Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1961
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: 173942
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
File 2 of 2
Found at i:123099 original size:22 final size:21
Alignment explanation
Indices: 123065--123115 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
123055 TTGTTATATT
* *
123065 ATTAAAATAATAT-TTTTAT-
1 ATTAAATTTATATATTTTATA
123084 ATTAATATTTATATATTTTATA
1 ATTAA-ATTTATATATTTTATA
123106 ATTAAATTTA
1 ATTAAATTTA
123116 AATAAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 5 0.19
20 6 0.22
21 11 0.41
22 5 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTAAATTTATATATTTTATA
Found at i:124137 original size:16 final size:16
Alignment explanation
Indices: 124118--124160 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
124108 ATAAGTTAAT
124118 AATTTATTTTATATAA
1 AATTTATTTTATATAA
* * *
124134 AATTTAATATATTTAA
1 AATTTATTTTATATAA
124150 ATATTTATTTT
1 A-ATTTATTTT
124161 GTATTTATAT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
AATTTATTTTATATAA
Found at i:124156 original size:33 final size:32
Alignment explanation
Indices: 124060--124160 Score: 111
Period size: 32 Copynumber: 3.1 Consensus size: 32
124050 TTATATTATT
124060 TTTTATATAAAA--TAA-AATTTAAGATATTATA
1 TTTTATATAAAATTTAATAATTTAA-ATATT-TA
* *
124091 TATTTATATAAATTTTAATAAGTT-AATAATTTA
1 T-TTTATATAAAATTTAATAATTTAAAT-ATTTA
124124 TTTTATATAAAATTTAATATATTTAAATATTTA
1 TTTTATATAAAATTTAATA-ATTTAAATATTTA
124157 TTTT
1 TTTT
124161 GTATTTATAT
Statistics
Matches: 59, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
31 1 0.02
32 27 0.46
33 17 0.29
34 10 0.17
35 4 0.07
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (32 bp):
TTTTATATAAAATTTAATAATTTAAATATTTA
Found at i:124210 original size:13 final size:13
Alignment explanation
Indices: 124141--124211 Score: 69
Period size: 13 Copynumber: 5.7 Consensus size: 13
124131 TAAAATTTAA
*
124141 TATATTTAAATAT
1 TATATTTATATAT
*
124154 T-TATTT-TGTATT
1 TATATTTATATA-T
* *
124166 TATATTTTTTTAT
1 TATATTTATATAT
124179 TATATTT-TA-AT
1 TATATTTATATAT
124190 TATATTTATATAT
1 TATATTTATATAT
124203 TATATTTAT
1 TATATTTAT
124212 GACGTATAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
11 11 0.22
12 10 0.20
13 25 0.51
14 3 0.06
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.66
Consensus pattern (13 bp):
TATATTTATATAT
Found at i:124264 original size:10 final size:10
Alignment explanation
Indices: 124229--124275 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
124219 AATTATTTAA
*
124229 TATTTAAAAT
1 TATTTAATAT
*
124239 TATTAAAT-T
1 TATTTAATAT
*
124248 TAATTAATAT
1 TATTTAATAT
124258 TATTTAATAT
1 TATTTAATAT
*
124268 TTTTTAAT
1 TATTTAAT
124276 TTTGTGTCAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
9 7 0.23
10 23 0.77
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
TATTTAATAT
Found at i:124328 original size:30 final size:30
Alignment explanation
Indices: 124292--124353 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
124282 TCATAAGTCG
124292 TTATGTCGATGTTACTTTTTATATTATATA
1 TTATGTCGATGTTACTTTTTATATTATATA
*
124322 TTATGTCGATGTTGCTTTTTATATTATATA
1 TTATGTCGATGTTACTTTTTATATTATATA
124352 TT
1 TT
124354 TATATAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.24, C:0.06, G:0.11, T:0.58
Consensus pattern (30 bp):
TTATGTCGATGTTACTTTTTATATTATATA
Found at i:124555 original size:26 final size:29
Alignment explanation
Indices: 124511--124570 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 29
124501 ATAAATTTTA
124511 ATTTTATATTATATATTAT-CAT-ATTAT
1 ATTTTATATTATATATTATACATAATTAT
* *
124538 ATTTT-TATTATTTTTTATAACATAATTAT
1 ATTTTATATTATATATTAT-ACATAATTAT
124567 ATTT
1 ATTT
124571 AAAATTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 11 0.39
27 5 0.18
28 3 0.11
29 9 0.32
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (29 bp):
ATTTTATATTATATATTATACATAATTAT
