Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold390
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: 272427
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
File 2 of 2
Found at i:124572 original size:18 final size:16
Alignment explanation
Indices: 124539--124606 Score: 50
Period size: 16 Copynumber: 4.1 Consensus size: 16
124529 ACAACATGAA
* *
124539 TATATATCTCAATATT
1 TATATATATAAATATT
124555 TATATAGTATAAATTATT
1 TATATA-TATAAA-TATT
*
124573 AATATAT-TAAA-ATT
1 TATATATATAAATATT
124587 TATATAAATATAAAATATT
1 TATAT--ATAT-AAATATT
124606 T
1 T
124607 TAAATACGAT
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
14 7 0.17
16 12 0.29
17 6 0.15
18 12 0.29
19 4 0.10
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (16 bp):
TATATATATAAATATT
Found at i:126610 original size:22 final size:23
Alignment explanation
Indices: 126575--126625 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
126565 TATTACATAT
*
126575 TTTATTTATTTTTAAAAT-TTAC
1 TTTATTTATATTTAAAATCTTAC
* *
126597 TTTATTTGTATTTATAATCTTAC
1 TTTATTTATATTTAAAATCTTAC
126620 TATTAT
1 T-TTAT
126626 CATTTATAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 15 0.62
23 5 0.21
24 4 0.17
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.63
Consensus pattern (23 bp):
TTTATTTATATTTAAAATCTTAC
Found at i:127287 original size:20 final size:22
Alignment explanation
Indices: 127245--127297 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
127235 ATCACAAAAA
* * *
127245 TAAAAATTCAAAAAGTTAGAAT
1 TAAAAAATAAAAAAATTAGAAT
127267 T-AAAAATAAAAAAATTA-AAT
1 TAAAAAATAAAAAAATTAGAAT
127287 TAAAAAATAAA
1 TAAAAAATAAA
127298 TTTATTATGC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 4 0.15
21 22 0.81
22 1 0.04
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.25
Consensus pattern (22 bp):
TAAAAAATAAAAAAATTAGAAT
Found at i:128860 original size:31 final size:31
Alignment explanation
Indices: 128825--128885 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
128815 AACTTAATCA
*
128825 TTTTATTTTATGCATAAATAAGTTCTTAACT
1 TTTTATTTTATACATAAATAAGTTCTTAACT
*
128856 TTTTATTTTATATATAAATAAGTTCTTAAC
1 TTTTATTTTATACATAAATAAGTTCTTAAC
128886 CTTTAATTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.34, C:0.08, G:0.05, T:0.52
Consensus pattern (31 bp):
TTTTATTTTATACATAAATAAGTTCTTAACT
Found at i:129895 original size:16 final size:17
Alignment explanation
Indices: 129876--129908 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
129866 AAATAATTTA
129876 ATATC-CAAATTTTTTT
1 ATATCTCAAATTTTTTT
*
129892 ATATCTTAAATTTTTTT
1 ATATCTCAAATTTTTTT
129909 TCCTTATCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (17 bp):
ATATCTCAAATTTTTTT
Found at i:130842 original size:2 final size:2
Alignment explanation
Indices: 130835--130859 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
130825 AGAAATATTT
130835 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 T
130860 TTGTATTTCT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:134653 original size:3 final size:3
Alignment explanation
Indices: 134645--134678 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
134635 CTTTCGATAG
134645 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
134679 ATATATTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:136103 original size:16 final size:18
Alignment explanation
Indices: 136078--136115 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
136068 ATATTAATTG
136078 TATAAAATAAT-TAAA-A
1 TATAAAATAATATAAATA
*
136094 TATAATATAATATAAATA
1 TATAAAATAATATAAATA
136112 TATA
1 TATA
136116 TTTTAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 10 0.53
17 4 0.21
18 5 0.26
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TATAAAATAATATAAATA
Found at i:136174 original size:34 final size:34
Alignment explanation
Indices: 136093--136174 Score: 96
Period size: 32 Copynumber: 2.4 Consensus size: 34
136083 AATAATTAAA
* *
136093 ATATAATATAATATAAATATATATTTTAAAATTT
1 ATATAATATAAAATAAATATATATATTAAAATTT
* * *
136127 AAATAATAT-AAATAATTA-ATATATTCAAATTT
1 ATATAATATAAAATAAATATATATATTAAAATTT
136159 ATATCAATATAAAATA
1 ATAT-AATATAAAATA
136175 TTTTAAAGCG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
32 15 0.38
33 12 0.30
34 13 0.32
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (34 bp):
ATATAATATAAAATAAATATATATATTAAAATTT
Found at i:137511 original size:14 final size:13
Alignment explanation
Indices: 137487--137522 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 13
137477 AATAAAAAAA
137487 TAAATTATAAATAT
1 TAAATT-TAAATAT
137501 TAAAATTTAAATAT
1 T-AAATTTAAATAT
137515 TAAATTTA
1 TAAATTTA
137523 TTAATTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 7 0.33
14 9 0.43
15 5 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TAAATTTAAATAT
Found at i:137572 original size:12 final size:12
Alignment explanation
Indices: 137555--137579 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
137545 ATATAAAAAA
137555 TCAAATTCAATT
1 TCAAATTCAATT
137567 TCAAATTCAATT
1 TCAAATTCAATT
137579 T
1 T
137580 TCCACTTTTG
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:0.16, G:0.00, T:0.44
Consensus pattern (12 bp):
TCAAATTCAATT
Found at i:137899 original size:18 final size:18
Alignment explanation
Indices: 137876--137910 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
137866 TAAAAATTTA
* *
137876 TTTTATTATTTAATAAAT
1 TTTTATAATTAAATAAAT
137894 TTTTATAATTAAATAAA
1 TTTTATAATTAAATAAA
137911 AATTTTATTT
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTTATAATTAAATAAAT
Found at i:137904 original size:21 final size:20
Alignment explanation
Indices: 137863--137922 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
137853 AATTTATTAA
*
137863 ATTTAAAAATTTATTTTATT
1 ATTTAAAAATTTATTTAATT
137883 ATTTAATAAATTT-TTATAATT
1 ATTTAA-AAATTTATT-TAATT
**
137904 AAATAAAAATTTTATTTAA
1 ATTTAAAAA-TTTATTTAA
137923 ATTCGATCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
20 11 0.33
21 20 0.61
22 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTTAAAAATTTATTTAATT
Found at i:137906 original size:37 final size:36
Alignment explanation
Indices: 137815--137921 Score: 87
Period size: 38 Copynumber: 2.8 Consensus size: 36
137805 TTGATTGAGT
*
137815 TAAATTTTT-TAAATAAAAAATTTTATTTATCTAAA
1 TAAATTTTTATAATTAAAAAATTTTATTTATCTAAA
*
137850 TATAATTTATTA-AATTTAAAAATTTATTTTA-TTAT-TTAA
1 TA-AATTT-TTATAA-TTAAAAA---ATTTTATTTATCTAAA
137889 TAAATTTTTATAATTAAATAAAAATTTTATTTA
1 TAAATTTTTATAATT--A-AAAAATTTTATTTA
137922 AATTCGATCA
Statistics
Matches: 58, Mismatches: 2, Indels: 21
0.72 0.02 0.26
Matches are distributed among these distances:
35 2 0.03
36 5 0.09
37 15 0.26
38 16 0.28
39 6 0.10
40 8 0.14
41 6 0.10
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (36 bp):
TAAATTTTTATAATTAAAAAATTTTATTTATCTAAA
Found at i:138290 original size:15 final size:16
Alignment explanation
