Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015354.1 Kokia drynarioides strain JFW-HI SEQ_130401, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1324750
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 502 characters in sequence are not A, C, G, or T
File 1 of 4
Found at i:20442 original size:15 final size:15
Alignment explanation
Indices: 20395--20444 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
20385 TTGCCTCAGA
*
20395 TTACATTTTAGTCAC
1 TTACGTTTTAGTCAC
* * *
20410 TTATGTTTAAAT--C
1 TTACGTTTTAGTCAC
20423 TTACGTTTTAGTCAC
1 TTACGTTTTAGTCAC
20438 TTACGTT
1 TTACGTT
20445 ATTGTGTTGT
Statistics
Matches: 26, Mismatches: 7, Indels: 4
0.70 0.19 0.11
Matches are distributed among these distances:
13 10 0.38
15 16 0.62
ACGTcount: A:0.24, C:0.16, G:0.10, T:0.50
Consensus pattern (15 bp):
TTACGTTTTAGTCAC
Found at i:23930 original size:15 final size:15
Alignment explanation
Indices: 23912--23961 Score: 50
Period size: 14 Copynumber: 3.3 Consensus size: 15
23902 AAGTTGTAGA
23912 TTTAATTTTTGTATT
1 TTTAATTTTTGTATT
* *
23927 TTT-ATTTAAT-TAAT
1 TTTAATTT-TTGTATT
23941 TTTAATTTTTGTACTT
1 TTTAATTTTTGTA-TT
23957 TTTAA
1 TTTAA
23962 ATTGATTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 7
0.71 0.11 0.18
Matches are distributed among these distances:
14 11 0.41
15 10 0.37
16 6 0.22
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68
Consensus pattern (15 bp):
TTTAATTTTTGTATT
Found at i:24243 original size:18 final size:18
Alignment explanation
Indices: 24220--24259 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
24210 TTCAGGAATA
24220 TTTTTATCTCAAAAGTAT
1 TTTTTATCTCAAAAGTAT
*
24238 TTTTTATTTCAAAAGTAT
1 TTTTTATCTCAAAAGTAT
24256 TTTT
1 TTTT
24260 GAGAAGCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.30, C:0.07, G:0.05, T:0.57
Consensus pattern (18 bp):
TTTTTATCTCAAAAGTAT
Found at i:24783 original size:32 final size:32
Alignment explanation
Indices: 24742--24805 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
24732 TAGCTTAAAT
24742 GACTTATTTAAACAATATTTTAATCTAATTCA
1 GACTTATTTAAACAATATTTTAATCTAATTCA
* *
24774 GACTTATTTAAATAATTTTTTAATCTAATTCA
1 GACTTATTTAAACAATATTTTAATCTAATTCA
24806 ATTAATTTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.39, C:0.11, G:0.03, T:0.47
Consensus pattern (32 bp):
GACTTATTTAAACAATATTTTAATCTAATTCA
Found at i:25048 original size:29 final size:29
Alignment explanation
Indices: 25002--25082 Score: 98
Period size: 29 Copynumber: 2.9 Consensus size: 29
24992 TTAATTGTAC
25002 AATTATTTTATATGTTTAATTATA-ATATGT
1 AATT-TTTTATATGTTTAATTATATAT-TGT
* *
25032 AATTTTTTATATTTTTAATTATATATTTT
1 AATTTTTTATATGTTTAATTATATATTGT
25061 AATTTTTTA-A-GTTTAATT-TATA
1 AATTTTTTATATGTTTAATTATATA
25083 AAAATTAACA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
26 4 0.09
27 7 0.15
28 1 0.02
29 29 0.62
30 6 0.13
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (29 bp):
AATTTTTTATATGTTTAATTATATATTGT
Found at i:31075 original size:19 final size:19
Alignment explanation
Indices: 31053--31097 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
31043 TTTTATTAGG
31053 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
31072 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
31091 ATTTAAT
1 ATTTAAT
31098 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:31905 original size:15 final size:16
Alignment explanation
Indices: 31887--31916 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31877 TTTCCCTATT
31887 TTCTA-TTTCTTTTAA
1 TTCTATTTTCTTTTAA
31902 TTCTATTTTCTTTTA
1 TTCTATTTTCTTTTA
31917 TTTTTAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (16 bp):
TTCTATTTTCTTTTAA
Found at i:31909 original size:22 final size:22
Alignment explanation
Indices: 31882--31926 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
31872 TTCGATTTCC
31882 CTATTTTCTATTT-CTTTTAATT
1 CTATTTTCT-TTTACTTTTAATT
*
31904 CTATTTTCTTTTATTTTTAATT
1 CTATTTTCTTTTACTTTTAATT
31926 C
1 C
31927 GGTTTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.18, C:0.13, G:0.00, T:0.69
Consensus pattern (22 bp):
CTATTTTCTTTTACTTTTAATT
Found at i:31936 original size:21 final size:22
Alignment explanation
Indices: 31896--31942 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
31886 TTTCTATTTC
*
31896 TTTTAATTCTATTTTCTTTTAT
1 TTTTAATTCGATTTTCTTTTAT
*
31918 TTTTAATTCGGTTTT-TTTTAT
1 TTTTAATTCGATTTTCTTTTAT
31939 TTTT
1 TTTT
31943 CCTCAGATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.15, C:0.06, G:0.04, T:0.74
Consensus pattern (22 bp):
TTTTAATTCGATTTTCTTTTAT
Found at i:32221 original size:19 final size:19
Alignment explanation
Indices: 32197--32251 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
32187 AAAATAAAAT
32197 AATTCAAAATAATTT-TAAA
1 AATTCAAAAT-ATTTATAAA
32216 AATTCAAAATATTTATAAA
1 AATTCAAAATATTTATAAA
32235 AATTTCAAAA-ATTTATA
1 AA-TTCAAAATATTTATA
32252 TATTTTCAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.12
19 23 0.68
20 7 0.21
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
AATTCAAAATATTTATAAA
Found at i:35599 original size:2 final size:2
Alignment explanation
Indices: 35560--35589 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
35550 TAATTAAAAT
35560 TA TA 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 TA TA
35590 CTTAATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35879 original size:17 final size:15
Alignment explanation
Indices: 35821--35894 Score: 53
Period size: 15 Copynumber: 4.7 Consensus size: 15
35811 CCATCCATAT
*
35821 TATTTTTAATTTTTAA
1 TATTTTTTA-TTTTAA
35837 -ATTGTTTTATTTTAA
1 TATT-TTTTATTTTAA
**
35852 TATTTAATATTTGTATA
1 TATTTTTTATTT-TA-A
35869 TATTTTTTATTTATTAA
1 TATTTTTTA-TT-TTAA
35886 T-TTTTTTAT
1 TATTTTTTAT
35895 ATAGTCATCT
Statistics
Matches: 47, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
15 16 0.34
16 16 0.34
17 10 0.21
18 4 0.09
19 1 0.02
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (15 bp):
TATTTTTTATTTTAA
Found at i:36351 original size:62 final size:61
Alignment explanation
Indices: 36232--36346 Score: 153
Period size: 60 Copynumber: 1.9 Consensus size: 61
36222 AAAATAAACA
* * * *
36232 AAATTATAATAGAGGCACTAAATCTACTAATAACATATAGTATAAGCACCTTTTAGAAATTT
1 AAATTATAATAGAAGCACTAAATC-ACTAAAAAAACATAGTATAAGCACCTTTTAGAAATTT
*
36294 AAATTATAATA-AAGCACTAAATC-CGTAAAAAAACATAGTATAAGGACCTTTTA
1 AAATTATAATAGAAGCACTAAATCAC-TAAAAAAACATAGTATAAGCACCTTTTA
36347 TAGAATTTCA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
59 1 0.02
60 24 0.51
61 11 0.23
62 11 0.23
ACGTcount: A:0.48, C:0.13, G:0.10, T:0.30
Consensus pattern (61 bp):
AAATTATAATAGAAGCACTAAATCACTAAAAAAACATAGTATAAGCACCTTTTAGAAATTT
Found at i:51854 original size:16 final size:17
Alignment explanation
Indices: 51835--51877 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
51825 AATAAAAAAT
*
51835 ATATTAAAATTATTA-A
1 ATATTAAAATTAATATA
51851 ATATTAAAA-TAATATA
1 ATATTAAAATTAATATA
51867 ATATTAAAATT
1 ATATTAAAATT
51878 TTTTTAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 4 0.17
16 19 0.79
17 1 0.04
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATATTAAAATTAATATA
Found at i:51860 original size:8 final size:8
Alignment explanation
Indices: 51835--51876 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
51825 AATAAAAAAT
51835 ATATTAAA
1 ATATTAAA
51843 ATTATT-AA
1 A-TATTAAA
51851 ATATTAAA
1 ATATTAAA
* *
51859 ATAATATA
1 ATATTAAA
51867 ATATTAAA
1 ATATTAAA
51875 AT
1 AT
51877 TTTTTTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 4 0.14
8 20 0.71
9 4 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
ATATTAAA
Found at i:51977 original size:66 final size:66
Alignment explanation
Indices: 51907--52039 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
51897 AATATGAACA
51907 AACCTAAATGAGCTTGAATTAATTTTTTGCAAATATAAATTTAAACAATTTTAAATTTAAATTTT
1 AACCTAAATGAGCTTGAATTAATTTTTTGCAAATATAAATTTAAACAATTTTAAATTTAAATTTT
51972 G
66 G
51973 AACCTAAATGAGCTTGAATTAATTTTTTGCAAATATAAATTTAAACAATTTTAAATTTAAATTTT
1 AACCTAAATGAGCTTGAATTAATTTTTTGCAAATATAAATTTAAACAATTTTAAATTTAAATTTT
52038 G
66 G
52039 A
1 A
52040 GTCAAATCCA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.42