Found at i:124585 original size:16 final size:17
Alignment explanation
Indices: 124564--124624 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 17
124554 ATAACATAAT
124564 TATATTTAAAATTTT-A
1 TATATTTAAAATTTTAA
124580 TATATTTATATAAATTTTAA
1 TATA-TT-TA-AAATTTTAA
*
124600 TATATTAAAAATTTATAA
1 TATATTTAAAATTT-TAA
124618 TATATTT
1 TATATTT
124625 TAATTATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
16 4 0.11
17 8 0.21
18 12 0.32
19 9 0.24
20 5 0.13
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TATATTTAAAATTTTAA
Found at i:124598 original size:27 final size:28
Alignment explanation
Indices: 124568--124627 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 28
124558 CATAATTATA
* * *
124568 TTTAAAATTTTATATATTTAT-ATAAAT
1 TTTAAAATATTAAAAATTTATAATAAAT
* *
124595 TTTAATATATTAAAAATTTATAATATAT
1 TTTAAAATATTAAAAATTTATAATAAAT
124623 TTTAA
1 TTTAA
124628 TTATTTTTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 17 0.63
28 10 0.37
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
TTTAAAATATTAAAAATTTATAATAAAT
Found at i:124627 original size:20 final size:19
Alignment explanation
Indices: 124571--124627 Score: 66
Period size: 20 Copynumber: 3.1 Consensus size: 19
124561 AATTATATTT
124571 AAAATTTT-ATATATTTATA
1 AAAATTTTAATATATTT-TA
*
124590 TAAATTTTAATATA--TTA
1 AAAATTTTAATATATTTTA
124607 AAAATTTATAATATATTTTA
1 AAAATTT-TAATATATTTTA
124627 A
1 A
124628 TTATTTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
17 8 0.25
18 8 0.25
19 7 0.22
20 9 0.28
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AAAATTTTAATATATTTTA
Found at i:125240 original size:36 final size:36
Alignment explanation
Indices: 125175--125244 Score: 90
Period size: 36 Copynumber: 1.9 Consensus size: 36
125165 AATTTTATAT
*
125175 AAATATTTATATATTTTTATAATTAAATTTAAATAA
1 AAATAATTATATATTTTTATAATTAAATTTAAATAA
*
125211 AAATAATTAT-TATTTATTA-AATATTAATTTAAAT
1 AAATAATTATATATTT-TTATAAT-TAAATTTAAAT
125245 TAATTTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
35 8 0.27
36 22 0.73
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (36 bp):
AAATAATTATATATTTTTATAATTAAATTTAAATAA
Found at i:126472 original size:14 final size:12
Alignment explanation
Indices: 126442--126479 Score: 53
Period size: 11 Copynumber: 3.2 Consensus size: 12
126432 TTATTTAAAA
126442 ATATTTTTTTAT
1 ATATTTTTTTAT
126454 A-ATTTTTTTA-
1 ATATTTTTTTAT
126464 ATATTATTTTTAT
1 ATATT-TTTTTAT
126477 ATA
1 ATA
126480 AAATAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
10 1 0.04
11 12 0.52
12 7 0.30
13 3 0.13
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATATTTTTTTAT
Found at i:126546 original size:32 final size:33
Alignment explanation
Indices: 126505--126576 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
126495 ATATTAAATA
*
126505 TTTATAT-AAATCTTGATA-AATTA-ATGATTTAT
1 TTTATATAAAAT-TTAATATAATTAGAT-ATTTAT
*
126537 TTTATATAAAATTTAATATATTTAGATATTTAT
1 TTTATATAAAATTTAATATAATTAGATATTTAT
126570 TTTATAT
1 TTTATAT
126577 TTATATTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
32 12 0.34
33 21 0.60
34 2 0.06
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.54
Consensus pattern (33 bp):
TTTATATAAAATTTAATATAATTAGATATTTAT
Found at i:126571 original size:21 final size:18
Alignment explanation
Indices: 126547--126616 Score: 54
Period size: 19 Copynumber: 3.6 Consensus size: 18
126537 TTTATATAAA
126547 ATTTAATATATTTAGATATTT
1 ATTT-ATATATTT--ATATTT
126568 ATTT-TATATTTATATTT
1 ATTTATATATTTATATTT
126585 ATTTTATCATATTT-TAATTAT
1 A-TTTAT-ATATTTAT-ATT-T
*
126606 ATTTAAATATT
1 ATTTATATATT
126617 ATGTTCATGA
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
17 7 0.16
18 3 0.07
19 14 0.33
20 13 0.30
21 6 0.14
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (18 bp):
ATTTATATATTTATATTT
Found at i:127003 original size:5 final size:5
Alignment explanation
Indices: 126993--127049 Score: 52