Indices: 138255--138293 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
138245 AACGAATTTG
*
138255 AAAATAATTTAAATCT
1 AAAATGATTTAAATCT
*
138271 AAAATGATTTAACT-T
1 AAAATGATTTAAATCT
138286 AAAATGAT
1 AAAATGAT
138294 CTGAATAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (16 bp):
AAAATGATTTAAATCT
Found at i:138375 original size:15 final size:15
Alignment explanation
Indices: 138355--138387 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
138345 CTGCGTATTT
*
138355 AATTTGATTAATCAA
1 AATTTGAATAATCAA
138370 AATTTGAATAATCAA
1 AATTTGAATAATCAA
138385 AAT
1 AAT
138388 CAAAATTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (15 bp):
AATTTGAATAATCAA
Found at i:139228 original size:16 final size:17
Alignment explanation
Indices: 139207--139274 Score: 74
Period size: 16 Copynumber: 4.2 Consensus size: 17
139197 ATAAATACCT
139207 TAAAAT-TTATATAATA
1 TAAAATATTATATAATA
139223 TAAAATATTA-AT-ATA
1 TAAAATATTATATAATA
139238 TTAAAAT-TTATATAAATA
1 -TAAAATATTATAT-AATA
*
139256 TAAAATATTTTA-AATA
1 TAAAATATTATATAATA
139272 TAA
1 TAA
139275 TTATATATAA
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
15 6 0.13
16 23 0.51
17 9 0.20
18 7 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAAATATTATATAATA
Found at i:139264 original size:33 final size:32
Alignment explanation
Indices: 139182--139264 Score: 112
Period size: 33 Copynumber: 2.5 Consensus size: 32
139172 AATAAAAAAA
* * *
139182 ATATGATATAAATATATAAATACCTTAAAATTT
1 ATATAATATAAA-ATATTAATACATTAAAATTT
*
139215 ATATAATATAAAATATTAATATATTAAAATTT
1 ATATAATATAAAATATTAATACATTAAAATTT
139247 ATATAAATATAAAATATT
1 ATAT-AATATAAAATATT
139265 TTAAATATAA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
32 21 0.47
33 24 0.53
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.41
Consensus pattern (32 bp):
ATATAATATAAAATATTAATACATTAAAATTT
Found at i:139282 original size:32 final size:33
Alignment explanation
Indices: 139207--139285 Score: 101
Period size: 32 Copynumber: 2.5 Consensus size: 33
139197 ATAAATACCT
*
139207 TAAAATTTATAT-AATATAAAATATTAATATAT
1 TAAAATTTATATAAATATAAAATATTAATATAA
*
139239 TAAAATTTATATAAATATAAAATATT-TTA-AA
1 TAAAATTTATATAAATATAAAATATTAATATAA
*
139270 TATAATTATATATAAA
1 TAAAATT-TATATAAA
139286 CACAATATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
31 7 0.17
32 22 0.52
33 13 0.31
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (33 bp):
TAAAATTTATATAAATATAAAATATTAATATAA
Found at i:139750 original size:11 final size:11
Alignment explanation
Indices: 139734--139765 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
139724 AAAATATTAT
139734 ATAATATAAAA
1 ATAATATAAAA
*
139745 ATAATATTAAA
1 ATAATATAAAA
139756 ATAATATAAA
1 ATAATATAAA
139766 CATATGAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
ATAATATAAAA
Found at i:139762 original size:27 final size:27
Alignment explanation
Indices: 139710--139764 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 27
139700 GTATTATACG
*
139710 ATATAAAAAATAATAAAATATTATATA
1 ATATAAAAAATAATAAAATATAATATA
139737 ATAT-AAAAATAATATTAAA-ATAATATA
1 ATATAAAAAATAATA--AAATATAATATA
139764 A
1 A
139765 ACATATGAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 10 0.40
27 12 0.48
28 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (27 bp):
ATATAAAAAATAATAAAATATAATATA
Found at i:139763 original size:29 final size:27
Alignment explanation
Indices: 139710--139763 Score: 72
Period size: 29 Copynumber: 1.9 Consensus size: 27
139700 GTATTATACG
*
139710 ATATAAAAAATAATAAAATATTATATA
1 ATATAAAAAATAATAAAATAATATATA
*
139737 ATATAAAAATAATATTAAAATAATATA
1 ATAT-AAAA-AATAATAAAATAATATA
139764 AACATATGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 4 0.17
28 4 0.17
29 15 0.65
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (27 bp):
ATATAAAAAATAATAAAATAATATATA
Found at i:140662 original size:25 final size:23
Alignment explanation
Indices: 140634--140681 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 23
140624 TTAATTTTAG
*
140634 GTGTGATTAAAATATGATATAATAT
1 GTGTAATTAAAATAT-ATA-AATAT
140659 GTGTAATTAAAATATATAAATAT
1 GTGTAATTAAAATATATAAATAT
140682 AAAAATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.23
24 3 0.14
25 14 0.64
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (23 bp):
GTGTAATTAAAATATATAAATAT
Found at i:141682 original size:13 final size:13
Alignment explanation
Indices: 141664--141694 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
141654 GCCCATCATT
141664 AAAAAAGTAAAAA
1 AAAAAAGTAAAAA
*
141677 AAAAAATTAAAAA
1 AAAAAAGTAAAAA
141690 AAAAA
1 AAAAA
141695 CAAAAGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.87, C:0.00, G:0.03, T:0.10
Consensus pattern (13 bp):
AAAAAAGTAAAAA
Found at i:142415 original size:5 final size:5
Alignment explanation
Indices: 142405--142453 Score: 57
Period size: 5 Copynumber: 9.8 Consensus size: 5
142395 TGATTTTTTT
*
142405 AATTA AATTA AGTTA AATTA AATTTA AATTCA AA-TA AATT- AATTA AATT
1 AATTA AATTA AATTA AATTA AA-TTA AATT-A AATTA AATTA AATTA AATT
142454 TTTAAAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
4 7 0.18
5 23 0.61
6 8 0.21
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (5 bp):
AATTA
Found at i:142997 original size:23 final size:21
Alignment explanation
Indices: 142956--142998 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
142946 ATATTATTTT
142956 TAAAATTTTTTTAAATAATAA
1 TAAAATTTTTTTAAATAATAA
*
142977 TAAAATTTATTTTTAACTAATA
1 TAAAA-TT-TTTTTAAATAATA
142999 TTTATATCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 2 0.11
23 12 0.63
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
TAAAATTTTTTTAAATAATAA
Found at i:143625 original size:18 final size:18
Alignment explanation
Indices: 143602--143636 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
143592 CTCTTTTCAA
*
143602 TTTATATGTATATATATT
1 TTTATATATATATATATT
143620 TTTATATATATATATAT
1 TTTATATATATATATAT
143637 CAATAGTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (18 bp):
TTTATATATATATATATT
Found at i:143856 original size:14 final size:15
Alignment explanation
Indices: 143831--143860 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
143821 TAATATGAAC
143831 TATTTAAGTTTAAAT
1 TATTTAAGTTTAAAT
143846 TATTTAA-TTTAAAT
1 TATTTAAGTTTAAAT
143860 T
1 T
143861 TTAATAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (15 bp):
TATTTAAGTTTAAAT
Found at i:143868 original size:15 final size:15
Alignment explanation
Indices: 143839--143905 Score: 66
Period size: 15 Copynumber: 4.6 Consensus size: 15
143829 ACTATTTAAG
*
143839 TTTAAATTAT-TTAA
1 TTTAAATTATAATAA
*
143853 TTTAAATTTTAATAA
1 TTTAAATTATAATAA
* * *
143868 TTTTAATCAAAATAA
1 TTTAAATTATAATAA
*
143883 TTT-TATTATAATAA
1 TTTAAATTATAATAA
143897 TTTAAATTA
1 TTTAAATTA
143906 GACTTATTTA
Statistics
Matches: 41, Mismatches: 10, Indels: 3
0.76 0.19 0.06
Matches are distributed among these distances:
14 20 0.49
15 21 0.51