Consensus pattern (66 bp):
AACCTAAATGAGCTTGAATTAATTTTTTGCAAATATAAATTTAAACAATTTTAAATTTAAATTTT
G
Found at i:52657 original size:23 final size:21
Alignment explanation
Indices: 52631--52677 Score: 51
Period size: 23 Copynumber: 2.1 Consensus size: 21
52621 ATAATTATGC
52631 TAATGTTAATA-TAACACTTATTA
1 TAATGTTAA-ACTAACA-TTA-TA
*
52654 TAATTTTAAACTAACATTATA
1 TAATGTTAAACTAACATTATA
52675 TAA
1 TAA
52678 AGGGTATTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 5 0.23
22 4 0.18
23 13 0.59
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.43
Consensus pattern (21 bp):
TAATGTTAAACTAACATTATA
Found at i:55533 original size:7 final size:7
Alignment explanation
Indices: 55521--55553 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
55511 GGAAAGGATA
55521 GGAATTG
1 GGAATTG
55528 GGAATTG
1 GGAATTG
55535 GGAATTG
1 GGAATTG
*
55542 GGAATTA
1 GGAATTG
55549 GGAAT
1 GGAAT
55554 CTGAGAGGGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.39, T:0.27
Consensus pattern (7 bp):
GGAATTG
Found at i:56503 original size:29 final size:28
Alignment explanation
Indices: 56449--56507 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 28
56439 TATAATGTGC
56449 AATTGTATACATGAATTTTGATTTTGTAT
1 AATTGTATACATGAATTTTGATTTTG-AT
56478 AATTGTATACATGAAATTTTGA-TTTGAT
1 AATTGTATACATG-AATTTTGATTTTGAT
56506 AA
1 AA
56508 AAGTTTTGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
28 4 0.14
29 17 0.59
30 8 0.28
ACGTcount: A:0.36, C:0.03, G:0.14, T:0.47
Consensus pattern (28 bp):
AATTGTATACATGAATTTTGATTTTGAT
Found at i:58209 original size:45 final size:45
Alignment explanation
Indices: 58158--58248 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
58148 CCGGTATAAG
58158 TCGAAATTGATCGAAATAAACAAAAACAATGAAACACAGATTACT
1 TCGAAATTGATCGAAATAAACAAAAACAATGAAACACAGATTACT
58203 TCGAAATTGATCGAAATAAACAAAAACAATGAAACACAGATTACT
1 TCGAAATTGATCGAAATAAACAAAAACAATGAAACACAGATTACT
58248 T
1 T
58249 GGCACCGGTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.53, C:0.15, G:0.11, T:0.21
Consensus pattern (45 bp):
TCGAAATTGATCGAAATAAACAAAAACAATGAAACACAGATTACT
Found at i:59317 original size:16 final size:16
Alignment explanation
Indices: 59284--59317 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
59274 GATCAAAATA
59284 TAATTCTATTATTTAT
1 TAATTCTATTATTTAT
59300 TAATT-TATTATTTCAT
1 TAATTCTATTATTT-AT
59316 TA
1 TA
59318 TTTTTGAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
TAATTCTATTATTTAT
Found at i:59389 original size:23 final size:23
Alignment explanation
Indices: 59363--59406 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
59353 ATTTTGAAAG
*
59363 ATTAAAATATAATTTCTTCATAT
1 ATTAAAATATAATTTCATCATAT
**
59386 ATTAATTTATAATTTCATCAT
1 ATTAAAATATAATTTCATCAT
59407 TTATGAACAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (23 bp):
ATTAAAATATAATTTCATCATAT
Found at i:59431 original size:88 final size:88
Alignment explanation
Indices: 59267--59432 Score: 203
Period size: 88 Copynumber: 1.9 Consensus size: 88
59257 ATTTCAAATA
* * * * * * **
59267 TTTGAGAGATCAAAATATAATTCTATTATTTATTAATTTATTATTTCATTATTTTTGAAGGAATT
1 TTTGAAAGATCAAAATATAATTCTATCATATATTAATTTATAATTTCATCATTTATGAAAAAATT
*
59332 AGATAAATTTTTTTTTTTTTCAT
66 ACATAAATTTTTTTTTTTTTCAT
*
59355 TTTGAAAGATTAAAATATAATTTCT-TCATATATTAATTTATAATTTCATCATTTATGAACAAAA
1 TTTGAAAGATCAAAATATAA-TTCTATCATATATTAATTTATAATTTCATCATTTATGAA-AAAA
59419 TTAC--AAATTTTTTT
64 TTACATAAATTTTTTT
59433 AGGGGGGAGG
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
87 10 0.15
88 47 0.71
89 9 0.14
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (88 bp):
TTTGAAAGATCAAAATATAATTCTATCATATATTAATTTATAATTTCATCATTTATGAAAAAATT
ACATAAATTTTTTTTTTTTTCAT
Found at i:60284 original size:16 final size:16
Alignment explanation
Indices: 60263--60309 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
60253 TTATGATATT
60263 TTTAAAATAATTTTAA
1 TTTAAAATAATTTTAA
*
60279 TTT-AAATTATTTATAA
1 TTTAAAATAATTT-TAA
*
60295 TTTATAA-AATTTTAA
1 TTTAAAATAATTTTAA
60310 ATTAGTAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 11 0.42
16 13 0.50
17 2 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTAAAATAATTTTAA
Found at i:61184 original size:2 final size:2
Alignment explanation
Indices: 61177--61214 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
61167 AAGTGAGATA
61177 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
61215 TTGAATTATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:63830 original size:6 final size:6
Alignment explanation
Indices: 63816--63854 Score: 69
Period size: 6 Copynumber: 6.3 Consensus size: 6
63806 ACAACAACAA
63816 CCCACAT CCCAAT CCCAAT CCCAAT CCCAAT CCCAAT CC
1 CCCA-AT CCCAAT CCCAAT CCCAAT CCCAAT CCCAAT CC
63855 ATTGATCAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 28 0.88
7 4 0.12
ACGTcount: A:0.31, C:0.54, G:0.00, T:0.15
Consensus pattern (6 bp):
CCCAAT
Found at i:74991 original size:44 final size:43
Alignment explanation
Indices: 74924--75011 Score: 131
Period size: 44 Copynumber: 2.0 Consensus size: 43
74914 ACTGTTTTAG
* *
74924 TTGTTGTTTTCATGTCATTTTGCTGTTATTTTTGTTGCTATTT
1 TTGTTGTTTTAATGTCATTTTGCTGTTATTTTTGCTGCTATTT
**
74967 TTGTTGTTTTTAATGTTGTTTTGCTGTTATTTTTGCTGCTATTT
1 TTGTTG-TTTTAATGTCATTTTGCTGTTATTTTTGCTGCTATTT
75011 T
1 T
75012 GGTTATTATT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
43 6 0.15
44 34 0.85
ACGTcount: A:0.09, C:0.08, G:0.17, T:0.66
Consensus pattern (43 bp):
TTGTTGTTTTAATGTCATTTTGCTGTTATTTTTGCTGCTATTT
Found at i:75000 original size:12 final size:12
Alignment explanation
Indices: 74941--75030 Score: 53
Period size: 12 Copynumber: 7.8 Consensus size: 12
74931 TTTCATGTCA
74941 TTTTGCTGTTAT
1 TTTTGCTGTTAT
* *
74953 TTTTGTTGCTA-
1 TTTTGCTGTTAT
*
74964 TTTT--TGTTGT
1 TTTTGCTGTTAT
** *
74974 TTTTAATGTT-G
1 TTTTGCTGTTAT
74985 TTTTGCTGTTAT
1 TTTTGCTGTTAT
*
74997 TTTTGCTGCTAT
1 TTTTGCTGTTAT
* * *
75009 TTTGGTTATTAT
1 TTTTGCTGTTAT
*
75021 TTTTGTTGTT
1 TTTTGCTGTT
75031 TAAATGTTAT
Statistics
Matches: 59, Mismatches: 15, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
9 3 0.05
10 4 0.07
11 12 0.20
12 40 0.68
ACGTcount: A:0.09, C:0.06, G:0.18, T:0.68
Consensus pattern (12 bp):
TTTTGCTGTTAT
Found at i:75003 original size:56 final size:55
Alignment explanation
Indices: 74925--75031 Score: 144
Period size: 56 Copynumber: 1.9 Consensus size: 55
74915 CTGTTTTAGT
* * *
74925 TGTTGTTTTCATGTCATTTTGCTGTTATTTTTGTTGCTATTTTTGTTGTTTTTAA
1 TGTTGTTTTCATGTCATTTTGCTGCTATTTTGGTTACTATTTTTGTTGTTTTTAA
* *
74980 TGTTGTTTTGC-TGTTATTTTTGCTGCTATTTTGGTTATTATTTTTGTTGTTT
1 TGTTGTTTT-CATGTCA-TTTTGCTGCTATTTTGGTTACTATTTTTGTTGTTT
75032 AAATGTTATT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
55 13 0.29
56 32 0.71
ACGTcount: A:0.09, C:0.07, G:0.18, T:0.66
Consensus pattern (55 bp):
TGTTGTTTTCATGTCATTTTGCTGCTATTTTGGTTACTATTTTTGTTGTTTTTAA
Found at i:75028 original size:44 final size:44
Alignment explanation
Indices: 74941--75031 Score: 130
Period size: 44 Copynumber: 2.1 Consensus size: 44
74931 TTTCATGTCA
* * *
74941 TTTTGCTGTTATTTTTGTTGCTATTTTTGTTGTTTTTAATGTTG
1 TTTTGCTGTTATTTTTGCTGCTATTTTGGTTATTTTTAATGTTG
*
74985 TTTTGCTGTTATTTTTGCTGCTATTTTGGTTATTATTT-TTGTTG
1 TTTTGCTGTTATTTTTGCTGCTATTTTGGTTATT-TTTAATGTTG
75029 TTT
1 TTT
75032 AAATGTTATT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 39 0.93
45 3 0.07
ACGTcount: A:0.09, C:0.05, G:0.18, T:0.68
Consensus pattern (44 bp):
TTTTGCTGTTATTTTTGCTGCTATTTTGGTTATTTTTAATGTTG
Found at i:75039 original size:44 final size:44
Alignment explanation
Indices: 74947--75044 Score: 117
Period size: 44 Copynumber: 2.2 Consensus size: 44
74937 GTCATTTTGC
* * * ***
74947 TGTTATTTTTGTTGCTATTTTTGTTGTTTTTAATGTTGTTTTGC
1 TGTTATTTTTGCTGCTATTTTGGTTATTTTTAATGTTGTTTAAA
*
74991 TGTTATTTTTGCTGCTATTTTGGTTATTATTT-TTGTTGTTTAAA
1 TGTTATTTTTGCTGCTATTTTGGTTATT-TTTAATGTTGTTTAAA
75035 TGTTATTTTT
1 TGTTATTTTT
75045 TATGCGTTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
44 43 0.93
45 3 0.07
ACGTcount: A:0.12, C:0.04, G:0.16, T:0.67
Consensus pattern (44 bp):
TGTTATTTTTGCTGCTATTTTGGTTATTTTTAATGTTGTTTAAA