Period size: 5 Copynumber: 12.2 Consensus size: 5
126983 TATTAAAATT
* *
126993 TTATA TTATA TTTTAA TTAT- TTATA TTATA TT-TA ATA-A TTATA TTAT-
1 TTATA TTATA TTAT-A TTATA TTATA TTATA TTATA TTATA TTATA TTATA
127040 TTA-A TTATA T
1 TTATA TTATA T
127050 CATGTATTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
4 16 0.38
5 22 0.52
6 4 0.10
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TTATA
Found at i:127003 original size:20 final size:19
Alignment explanation
Indices: 126943--127032 Score: 73
Period size: 20 Copynumber: 4.8 Consensus size: 19
126933 TTATATGATA
* *
126943 ATTACATTTAAAATATTAT
1 ATTATATTTAAAATTTTAT
126962 A-TAT-TTATATAAATTTTA-
1 ATTATATT-TA-AAATTTTAT
126980 A-TATA-TTAAAATTTTAT
1 ATTATATTTAAAATTTTAT
* *
126997 ATTATATTTTAATTATTTAT
1 ATTATATTTAAAAT-TTTAT
127017 ATTATATTTAATAATT
1 ATTATATTTAA-AATT
127033 ATATTATTTA
Statistics
Matches: 57, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
16 8 0.14
17 5 0.09
18 13 0.23
19 13 0.23
20 16 0.28
21 2 0.04
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTATATTTAAAATTTTAT
Found at i:127036 original size:18 final size:20
Alignment explanation
Indices: 126993--127039 Score: 71
Period size: 18 Copynumber: 2.5 Consensus size: 20
126983 TATTAAAATT
*
126993 TTATATTATATTTTAATTAT
1 TTATATTATATTTTAATTAA
127013 TTATATTATA-TTTAA-TAA
1 TTATATTATATTTTAATTAA
127031 TTATATTAT
1 TTATATTAT
127040 TTAATTATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 11 0.42
19 5 0.19
20 10 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATATTATATTTTAATTAA
Found at i:127044 original size:13 final size:13
Alignment explanation
Indices: 127008--127049 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
126998 TTATATTTTA
127008 ATTATTTATATTAT
1 ATTATTTA-ATTAT
*
127022 ATT-TAATAATTAT
1 ATTAT-TTAATTAT
127035 ATTATTTAATTAT
1 ATTATTTAATTAT
127048 AT
1 AT
127050 CATGTATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
13 18 0.75
14 6 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
ATTATTTAATTAT
Found at i:127291 original size:2 final size:2
Alignment explanation
Indices: 127284--127355 Score: 51
Period size: 2 Copynumber: 36.5 Consensus size: 2
127274 TGCTGGACCT
* * * **
127284 TA TA TA TA TA TA TA TA TA TA TG GA TGA TGA TG T- TA TA GC TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A T-A TA TA TA TA TA TA TA
*
127326 TA T- TT 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 T
127356 GGATGATGAT
Statistics
Matches: 56, Mismatches: 10, Indels: 8
0.76 0.14 0.11
Matches are distributed among these distances:
1 3 0.05
2 48 0.86
3 5 0.09
ACGTcount: A:0.42, C:0.01, G:0.08, T:0.49
Consensus pattern (2 bp):
TA
Found at i:127356 original size:51 final size:51
Alignment explanation
Indices: 127284--127384 Score: 193
Period size: 51 Copynumber: 2.0 Consensus size: 51
127274 TGCTGGACCT
*
127284 TATATATATATATATATATATGGATGATGATGTTATAGCTAATATTTTATA
1 TATATATATATATATATATATGGATGATGATGTTACAGCTAATATTTTATA
127335 TATATATATATATATATATATGGATGATGATGTTACAGCTAATATTTTAT
1 TATATATATATATATATATATGGATGATGATGTTACAGCTAATATTTTAT
127385 GTGGATGATA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.39, C:0.03, G:0.12, T:0.47
Consensus pattern (51 bp):
TATATATATATATATATATATGGATGATGATGTTACAGCTAATATTTTATA
Found at i:127621 original size:12 final size:12
Alignment explanation
Indices: 127604--127638 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
127594 TAAAATATTA
127604 ATAAATTTTTAT
1 ATAAATTTTTAT
127616 ATAAATTTTTAT
1 ATAAATTTTTAT
127628 AT--ATTTTTAT
1 ATAAATTTTTAT
127638 A
1 A
127639 ATTAAATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 9 0.39
12 14 0.61
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
ATAAATTTTTAT
Found at i:127689 original size:10 final size:10
Alignment explanation
Indices: 127665--127707 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
127655 AATAATTATT
*
127665 ATTAATTAAA