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (15 bp):
TTTAAATTATAATAA
Found at i:143870 original size:20 final size:20
Alignment explanation
Indices: 143832--143870 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
143822 AATATGAACT
* *
143832 ATTTAAGTTTAAATTATTTA
1 ATTTAAATTTAAATAATTTA
*
143852 ATTTAAATTTTAATAATTT
1 ATTTAAATTTAAATAATTT
143871 TAATCAAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (20 bp):
ATTTAAATTTAAATAATTTA
Found at i:143897 original size:14 final size:15
Alignment explanation
Indices: 143862--143899 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
143852 ATTTAAATTT
143862 TAATAATTTTAATCA
1 TAATAATTTTAATCA
* *
143877 AAATAATTTT-ATTA
1 TAATAATTTTAATCA
143891 TAATAATTT
1 TAATAATTT
143900 AAATTAGACT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 11 0.55
15 9 0.45
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATAATTTTAATCA
Found at i:144199 original size:17 final size:17
Alignment explanation
Indices: 144177--144212 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
144167 TATAAAACTT
* *
144177 AAATATTTTGAAATTAA
1 AAATATTATCAAATTAA
144194 AAATATTATCAAATTAA
1 AAATATTATCAAATTAA
144211 AA
1 AA
144213 TGACCTCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (17 bp):
AAATATTATCAAATTAA
Found at i:144513 original size:21 final size:22
Alignment explanation
Indices: 144487--144542 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
144477 ATCTAATTTA
* * *
144487 TAAATATTTTTATTAT-AAATT
1 TAAATATTTTAAATATAAAACT
*
144508 TAAATAATTTAAATATAAAACT
1 TAAATATTTTAAATATAAAACT
144530 TAAATATTTTAAA
1 TAAATATTTTAAA
144543 ATTCAAAATG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 13 0.45
22 16 0.55
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (22 bp):
TAAATATTTTAAATATAAAACT
Found at i:144967 original size:21 final size:21
Alignment explanation
Indices: 144928--144973 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
144918 ATATTTTTAT
*
144928 TTATTATAATTATTTTTAAAA
1 TTATTATAATTATTATTAAAA
*
144949 TTATTATATATTA-TATTAAAT
1 TTATTATA-ATTATTATTAAAA
144970 TTAT
1 TTAT
144974 ATTTTAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTATTATAATTATTATTAAAA
Found at i:147966 original size:45 final size:45
Alignment explanation
Indices: 147892--147980 Score: 133
Period size: 45 Copynumber: 2.0 Consensus size: 45
147882 GATTACTTCA
* * *
147892 ATAACTTATGCTACTCAACCATAAGCTCGAGCCAACAATTATTGG
1 ATAACTTATACTACTCAACCAAAAACTCGAGCCAACAATTATTGG
* *
147937 ATAACTTATACTACTCAATCAAAAACTCGAGCCAATAATTATTG
1 ATAACTTATACTACTCAACCAAAAACTCGAGCCAACAATTATTG
147981 AATGAAATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.28
Consensus pattern (45 bp):
ATAACTTATACTACTCAACCAAAAACTCGAGCCAACAATTATTGG
Found at i:148471 original size:25 final size:25
Alignment explanation
Indices: 148393--148474 Score: 75
Period size: 25 Copynumber: 3.3 Consensus size: 25
148383 AAAAAACAAT
*
148393 TTTTATTTATTTTT-AAAAT--TTTA
1 TTTT-TTTATTTTTAAAAATAATGTA
*
148416 TTTTTTTAATTTTTAAATAATTAAAG-A
1 TTTTTTT-ATTTTTAAA-AA-TAATGTA
148443 -TTTTTTATTTTTAAAAATAATGTA
1 TTTTTTTATTTTTAAAAATAATGTA
148467 TTTTTTTA
1 TTTTTTTA
148475 GAATATCCTT
Statistics
Matches: 48, Mismatches: 3, Indels: 14
0.74 0.05 0.22
Matches are distributed among these distances:
22 3 0.06
23 14 0.29
24 5 0.10
25 18 0.38
26 7 0.15
27 1 0.02
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (25 bp):
TTTTTTTATTTTTAAAAATAATGTA
Found at i:149131 original size:17 final size:16
Alignment explanation
Indices: 149098--149144 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
149088 ATTATAAATT
149098 TATTTTAAATAAA-AA
1 TATTTTAAATAAATAA
149113 TATTATTAAATAAATAA
1 TATT-TTAAATAAATAA
*
149130 TAATTTAAATCAAAT
1 TATTTTAAAT-AAAT
149145 CAATTCGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 4 0.14
16 15 0.54
17 9 0.32
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (16 bp):
TATTTTAAATAAATAA
Found at i:150150 original size:2 final size:2
Alignment explanation
Indices: 150143--150175 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
150133 GATCTTACAC
150143 TA TA TA 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 T
150176 CCCATTTCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:151711 original size:21 final size:21
Alignment explanation
Indices: 151660--151717 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 21
151650 TTTATTATAT
* *
151660 AAATAA-TTATTTTAATCAAA
1 AAATAATTTATTTAAATTAAA
* *
151680 ACAT-ATGTATTTAAATTAAA
1 AAATAATTTATTTAAATTAAA
151700 AAATAATTTATTTAAATT
1 AAATAATTTATTTAAATT
151718 CGATATAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
19 1 0.03
20 17 0.57
21 12 0.40
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (21 bp):
AAATAATTTATTTAAATTAAA
Found at i:156545 original size:20 final size:20
Alignment explanation
Indices: 156516--156590 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
156506 AAAAAGACAT
*
156516 AATGTATCGATACATTGCAG
1 AATGTATCGATACATTGCAA
*
156536 AATATATCGATACATT-CATA
1 AATGTATCGATACATTGCA-A
* * *
156556 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTGCAA
156576 AATGTATCGATACAT
1 AATGTATCGATACAT
156591 CTGGGTAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
19 2 0.04
20 42 0.93
21 1 0.02
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTGCAA
Found at i:156584 original size:40 final size:39
Alignment explanation
Indices: 156513--156590 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
156503 GGTAAAAAGA
* *
156513 CATAATGTATCGATACATTGCAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
156552 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
156591 CTGGGTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:158619 original size:48 final size:47
Alignment explanation
Indices: 158549--158644 Score: 165
Period size: 48 Copynumber: 2.0 Consensus size: 47
158539 TTAATTTAAT
* *
158549 TTGACAAAAACTATCAATAAGTCAAATCGACTAGCATAAACTCAATA
1 TTGACAAAAAATATCAATAAGTCAAATCGACTAACATAAACTCAATA
158596 TTGACAAAAAAATATCAATAAGTCAAATCGACTAACATAAACTCAATA
1 TTGAC-AAAAAATATCAATAAGTCAAATCGACTAACATAAACTCAATA
158644 T
1 T
158645 GACTCAAACA
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
47 5 0.11
48 41 0.89
ACGTcount: A:0.51, C:0.18, G:0.07, T:0.24
Consensus pattern (47 bp):
TTGACAAAAAATATCAATAAGTCAAATCGACTAACATAAACTCAATA
Found at i:158672 original size:23 final size:23
Alignment explanation
Indices: 158646--158690 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
158636 ACTCAATATG
158646 ACTCAAACAATTAAATT-AAAATA
1 ACTCAAACAATT-AATTCAAAATA
*
158669 ACTCAAATAATTAATTCAAAAT
1 ACTCAAACAATTAATTCAAAAT
158691 GATCCAAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.58, C:0.13, G:0.00, T:0.29
Consensus pattern (23 bp):
ACTCAAACAATTAATTCAAAATA
Found at i:161621 original size:100 final size:100
Alignment explanation
Indices: 161375--161623 Score: 329
Period size: 100 Copynumber: 2.5 Consensus size: 100