Found at i:76805 original size:35 final size:35
Alignment explanation
Indices: 76758--76837 Score: 144
Period size: 35 Copynumber: 2.3 Consensus size: 35
76748 AAATTTAATT
76758 TTTAA-AATTTATATATTTCATCAATTTAATCTTGA
1 TTTAACAA-TTATATATTTCATCAATTTAATCTTGA
76793 TTTAACAATTATATATTTCATCAATTTAATCTTGA
1 TTTAACAATTATATATTTCATCAATTTAATCTTGA
76828 TTTAACAATT
1 TTTAACAATT
76838 TAACTCACAA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
35 42 0.95
36 2 0.05
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.50
Consensus pattern (35 bp):
TTTAACAATTATATATTTCATCAATTTAATCTTGA
Found at i:76838 original size:19 final size:19
Alignment explanation
Indices: 76779--76840 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 19
76769 TATATTTCAT
76779 CAATTTAATCTTGATTTAA
1 CAATTTAATCTTGATTTAA
* *
76798 CAA-TT-AT-AT-ATTTCAT
1 CAATTTAATCTTGATTT-AA
76814 CAATTTAATCTTGATTTAA
1 CAATTTAATCTTGATTTAA
76833 CAATTTAA
1 CAATTTAA
76841 CTCACAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
15 4 0.12
16 5 0.15
17 4 0.12
18 4 0.12
19 13 0.38
20 4 0.12
ACGTcount: A:0.39, C:0.11, G:0.03, T:0.47
Consensus pattern (19 bp):
CAATTTAATCTTGATTTAA
Found at i:79442 original size:16 final size:16
Alignment explanation
Indices: 79423--79469 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
79413 AATTTTCAAT
79423 AAATAAAAAATATATA
1 AAATAAAAAATATATA
**
79439 AAATTATTAAATAT-TA
1 AAA-TAAAAAATATATA
79455 AAATAAAATAATATA
1 AAATAAAA-AATATA
79470 AATATATATT
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
15 3 0.12
16 13 0.54
17 8 0.33
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATAAAAAATATATA
Found at i:84056 original size:17 final size:18
Alignment explanation
Indices: 84031--84064 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
84021 GAACAATATA
*
84031 ATTATTAAATAAATACAC
1 ATTATTAAAAAAATACAC
84049 ATTA-TAAAAAAATACA
1 ATTATTAAAAAAATACA
84065 TGGCAGAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (18 bp):
ATTATTAAAAAAATACAC
Found at i:90677 original size:18 final size:17
Alignment explanation
Indices: 90650--90683 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
90640 TAATTTTTTA
*
90650 ATCAATTCAATCAAATCG
1 ATCAAATCAAT-AAATCG
90668 ATCAAATCAATAAATC
1 ATCAAATCAATAAATC
90684 AGTAATCTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.21, G:0.03, T:0.26
Consensus pattern (17 bp):
ATCAAATCAATAAATCG
Found at i:97579 original size:22 final size:22
Alignment explanation
Indices: 97553--97595 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
97543 TTGATTTTAT
97553 AAATAAAAGAATTAAAAATAAA
1 AAATAAAAGAATTAAAAATAAA
* **
97575 AAATATATTAATTAAAAATAA
1 AAATAAAAGAATTAAAAATAA
97596 GAATAATTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (22 bp):
AAATAAAAGAATTAAAAATAAA
Found at i:103009 original size:30 final size:30
Alignment explanation
Indices: 102955--103155 Score: 151
Period size: 30 Copynumber: 6.8 Consensus size: 30
102945 GGAAAAATAG
* * * *
102955 GGGT-AAAATCAAAATTTTGGAAAGTTTTAG
1 GGGTCAAAATGAAATTTTTAGAAAG-TTTAA
* *
102985 GGGTCAAAATGAAATTTTTA-AAAGTTCAT
1 GGGTCAAAATGAAATTTTTAGAAAGTTTAA
* *
103014 GGATCAAAAATGAAA-TTTTAGAAAGTTTAG
1 GGGTC-AAAATGAAATTTTTAGAAAGTTTAA
* * * * *
103044 GGGTTAAAAAT-ACATTTTCAAAAAGTTCAA
1 GGG-TCAAAATGAAATTTTTAGAAAGTTTAA
* *
103074 GGGTCAAAATGACATTTTTAGAAAGTTAAA
1 GGGTCAAAATGAAATTTTTAGAAAGTTTAA
* * * *
103104 GGGTCGAAATGACATTTTCATAAAGTTTAA
1 GGGTCAAAATGAAATTTTTAGAAAGTTTAA
* *
103134 GGATCAAAATGTAA-TTTTAGAA
1 GGGTCAAAATGAAATTTTTAGAA
103156 CAAAATAAGG
Statistics
Matches: 136, Mismatches: 29, Indels: 13
0.76 0.16 0.07
Matches are distributed among these distances:
29 26 0.19
30 97 0.71
31 13 0.10
ACGTcount: A:0.43, C:0.06, G:0.19, T:0.32
Consensus pattern (30 bp):
GGGTCAAAATGAAATTTTTAGAAAGTTTAA
Found at i:103083 original size:59 final size:59
Alignment explanation
Indices: 102966--103155 Score: 213
Period size: 60 Copynumber: 3.2 Consensus size: 59
102956 GGTAAAATCA
* * * *
102966 AAATTTTGGAAAGTTTTAGGGGTCAAAATGAAATTTT-TAAAAGTTCATGGATCAAAAATG
1 AAATTTTAGAAAG-TTTAGGGGTCAAAATGACATTTTCAAAAAGTTCAAGGATC-AAAATG
* *
103026 AAATTTTAGAAAGTTTAGGGGTTAAAAAT-ACATTTTCAAAAAGTTCAAGGGTCAAAATG
1 AAATTTTAGAAAGTTTAGGGG-TCAAAATGACATTTTCAAAAAGTTCAAGGATCAAAATG
* * * * * *
103085 ACATTTTTAGAAAGTTAAAGGGTCGAAATGACATTTTCATAAAGTTTAAGGATCAAAATG
1 A-AATTTTAGAAAGTTTAGGGGTCAAAATGACATTTTCAAAAAGTTCAAGGATCAAAATG
*
103145 TAATTTTAGAA
1 AAATTTTAGAA
103156 CAAAATAAGG
Statistics
Matches: 110, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
59 35 0.32
60 75 0.68
ACGTcount: A:0.43, C:0.06, G:0.18, T:0.33
Consensus pattern (59 bp):
AAATTTTAGAAAGTTTAGGGGTCAAAATGACATTTTCAAAAAGTTCAAGGATCAAAATG
Found at i:105086 original size:42 final size:42
Alignment explanation
Indices: 104947--105385 Score: 562
Period size: 42 Copynumber: 10.6 Consensus size: 42
104937 CTTGATCTTA
* * * *
104947 GGGGTAAAAGATTGGAT-AGTGGCTTCAATCTGCCTCTATTGACTTA
1 GGGGTAAGAGATTGGATGA-TGTCTTCAATCTGCC-CCA-TGA--TC
* *
104993 GGGGTAAAAGATTGGATG--G-CTTCAATCTGCCTCATGATC
1 GGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATC
* * ** * *
105032 GGGGTAAAAGATTGGATGATGTCTTTAATCAACCCTATGATT
1 GGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATC
105074 GGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATC
1 GGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATC
*
105116 GGGGTAAAAGATTGGATGATGTCTTCAATCTGCCCCATGATC
1 GGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATC
*
105158 GGGGTAAGAGATTGGATGA---CTTCAATCTGCCTCATGATC
1 GGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATC
*
105197 GGGGTAAGAGATTGGATGATGTCTTTAATCTGCCCCATGATC
1 GGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATC
* *
105239 GGGGTAAGAGATTGGATGA--T-TTCAATCTACCCCATGATT
1 GGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATC
* *
105278 GGGGTAAGAGATTGGATAATGTCTTCAATCTGCCTCATGATC
1 GGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATC
105320 GGGGTAAGAGATTGGATG--G-CTTCAATCTGCCCCATGATC
1 GGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATC
*
105359 GGGGTAAGATATTGGATGATGTCTTCA
1 GGGGTAAGAGATTGGATGATGTCTTCA
105386 CTTTGCTCTA
Statistics
Matches: 350, Mismatches: 30, Indels: 30
0.85 0.07 0.07
Matches are distributed among these distances:
39 127 0.36
40 2 0.01
41 6 0.02
42 185 0.53
43 12 0.03
44 1 0.00
46 17 0.05
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (42 bp):
GGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATC
Found at i:105091 original size:81 final size:81
Alignment explanation
Indices: 104947--105385 Score: 585
Period size: 81 Copynumber: 5.3 Consensus size: 81
104937 CTTGATCTTA
* * *
104947 GGGGTAAAAGATTGGAT-AGTGGCTTCAATCTGCCTCTATTGACTTAGGGGTAAAAGATTGGATG
1 GGGGTAAAAGATTGGATGA-TGTCTTCAATCTGCC-CTA-TGA--TCGGGGTAAGAGATTGGATG
*
105011 GCTTCAATCTGCCTCATGATC
61 GCTTCAATCTGCCCCATGATC
* ** *
105032 GGGGTAAAAGATTGGATGATGTCTTTAATCAACCCTATGATTGGGGTAAGAGATTGGATGATGTC
1 GGGGTAAAAGATTGGATGATGTCTTCAATCTGCCCTATGATCGGGGTAAGAGATTGGATG--G-C
105097 TTCAATCTGCCCCATGATC
63 TTCAATCTGCCCCATGATC
* *
105116 GGGGTAAAAGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGACTTC
1 GGGGTAAAAGATTGGATGATGTCTTCAATCTGCCCTATGATCGGGGTAAGAGATTGGATGGCTTC
*
105181 AATCTGCCTCATGATC
66 AATCTGCCCCATGATC
* * * **
105197 GGGGTAAGAGATTGGATGATGTCTTTAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATTTC
1 GGGGTAAAAGATTGGATGATGTCTTCAATCTGCCCTATGATCGGGGTAAGAGATTGGATGGCTTC
* *
105262 AATCTACCCCATGATT
66 AATCTGCCCCATGATC
* *
105278 GGGGTAAGAGATTGGATAATGTCTTCAATCTG-CCTCATGATCGGGGTAAGAGATTGGATGGCTT
1 GGGGTAAAAGATTGGATGATGTCTTCAATCTGCCCT-ATGATCGGGGTAAGAGATTGGATGGCTT
105342 CAATCTGCCCCATGATC
65 CAATCTGCCCCATGATC
* *
105359 GGGGTAAGATATTGGATGATGTCTTCA
1 GGGGTAAAAGATTGGATGATGTCTTCA
105386 CTTTGCTCTA
Statistics
Matches: 320, Mismatches: 29, Indels: 14
0.88 0.08 0.04
Matches are distributed among these distances:
80 2 0.01
81 208 0.65
83 4 0.01
84 77 0.24
85 28 0.09
86 1 0.00
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (81 bp):
GGGGTAAAAGATTGGATGATGTCTTCAATCTGCCCTATGATCGGGGTAAGAGATTGGATGGCTTC
AATCTGCCCCATGATC
Found at i:105210 original size:123 final size:122