1 ATTAATTTAA
127675 TATTAATTTAA
1 -ATTAATTTAA
*
127686 ATTAACTTAA
1 ATTAATTTAA
*
127696 ATTAATCTAA
1 ATTAATTTAA
127706 AT
1 AT
127708 AAAAAAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
10 19 0.68
11 9 0.32
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (10 bp):
ATTAATTTAA
Found at i:127987 original size:22 final size:24
Alignment explanation
Indices: 127955--128013 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 24
127945 AATTCATAAA
*
127955 TTTATTTATTA-TTAAA-AAATTAT
1 TTTATTAATTATTTAAATAAATT-T
127978 TTTA-TAATTAAATTTAAATAAATTT
1 TTTATTAATT--ATTTAAATAAATTT
128003 TTTATTAATTA
1 TTTATTAATTA
128014 AATAATAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
22 4 0.13
23 4 0.13
24 2 0.07
25 10 0.33
26 10 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
TTTATTAATTATTTAAATAAATTT
Found at i:128005 original size:25 final size:26
Alignment explanation
Indices: 127966--128016 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
127956 TTATTTATTA
127966 TTAAAAAATTATTTTA-TAATTAAAT
1 TTAAAAAATTATTTTATTAATTAAAT
127991 TTAAATAAATT-TTTTATTAATTAAAT
1 TTAAA-AAATTATTTTATTAATTAAAT
128017 AATAATTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 10 0.42
26 14 0.58
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
TTAAAAAATTATTTTATTAATTAAAT
Found at i:128415 original size:10 final size:10
Alignment explanation
Indices: 128397--128438 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
128387 TTATTAATAT
128397 TTATAATAAAA
1 TTAT-ATAAAA
128408 TTATATAAAA
1 TTATATAAAA
*
128418 -TATTATTAAA
1 TTA-TATAAAA
128428 TTATATAAAA
1 TTATATAAAA
128438 T
1 T
128439 AATAATTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
9 2 0.07
10 19 0.70
11 6 0.22
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
TTATATAAAA
Found at i:128430 original size:20 final size:21
Alignment explanation
Indices: 128405--128485 Score: 87
Period size: 20 Copynumber: 3.9 Consensus size: 21
128395 ATTTATAATA
128405 AAATTATATAAAATATTA-TT
1 AAATTATATAAAATATTATTT
*
128425 AAATTATATAAAATAATAATTT
1 AAATTATATAAAAT-ATTATTT
* *
128447 AAATTAAAT-TAAT-TTAATTT
1 AAATTATATAAAATATT-ATTT
*
128467 AAATTATAAAAAATATTAT
1 AAATTATATAAAATATTAT
128486 ACAAACTTAA
Statistics
Matches: 49, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
19 1 0.02
20 25 0.51
21 11 0.22
22 12 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AAATTATATAAAATATTATTT
Found at i:128461 original size:15 final size:15
Alignment explanation
Indices: 128441--128472 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
128431 TATAAAATAA
128441 TAATTTAAATTAAAT
1 TAATTTAAATTAAAT
*
128456 TAATTTAATTTAAAT
1 TAATTTAAATTAAAT
128471 TA
1 TA
128473 TAAAAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATTTAAATTAAAT
Found at i:132922 original size:15 final size:16
Alignment explanation
Indices: 132896--132937 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
132886 ATTTTAATTT
132896 TTTAAA-ATATTTT-A
1 TTTAAATATATTTTAA
*
132910 TTTAATTATATTTTAA
1 TTTAAATATATTTTAA
132926 TTTAAATATATT
1 TTTAAATATATT
132938 AATTCATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 5 0.21
15 7 0.29
16 12 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTAAATATATTTTAA
Found at i:132927 original size:33 final size:30
Alignment explanation
Indices: 132868--132928 Score: 86
Period size: 33 Copynumber: 1.9 Consensus size: 30
132858 TAGTTTCATA
132868 TAAAATATTTATAAATTTATTTTAATTTTT
1 TAAAATATTTATAAATTTATTTTAATTTTT
*
132898 TAAAATATTTTATTTAATTATATTTTAATTT
1 TAAAATA-TTTA-TAAATT-TATTTTAATTT
132929 AAATATATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 7 0.26
31 4 0.15
32 5 0.19
33 11 0.41
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (30 bp):
TAAAATATTTATAAATTTATTTTAATTTTT
Found at i:133045 original size:15 final size:16
Alignment explanation
Indices: 133015--133049 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