161365 AAATAGGATC
* * * * * *
161375 TGAAAAGGTTTAAAATCTCATTAAAAACTTTAACTTGTCAAGTATACTGCTACTAAAAACTGGTT
1 TGAAAAGGTTTAAAATCTCATTAAAAACTTTAACTTATCAAGTATATTACCACTAAAAAATAGTT
*
161440 AAACTTTCCAGTTTTCTTGAGTCATATCTATTATA
66 AAACTTTCCAGTTTTCTTCAGTCATATCTATTATA
* * * *
161475 TGAAAAAGTTTAAAATCTCATTAAAAAATTTAACCTATCAAGTATATTACCA-TCAAAAAATATT
1 TGAAAAGGTTTAAAATCTCATTAAAAACTTTAACTTATCAAGTATATTACCACT-AAAAAATAGT
* * *
161539 TAAACTTTCCAGTTTTCTTCATTCATTTCTGTTATA
65 TAAACTTTCCAGTTTTCTTCAGTCATATCTATTATA
* * *
161575 TGAAAGGGTTTAAAATCTCATTACAAACTTTAAATTATCAAGTATATTA
1 TGAAAAGGTTTAAAATCTCATTAAAAACTTTAACTTATCAAGTATATTA
161624 AAAATGGGCT
Statistics
Matches: 128, Mismatches: 20, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
99 1 0.01
100 127 0.99
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39
Consensus pattern (100 bp):
TGAAAAGGTTTAAAATCTCATTAAAAACTTTAACTTATCAAGTATATTACCACTAAAAAATAGTT
AAACTTTCCAGTTTTCTTCAGTCATATCTATTATA
Found at i:162327 original size:22 final size:22
Alignment explanation
Indices: 162302--162354 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
162292 TTAAATTATT
**
162302 ATTTAATAATAAAAATATTTAA
1 ATTTAATAATAAAAATACATAA
* *
162324 ATTTAATTATAAGAATACATAA
1 ATTTAATAATAAAAATACATAA
162346 ATATTAATA
1 AT-TTAATA
162355 TATATATTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (22 bp):
ATTTAATAATAAAAATACATAA
Found at i:162340 original size:28 final size:30
Alignment explanation
Indices: 162292--162350 Score: 70
Period size: 28 Copynumber: 2.0 Consensus size: 30
162282 TTAATTTGAA
* *
162292 TTAAATTATTATTTAATAATA-A-AAATAT
1 TTAAATTATAATTTAAGAATACATAAATAT
162320 TTAAATT-TAATTATAAGAATACATAAATAT
1 TTAAATTATAATT-TAAGAATACATAAATAT
162350 T
1 T
162351 AATATATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
27 4 0.15
28 14 0.54
29 1 0.04
30 7 0.27
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (30 bp):
TTAAATTATAATTTAAGAATACATAAATAT
Found at i:163231 original size:18 final size:19
Alignment explanation
Indices: 163201--163247 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
163191 TTTGTTATAA
163201 AATATTTATATATTGTTTAT
1 AATATTTA-ATATTGTTTAT
* *
163221 AAT-TTTAATATTATATAT
1 AATATTTAATATTGTTTAT
163239 AATATTTAA
1 AATATTTAA
163248 ATTTAATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 12 0.50
19 9 0.38
20 3 0.12
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (19 bp):
AATATTTAATATTGTTTAT
Found at i:163252 original size:25 final size:26
Alignment explanation
Indices: 163201--163258 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
163191 TTTGTTATAA
* *
163201 AATATTTATATATTGTTTATAATTTT
1 AATATTTATATAATATTTATAATTTT
163227 AATATTATATATAATATTTA-AA-TTT
1 AATATT-TATATAATATTTATAATTTT
163252 AATATTT
1 AATATTT
163259 TTGTAACGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 1 0.03
25 9 0.31
26 8 0.28
27 11 0.38
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (26 bp):
AATATTTATATAATATTTATAATTTT
Found at i:163606 original size:2 final size:2
Alignment explanation
Indices: 163591--163626 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
163581 GTCACTCTTT
*
163591 TA TA TA GTA AA 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
163627 TTTTTTCGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:165332 original size:19 final size:19
Alignment explanation
Indices: 165308--165346 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
165298 CGTTGCTAAT
165308 GACATGGACACGCTAAGGC
1 GACATGGACACGCTAAGGC
165327 GACATGGACACGCTAAGGC
1 GACATGGACACGCTAAGGC
165346 G
1 G
165347 CCAAGCGCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.26, G:0.33, T:0.10
Consensus pattern (19 bp):
GACATGGACACGCTAAGGC
Found at i:167213 original size:20 final size:19
Alignment explanation
Indices: 167162--167216 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
167152 TGACTTAATA
*
167162 AAAAAT-TATTTAAATATT
1 AAAAATATATTTTAATATT
*
167180 AAATATATATTTTAATATT
1 AAAAATATATTTTAATATT
*
167199 AAAAATATGTCTTTAATA
1 AAAAATATAT-TTTAATA
167217 GCATAAAATC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 5 0.16
19 19 0.61
20 7 0.23
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (19 bp):
AAAAATATATTTTAATATT
Found at i:167786 original size:3 final size:3
Alignment explanation
Indices: 167778--167816 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
167768 TTTCTGCGTA
167778 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
167817 TAGGTTAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:169190 original size:14 final size:14
Alignment explanation
Indices: 169171--169197 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
169161 TATTTTGATC
169171 TTAAAAAATAACTA
1 TTAAAAAATAACTA
169185 TTAAAAAATAACT
1 TTAAAAAATAACT
169198 TTTATATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (14 bp):
TTAAAAAATAACTA
Found at i:169304 original size:18 final size:18
Alignment explanation
Indices: 169276--169310 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
169266 TTTTAAATTT
169276 ATTATTTTTAAATAAAATA
1 ATTATTTTTAAA-AAAATA
169295 ATTA-TTTTAAAAAAAT
1 ATTATTTTTAAAAAAAT
169311 TTCACCAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 7 0.44
19 4 0.25
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTATTTTTAAAAAAATA
Found at i:170121 original size:25 final size:21
Alignment explanation
Indices: 170097--170137 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
170087 AGTATGAATA
*
170097 AAATAAT-TATTTATTTAATT
1 AAATAATATTTTTATTTAATT
170117 AAATAATATTTTTATTTAATT
1 AAATAATATTTTTATTTAATT
170138 TTAATTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
AAATAATATTTTTATTTAATT
Found at i:170456 original size:2 final size:2
Alignment explanation
Indices: 170449--170481 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
170439 ACAAAAGAAC
170449 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 A
170482 AAACAAGAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:171112 original size:2 final size:2
Alignment explanation
Indices: 171105--171131 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
171095 CTTTAGAGGA
171105 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 A
171132 ATTTTCTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:171267 original size:29 final size:28
Alignment explanation
Indices: 171190--171277 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 28
171180 TTTAAAAATG
* *
171190 AAATA-ATT-TTATTTAATATAGTTAAT-
1 AAATATATTATTATATAATA-AATTAATA
171216 AAAT-T-TTATTATATAATAAATTAATA
1 AAATATATTATTATATAATAAATTAATA
* *
171242 AACATATATTATTAT-TAATATGATTAATC
1 AA-ATATATTATTATATAATA-AATTAATA
171271 AAATATA
1 AAATATA
171278 AGTAATTACA
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
25 8 0.16
26 15 0.29
27 2 0.04
28 11 0.22
29 15 0.29
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (28 bp):
AAATATATTATTATATAATAAATTAATA