Alignment explanation
Indices: 104947--105385 Score: 536
Period size: 123 Copynumber: 3.6 Consensus size: 122
104937 CTTGATCTTA
* * * *
104947 GGGGTAAAAGATTGGAT-AGTGGCTTCAATCTGCCTCTATTGACTTAGGGGTAAAAGATTGGATG
1 GGGGTAAGAGATTGGATGA-TGTCTTCAATCTGCC-CCA-TGA--TCGGGGTAAAAGATTGGATG
* * * **
105011 -G-CTTCAATCTGCCTCATGATCGGGGTAAAAGATTGGATGATGTCTTTAATCAACC-CTATGAT
61 AGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGA---CTTCAATCTGCCTC-ATGAT
*
105073 T
122 C
105074 GGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAAAGATTGGATGATGTC
1 GGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAAAGATTGGATGA-GTC
105139 TTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGACTTCAATCTGCCTCATGATC
65 TTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGACTTCAATCTGCCTCATGATC
* *
105197 GGGGTAAGAGATTGGATGATGTCTTTAATCTGCCCCATGATCGGGGTAAGAGATTGGATGA-T-T
1 GGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAAAGATTGGATGAGTCT
* * *
105260 TCAATCTACCCCATGATTGGGGTAAGAGATTGGATAATGTCTTCAATCTGCCTCATGATC
66 TCAATCTGCCCCATGATCGGGGTAAGAGATTGG---ATGACTTCAATCTGCCTCATGATC
* *
105320 GGGGTAAGAGATTGGATG--G-CTTCAATCTGCCCCATGATCGGGGTAAGATATTGGATGATGTC
1 GGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAAAGATTGGATGA-GTC
105382 TTCA
65 TTCA
105386 CTTTGCTCTA
Statistics
Matches: 284, Mismatches: 17, Indels: 26
0.87 0.05 0.08
Matches are distributed among these distances:
120 69 0.24
121 2 0.01
122 1 0.00
123 137 0.48
124 1 0.00
125 4 0.01
126 39 0.14
127 30 0.11
128 1 0.00
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (122 bp):
GGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAAAGATTGGATGAGTCT
TCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGACTTCAATCTGCCTCATGATC
Found at i:105777 original size:50 final size:51
Alignment explanation
Indices: 105723--106427 Score: 443
Period size: 50 Copynumber: 14.2 Consensus size: 51
105713 ATTGCGGTTG
* * ** *
105723 CAATCC-TTCCTATCACATCTTCTAAGGTATCGGGCTCATCGTTGCGACCT
1 CAATCCTTTCCTATCACATCTTCTAAGGTACCGGGTTCGCCGTTGCGGCCT
* * * *
105773 CAATCC-TTCCCATCGCATCTTCTAAGGTACCGGGTTCACCGTTACGGCCT
1 CAATCCTTTCCTATCACATCTTCTAAGGTACCGGGTTCGCCGTTGCGGCCT
* * * * *
105823 CAA-CCTTTCCCT-TCATATCTTC-ATGGTACCGGATTCGCCGTTGCAGACT
1 CAATCCTTT-CCTATCACATCTTCTAAGGTACCGGGTTCGCCGTTGCGGCCT
* * *
105872 CAAT-CTTTCCCATCACATCTTCTAAGGTACCGGATTCGCCATTGCGGCCT
1 CAATCCTTTCCTATCACATCTTCTAAGGTACCGGGTTCGCCGTTGCGGCCT
* * * *
105922 CAA-CCTTTCCCT-TCACATCTTTTAAGGTATCAGGTTCGCCGTTGTGGCCT
1 CAATCCTTT-CCTATCACATCTTCTAAGGTACCGGGTTCGCCGTTGCGGCCT
* * * * * * ** *
105972 CAA-CCTATCCTTTCATATCTT-TATGGTACTGGATTCATCGTTGCAGCCT
1 CAATCCTTTCCTATCACATCTTCTAAGGTACCGGGTTCGCCGTTGCGGCCT
* * * * *
106021 CAGT-CTTTCCCATCACATCTTTTAAGTTACCGGGTTCGCTGTTGCGGCCT
1 CAATCCTTTCCTATCACATCTTCTAAGGTACCGGGTTCGCCGTTGCGGCCT
* * * * * * * **
106071 CCA-CCTTTCCCT-TCATATCTT-TATGGTATCGGATTTGTCGTTATGGCCT
1 CAATCCTTT-CCTATCACATCTTCTAAGGTACCGGGTTCGCCGTTGCGGCCT
* * * * * * *
106120 TAATCCTTTCC-ACCACATCTTCTAAGGTATCGGGTTTGCCATTACGACCT
1 CAATCCTTTCCTATCACATCTTCTAAGGTACCGGGTTCGCCGTTGCGGCCT
*** * * *
106170 CAATCCTTTCC-ATCACATCTTCTAAGGTACTTAGTTCACTGTTACGGCCT
1 CAATCCTTTCCTATCACATCTTCTAAGGTACCGGGTTCGCCGTTGCGGCCT
* * * * * * * **
106220 CCA-CCTTTCCCT-TCATATCTTC-ATGATACCAGATTCTCCGTTGCGGTTT
1 CAATCCTTT-CCTATCACATCTTCTAAGGTACCGGGTTCGCCGTTGCGGCCT
* * * * **
106269 TAATCC-TTCCCATCACATCTTCTAGGGTACCGAGTTCGCCGTTGTAGCCT
1 CAATCCTTTCCTATCACATCTTCTAAGGTACCGGGTTCGCCGTTGCGGCCT
* * ** * * *
106319 CAAT-CTTTCCCT-TCATATCTTC-ATGGTACTAGATTCGCTGTTGCGGTCT
1 CAATCCTTT-CCTATCACATCTTCTAAGGTACCGGGTTCGCCGTTGCGGCCT
* * * *
106368 CAATCC-TTCCTATCACATCTTTTAAGGTACCGGATTCGCTGTTGCGGTCT
1 CAATCCTTTCCTATCACATCTTCTAAGGTACCGGGTTCGCCGTTGCGGCCT
106418 CAA-CCTTTCC
1 CAATCCTTTCC
106428 CTTCATATCT
Statistics
Matches: 498, Mismatches: 131, Indels: 52
0.73 0.19 0.08
Matches are distributed among these distances:
48 7 0.01
49 173 0.35
50 310 0.62
51 8 0.02
ACGTcount: A:0.18, C:0.31, G:0.16, T:0.35
Consensus pattern (51 bp):
CAATCCTTTCCTATCACATCTTCTAAGGTACCGGGTTCGCCGTTGCGGCCT
Found at i:105933 original size:99 final size:99
Alignment explanation
Indices: 105762--106442 Score: 500
Period size: 99 Copynumber: 6.9 Consensus size: 99
105752 TCGGGCTCAT
* * * * *
105762 CGTTGC-GACCTCAATCCTTCCCATCGCATCTTCTAAGGTACCGGGTTCACCGTTACGGCCTCAA
1 CGTTGCGGA-CTCAATCTTTCCCATCACATCTTCTAAGGTACCGGATTCGCCGTTGCGGCCTCAA
105826 CCTTTCCCTTCATATCTTCATGGTACCGGATTCGC
65 CCTTTCCCTTCATATCTTCATGGTACCGGATTCGC
* *
105861 CGTTGCAGACTCAATCTTTCCCATCACATCTTCTAAGGTACCGGATTCGCCATTGCGGCCTCAAC
1 CGTTGCGGACTCAATCTTTCCCATCACATCTTCTAAGGTACCGGATTCGCCGTTGCGGCCTCAAC
* * * *
105926 CTTTCCCTTCACATCTTTTAAGGTATCAGG-TTCGC
66 CTTTCCCTTCATATC-TTCATGGTA-CCGGATTCGC
* * * * ** * * * ** * **
105961 CGTTGTGGCCTCAACCTATCCTTTCATATCTT-TATGGTACTGGATTCATCGTTGCAGCCTCAGT
1 CGTTGCGGACTCAATCTTTCCCATCACATCTTCTAAGGTACCGGATTCGCCGTTGCGGCCTCAAC
* * * * * *
106025 CTTTCCCATCACATCTTTTAAGTTACCGGGTTCGC
66 CTTTCCCTTCATATC-TTCATGGTACCGGATTCGC
* * * * * * * * * * ** *
106060 TGTTGCGGCCTCCACCTTTCCCTTCATATCTT-TATGGTATCGGATTTGTCGTTATGGCCTTAAT
1 CGTTGCGGACTCAATCTTTCCCATCACATCTTCTAAGGTACCGGATTCGCCGTTGCGGCCTCAA-
* * * * *
106124 CCTTTCCAC--CACATCTTCTAAGGTATCGGGTTTGC
65 CCTTTCC-CTTCATATCTTC-ATGGTACCGGATTCGC
* * ** * * *
106159 CATTAC-GACCTCAATCCTTT-CCATCACATCTTCTAAGGTA-CTTAGTTCACTGTTACGGCCTC
1 CGTTGCGGA-CTCAAT-CTTTCCCATCACATCTTCTAAGGTACCGGA-TTCGCCGTTGCGGCCTC
* * * *
106221 CACCTTTCCCTTCATATCTTCATGATACCAGATTCTC
63 AACCTTTCCCTTCATATCTTCATGGTACCGGATTCGC
** * * * **
106258 CGTTGCGGTTTTAATCCTTCCCATCACATCTTCTAGGGTACC-GAGTTCGCCGTTGTAGCCTCAA
1 CGTTGCGGACTCAATCTTTCCCATCACATCTTCTAAGGTACCGGA-TTCGCCGTTGCGGCCTCAA
* **
106322 TCTTTCCCTTCATATCTTCATGGTACTAGATTCGC
65 CCTTTCCCTTCATATCTTCATGGTACCGGATTCGC
* * * * * * *
106357 TGTTGCGGTCTCAATCCTTCCTATCACATCTTTTAAGGTACCGGATTCGCTGTTGCGGTCTCAAC
1 CGTTGCGGACTCAATCTTTCCCATCACATCTTCTAAGGTACCGGATTCGCCGTTGCGGCCTCAAC
106422 CTTTCCCTTCATATCTTCATG
66 CTTTCCCTTCATATCTTCATG
106443 TTCCCTCGGT
Statistics
Matches: 462, Mismatches: 103, Indels: 34
0.77 0.17 0.06
Matches are distributed among these distances:
98 10 0.02
99 370 0.80
100 78 0.17
101 4 0.01
ACGTcount: A:0.18, C:0.31, G:0.16, T:0.36
Consensus pattern (99 bp):
CGTTGCGGACTCAATCTTTCCCATCACATCTTCTAAGGTACCGGATTCGCCGTTGCGGCCTCAAC
CTTTCCCTTCATATCTTCATGGTACCGGATTCGC
Found at i:106059 original size:149 final size:149
Alignment explanation
Indices: 105617--106442 Score: 471
Period size: 149 Copynumber: 5.6 Consensus size: 149
105607 GATTCGTCGC
* * * * * * * * *
105617 TGCGGCCTCAATCTTTCCCTTCATATC-TCTAAGGTATAAAGTTCACCGTTGCAGCTTCAACCTT
1 TGCGGCCTCAACCTTTCCCTTCACATCTTTTAAGGTATCAGGTTCACCGTTACGGCCTCAACCTA
* * *** * * ** * *
105681 TCCCTCCATATTTTCATGGTAGAAGATTCTCCATTGC-GGTTGCAATCCTTCCTATCACATCTTC
66 TCCCTTCATATCTTCATGGTACCGGATTCACCGTTGCAGACT-CAATCTTTCCCATCACATCTTC
* ** ** *
105745 TAAGGTATCGGGCTCATCGT
130 TAAGGTACCGGATTCGCCAT
* * * * * *
105765 TGCGACCTCAATCC-TTCCCATCGCATCTTCTAAGGTACCGGGTTCACCGTTACGGCCTCAACCT
1 TGCGGCCTCAA-CCTTTCCCTTCACATCTTTTAAGGTATCAGGTTCACCGTTACGGCCTCAACCT
* *
105829 TTCCCTTCATATCTTCATGGTACCGGATTCGCCGTTGCAGACTCAATCTTTCCCATCACATCTTC
65 ATCCCTTCATATCTTCATGGTACCGGATTCACCGTTGCAGACTCAATCTTTCCCATCACATCTTC
105894 TAAGGTACCGGATTCGCCAT
130 TAAGGTACCGGATTCGCCAT
* **
105914 TGCGGCCTCAACCTTTCCCTTCACATCTTTTAAGGTATCAGGTTCGCCGTTGTGGCCTCAACCTA
1 TGCGGCCTCAACCTTTCCCTTCACATCTTTTAAGGTATCAGGTTCACCGTTACGGCCTCAACCTA
* * * * * * *
105979 TCCTTTCATATCTTTATGGTACTGGATTCATCGTTGCAGCCTCAGTCTTTCCCATCACATCTTTT
66 TCCCTTCATATCTTCATGGTACCGGATTCACCGTTGCAGACTCAATCTTTCCCATCACATCTTCT
* * **
106044 AAGTTACCGGGTTCGCTGT
131 AAGGTACCGGATTCGCCAT
* * * *** * *
106063 TGCGGCCTCCACCTTTCCCTTCATATC-TTTATGGTATC-GGATTTGTCGTTATGGCCTTAATCC
1 TGCGGCCTCAACCTTTCCCTTCACATCTTTTAAGGTATCAGG-TTCACCGTTACGGCCTCAA-CC
* * * * * ** * *
106126 TTTCCAC--CACATCTTCTAAGGTATCGGGTTTGCCATTAC-GACCTCAATCCTTT-CCATCACA
64 TATCC-CTTCATATCTTC-ATGGTACCGGATTCACCGTTGCAGA-CTCAAT-CTTTCCCATCACA
** * **
106187 TCTTCTAAGGTA-CTTAGTTCACTGT
125 TCTTCTAAGGTACCGGA-TTCGCCAT
* * * * * * * * * * ** *
106212 TACGGCCTCCACCTTTCCCTTCATATC-TTCATGATACCAGATTCTCCGTTGCGGTTTTAATCCT