133005 ATTTTTTATT
133015 AATTAAATAATAATTTA
1 AATTAAAT-ATAATTTA
133032 AATTAAAT-TAATTTA
1 AATTAAATATAATTTA
133047 AAT
1 AAT
133050 AAAAAAAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 10 0.56
17 8 0.44
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AATTAAATATAATTTA
Found at i:136145 original size:21 final size:21
Alignment explanation
Indices: 136121--136161 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
136111 TATTAAAATA
136121 ATATTTTAT-ATTAATATTTAT
1 ATATTTTATAATTAA-ATTTAT
136142 ATATTTTATAATTAAATTTA
1 ATATTTTATAATTAAATTTA
136162 AATAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATATTTTATAATTAAATTTAT
Found at i:136802 original size:32 final size:33
Alignment explanation
Indices: 136727--136828 Score: 99
Period size: 33 Copynumber: 3.1 Consensus size: 33
136717 TTTATATTAT
*
136727 TTTTATATAAAA--TAA-AAATTTAAGATATTAAA
1 TTTTATATAAAATTTAATAAATTT-AGATATT-TA
*
136759 TATTTATAT-AAATCTTGATAAA-TTA-ATAATTTA
1 T-TTTATATAAAAT-TTAATAAATTTAGAT-ATTTA
136792 TTTTATATAAAATTTAATAAATTTAGATATTTA
1 TTTTATATAAAATTTAATAAATTTAGATATTTA
136825 TTTT
1 TTTT
136829 GTATTTATAT
Statistics
Matches: 58, Mismatches: 3, Indels: 17
0.74 0.04 0.22
Matches are distributed among these distances:
32 18 0.31
33 27 0.47
34 6 0.10
35 4 0.07
36 3 0.05
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (33 bp):
TTTTATATAAAATTTAATAAATTTAGATATTTA
Found at i:137233 original size:27 final size:27
Alignment explanation
Indices: 137203--137278 Score: 75
Period size: 27 Copynumber: 2.9 Consensus size: 27
137193 CATAATTATA
137203 TTTAAAATATTATATATTTATATAAAT
1 TTTAAAATATTATATATTTATATAAAT
* * * *
137230 TTTAATATATTAAAAATTTATATTATAT
1 TTTAAAATATTATATATTTATA-TAAAT
* *
137258 TTT-AATTATTTTATA-TTATAT
1 TTTAAAATATTATATATTTATAT
137279 TTAATAATTA
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
25 1 0.03
26 5 0.13
27 26 0.67
28 7 0.18
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
TTTAAAATATTATATATTTATATAAAT
Found at i:137257 original size:5 final size:5
Alignment explanation
Indices: 137247--137307 Score: 58
Period size: 5 Copynumber: 12.8 Consensus size: 5
137237 TATTAAAAAT
* * *
137247 TTATA TTATA TTTTAA TTATT TTATA TTATA TT-TA ATA-A TTATA TTAT-
1 TTATA TTATA TTAT-A TTATA TTATA TTATA TTATA TTATA TTATA TTATA
137295 TTA-A TTATA TTAT
1 TTATA TTATA TTAT
137308 GTATTATAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
4 12 0.27
5 29 0.64
6 4 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:137266 original size:16 final size:16
Alignment explanation
Indices: 137247--137307 Score: 59
Period size: 16 Copynumber: 3.6 Consensus size: 16
137237 TATTAAAAAT
137247 TTATATTATATTTTAA
1 TTATATTATATTTTAA
* * *
137263 TTATTTTATATTATAT
1 TTATATTATATTTTAA
137279 TTAATAATTATATTATTTAA
1 TT-AT-ATTATA-T-TTTAA
137299 TTATATTAT
1 TTATATTAT
137308 GTATTATAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
16 15 0.43
17 2 0.06
18 10 0.29
19 3 0.09
20 5 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTATATTATATTTTAA
Found at i:137272 original size:21 final size:22
Alignment explanation
Indices: 137246--137294 Score: 73
Period size: 21 Copynumber: 2.2 Consensus size: 22
137236 ATATTAAAAA
137246 TTTATATTATATTT-TAATTAT
1 TTTATATTATATTTATAATTAT
137267 TTTATATTATATTTAATAATTAT
1 TTTATATTATATTT-ATAATTAT
*
137290 ATTAT
1 TTTAT
137295 TTAATTATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 14 0.56
23 11 0.44
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTATATTATATTTATAATTAT
Found at i:137290 original size:13 final size:12
Alignment explanation
Indices: 137245--137305 Score: 67
Period size: 13 Copynumber: 5.2 Consensus size: 12
137235 TATATTAAAA
137245 ATTTAT-ATTAT
1 ATTTATAATTAT
137256 ATTT-TAATTAT
1 ATTTATAATTAT
137267 -TTTAT-ATTAT
1 ATTTATAATTAT
137277 ATTTAATAATTAT
1 ATTT-ATAATTAT
*
137290 ATTATTTAATTAT
1 ATT-TATAATTAT
137303 ATT
1 ATT
137306 ATGTATTATA