Found at i:171580 original size:21 final size:21
Alignment explanation
Indices: 171535--171589 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
171525 TTAATAATTT
* * **
171535 TAATTTTATAATTATAAGATC
1 TAATTTTATTATTATAAAAAA
171556 TAATTTTATTATTATAAAAAA
1 TAATTTTATTATTATAAAAAA
171577 TAATTTTATTATT
1 TAATTTTATTATT
171590 TTTTAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (21 bp):
TAATTTTATTATTATAAAAAA
Found at i:172589 original size:19 final size:21
Alignment explanation
Indices: 172564--172620 Score: 82
Period size: 19 Copynumber: 2.8 Consensus size: 21
172554 TGAATTAATA
172564 TTAAATTTTATTATTATA-TT
1 TTAAATTTTATTATTATATTT
*
172584 TT-AATTTTATCATTATATTT
1 TTAAATTTTATTATTATATTT
*
172604 TTAAATTTTAATATTAT
1 TTAAATTTTATTATTAT
172621 TCGAACACAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 14 0.44
20 6 0.19
21 12 0.38
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (21 bp):
TTAAATTTTATTATTATATTT
Found at i:173208 original size:21 final size:21
Alignment explanation
Indices: 173173--173236 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 21
173163 AGTTAAAACT
*
173173 TAAATAAAATTTTTTATAATTAA
1 TAAAT-AAATATTTTATAA-TAA
173196 -AAATAAATATTTT-T-ATAA
1 TAAATAAATATTTTATAATAA
* *
173214 TAAATATATATTTTATAGTAA
1 TAAATAAATATTTTATAATAA
173235 TA
1 TA
173237 GTTATAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
18 3 0.09
19 13 0.37
20 2 0.06
21 13 0.37
22 4 0.11
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
TAAATAAATATTTTATAATAA
Found at i:173242 original size:21 final size:20
Alignment explanation
Indices: 173196--173249 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
173186 TTATAATTAA
*
173196 AAATAAATATTTT-TATAAT
1 AAATATATATTTTATATAAT
173215 AAATATATATTTTATAGTAAT
1 AAATATATATTTTATA-TAAT
**
173236 AGTTATA-ATTTTAT
1 AAATATATATTTTAT
173250 TTTATTAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 12 0.40
20 9 0.30
21 9 0.30
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (20 bp):
AAATATATATTTTATATAAT
Found at i:173444 original size:35 final size:36
Alignment explanation
Indices: 173394--173483 Score: 92
Period size: 35 Copynumber: 2.5 Consensus size: 36
173384 TTAAAAATAA
* *
173394 AAAATAAGATTATTTATATATAATATAAAT-AAATT
1 AAAATAAAATAATTTATATATAATATAAATCAAATT
** * *
173429 AAAATAAAATAATTTACCTATATTTTAAATCAAATT
1 AAAATAAAATAATTTATATATAATATAAATCAAATT
* *
173465 AAATTTAAATAAATTTATA
1 AAAATAAAAT-AATTTATA
173484 ATATTATTAA
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
35 24 0.56
36 13 0.30
37 6 0.14
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (36 bp):
AAAATAAAATAATTTATATATAATATAAATCAAATT
Found at i:173653 original size:3 final size:3
Alignment explanation
Indices: 173645--173685 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
173635 CTTCCGAACA
*
173645 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
173686 CATGAGGCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:179486 original size:24 final size:24
Alignment explanation
Indices: 179450--179496 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
179440 GAAGCAAAAA
* *
179450 GAGAAGCATAAGAAAGAGAAGAAG
1 GAGAAGCAGAAGAAAGAAAAGAAG
* *
179474 GAGAAGGAGAAGAGAGAAAAGAA
1 GAGAAGCAGAAGAAAGAAAAGAA
179497 AGAAAAAAAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.60, C:0.02, G:0.36, T:0.02
Consensus pattern (24 bp):
GAGAAGCAGAAGAAAGAAAAGAAG
Found at i:181712 original size:22 final size:22
Alignment explanation
Indices: 181684--181727 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
181674 TAAGATAAGA
181684 GGGAAAAAGAAAGTAGTGGCAT
1 GGGAAAAAGAAAGTAGTGGCAT
181706 GGGAAAAAGAAAGTAGTGGCAT
1 GGGAAAAAGAAAGTAGTGGCAT
181728 TCATTTATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.05, G:0.36, T:0.14
Consensus pattern (22 bp):
GGGAAAAAGAAAGTAGTGGCAT
Found at i:182134 original size:28 final size:28
Alignment explanation
Indices: 182116--182183 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 28
182106 ATTTTATTTT
182116 TTTAATATTTATATTATAATATTATATA
1 TTTAATATTTATATTATAATATTATATA
* * *
182144 TTTAATTTTTATA-TAAAATA-TAAATGA
1 TTTAATATTTATATTATAATATTATAT-A
*
182171 TATAATATTTATA
1 TTTAATATTTATA
182184 AAAAATTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 4 0.12
27 18 0.53
28 12 0.35
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (28 bp):
TTTAATATTTATATTATAATATTATATA
Found at i:182366 original size:49 final size:49
Alignment explanation
Indices: 182308--182407 Score: 200
Period size: 49 Copynumber: 2.0 Consensus size: 49
182298 AGTTTTCAAG
182308 TGTAATATTTTTGTTTATATTTTTATAAATATCGAGCTCTACTTGGTAT
1 TGTAATATTTTTGTTTATATTTTTATAAATATCGAGCTCTACTTGGTAT
182357 TGTAATATTTTTGTTTATATTTTTATAAATATCGAGCTCTACTTGGTAT
1 TGTAATATTTTTGTTTATATTTTTATAAATATCGAGCTCTACTTGGTAT
182406 TG
1 TG
182408 GGATTAAGCA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (49 bp):
TGTAATATTTTTGTTTATATTTTTATAAATATCGAGCTCTACTTGGTAT
Found at i:186148 original size:19 final size:18
Alignment explanation
Indices: 186112--186146 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
186102 ATTTTTTATA
186112 ATTTTATATATAATTAAT
1 ATTTTATATATAATTAAT
186130 ATTTTA-ATAT-ATTAAT
1 ATTTTATATATAATTAAT
186146 A
1 A
186147 ATTAAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTTTATATATAATTAAT
Found at i:186471 original size:19 final size:19
Alignment explanation
Indices: 186406--186472 Score: 50
Period size: 19 Copynumber: 3.5 Consensus size: 19
186396 GTTAATTTTA
186406 AATACAATAT-AAA-AATAT
1 AATA-AATATAAAATAATAT
* * *
186424 AAAAAAATCATAACATATTA-
1 -AATAAAT-ATAAAATAATAT
*
186444 AATAGATATAAAATAATAT
1 AATAAATATAAAATAATAT
186463 AATAAATATA
1 AATAAATATA
186473 TTATAATTAT
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
18 12 0.33
19 19 0.53
20 2 0.06
21 3 0.08
ACGTcount: A:0.66, C:0.04, G:0.01, T:0.28
Consensus pattern (19 bp):
AATAAATATAAAATAATAT
Found at i:187731 original size:24 final size:25
Alignment explanation
Indices: 187703--187752 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
187693 TCTAAATTTG
187703 AGTTTT-TTAAATTTATTTT-TAATT
1 AGTTTTATT-AATTTATTTTATAATT
*
187727 AGTTTTATTTATTTATTTTATAATT
1 AGTTTTATTAATTTATTTTATAATT
187752 A
1 A
187753 AATAATATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (25 bp):
AGTTTTATTAATTTATTTTATAATT
Found at i:188526 original size:24 final size:22
Alignment explanation
Indices: 188489--188558 Score: 70
Period size: 22 Copynumber: 3.1 Consensus size: 22
188479 CAATTTACAT
188489 AAAA-ACTTAATAAATTAATTAA
1 AAAATACTT-ATAAATTAATTAA
* * *
188511 AAAATATTTTTATAAAATCATTAA
1 AAAATA--CTTATAAATTAATTAA
*
188535 AAAATACTTATAAATAAATTAA
1 AAAATACTTATAAATTAATTAA
188557 AA
1 AA
188559 TCCTAACTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
22 18 0.47
23 1 0.03
24 17 0.45
25 2 0.05
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.34
Consensus pattern (22 bp):
AAAATACTTATAAATTAATTAA