1 TGCGGCCTCAACCTTTCCCTTCACATCTTTTAAGGTATCAGGTTCACCGTTACGGCCTCAA-CCT
* * * * * * * *
106276 -TCCCATCACATCTTCTAGGGTACC-GAGTTCGCCGTTGTAGCCTCAATCTTTCCCTTCATATCT
65 ATCCCTTCATATCTTC-ATGGTACCGGA-TTCACCGTTGCAGACTCAATCTTTCCCATCACATCT
* ** **
106339 TC-ATGGTACTAGATTCGCTGT
128 TCTAAGGTACCGGATTCGCCAT
* * * * * *
106360 TGCGGTCTCAATCC-TT-CCTATCACATCTTTTAAGGTA-CCGGATTCGCTGTTGCGGTCTCAAC
1 TGCGGCCTCAA-CCTTTCCCT-TCACATCTTTTAAGGTATCAGG-TTCACCGTTACGGCCTCAAC
*
106422 CTTTCCCTTCATATCTTCATG
63 CTATCCCTTCATATCTTCATG
106443 TTCCCTCGGT
Statistics
Matches: 533, Mismatches: 122, Indels: 46
0.76 0.17 0.07
Matches are distributed among these distances:
147 6 0.01
148 99 0.19
149 420 0.79
150 8 0.02
ACGTcount: A:0.19, C:0.30, G:0.16, T:0.35
Consensus pattern (149 bp):
TGCGGCCTCAACCTTTCCCTTCACATCTTTTAAGGTATCAGGTTCACCGTTACGGCCTCAACCTA
TCCCTTCATATCTTCATGGTACCGGATTCACCGTTGCAGACTCAATCTTTCCCATCACATCTTCT
AAGGTACCGGATTCGCCAT
Found at i:106082 original size:248 final size:247
Alignment explanation
Indices: 105758--106439 Score: 760
Period size: 248 Copynumber: 2.7 Consensus size: 247
105748 GGTATCGGGC
* * *
105758 TCATCGTTGCGACCTCAATCCTTCCCATCGCATCTTCTAAGGTACCGGGTTCACCGTTACGGCCT
1 TCATCGTTGCG-CCTCAATCCTTCCCATCACATCTTCTAAGGTACCGGGTTCGCCGTTGCGGCCT
*
105823 CAACCTTTCCCTTCATATCTTCATGGTACCGGATTCGCCGTTGCAGACTCAATCTTTCCCATCAC
65 CAACCTTTCCCTTCATATCTTCATGGTACCGGATTCGCCGTTGCGGACTCAATCTTTCCCATCAC
*
105888 ATCTTCTAAGGTACCGGATTCGCCATTGCGGCCTCAACCTTTCCCTTCACATCTTTTAAGGTA-T
130 ATCTTCTAAGGTACCGGATTCGCCATTGCGGCCTCAACCTTTCCCTTCACATCTTCTAAGGTACT
* ** * * * **
105952 CAGGTTCGCCGTTGTGGCCTCAACCTATCCTTTCATATCTTTATGGTACTGGAT
195 CA-GTTCACCGTTACGGCCTCAACCTATCCCTTCATATCTTCATGATACCAGAT
* * * * *
106006 TCATCGTTGCAGCCTCAGTCTTTCCCATCACATCTTTTAAGTTACCGGGTTCGCTGTTGCGGCCT
1 TCATCGTTGC-GCCTCAATCCTTCCCATCACATCTTCTAAGGTACCGGGTTCGCCGTTGCGGCCT
* * * * * ** * * *
106071 CCACCTTTCCCTTCATATCTTTATGGTATCGGATTTGTCGTTATGGCCTTAATCCTTT-CCACCA
65 CAACCTTTCCCTTCATATCTTCATGGTACCGGATTCGCCGTTGCGGACTCAAT-CTTTCCCATCA
* * * * * *
106135 CATCTTCTAAGGTATCGGGTTTGCCATTACGACCTCAATCCTTT-CCATCACATCTTCTAAGGTA
129 CATCTTCTAAGGTACCGGATTCGCCATTGCGGCCTCAA-CCTTTCCCTTCACATCTTCTAAGGTA
* * * *
106199 CTTAGTTCACTGTTACGGCCTCCACCTTTCCCTTCATATCTTCATGATACCAGAT
193 CTCAGTTCACCGTTACGGCCTCAACCTATCCCTTCATATCTTCATGATACCAGAT
** * * * **
106254 TC-TCCGTTGCGGTTTTAATCCTTCCCATCACATCTTCTAGGGTACCGAGTTCGCCGTTGTAGCC
1 TCAT-CGTTGC-GCCTCAATCCTTCCCATCACATCTTCTAAGGTACCGGGTTCGCCGTTGCGGCC
* ** * * * *
106318 TCAATCTTTCCCTTCATATCTTCATGGTACTAGATTCGCTGTTGCGGTCTCAATCCTTCCTATCA
64 TCAACCTTTCCCTTCATATCTTCATGGTACCGGATTCGCCGTTGCGGACTCAATCTTTCCCATCA
* ** * *
106383 CATCTTTTAAGGTACCGGATTCGCTGTTGCGGTCTCAACCTTTCCCTTCATATCTTC
129 CATCTTCTAAGGTACCGGATTCGCCATTGCGGCCTCAACCTTTCCCTTCACATCTTC
106440 ATGTTCCCTC
Statistics
Matches: 349, Mismatches: 78, Indels: 14
0.79 0.18 0.03
Matches are distributed among these distances:
247 9 0.03
248 328 0.94
249 12 0.03
ACGTcount: A:0.18, C:0.31, G:0.16, T:0.36
Consensus pattern (247 bp):
TCATCGTTGCGCCTCAATCCTTCCCATCACATCTTCTAAGGTACCGGGTTCGCCGTTGCGGCCTC
AACCTTTCCCTTCATATCTTCATGGTACCGGATTCGCCGTTGCGGACTCAATCTTTCCCATCACA
TCTTCTAAGGTACCGGATTCGCCATTGCGGCCTCAACCTTTCCCTTCACATCTTCTAAGGTACTC
AGTTCACCGTTACGGCCTCAACCTATCCCTTCATATCTTCATGATACCAGAT
Found at i:107003 original size:112 final size:115
Alignment explanation
Indices: 106803--107014 Score: 297
Period size: 112 Copynumber: 1.9 Consensus size: 115
106793 TCCTTATATC
* * *
106803 ATTAGACCACTAACCGTTGTTTCAAATGCAAAAAATGCTTGTATCAAGGTTGTAAGGCAGATGAA
1 ATTAGACCACTAACCGTTATTTCAAATGCAAAAAATGCTTGTAACAAGGTTGTAAGGCAGATAAA
*
106868 ATTGAATTTGATTGGTGGAAAAGCTCGTATGAATGAAAAGATTAAAAATT
66 ATTGAATTTGATTGGAGGAAAAGCTCGTATGAATGAAAAGATTAAAAATT
* * * *
106918 ATTAGTCCACTAACCGTTATTTC-AATGC-AAAAATGCTTG-AACATGGTTGTGAGG-TGAATAA
1 ATTAGACCACTAACCGTTATTTCAAATGCAAAAAATGCTTGTAACAAGGTTGTAAGGCAG-ATAA
* *
106979 AATTGAATTTTATTGGAGGCAAAGCTCGTATGAATG
65 AATTGAATTTGATTGGAGGAAAAGCTCGTATGAATG
107015 CAAATATTGA
Statistics
Matches: 86, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
111 1 0.01
112 48 0.56
113 11 0.13
114 5 0.06
115 21 0.24
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.31
Consensus pattern (115 bp):
ATTAGACCACTAACCGTTATTTCAAATGCAAAAAATGCTTGTAACAAGGTTGTAAGGCAGATAAA
ATTGAATTTGATTGGAGGAAAAGCTCGTATGAATGAAAAGATTAAAAATT
Found at i:107361 original size:17 final size:17
Alignment explanation
Indices: 107332--107379 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
107322 ATTTTTCTTT
*
107332 TTCCTTATTTTTTTCT-
1 TTCCTTTTTTTTTTCTC
*
107348 TTCTTTTTTCTTTTTCTC
1 TTCCTTTTT-TTTTTCTC
107366 TTCCTTTTTTTTTT
1 TTCCTTTTTTTTTT
107380 GGGGTGAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 7 0.26
17 12 0.44
18 8 0.30
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (17 bp):
TTCCTTTTTTTTTTCTC
Found at i:107938 original size:81 final size:81
Alignment explanation
Indices: 107803--107973 Score: 290
Period size: 81 Copynumber: 2.1 Consensus size: 81
107793 CCTAACAAAA
*
107803 TCTTGATTAATGTTCAATAAGCGTAAAGAGCAAATGATAACTTCTCATGCCAATCTTTGTAAGTC
1 TCTTGATTAATGTTCAATAAGCGTAAAGAGCAAATGATAACTTCTCATGCCAATCTTTGTAAGCC
107868 TCGATCTTCTTGATAT
66 TCGATCTTCTTGATAT
* * * *
107884 TCTTGATTGATGTTCAATAAGCGTAGAGAGTAAATGATAACTTCTCATGCCAATCTTTGTAGGCC
1 TCTTGATTAATGTTCAATAAGCGTAAAGAGCAAATGATAACTTCTCATGCCAATCTTTGTAAGCC
107949 TCGATCTTCTTGATAT
66 TCGATCTTCTTGATAT
107965 TCTTG-TTAA
1 TCTTGATTAA
107974 CTGCCTCCAT
Statistics
Matches: 84, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
80 3 0.04
81 81 0.96
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (81 bp):
TCTTGATTAATGTTCAATAAGCGTAAAGAGCAAATGATAACTTCTCATGCCAATCTTTGTAAGCC
TCGATCTTCTTGATAT
Found at i:112752 original size:30 final size:30
Alignment explanation
Indices: 112712--112951 Score: 225
Period size: 30 Copynumber: 8.0 Consensus size: 30
112702 TAAGGAAAAA
* *
112712 TAAGGGTAAAAATGAAATTTTTGGAAAGTT
1 TAAGGGTTAAAATGAAATTTTTAGAAAGTT
* *
112742 TTA-GGTTAAAATGTAATTTTTAGAAAG-T
1 TAAGGGTTAAAATGAAATTTTTAGAAAGTT
* * * *
112770 TAGGGGATCAAAATGGAATTTTTATAAAGTT
1 TAAGGG-TTAAAATGAAATTTTTAGAAAGTT
* * *
112801 CATGGATTAAAATTGAAA-TTTTAGAAAGTT
1 TAAGGGTTAAAA-TGAAATTTTTAGAAAGTT
*
112831 TAAGGGTTAAAATGTAATTTTTAGAAAGTT
1 TAAGGGTTAAAATGAAATTTTTAGAAAGTT
* * * ** *
112861 TATGGGTCAAAATGACATTTCCAAAAAGTT
1 TAAGGGTTAAAATGAAATTTTTAGAAAGTT
* *
112891 TAGGGGTTAAAATGATATTTTTAGAAAGTT
1 TAAGGGTTAAAATGAAATTTTTAGAAAGTT
* ** *
112921 AAAGGGTCGAAATGACATTTTTAGAAAGTT
1 TAAGGGTTAAAATGAAATTTTTAGAAAGTT
112951 T
1 T
112952 GGGGATGAAA
Statistics
Matches: 167, Mismatches: 38, Indels: 10
0.78 0.18 0.05
Matches are distributed among these distances:
28 2 0.01
29 27 0.16
30 130 0.78
31 8 0.05
ACGTcount: A:0.40, C:0.03, G:0.20, T:0.36
Consensus pattern (30 bp):
TAAGGGTTAAAATGAAATTTTTAGAAAGTT
Found at i:112841 original size:90 final size:89
Alignment explanation
Indices: 112720--112971 Score: 278
Period size: 90 Copynumber: 2.8 Consensus size: 89
112710 AATAAGGGTA
* *
112720 AAAATGAAATTTTTGGAAAGTTTTA-GGTTAAAATGTAATTTTTAGAAAGTTAGGGGATCAAAAT
1 AAAATGAAA-TTTTAGAAAGTTTAAGGGTTAAAATGTAATTTTTAGAAAGTTAGGGGATCAAAAT
* * *
112784 GGAATTTTTATAAAGTTCATGGATT
65 GGAATTTTCAAAAAGTTCAGGGATT
*
112809 AAAATTGAAATTTTAGAAAGTTTAAGGGTTAAAATGTAATTTTTAGAAAGTTTATGGG-TCAAAA
1 AAAA-TGAAATTTTAGAAAGTTTAAGGGTTAAAATGTAATTTTTAGAAAG-TTAGGGGATCAAAA
* * *
112873 T-GACATTTCCAAAAAGTTTAGGGGTT
64 TGGA-ATTTTCAAAAAGTTCAGGGATT
* * ** * *
112899 AAAATGATATTTTTAGAAAGTTAAAGGGTCGAAATG-ACATTTTTAGAAAGTTTGGGGATGAAAA
1 AAAATGA-AATTTTAGAAAGTTTAAGGGTTAAAATGTA-ATTTTTAGAAAGTTAGGGGATCAAAA
*
112963 TGTAATTTT
64 TGGAATTTT
112972 AGAACAAAAT
Statistics
Matches: 137, Mismatches: 18, Indels: 15
0.81 0.11 0.09
Matches are distributed among these distances:
89 28 0.20
90 102 0.74
91 7 0.05
ACGTcount: A:0.40, C:0.03, G:0.21, T:0.37
Consensus pattern (89 bp):
AAAATGAAATTTTAGAAAGTTTAAGGGTTAAAATGTAATTTTTAGAAAGTTAGGGGATCAAAATG
GAATTTTCAAAAAGTTCAGGGATT
Found at i:112986 original size:60 final size:59
Alignment explanation
Indices: 112819--112986 Score: 169
Period size: 60 Copynumber: 2.8 Consensus size: 59
112809 AAAATTGAAA
* ** *