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
10 9 0.21
11 13 0.30
12 2 0.05
13 18 0.42
14 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
ATTTATAATTAT
Found at i:137291 original size:39 final size:40
Alignment explanation
Indices: 137209--137304 Score: 101
Period size: 39 Copynumber: 2.4 Consensus size: 40
137199 TATATTTAAA
137209 ATATTATATATTTATATAAATTTTAATATATTAAAAATTT
1 ATATTATATATTTATATAAATTTTAATATATTAAAAATTT
* *
137249 ATATTATAT-TTTA-AT-TATTTTATATTATATTTAATAA-TT
1 ATATTATATATTTATATAAATTTTA-A-TATA-TTAAAAATTT
* *
137288 ATATTATTTAATTATAT
1 ATATTATATATTTATAT
137305 TATGTATTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
37 6 0.13
38 3 0.06
39 18 0.38
40 18 0.38
41 2 0.04
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (40 bp):
ATATTATATATTTATATAAATTTTAATATATTAAAAATTT
Found at i:137812 original size:22 final size:24
Alignment explanation
Indices: 137785--137844 Score: 63
Period size: 22 Copynumber: 2.6 Consensus size: 24
137775 TAAAATATTA
137785 AAATATTAATAAAATTTTAT-A-T
1 AAATATTAATAAAATTTTATAATT
* * *
137807 AAATATTTATATATTTTTATAATT
1 AAATATTAATAAAATTTTATAATT
137831 AAAT-TTAAATAAAA
1 AAATATT-AATAAAA
137845 ATAATTTTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
22 17 0.59
23 3 0.10
24 9 0.31
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
AAATATTAATAAAATTTTATAATT
Found at i:137878 original size:10 final size:10
Alignment explanation
Indices: 137854--137896 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
137844 AATAATTTTT
*
137854 ATTAATTAAA
1 ATTAATTTAA
137864 TATTAATTTAA
1 -ATTAATTTAA
*
137875 ATTAACTTAA
1 ATTAATTTAA
*
137885 ATTAATCTAA
1 ATTAATTTAA
137895 AT
1 AT
137897 AAAAAAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
10 19 0.68
11 9 0.32
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (10 bp):
ATTAATTTAA
Found at i:138130 original size:22 final size:22
Alignment explanation
Indices: 138080--138131 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
138070 AATTTGATTA
138080 TAAATTTAATTTTTTTAAATAT
1 TAAATTTAATTTTTTTAAATAT
**
138102 TTTATTTAATTTTAATTT-AA-AT
1 TAAATTTAATTTT--TTTAAATAT
138124 TAAATTTA
1 TAAATTTA
138132 TATCCATTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
22 19 0.79
23 2 0.08
24 3 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TAAATTTAATTTTTTTAAATAT
Found at i:138695 original size:10 final size:10
Alignment explanation
Indices: 138682--138710 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
138672 AAAATAAAAT
138682 TTTAAATTAA
1 TTTAAATTAA
138692 TTTAAATTAA
1 TTTAAATTAA
138702 TTTAAATTA
1 TTTAAATTA
138711 TAAAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
TTTAAATTAA
Found at i:147291 original size:16 final size:16
Alignment explanation
Indices: 147272--147302 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
147262 TTTCAGATTC
147272 GAATCATTTTAAGTTT
1 GAATCATTTTAAGTTT
*
147288 GAATTATTTTAAGTT
1 GAATCATTTTAAGTT
147303 CAGATCATTT
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:0.32, C:0.03, G:0.13, T:0.52
Consensus pattern (16 bp):
GAATCATTTTAAGTTT
Found at i:147312 original size:16 final size:16
Alignment explanation
Indices: 147272--147313 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
147262 TTTCAGATTC
*
147272 GAATCATTTTAAGTTT
1 GAATCATTTTAAGTTA
*
147288 GAATTATTTTAAGTTCA
1 GAATCATTTTAAGTT-A
147305 G-ATCATTTT
1 GAATCATTTT
147314 CGATTTTGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 21 0.95
17 1 0.05
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.50
Consensus pattern (16 bp):
GAATCATTTTAAGTTA
Found at i:149203 original size:2 final size:2
Alignment explanation
Indices: 149196--149241 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
149186 AATTTTATGC
149196 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
149238 AT AT
1 AT AT
149242 CTCAATCTTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:151727 original size:24 final size:24