Found at i:188545 original size:22 final size:22
Alignment explanation
Indices: 188489--188558 Score: 63
Period size: 24 Copynumber: 3.1 Consensus size: 22
188479 CAATTTACAT
*
188489 AAAA-ACTTAATAAATTAATTAA
1 AAAATACTT-ATAAAATAATTAA
* *
188511 AAAATATTTTTATAAAATCATTAA
1 AAAATA--CTTATAAAATAATTAA
188535 AAAATACTTAT-AAATAAATTAA
1 AAAATACTTATAAAAT-AATTAA
188557 AA
1 AA
188559 TCCTAACTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
21 4 0.10
22 15 0.38
23 1 0.03
24 17 0.44
25 2 0.05
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.34
Consensus pattern (22 bp):
AAAATACTTATAAAATAATTAA
Found at i:190488 original size:12 final size:12
Alignment explanation
Indices: 190472--190530 Score: 66
Period size: 12 Copynumber: 4.8 Consensus size: 12
190462 GGAAAGAGGG
190472 GAAAAAAGAAAAA
1 GAAAAAA-AAAAA
190485 -AAAAAAAAAAA
1 GAAAAAAAAAAA
** *
190496 GGAACGAAAAAAG
1 -GAAAAAAAAAAA
190509 GAAAAAAAAAAA
1 GAAAAAAAAAAA
190521 GAAAAAAAAA
1 GAAAAAAAAA
190531 TACAGGCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
11 5 0.13
12 25 0.66
13 8 0.21
ACGTcount: A:0.85, C:0.02, G:0.14, T:0.00
Consensus pattern (12 bp):
GAAAAAAAAAAA
Found at i:196221 original size:2 final size:2
Alignment explanation
Indices: 196214--196239 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
196204 ATCTATCTTC
196214 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
196240 ACTAAACAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:196824 original size:10 final size:10
Alignment explanation
Indices: 196809--196849 Score: 50
Period size: 9 Copynumber: 4.2 Consensus size: 10
196799 ATGTTATTAT
196809 TTAAAATATA
1 TTAAAATATA
196819 TTAAAATAT-
1 TTAAAATATA
*
196828 TAAAAATAATA
1 TTAAAAT-ATA
196839 TTAAAA-ATA
1 TTAAAATATA
196848 TT
1 TT
196850 TTTATATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
9 11 0.41
10 11 0.41
11 5 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
TTAAAATATA
Found at i:196840 original size:12 final size:12
Alignment explanation
Indices: 196823--196847 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
196813 AATATATTAA
196823 AATATTAAAAAT
1 AATATTAAAAAT
196835 AATATTAAAAAT
1 AATATTAAAAAT
196847 A
1 A
196848 TTTTTATATT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AATATTAAAAAT
Found at i:196858 original size:17 final size:18
Alignment explanation
Indices: 196836--196878 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
196826 ATTAAAAATA
196836 ATATTAAAAATAT-TTTT
1 ATATTAAAAATATATTTT
*
196853 ATATT-AATATATATTTT
1 ATATTAAAAATATATTTT
196870 ATAATTAAA
1 AT-ATTAAA
196879 TTGAATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 6 0.27
17 11 0.50
18 3 0.14
19 2 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATATTAAAAATATATTTT
Found at i:197272 original size:22 final size:22
Alignment explanation
Indices: 197225--197284 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
197215 TAAAATATTA
* *
197225 TTTTAT-ATTAATATTTATATAC
1 TTTTATAATTAA-ATATAAATAC
*
197247 TTTTATAATTAAATATAAATAT
1 TTTTATAATTAAATATAAATAC
*
197269 TTTTATTAAATAAATA
1 TTTTA-TAATTAAATA
197285 ATAATTTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 18 0.56
23 14 0.44
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTTATAATTAAATATAAATAC
Found at i:198037 original size:25 final size:25
Alignment explanation
Indices: 198009--198056 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
197999 ACTTACCTAA
*
198009 TTTTTACATATTTATTTCA-CTTTTG
1 TTTTTA-ATATGTATTTCATCTTTTG
*
198034 TTTTTATTATGTATTTCATCTTT
1 TTTTTAATATGTATTTCATCTTT
198057 AGGTTTGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.19, C:0.10, G:0.04, T:0.67
Consensus pattern (25 bp):
TTTTTAATATGTATTTCATCTTTTG
Found at i:198251 original size:21 final size:21
Alignment explanation
Indices: 198227--198269 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
198217 AATTATTATT
198227 TAAAT-TTAATTATAAAATATA
1 TAAATATTAA-TATAAAATATA
198248 TAAATATTAATATAAAATATA
1 TAAATATTAATATAAAATATA
198269 T
1 T
198270 TTTTTAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAATATTAATATAAAATATA
Found at i:198279 original size:46 final size:45
Alignment explanation
Indices: 198205--198307 Score: 111
Period size: 46 Copynumber: 2.3 Consensus size: 45
198195 GATTAATATT
* *
198205 TAATAATTAAAAAATTATTATTTAAATTTAATTATAAAATATATAAA
1 TAATAAATATAAAATTATTATTTAAATTTAATTAT-AAAT-TATAAA
* * **
198252 T-ATTAATATAAAATATATT-TTTTAATTTTTTTATAAATTATAAA
1 TAATAAATATAAAAT-TATTATTTAAATTTAATTATAAATTATAAA
198296 TAATAAATATAA
1 TAATAAATATAA
198308 GTAACATAGA
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
44 7 0.15
45 13 0.28
46 22 0.47
47 5 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (45 bp):
TAATAAATATAAAATTATTATTTAAATTTAATTATAAATTATAAA
Found at i:199105 original size:25 final size:25
Alignment explanation
Indices: 199063--199110 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
199053 AATAGCATTT
* **
199063 TAAAAATTTATATTTAATTTTTATG
1 TAAAAATTTAAAAATAATTTTTATG
199088 TAAAAATTTAAAAATAATTTTTA
1 TAAAAATTTAAAAATAATTTTTA
199111 AATTTTATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (25 bp):
TAAAAATTTAAAAATAATTTTTATG
Found at i:200112 original size:13 final size:13
Alignment explanation
Indices: 200094--200120 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
200084 ATTTTATAAG
200094 TATTTATATTTGA
1 TATTTATATTTGA
200107 TATTTATATTTGA
1 TATTTATATTTGA
200120 T
1 T
200121 GTATATTCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (13 bp):
TATTTATATTTGA
Found at i:201251 original size:15 final size:15
Alignment explanation
Indices: 201228--201260 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
201218 CACAATAAAA
201228 ATTAAATATATTTAT
1 ATTAAATATATTTAT
*
201243 ATTAGATATATTTAT
1 ATTAAATATATTTAT
201258 ATT
1 ATT
201261 CAACTTATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
ATTAAATATATTTAT
Found at i:202032 original size:129 final size:130
Alignment explanation
Indices: 201766--202032 Score: 362
Period size: 129 Copynumber: 2.1 Consensus size: 130
201756 TATATAAAAG
* * *
201766 AATTTCTAATTCCTTCCCTGGTTTTGATGGTCAGATCTTTTAAGCCAATTGAATTTGTTTTTTCC
1 AATTT-TAATTCCTTCCCTGGTTTCGATGGTCAGATCTTTCAAGCCAATTGAATTTGTTTCTTCC
* ** *
201831 CTGGTTTTGCCATTGTTGGTCTAATCATTCTGTTGCCCAACTCGGTCCTGTCAAATCAAACTCTA
65 CTGGTCTTGCCACCGTTGCTCTAATCATTCTGTTGCCCAACTCGGTCCTGTCAAATCAAACTCTA
201896 T
130 T
*
201897 -ACTTTAATTCCTTCCCTGGTTTCGATGGTCAGATCTTTCAAGCCAATTGAATTTGTTTCTTCCC
1 AATTTTAATTCCTTCCCTGGTTTCGATGGTCAGATCTTTCAAGCCAATTGAATTTGTTTCTTCCC
** * * *
201961 TGGTCTTGTCC-CCGTTGCTCTAATCATTCTGTTGCTGAGCTTGGT-CTGTGAAATC-AACTTCT
66 TGGTCTTG-CCACCGTTGCTCTAATCATTCTGTTGCCCAACTCGGTCCTGTCAAATCAAAC-TCT
202023 AT
129 AT
202025 AATTTTAA
1 AATTTTAA
202033 GGTTTTTGAA
Statistics
Matches: 119, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
127 3 0.03
128 14 0.12
129 97 0.82
130 5 0.04
ACGTcount: A:0.19, C:0.22, G:0.16, T:0.42