112819 TTTTAGAAAGTTTAAGGGTTAAAATGTAATTTTTAGAAAGTTTATGGGTCAAAATGACAT
1 TTTTAGAAAGTTTAGGGGTTAAAATGTAA-TTTTAGAAAAATTAAGGGTCAAAATGACAT
** * * * *
112879 TTCCAAAAAGTTTAGGGGTTAAAATGATATTTTTAG-AAAGTTAAAGGGTCGAAATGACAT
1 TTTTAGAAAGTTTAGGGGTTAAAATG-TAATTTTAGAAAAATT-AAGGGTCAAAATGACAT
* *
112939 TTTTAGAAAGTTT-GGGGATGAAAATGTAATTTTAGAACAAAATAAGGG
1 TTTTAGAAAGTTTAGGGG-TTAAAATGTAATTTTAGAA-AAATTAAGGG
112987 CTTCGAGAGC
Statistics
Matches: 87, Mismatches: 16, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
59 16 0.18
60 66 0.76
61 5 0.06
ACGTcount: A:0.40, C:0.04, G:0.22, T:0.34
Consensus pattern (59 bp):
TTTTAGAAAGTTTAGGGGTTAAAATGTAATTTTAGAAAAATTAAGGGTCAAAATGACAT
Found at i:113146 original size:32 final size:33
Alignment explanation
Indices: 113084--113147 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
113074 TCAAATGGGA
* **
113084 AAATTGAAATAAATTAAAAATAGCAAAAGGACT
1 AAATTGAAACAAACAAAAAATAGCAAAAGGACT
*
113117 AAATTGAAACAAACAAAAAAT-GCAGAAGGAC
1 AAATTGAAACAAACAAAAAATAGCAAAAGGAC
113148 CAAAGGCGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 9 0.33
33 18 0.67
ACGTcount: A:0.61, C:0.09, G:0.14, T:0.16
Consensus pattern (33 bp):
AAATTGAAACAAACAAAAAATAGCAAAAGGACT
Found at i:126561 original size:2 final size:2
Alignment explanation
Indices: 126554--126593 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
126544 CACATTCATT
126554 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
126594 TATATATAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:127861 original size:23 final size:23
Alignment explanation
Indices: 127831--127893 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
127821 CAGTCAATGA
127831 TTGGTCAAAGTCAATGGTTCGAT
1 TTGGTCAAAGTCAATGGTTCGAT
* *
127854 TTGGTCAAAGTCAACT-ATTCGGT
1 TTGGTCAAAGTCAA-TGGTTCGAT
* *
127877 TCGATCAAAGTCAATGG
1 TTGGTCAAAGTCAATGG
127894 GTCAGGTTGG
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
22 1 0.03
23 31 0.94
24 1 0.03
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.32
Consensus pattern (23 bp):
TTGGTCAAAGTCAATGGTTCGAT
Found at i:127927 original size:22 final size:22
Alignment explanation
Indices: 127887--127928 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
127877 TCGATCAAAG
* *
127887 TCAATGGGTCAGGTTGGGTCGA
1 TCAATGGGTCAAGTCGGGTCGA
*
127909 TCAATGGGTTAAGTCGGGTC
1 TCAATGGGTCAAGTCGGGTC
127929 ATATAATTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.19, C:0.14, G:0.38, T:0.29
Consensus pattern (22 bp):
TCAATGGGTCAAGTCGGGTCGA
Found at i:129062 original size:173 final size:173
Alignment explanation
Indices: 128773--129096 Score: 576
Period size: 173 Copynumber: 1.9 Consensus size: 173
128763 AGGGTGTTAT
* * *
128773 AGTTAGTTTCGAGGTTCAAAGGGTAATAACAAGTTATCGAATGACAACATACACTAAGAATTAGG
1 AGTTAGTTTCGAGGTTCAAAGGGTAATAACAAGTTATAGAATGAAAACATACACTAAGAATCAGG
128838 ATTTAGTGTTTATATTTTAGGAGGATGTGTTTTACTCTTAATGGATGGACATTAATTGTCATGAA
66 ATTTAGTGTTTATATTTTAGGAGGATGTGTTTTACTCTTAATGGATGGACATTAATTGTCATGAA
*
128903 ATCCACTTATATGGACATGAAACCCTACCTTATTCTAGTCAAA
131 ATCCACCTATATGGACATGAAACCCTACCTTATTCTAGTCAAA
* * *
128946 AGTTAGTTTCGAGGTTTAAAGGGTAATAACAAGTTATAGAATGAAAACGTGCACTAAGAATCAGG
1 AGTTAGTTTCGAGGTTCAAAGGGTAATAACAAGTTATAGAATGAAAACATACACTAAGAATCAGG
129011 ATTTAGTGTTTATATTTTAGGAGGATGTGTTTTACTCTTAATGGATGGACATTAATTGTCATGAA
66 ATTTAGTGTTTATATTTTAGGAGGATGTGTTTTACTCTTAATGGATGGACATTAATTGTCATGAA
*
129076 ATCCACCTATATGGGCATGAA
131 ATCCACCTATATGGACATGAA
129097 GTGGTGCCGC
Statistics
Matches: 143, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
173 143 1.00
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.34
Consensus pattern (173 bp):
AGTTAGTTTCGAGGTTCAAAGGGTAATAACAAGTTATAGAATGAAAACATACACTAAGAATCAGG
ATTTAGTGTTTATATTTTAGGAGGATGTGTTTTACTCTTAATGGATGGACATTAATTGTCATGAA
ATCCACCTATATGGACATGAAACCCTACCTTATTCTAGTCAAA
Found at i:132534 original size:2 final size:2
Alignment explanation
Indices: 132527--132557 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
132517 AATATGGCAT
132527 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 T
132558 TTAATTATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:135825 original size:41 final size:41
Alignment explanation
Indices: 135747--136075 Score: 383
Period size: 41 Copynumber: 8.1 Consensus size: 41
135737 AAAGATAAGA
* * *
135747 TCAGAGCAATAGC-GCACTTATGGGAAAGCGCCACTAAAGA
1 TCAGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGG
* * *
135787 TCAGAGCAATAGCGGTGCTTATGGGCAAGCGCTGCTAAAGG
1 TCAGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGG
* * *
135828 TCAGTGTAATA-CGGTGCTTATGGGAAAGCGCCGCTAAAGG
1 TCAGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGG
* * *
135868 TTAAAGCAATAACGGCGCTTATGGGAAAGCGCCGCTAAAGG
1 TCAGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGG
* * * **
135909 TCAGAGCAATAGCGGCGCTTATGGGCAAGCACCACTAAATA
1 TCAGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGG
* * * * *
135950 TCAAAGCAATAGCGGTGCTTAAGGGCAAGCGCTGCTAAAGG
1 TCAGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGG
* * ** **
135991 TCAGAACAGTAGCGGCGCTTATGAAAAAGCATCGCTAAAGG
1 TCAGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGG
*
136032 TCAGAGCAATAGCGGCGCTTTTGGGAAAGCGCCGCTAAAGG
1 TCAGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGG
136073 TCA
1 TCA
136076 TTTAATTGAT
Statistics
Matches: 238, Mismatches: 49, Indels: 3
0.82 0.17 0.01
Matches are distributed among these distances:
40 47 0.20
41 191 0.80
ACGTcount: A:0.32, C:0.21, G:0.29, T:0.18
Consensus pattern (41 bp):
TCAGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGG
Found at i:136211 original size:19 final size:19
Alignment explanation
Indices: 136173--136211 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
136163 CCGCTAAAGA
* **
136173 TCAGAGCAATAGTGGTGCT
1 TCAGAGCAATAGCGACGCT
136192 TCAGAGCAATAGCGACGCT
1 TCAGAGCAATAGCGACGCT
136211 T
1 T
136212 ATGGGCAAGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (19 bp):
TCAGAGCAATAGCGACGCT
Found at i:136251 original size:24 final size:24
Alignment explanation
Indices: 136219--136275 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
136209 CTTATGGGCA
*
136219 AGCGCCGCTAAAGGTCA-ATGTAAT
1 AGCGGCGCTAAAGGTCAGA-GTAAT
*
136243 AGCGGCGCTAAAGGTTAGAGTAAT
1 AGCGGCGCTAAAGGTCAGAGTAAT
136267 AGCGGCGCT
1 AGCGGCGCT
136276 TATGGGAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 29 0.97
25 1 0.03
ACGTcount: A:0.30, C:0.19, G:0.32, T:0.19
Consensus pattern (24 bp):
AGCGGCGCTAAAGGTCAGAGTAAT
Found at i:136314 original size:41 final size:41
Alignment explanation
Indices: 136243--136399 Score: 206
Period size: 41 Copynumber: 3.8 Consensus size: 41
136233 TCAATGTAAT
* * *
136243 AGCGGCGCTAAAGGTTAGAGTAATAGCGGCGCTTATGGGAA
1 AGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAA
* * *
136284 AGCGCCGCTAAAGGTCAGAGCAATAACGGCGCTTAAGGGCA
1 AGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAA
* * **
136325 AGCGCCGCTAAAGGTCAGAGCAGTAGCGACGCTTATGAAAA
1 AGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAA
* *
136366 AGCACCGCTAAAGGTCAGAGCAATAGCGGGGCTT
1 AGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTT
136400 TCCCAAAAGC
Statistics
Matches: 99, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 99 1.00
ACGTcount: A:0.31, C:0.21, G:0.32, T:0.15
Consensus pattern (41 bp):
AGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAA
Found at i:136314 original size:65 final size:65
Alignment explanation
Indices: 136194--136321 Score: 186
Period size: 65 Copynumber: 2.0 Consensus size: 65
136184 GTGGTGCTTC
* * *
136194 AGAGCAATAGCGACGCTTATGGGCAAGCGCCGCTAAAGGTCAATGTAATAGCGGCGCTAAAGGTT
1 AGAGCAATAGCGACGCTTATGGGAAAGCGCCGCTAAAGGTCAATGCAATAACGGCGCTAAAGGTT
* * *
136259 AGAGTAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTCAGA-GCAATAACGGCGCTTAAGG
1 AGAGCAATAGCGACGCTTATGGGAAAGCGCCGCTAAAGGTCA-ATGCAATAACGGCGCTAAAGG
136322 GCAAGCGCCG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
65 55 0.98
66 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.32, T:0.17
Consensus pattern (65 bp):
AGAGCAATAGCGACGCTTATGGGAAAGCGCCGCTAAAGGTCAATGCAATAACGGCGCTAAAGGTT
Found at i:136408 original size:41 final size:40
