAGAATGCAACCACA
*
112331 AGCTAGAATGCAGCCACA
1 AGCTAGAATGCAACCACA
112349 A
1 A
112350 CAGACTGCGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.42, C:0.28, G:0.19, T:0.11
Consensus pattern (18 bp):
AGCTAGAATGCAACCACA
Found at i:124037 original size:23 final size:22
Alignment explanation
Indices: 124004--124083 Score: 88
Period size: 23 Copynumber: 3.5 Consensus size: 22
123994 GCTAGGGAAA
*
124004 CAGTAAACACACACAGTGCAAT
1 CAGTAAGCACACACAGTGCAAT
*
124026 CCAGTAAGCACACACTGTGCAAT
1 -CAGTAAGCACACACAGTGCAAT
* * * *
124049 CAGTAGGCGCACATAGCGCAAAT
1 CAGTAAGCACACACAGTGC-AAT
124072 CAGTAAGCACAC
1 CAGTAAGCACAC
124084 GAAGTACAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
22 14 0.30
23 33 0.70
ACGTcount: A:0.39, C:0.29, G:0.19, T:0.14
Consensus pattern (22 bp):
CAGTAAGCACACACAGTGCAAT
Found at i:127026 original size:23 final size:22
Alignment explanation
Indices: 126999--127048 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 22
126989 GTTAGGGAAA
*
126999 CAGTAAGCACACACAGTGCAAT
1 CAGTAAGCACAAACAGTGCAAT
*
127021 CCAGTAAGCACAAACTGTGCAAT
1 -CAGTAAGCACAAACAGTGCAAT
127044 CAGTA
1 CAGTA
127049 GGCGCACATG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 5 0.20
23 20 0.80
ACGTcount: A:0.40, C:0.26, G:0.18, T:0.16
Consensus pattern (22 bp):
CAGTAAGCACAAACAGTGCAAT
Found at i:127105 original size:23 final size:23
Alignment explanation
Indices: 127075--127120 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
127065 ATCAATAGGG
127075 ACACGAAGTGCGAAACAGTAAGC
1 ACACGAAGTGCGAAACAGTAAGC
127098 ACACGAAGTGCGAAACAGTAAGC
1 ACACGAAGTGCGAAACAGTAAGC
127121 GCGCTAGCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.22, G:0.26, T:0.09
Consensus pattern (23 bp):
ACACGAAGTGCGAAACAGTAAGC
Found at i:127750 original size:11 final size:11
Alignment explanation
Indices: 127724--127753 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
127714 TCAGTATCTA
127724 ATAATTTTTCT
1 ATAATTTTTCT
127735 A-AATTTTTCT
1 ATAATTTTTCT
127745 ATAATTTTT
1 ATAATTTTT
127754 AAAAGTCAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (11 bp):
ATAATTTTTCT
Done.