Consensus pattern (130 bp):
AATTTTAATTCCTTCCCTGGTTTCGATGGTCAGATCTTTCAAGCCAATTGAATTTGTTTCTTCCC
TGGTCTTGCCACCGTTGCTCTAATCATTCTGTTGCCCAACTCGGTCCTGTCAAATCAAACTCTAT
Found at i:209868 original size:58 final size:57
Alignment explanation
Indices: 209793--209968 Score: 226
Period size: 58 Copynumber: 3.0 Consensus size: 57
209783 CTTAGATCGC
* ***
209793 CACTAAGTGACGCCAAGTCACCCAAACTTAGATCGCCACCAAGGCGACCAGATTCGTG
1 CACTAGGTGACGCCAAGTCACCCAAACTTAGATCGCCACCAAGGCGACC-GATTCACA
* *
209851 CACTAGGTGACGGCAAGTCACCCAAACTTAGATCGCCACCAGGGCGACTCGATTCACA
1 CACTAGGTGACGCCAAGTCACCCAAACTTAGATCGCCACCAAGGCGAC-CGATTCACA
* * * * *
209909 CACTAGGTGATGCCAAGTTACCTAAACTTAGATCGCCACTAAGGTGACCCGATTCACA
1 CACTAGGTGACGCCAAGTCACCCAAACTTAGATCGCCACCAAGGCGA-CCGATTCACA
209967 CA
1 CA
209969 TCACATGATA
Statistics
Matches: 103, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
58 101 0.98
59 2 0.02
ACGTcount: A:0.31, C:0.31, G:0.20, T:0.18
Consensus pattern (57 bp):
CACTAGGTGACGCCAAGTCACCCAAACTTAGATCGCCACCAAGGCGACCGATTCACA
Found at i:209983 original size:58 final size:58
Alignment explanation
Indices: 209805--209987 Score: 188
Period size: 58 Copynumber: 3.2 Consensus size: 58
209795 CTAAGTGACG
* *** ** **
209805 CCAAGTCACCCAAACTTAGATCGCCACCAAGGCGACCAGATTCGTGCACTAGGTGACG
1 CCAAGTCACCCAAACTTAGATCGCCACCAAGGCGACCCGATTCACACACTACATGATA
* * * ** *
209863 GCAAGTCACCCAAACTTAGATCGCCACCAGGGCGACTCGATTCACACACTAGGTGATG
1 CCAAGTCACCCAAACTTAGATCGCCACCAAGGCGACCCGATTCACACACTACATGATA
* * * *
209921 CCAAGTTACCTAAACTTAGATCGCCACTAAGGTGACCCGATTCACACA-TCACATGATA
1 CCAAGTCACCCAAACTTAGATCGCCACCAAGGCGACCCGATTCACACACT-ACATGATA
209979 CCAAGTCAC
1 CCAAGTCAC
209988 TCAGACTCGA
Statistics
Matches: 105, Mismatches: 19, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
57 1 0.01
58 104 0.99
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.18
Consensus pattern (58 bp):
CCAAGTCACCCAAACTTAGATCGCCACCAAGGCGACCCGATTCACACACTACATGATA
Found at i:213829 original size:10 final size:10
Alignment explanation
Indices: 213812--213851 Score: 66
Period size: 10 Copynumber: 4.2 Consensus size: 10
213802 TCTCTTTTCA
213812 AAAT-TTTTT
1 AAATATTTTT
213821 AAATATTTTT
1 AAATATTTTT
213831 AAATATTTTT
1 AAATATTTTT
213841 AAA-ATTTTT
1 AAATATTTTT
213850 AA
1 AA
213852 TTTTGAACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
9 12 0.40
10 18 0.60
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
AAATATTTTT
Found at i:213839 original size:19 final size:19
Alignment explanation
Indices: 213812--213851 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
213802 TCTCTTTTCA
213812 AAAT-TTTTTAAATATTTTT
1 AAATATTTTTAAA-ATTTTT
213831 AAATATTTTTAAAATTTTT
1 AAATATTTTTAAAATTTTT
213850 AA
1 AA
213852 TTTTGAACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
AAATATTTTTAAAATTTTT
Found at i:218040 original size:129 final size:129
Alignment explanation
Indices: 217810--218068 Score: 437
Period size: 129 Copynumber: 2.0 Consensus size: 129
217800 GGTGGTGCAA
* *
217810 TACCACCATTACCATGATCTTTGCACCAGCGTGAAATCAATCCCCGCACCAAGCAATTAGGGTTC
1 TACCACCATTACCATGATCTTTGCACCAGCGAGAAATCAATCCCCACACCAAGCAATTAGGGTTC
*
217875 AACATAGAGCGGGAGAGTTCTTGTTTCGATGGGGGGAATGTTAGCTTACGTTCATTCAACCGCT
66 AACATAGAGCGGGAGAGTTCTTGTTGCGATGGGGGGAATGTTAGCTTACGTTCATTCAACCGCT
* * * * *
217939 TACCACCATTACCTTGATCTTTGCGCCAGTGAGAAATCAATCCCCACGCCAAGCAGTTAGGGTTC
1 TACCACCATTACCATGATCTTTGCACCAGCGAGAAATCAATCCCCACACCAAGCAATTAGGGTTC
*
218004 ACCATAGAGCGGGAGAGTTCTTGTTGCGATGGGGGGAATGTTAGCTTACGTTCATTCAACCGCT
66 AACATAGAGCGGGAGAGTTCTTGTTGCGATGGGGGGAATGTTAGCTTACGTTCATTCAACCGCT
218068 T
1 T
218069 CTGGATTTCT
Statistics
Matches: 121, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
129 121 1.00
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.27
Consensus pattern (129 bp):
TACCACCATTACCATGATCTTTGCACCAGCGAGAAATCAATCCCCACACCAAGCAATTAGGGTTC
AACATAGAGCGGGAGAGTTCTTGTTGCGATGGGGGGAATGTTAGCTTACGTTCATTCAACCGCT
Found at i:220331 original size:17 final size:18
Alignment explanation
Indices: 220309--220347 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
220299 ACAATGATAG
220309 AAAAGACAAG-GAG-ATTA
1 AAAAGA-AAGAGAGCATTA
220326 AAAAGAAAGAGAGCATTA
1 AAAAGAAAGAGAGCATTA
220344 AAAA
1 AAAA
220348 TGGTTGTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 3 0.15
17 9 0.45
18 8 0.40
ACGTcount: A:0.64, C:0.05, G:0.21, T:0.10
Consensus pattern (18 bp):
AAAAGAAAGAGAGCATTA
Found at i:224210 original size:6 final size:6
Alignment explanation
Indices: 224199--224236 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
224189 CATTGGGACC
*
224199 AAAAA- AAAAAA AAAAAG AAAAAG AAAAAG AAAAAG AAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAA
224237 GAGGTTCTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:225888 original size:20 final size:20
Alignment explanation
Indices: 225851--225903 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
225841 TATTTAAAAA
* *
225851 ATTATTAAAATAATATTTTT
1 ATTATTAAATTTATATTTTT
225871 A-TATTAATATTTATATTTTT
1 ATTATTAA-ATTTATATTTTT
225891 ATTATTAAATTTA
1 ATTATTAAATTTA
225904 AATAAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 6 0.21
20 17 0.59
21 6 0.21
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTATTAAATTTATATTTTT
Found at i:228485 original size:44 final size:44
Alignment explanation
Indices: 228422--228511 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
228412 CTTTCCTACA
228422 AATACATCATTCTTAAGTAAGATTGCCTTATTGGATTCTAGGAT
1 AATACATCATTCTTAAGTAAGATTGCCTTATTGGATTCTAGGAT
228466 AATACATCATTCTTAAGTAAGATTGCCTTATTGGATTCTAGGAT
1 AATACATCATTCTTAAGTAAGATTGCCTTATTGGATTCTAGGAT
228510 AA
1 AA
228512 CTTTAGAACT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (44 bp):
AATACATCATTCTTAAGTAAGATTGCCTTATTGGATTCTAGGAT
Found at i:230311 original size:13 final size:13
Alignment explanation
Indices: 230293--230320 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
230283 GAAAATTTTT
230293 CTATTAAAACTTA
1 CTATTAAAACTTA
230306 CTATTAAAACTTA
1 CTATTAAAACTTA
230319 CT
1 CT
230321 TCTTTCATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.18, G:0.00, T:0.39
Consensus pattern (13 bp):
CTATTAAAACTTA
Found at i:232780 original size:15 final size:16
Alignment explanation
Indices: 232750--232783 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
232740 AATATCACAA
*
232750 ATTTTATTTTTTCTTT
1 ATTTTATTTTTGCTTT
232766 ATTTTA-TTTTGCTTT
1 ATTTTATTTTTGCTTT
232781 ATT
1 ATT
232784 AGATTCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.15, C:0.06, G:0.03, T:0.76
Consensus pattern (16 bp):
ATTTTATTTTTGCTTT
Found at i:234287 original size:15 final size:16
Alignment explanation
Indices: 234267--234301 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
234257 GGTTTTAAGC
*
234267 TTTTTC-AAGTTTGGA
1 TTTTTCTAAATTTGGA
234282 TTTTTCTAAATTTGGA
1 TTTTTCTAAATTTGGA
234298 TTTT
1 TTTT