Alignment explanation
Indices: 136243--136423 Score: 173
Period size: 41 Copynumber: 4.4 Consensus size: 40
136233 TCAATGTAAT
* * * **
136243 AGCGGCGCTAAAGGTTAGAGTAATAGCGGCGCTTATGGGAA
1 AGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTT-TGAAAA
* * ***
136284 AGCGCCGCTAAAGGTCAGAGCAATAACGGCGCTTAAGGGCA
1 AGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTT-TGAAAA
* *
136325 AGCGCCGCTAAAGGTCAGAGCAGTAGCGACGCTTATGAAAA
1 AGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTT-TGAAAA
* * **
136366 AGCACCGCTAAAGGTCAGAGCAATAGCGGGGCTTTCCCAAA
1 AGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTT-GAAAA
*
136407 AGCGCCACTAAAGGTCA
1 AGCGCCGCTAAAGGTCA
136424 TTTAATTGAT
Statistics
Matches: 118, Mismatches: 21, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
40 1 0.01
41 117 0.99
ACGTcount: A:0.32, C:0.23, G:0.30, T:0.15
Consensus pattern (40 bp):
AGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTTGAAAA
Found at i:136410 original size:82 final size:82
Alignment explanation
Indices: 136243--136423 Score: 209
Period size: 82 Copynumber: 2.2 Consensus size: 82
136233 TCAATGTAAT
* * * * ** *
136243 AGCGGCGCTAAAGGTTAGAGTAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTCAGAGCAAT
1 AGCGCCGCTAAAGGTCAGAGCAATAGCGACGCTTATGAAAAAGCACCGCTAAAGGTCAGAGCAAT
****
136308 AACGGCGCTTAAGGGCA
66 AACGGCGCTTAACCAAA
*
136325 AGCGCCGCTAAAGGTCAGAGCAGTAGCGACGCTTATGAAAAAGCACCGCTAAAGGTCAGAGCAAT
1 AGCGCCGCTAAAGGTCAGAGCAATAGCGACGCTTATGAAAAAGCACCGCTAAAGGTCAGAGCAAT
* * **
136390 AGCGGGGCTTTCCCAAA
66 AACGGCGCTTAACCAAA
*
136407 AGCGCCACTAAAGGTCA
1 AGCGCCGCTAAAGGTCA
136424 TTTAATTGAT
Statistics
Matches: 82, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
82 82 1.00
ACGTcount: A:0.32, C:0.23, G:0.30, T:0.15
Consensus pattern (82 bp):
AGCGCCGCTAAAGGTCAGAGCAATAGCGACGCTTATGAAAAAGCACCGCTAAAGGTCAGAGCAAT
AACGGCGCTTAACCAAA
Found at i:136783 original size:21 final size:20
Alignment explanation
Indices: 136759--136797 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
136749 TTCAAAATTC
136759 AAATTTAAACCGAAAAAAACA
1 AAATTTAAA-CGAAAAAAACA
*
136780 AAATTTAAAGGAAAAAAA
1 AAATTTAAACGAAAAAAA
136798 TGCTCGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.69, C:0.08, G:0.08, T:0.15
Consensus pattern (20 bp):
AAATTTAAACGAAAAAAACA
Found at i:140556 original size:19 final size:18
Alignment explanation
Indices: 140528--140590 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 18
140518 TAAAATAGAG
*
140528 AAAATTATAAAAATAATAA
1 AAAATCATAAAAAT-ATAA
*
140547 AAAATCATAAATATATACA
1 AAAATCATAAAAATATA-A
140566 TAAAA-CATAAAAAATTATAA
1 -AAAATCAT-AAAAA-TATAA
140586 AAAAT
1 AAAAT
140591 TAACAAATGA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
18 3 0.08
19 20 0.56
20 9 0.25
21 4 0.11
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (18 bp):
AAAATCATAAAAATATAA
Found at i:142256 original size:43 final size:43
Alignment explanation
Indices: 142192--142462 Score: 344
Period size: 43 Copynumber: 6.3 Consensus size: 43
142182 ATTTGTTAAT
* *
142192 TTTAGTGGCGTTTGTGGGAAAAGCACCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTC
* * * *
142235 TTTAGTGGCGTTTGTGAGAAAAGCGCCACTAAAGAACATGTTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTC
* ** * * * * *
142278 TTTAGCGGCATTTGCAGAAAAAGCACTGCTAAAGACTATGTTA
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTC
*
142321 TTTAGCGGCGTTTGTGGGAAAAGCGCTGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTC
* * * *
142364 TTTAGCAGTGTTTGTGGTAAAAGCGCTGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTC
** *
142407 TTTAGCAACATTTGTGGGAAAAGCGCCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTC
142450 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
142463 TTCCAAATAA
Statistics
Matches: 194, Mismatches: 34, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 194 1.00
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTC
Found at i:155293 original size:18 final size:18
Alignment explanation
Indices: 155267--155301 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
155257 ATAATTCAAT
*
155267 AAAAAAAACACAATCCAC
1 AAAAAAAACAAAATCCAC
*
155285 AAAACAAACAAAATCCA
1 AAAAAAAACAAAATCCA
155302 AAGAGAAAAG
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:0.69, C:0.26, G:0.00, T:0.06
Consensus pattern (18 bp):
AAAAAAAACAAAATCCAC
Found at i:169629 original size:22 final size:20
Alignment explanation
Indices: 169601--169640 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
169591 TCTTGATTAA
169601 CTTAATTAATCACTTATTTAGC
1 CTTAATTAATC-C-TATTTAGC
169623 CTTAATTAATCCTATTTA
1 CTTAATTAATCCTATTTA
169641 TAATCAACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 1 0.06
22 11 0.61
ACGTcount: A:0.33, C:0.17, G:0.03, T:0.47
Consensus pattern (20 bp):
CTTAATTAATCCTATTTAGC
Found at i:176141 original size:23 final size:23
Alignment explanation
Indices: 176114--176170 Score: 80
Period size: 23 Copynumber: 2.4 Consensus size: 23
176104 TCATTAGTTC
176114 ATTTACACATAAATCACATTAAT
1 ATTTACACATAAATCACATTAAT
*
176137 ATTTA-AGTATAAATCACATTAAT
1 ATTTACA-CATAAATCACATTAAT
176160 ATTTAACACAT
1 ATTT-ACACAT
176171 TTAACGATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
22 1 0.03
23 24 0.83
24 3 0.10
25 1 0.03
ACGTcount: A:0.47, C:0.14, G:0.02, T:0.37
Consensus pattern (23 bp):
ATTTACACATAAATCACATTAAT
Found at i:177886 original size:23 final size:23
Alignment explanation
Indices: 177830--177888 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
177820 CAACGACCAA
* *
177830 TCAAAGTCAACGATTTGATTCGG
1 TCAAAGTCAATGGTTTGATTCGG
*
177853 TAAAAGTCAATGGTTTGATTCGG
1 TCAAAGTCAATGGTTTGATTCGG
177876 TCAAAGTCAATGG
1 TCAAAGTCAATGG
177889 GTCGGGTTGG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.31
Consensus pattern (23 bp):
TCAAAGTCAATGGTTTGATTCGG
Found at i:177909 original size:22 final size:23
Alignment explanation
Indices: 177881--177927 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
177871 TTCGGTCAAA
*
177881 GTCAATGGGTCGGGTTGGG-TTG
1 GTCAATGGGTCAGGTTGGGCTTG
177903 GTCAATGGGTCAGGTTGGGCTTG
1 GTCAATGGGTCAGGTTGGGCTTG
177926 GT
1 GT
177928 TTGATTCGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.11, C:0.11, G:0.47, T:0.32
Consensus pattern (23 bp):
GTCAATGGGTCAGGTTGGGCTTG
Found at i:187117 original size:20 final size:20
Alignment explanation
Indices: 187092--187135 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
187082 TGTCAATGCA
187092 TTTTTACATTTACTT-TTATC
1 TTTTTACATTTACTTGTT-TC
*
187112 TTTTTACTTTTACTTGTTTC
1 TTTTTACATTTACTTGTTTC
187132 TTTT
1 TTTT
187136 AAATCTTATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.14, C:0.14, G:0.02, T:0.70
Consensus pattern (20 bp):
TTTTTACATTTACTTGTTTC
Found at i:187136 original size:13 final size:14
Alignment explanation
Indices: 187100--187136 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
187090 CATTTTTACA
187100 TTTACTTTTATCTT
1 TTTACTTTTATCTT
187114 TTTACTTTTA-CTT
1 TTTACTTTTATCTT
187127 GTTT-CTTTTA
1 -TTTACTTTTA
187137 AATCTTATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 9 0.41
14 13 0.59
ACGTcount: A:0.14, C:0.14, G:0.03, T:0.70
Consensus pattern (14 bp):
TTTACTTTTATCTT
Found at i:187621 original size:26 final size:26
Alignment explanation
Indices: 187592--187645 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
187582 CAACCCCCAC
187592 AAAATGAACCAGTCTTATTTTTGTCT
1 AAAATGAACCAGTCTTATTTTTGTCT
187618 AAAATGAACCAGTCTTATTTTTGTCT
1 AAAATGAACCAGTCTTATTTTTGTCT
187644 AA
1 AA
187646 GGCAACGAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (26 bp):
AAAATGAACCAGTCTTATTTTTGTCT
Found at i:190119 original size:10 final size:11
Alignment explanation
Indices: 190104--190149 Score: 60
Period size: 10 Copynumber: 4.3 Consensus size: 11
190094 ATAAAATCAC
190104 AAAAAG-AAAG
1 AAAAAGAAAAG
190114 AAAAAG-AAAG
1 AAAAAGAAAAG
*
190124 AAGAAGAAAAG
1 AAAAAGAAAAG
190135 AGAAAAGAAAAG
1 A-AAAAGAAAAG
190147 AAA
1 AAA
190150 TACATTGCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
10 15 0.47
11 7 0.22
12 10 0.31
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:203796 original size:21 final size:22