Alignment explanation
Indices: 151700--151801 Score: 82
Period size: 24 Copynumber: 4.2 Consensus size: 24
151690 AGGAGAGGGT
151700 GATCTACGTCG-CAAGGGTGATGGA
1 GATCTACGTCGACAA-GGTGATGGA
* *
151724 GATCTACGGCGACCAGGTGATGGA
1 GATCTACGTCGACAAGGTGATGGA
* * * ** *
151748 CATCTACGACGTCTGGGTGAAGGA
1 GATCTACGTCGACAAGGTGATGGA
* *
151772 GATCTGCGTCG-CACATGTGATGGA
1 GATCTACGTCGACA-AGGTGATGGA
151796 GATCTA
1 GATCTA
151802 TGACGTCGAA
Statistics
Matches: 60, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
23 1 0.02
24 57 0.95
25 2 0.03
ACGTcount: A:0.25, C:0.20, G:0.34, T:0.22
Consensus pattern (24 bp):
GATCTACGTCGACAAGGTGATGGA
Found at i:151773 original size:48 final size:48
Alignment explanation
Indices: 151714--151808 Score: 120
Period size: 48 Copynumber: 2.0 Consensus size: 48
151704 TACGTCGCAA
*
151714 GGGTGATGGAGATCTACGGCG-ACCAGGTGATGGACATCTACGACGTCT
1 GGGTGAAGGAGATCTACGGCGCA-CAGGTGATGGACATCTACGACGTCT
* * * * *
151762 GGGTGAAGGAGATCTGCGTCGCACATGTGATGGAGATCTATGACGTC
1 GGGTGAAGGAGATCTACGGCGCACAGGTGATGGACATCTACGACGTC
151809 GAACAGGAGA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
48 39 0.98
49 1 0.03
ACGTcount: A:0.23, C:0.19, G:0.36, T:0.22
Consensus pattern (48 bp):
GGGTGAAGGAGATCTACGGCGCACAGGTGATGGACATCTACGACGTCT
Found at i:151820 original size:27 final size:27
Alignment explanation
Indices: 151790--151885 Score: 99
Period size: 27 Copynumber: 3.6 Consensus size: 27
151780 TCGCACATGT
*
151790 GATGGAGATCTATGACGTCGAACAGGA
1 GATGGTGATCTATGACGTCGAACAGGA
**
151817 GATGGTGATCTGCGACGTCGAATC--GA
1 GATGGTGATCTATGACGTCGAA-CAGGA
* *
151843 TAATGGTGATCTATGACGTCTG-ACAGGT
1 -GATGGTGATCTATGACGTC-GAACAGGA
151871 GATGGTGATCTATGA
1 GATGGTGATCTATGA
151886 TGTCCGATAG
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
26 3 0.05
27 50 0.89
28 3 0.05
ACGTcount: A:0.27, C:0.15, G:0.32, T:0.26
Consensus pattern (27 bp):
GATGGTGATCTATGACGTCGAACAGGA
Found at i:151897 original size:27 final size:27
Alignment explanation
Indices: 151788--151899 Score: 95
Period size: 27 Copynumber: 4.1 Consensus size: 27
151778 CGTCGCACAT
*
151788 GTGATGGAGATCTATGACGT-CGAACAG
1 GTGATGGTGATCTATGACGTCCG-ACAG
* **
151815 GAGATGGTGATCTGCGACGT-CGA-ATCG
1 GTGATGGTGATCTATGACGTCCGACA--G
* * *
151842 ATAATGGTGATCTATGACGTCTGACAG
1 GTGATGGTGATCTATGACGTCCGACAG
* *
151869 GTGATGGTGATCTATGATGTCCGATAG
1 GTGATGGTGATCTATGACGTCCGACAG
151896 GTGA
1 GTGA
151900 CCGATATCTA
Statistics
Matches: 66, Mismatches: 15, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
25 1 0.02
26 1 0.02
27 61 0.92
28 2 0.03
29 1 0.02
ACGTcount: A:0.26, C:0.14, G:0.33, T:0.27
Consensus pattern (27 bp):
GTGATGGTGATCTATGACGTCCGACAG
Found at i:155567 original size:20 final size:20
Alignment explanation
Indices: 155500--155585 Score: 71
Period size: 19 Copynumber: 4.5 Consensus size: 20
155490 ATAAATTATT
*
155500 AATATATCAA-AATTTATATA
1 AATATATAAATAATTTA-ATA
155520 AATATA-AAAT-ATTT--TA
1 AATATATAAATAATTTAATA
155536 AATATGAT-AATAATTTAATA
1 AATAT-ATAAATAATTTAATA
*
155556 AATATATAAATACA-ATAA-A
1 AATATATAAATA-ATTTAATA
155575 AATATATAAAT
1 AATATATAAAT
155586 TAACAAATTT
Statistics
Matches: 56, Mismatches: 2, Indels: 17
0.75 0.03 0.23
Matches are distributed among these distances:
16 7 0.12
17 4 0.07
18 4 0.07
19 20 0.36
20 20 0.36
21 1 0.02
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.37
Consensus pattern (20 bp):
AATATATAAATAATTTAATA
Found at i:161024 original size:16 final size:16
Alignment explanation
Indices: 161005--161035 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
160995 TTTTTAAAAT
161005 TTAAATATTAAATTTA
1 TTAAATATTAAATTTA
*
161021 TTAAATATTATATTT
1 TTAAATATTAAATTT
161036 TAAAAAATTA
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:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTAAATATTAAATTTA
Found at i:161958 original size:30 final size:30
Alignment explanation