234302 CTCATATTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.20, C:0.06, G:0.14, T:0.60
Consensus pattern (16 bp):
TTTTTCTAAATTTGGA
Found at i:234332 original size:14 final size:15
Alignment explanation
Indices: 234307--234338 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
234297 ATTTTCTCAT
234307 ATTCAGATTTTTTAG
1 ATTCAGATTTTTTAG
234322 ATTCA-ATTTTTTAG
1 ATTCAGATTTTTTAG
234336 ATT
1 ATT
234339 TAAGCTTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.28, C:0.06, G:0.09, T:0.56
Consensus pattern (15 bp):
ATTCAGATTTTTTAG
Found at i:235739 original size:27 final size:27
Alignment explanation
Indices: 235708--235809 Score: 161
Period size: 27 Copynumber: 3.8 Consensus size: 27
235698 AAAGCAACCT
*
235708 TTTGTGTTTGTTAAAAATGGTGGTTCC
1 TTTGTGTTTGTCAAAAATGGTGGTTCC
*
235735 TTTGTGTTTGTCAAAAATGGAGGTTCC
1 TTTGTGTTTGTCAAAAATGGTGGTTCC
*
235762 TTTGTGTTTGTCAAAAATGGTAGTTCCC
1 TTTGTGTTTGTCAAAAATGGTGGTT-CC
235790 TTT-TGTTTGTCAAAAATGGT
1 TTTGTGTTTGTCAAAAATGGT
235810 AGCTTGTTAT
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
27 65 0.93
28 5 0.07
ACGTcount: A:0.22, C:0.10, G:0.24, T:0.45
Consensus pattern (27 bp):
TTTGTGTTTGTCAAAAATGGTGGTTCC
Found at i:235827 original size:24 final size:24
Alignment explanation
Indices: 235714--235828 Score: 72
Period size: 27 Copynumber: 4.4 Consensus size: 24
235704 ACCTTTTGTG
* * *
235714 TTTGTTAAAAATGGTGGTTCCTTTGTG
1 TTTGTCAAAAATGGTAG--CCTTT-TA
*
235741 TTTGTCAAAAATGG-AGGTTCCTTTGTG
1 TTTGTCAAAAATGGTA-G--CCTTT-TA
*
235768 TTTGTCAAAAATGGTAGTTCCCTTTTG
1 TTTGTCAAAAATGGTAG---CCTTTTA
235795 TTTGTCAAAAATGGTAG-CTTGTTA
1 TTTGTCAAAAATGGTAGCCTT-TTA
235819 TTTGTCAAAA
1 TTTGTCAAAA
235829 TTAGTGACTA
Statistics
Matches: 80, Mismatches: 4, Indels: 11
0.84 0.04 0.12
Matches are distributed among these distances:
23 3 0.04
24 12 0.15
27 58 0.73
28 7 0.09
ACGTcount: A:0.24, C:0.10, G:0.22, T:0.43
Consensus pattern (24 bp):
TTTGTCAAAAATGGTAGCCTTTTA
Found at i:238146 original size:27 final size:27
Alignment explanation
Indices: 238116--238189 Score: 103
Period size: 27 Copynumber: 2.7 Consensus size: 27
238106 CAAAAGCCAC
* **
238116 CCTTTGTGTTTGTAAAAAATGGTGGTT
1 CCTTTGTGTTTGTCAAAAATGGTAATT
*
238143 CCTTTGTGTTTATCAAAAATGGTAATT
1 CCTTTGTGTTTGTCAAAAATGGTAATT
*
238170 CCTTTTTGTTTGTCAAAAAT
1 CCTTTGTGTTTGTCAAAAAT
238190 TGTTGTTTGT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.26, C:0.11, G:0.18, T:0.46
Consensus pattern (27 bp):
CCTTTGTGTTTGTCAAAAATGGTAATT
Found at i:241553 original size:5 final size:5
Alignment explanation
Indices: 241539--241570 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
241529 GACCTGATAT
241539 TAAAA T-AAA TAAAA TAAAA TAAAA TAAAA TAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAA
241571 GATTTATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
TAAAA
Found at i:245661 original size:12 final size:13
Alignment explanation
Indices: 245639--245676 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
245629 GATAAATTAT
245639 TTTAGAATTTAAA
1 TTTAGAATTTAAA
245652 TTTA-AATTTAAA
1 TTTAGAATTTAAA
*
245664 TTTTGAGATTTAA
1 TTTAGA-ATTTAA
245677 TAAGTTGATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 11 0.50
13 5 0.23
14 6 0.27
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (13 bp):
TTTAGAATTTAAA
Found at i:245782 original size:2 final size:2
Alignment explanation
Indices: 245775--245807 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
245765 TACCTTGGTT
245775 TA TA TA 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 T
245808 GATTGAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:252015 original size:24 final size:24
Alignment explanation
Indices: 251970--252017 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
251960 GAAGATTATT
*
251970 TTCTTTGAGTAATGAAGGGGCAAA
1 TTCTTTGAGTAATGAACGGGCAAA
*
251994 TTCTTTGAGTAATGAACTGGCAAA
1 TTCTTTGAGTAATGAACGGGCAAA
252018 AAGAACCAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.33, C:0.10, G:0.25, T:0.31
Consensus pattern (24 bp):
TTCTTTGAGTAATGAACGGGCAAA
Found at i:253330 original size:2 final size:2
Alignment explanation
Indices: 253323--253357 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
253313 TACCTTAGTT
253323 TA TA TA TA 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
253358 GATTGGAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:255599 original size:2 final size:2
Alignment explanation
Indices: 255592--255633 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
255582 TTGATGAGTG
255592 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
255633 T
1 T
255634 CAAGTACTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:255783 original size:2 final size:2
Alignment explanation
Indices: 255776--255810 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
255766 TGCACAATTT
255776 TA TA TA TA 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
255811 GCATAATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:256563 original size:24 final size:24
Alignment explanation
Indices: 256518--256565 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
256508 GAAGATTATT
*
256518 TTCTTTGAGTAATAAACGGGCAAA
1 TTCTTTGAGTAAGAAACGGGCAAA
* *
256542 TTCTTTGAGTAAGGAACTGGCAAA
1 TTCTTTGAGTAAGAAACGGGCAAA
256566 AAGAGCCAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.29
Consensus pattern (24 bp):
TTCTTTGAGTAAGAAACGGGCAAA
Found at i:258475 original size:24 final size:24
Alignment explanation
Indices: 258430--258477 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
258420 GAAGATTATT
**
258430 TTCTTTGAGTAATAAATGGGCAAA
1 TTCTTTGAGTAATAAACAGGCAAA
*
258454 TTCTTTGAGTAATGAACAGGCAAA
1 TTCTTTGAGTAATAAACAGGCAAA
258478 AAGACCCAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (24 bp):
TTCTTTGAGTAATAAACAGGCAAA
Found at i:260839 original size:2 final size:2
Alignment explanation
Indices: 260826--260866 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
260816 ATTCCAAATT
* *
260826 TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
260867 TAGACTTGGC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:262715 original size:16 final size:16
Alignment explanation
Indices: 262694--262757 Score: 85
Period size: 16 Copynumber: 4.0 Consensus size: 16
262684 AATATAAAAT
262694 TTTAAACTTAAAATAA
1 TTTAAACTTAAAATAA
*
262710 TTTAAATTTAAAATAA
1 TTTAAACTTAAAATAA
*
262726 TTTAAATCTAAAAAT-A
1 TTTAAA-CTTAAAATAA
*
262742 TTTAAACTCAAAATAA
1 TTTAAACTTAAAATAA
262758 CCAAACTTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
15 7 0.17
16 29 0.69
17 6 0.14
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (16 bp):
TTTAAACTTAAAATAA
Found at i:262848 original size:2 final size:2
Alignment explanation
Indices: 262843--262871 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
262833 TTATTATTGC
262843 TA 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 T
262872 TAGTCTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.