Indices: 161902--161959 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
161892 AATATGACGA
* *
161902 TTAATAAATTTTTTATTTTTTATTAAAAAC
1 TTAATAAATTTGTTATTATTTATTAAAAAC
161932 TTAATAAATTTGTTATTAATTT-TTAAAA
1 TTAATAAATTTGTTATT-ATTTATTAAAA
161960 TTTTATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 22 0.88
31 3 0.12
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (30 bp):
TTAATAAATTTGTTATTATTTATTAAAAAC
Found at i:162802 original size:17 final size:18
Alignment explanation
Indices: 162780--162813 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
162770 TACTAAGTTG
*
162780 TTTTAAT-TTTTTATTTT
1 TTTTAATATTTATATTTT
162797 TTTTAATATTTATATTT
1 TTTTAATATTTATATTT
162814 GATATATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTAATATTTATATTTT
Found at i:162875 original size:18 final size:18
Alignment explanation
Indices: 162852--162886 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
162842 TATAATTTTT
* *
162852 TAAAAATTTTAAAATATA
1 TAAAAAATTAAAAATATA
162870 TAAAAAATTAAAAATAT
1 TAAAAAATTAAAAATAT
162887 TTATATTAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
TAAAAAATTAAAAATATA
Found at i:168744 original size:32 final size:31
Alignment explanation
Indices: 168703--168762 Score: 111
Period size: 32 Copynumber: 1.9 Consensus size: 31
168693 AGATGAATAT
168703 TTTAAAAAAATAAAAAACTTAAATAACATAGA
1 TTTAAAAAAATAAAAAA-TTAAATAACATAGA
168735 TTTAAAAAAATAAAAAATTAAATAACAT
1 TTTAAAAAAATAAAAAATTAAATAACAT
168763 GGATATTAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 11 0.39
32 17 0.61
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.27
Consensus pattern (31 bp):
TTTAAAAAAATAAAAAATTAAATAACATAGA
Found at i:168750 original size:31 final size:32
Alignment explanation
Indices: 168703--168762 Score: 104
Period size: 31 Copynumber: 1.9 Consensus size: 32
168693 AGATGAATAT
*
168703 TTTAAAAAAATAAAAAACTTAAATAACATAGA
1 TTTAAAAAAATAAAAAAATTAAATAACATAGA
168735 TTTAAAAAAAT-AAAAAATTAAATAACAT
1 TTTAAAAAAATAAAAAAATTAAATAACAT
168763 GGATATTAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 16 0.59
32 11 0.41
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.27
Consensus pattern (32 bp):
TTTAAAAAAATAAAAAAATTAAATAACATAGA
Found at i:171675 original size:23 final size:22
Alignment explanation
Indices: 171632--171676 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
171622 ATAAGCATTT
*
171632 TAATTATTTTTTATATTATACA
1 TAATTATTTTTTATATCATACA
*
171654 TAATTATTTTTTCATGTCATACA
1 TAATTATTTTTT-ATATCATACA
171677 GTATAGGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.33, C:0.09, G:0.02, T:0.56
Consensus pattern (22 bp):
TAATTATTTTTTATATCATACA
Found at i:171837 original size:2 final size:2
Alignment explanation
Indices: 171830--171854 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
171820 TCTAAATTGG
171830 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 A
171855 GACATACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:173460 original size:23 final size:26
Alignment explanation
Indices: 173411--173460 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 26
173401 GCTCGTTTCG
**
173411 CCCCCCGGGTCGCTCCCCCTCTTGGC
1 CCCCCCGGGTCGCTCCCCCTCCCGGC
173437 CCCCCCGGG-C-C-CCCCCTCCCGGC
1 CCCCCCGGGTCGCTCCCCCTCCCGGC
173460 C
1 C
173461 GTCCCGTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 11 0.50
24 1 0.05
25 1 0.05
26 9 0.41
ACGTcount: A:0.00, C:0.66, G:0.22, T:0.12
Consensus pattern (26 bp):
CCCCCCGGGTCGCTCCCCCTCCCGGC
Found at i:173685 original size:11 final size:11
Alignment explanation
Indices: 173654--173687 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
173644 TGTCCGCCGG
*
173654 CCCCCCCCCCT
1 CCCCCCCCCTT
173665 CCCCCCCCCTT
1 CCCCCCCCCTT
*
173676 CTCCCCCCCTT
1 CCCCCCCCCTT
173687 C
1 C
173688 GCGGCCCCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.00, C:0.82, G:0.00, T:0.18
Consensus pattern (11 bp):
CCCCCCCCCTT
Done.