Alignment explanation
Indices: 203767--203810 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
203757 AAAAAATTAC
203767 AAATCGAATCAAGT-GAAATGA
1 AAATCGAATCAAGTCGAAATGA
* *
203788 AAATTGAATCAAGTCGAATTGA
1 AAATCGAATCAAGTCGAAATGA
203810 A
1 A
203811 TTGAATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.50, C:0.09, G:0.18, T:0.23
Consensus pattern (22 bp):
AAATCGAATCAAGTCGAAATGA
Found at i:205280 original size:24 final size:24
Alignment explanation
Indices: 205244--205303 Score: 111
Period size: 24 Copynumber: 2.5 Consensus size: 24
205234 TCTTTCAGTT
*
205244 AAACTCTGTTTATTTGTTTTAATC
1 AAACTCTGATTATTTGTTTTAATC
205268 AAACTCTGATTATTTGTTTTAATC
1 AAACTCTGATTATTTGTTTTAATC
205292 AAACTCTGATTA
1 AAACTCTGATTA
205304 GTCTAGATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.30, C:0.13, G:0.08, T:0.48
Consensus pattern (24 bp):
AAACTCTGATTATTTGTTTTAATC
Found at i:210568 original size:34 final size:34
Alignment explanation
Indices: 210525--210590 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
210515 AGATCCGAGT
*
210525 AAGGTTTCTTCCATCCTTGATTTGAAGGTTACAA
1 AAGGTTTCTTCCAACCTTGATTTGAAGGTTACAA
*
210559 AAGGTTTCTTCTAACCTTGATTTGAAGGTTAC
1 AAGGTTTCTTCCAACCTTGATTTGAAGGTTAC
210591 GAAGAATGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.39
Consensus pattern (34 bp):
AAGGTTTCTTCCAACCTTGATTTGAAGGTTACAA
Found at i:216290 original size:17 final size:17
Alignment explanation
Indices: 216259--216316 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
216249 TAATTGTCCA
* *
216259 TGCATTATTAATGTCAT
1 TGCATTTTTATTGTCAT
**
216276 TGCATTTTTATTGTCGC
1 TGCATTTTTATTGTCAT
* **
216293 TGCATCTACATTGTCAT
1 TGCATTTTTATTGTCAT
216310 TGCATTT
1 TGCATTT
216317 CCATATATAT
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.21, C:0.17, G:0.14, T:0.48
Consensus pattern (17 bp):
TGCATTTTTATTGTCAT
Found at i:216297 original size:34 final size:34
Alignment explanation
Indices: 216251--216316 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 34
216241 CTGTAGTATA
*
216251 ATTGTCCATGCAT-TATTAATGTCATTGCATTTTT
1 ATTGTCCATGCATCTA-CAATGTCATTGCATTTTT
*
216285 ATTGTCGC-TGCATCTACATTGTCATTGCATTT
1 ATTGTC-CATGCATCTACAATGTCATTGCATTT
216317 CCATATATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
34 25 0.89
35 3 0.11
ACGTcount: A:0.21, C:0.18, G:0.14, T:0.47
Consensus pattern (34 bp):
ATTGTCCATGCATCTACAATGTCATTGCATTTTT
Found at i:220190 original size:21 final size:22
Alignment explanation
Indices: 220165--220211 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
220155 GTATTTTCAG
*
220165 TTTTGTT-A-TGATATTTGATTA
1 TTTTGTTAAGTGAT-TTTGATGA
220186 TTTTGTTAAGTGATTTTGATGA
1 TTTTGTTAAGTGATTTTGATGA
220208 TTTT
1 TTTT
220212 AGGATTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 7 0.30
22 12 0.52
23 4 0.17
ACGTcount: A:0.21, C:0.00, G:0.17, T:0.62
Consensus pattern (22 bp):
TTTTGTTAAGTGATTTTGATGA
Found at i:225277 original size:16 final size:16
Alignment explanation
Indices: 225243--225294 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
225233 ACAACACAAC
*
225243 AAAAAGTAAA-ATAACT
1 AAAAAGTAAATA-AAAT
225259 AAAAAGTAAATAAAAT
1 AAAAAGTAAATAAAAT
* *
225275 AAAAAATAATTAAAAT
1 AAAAAGTAAATAAAAT
225291 AAAA
1 AAAA
225295 TGCATCGACA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
16 31 0.97
17 1 0.03
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.19
Consensus pattern (16 bp):
AAAAAGTAAATAAAAT
Found at i:232606 original size:18 final size:19
Alignment explanation
Indices: 232585--232620 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
232575 TAGCTCATTT
*
232585 GAGCA-TACTGGCTTGTAA
1 GAGCATTACTGGATTGTAA
232603 GAGCATTACTGGATTGTA
1 GAGCATTACTGGATTGTA
232621 GAAGTTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.31
Consensus pattern (19 bp):
GAGCATTACTGGATTGTAA
Found at i:233362 original size:19 final size:21
Alignment explanation
Indices: 233311--233384 Score: 57
Period size: 21 Copynumber: 3.6 Consensus size: 21
233301 GGATTTTTTA
*
233311 GTATTGGTAGAAGCATGACTT
1 GTATTGGTAGAAGCATGACAT
*
233332 GT-TTCAGTAGAAG-A-GACAT
1 GTATT-GGTAGAAGCATGACAT
* *
233351 GTATTGGTAGAACCATCAC-T
1 GTATTGGTAGAAGCATGACAT
*
233371 AGTATCGGTAGAAG
1 -GTATTGGTAGAAG
233385 TCTGCTATTA
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
19 12 0.29
20 7 0.17
21 22 0.54
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.28
Consensus pattern (21 bp):
GTATTGGTAGAAGCATGACAT
Found at i:239568 original size:10 final size:10
Alignment explanation
Indices: 239553--239658 Score: 79
Period size: 10 Copynumber: 10.3 Consensus size: 10
239543 AAACATTTAT
239553 TATATA-ATAA
1 TATATACAT-A
239563 TATATACATA
1 TATATACATA
239573 TATATACATA
1 TATATACATA
* *
239583 TATGTATATA
1 TATATACATA
* *
239593 TATAATATACA
1 TAT-ATACATA
239604 TATATACATA
1 TATATACATA
**
239614 TATATATGTA
1 TATATACATA
*
239624 TACATACATACA
1 TATATACAT--A
*
239636 TACATACATA
1 TATATACATA
* *
239646 TATTTATATA
1 TATATACATA
239656 TAT
1 TAT
239659 GTGATTGAGA
Statistics
Matches: 78, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
10 58 0.74
11 10 0.13
12 10 0.13
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (10 bp):
TATATACATA
Found at i:239594 original size:4 final size:4
Alignment explanation
Indices: 239553--239658 Score: 83
Period size: 4 Copynumber: 27.2 Consensus size: 4
239543 AAACATTTAT
* * *
239553 TATA TA-A TA-A TATA TACA TATA TATA CATA TATG TATA TATA TA-A
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * * * * * *
239598 TATA CATA TATA CATA TATA TATG TATA CATA CATA CATA CATA CATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
*
239646 TATT TATA TATA T
1 TATA TATA TATA T
239659 GTGATTGAGA
Statistics
Matches: 84, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
3 9 0.11
4 75 0.89
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (4 bp):
TATA
Found at i:240266 original size:17 final size:17
Alignment explanation
Indices: 240219--240275 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
240209 TATATATATG
240219 AAAATGCAA-TGACAATA
1 AAAATG-AAGTGACAATA
* * * *
240236 TAGATGCAGCGACAATA
1 AAAATGAAGTGACAATA
240253 AAAATGAAGTGACAATA
1 AAAATGAAGTGACAATA
240270 AAAATG
1 AAAATG
240276 CAATTACATG
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
16 1 0.03
17 30 0.97
ACGTcount: A:0.54, C:0.11, G:0.18, T:0.18
Consensus pattern (17 bp):
AAAATGAAGTGACAATA
Found at i:252039 original size:21 final size:21
Alignment explanation
Indices: 252013--252067 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
252003 TAGTTTGTAT
*
252013 ACTTGTTTCGATAGAAGAGTC
1 ACTTGTATCGATAGAAGAGTC
* **
252034 ACTTGTATCGGTAGAATTGTC
1 ACTTGTATCGATAGAAGAGTC
*
252055 ATTTGTATCGATA
1 ACTTGTATCGATA
252068 TAACTCTGCA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (21 bp):
ACTTGTATCGATAGAAGAGTC
Found at i:256309 original size:16 final size:16
Alignment explanation
Indices: 256264--256314 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 16
256254 AGTAATATAT
*
256264 TTTTTCTGCTT-TTCTC
1 TTTTTCTTCTTCTT-TC
*
256280 TTTTTCTT-TACTTTC
1 TTTTTCTTCTTCTTTC
256295 TTTTTCTTCTTCTTT-
1 TTTTTCTTCTTCTTTC
256310 TTTTT
1 TTTTT
256315 ATATATGTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 16 0.53
16 14 0.47
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (16 bp):
TTTTTCTTCTTCTTTC
Found at i:266402 original size:41 final size:41
Alignment explanation
Indices: 266160--266416 Score: 293
Period size: 41 Copynumber: 6.2 Consensus size: 41
266150 ACTTGAAGTA
*
266160 TAAATGGAAGACTCATGTCTCGGGATGAGCATGAGATTATAT
1 TAAA-GGAAGACTCATGACTCGGGATGAGCATGAGATTATAT
* ***
266202 TAAAGGAAGACTCGTGACTCAAAATGAGCATGAGATTATAT
1 TAAAGGAAGACTCATGACTCGGGATGAGCATGAGATTATAT
* **** *
266243 TAAAGGAAGACTCGTGACTAAAAATGAGCATGAGATTAAAT
1 TAAAGGAAGACTCATGACTCGGGATGAGCATGAGATTATAT
* * *
266284 TAAAGGAAGACTTATGTCTCGGGATGAGCATAAGATTATAT
1 TAAAGGAAGACTCATGACTCGGGATGAGCATGAGATTATAT
* *
266325 TAAAGGAAGACTCGTGACTCGGGATGAGTATGAGATTATATT
1 TAAAGGAAGACTCATGACTCGGGATGAGCATGAGATTATA-T
* * * *
266367 TAAAGGAAGACTTATGACTCGGTA-GAGCATAAGATTGT-T
1 TAAAGGAAGACTCATGACTCGGGATGAGCATGAGATTATAT
266406 TAAAAGGAAGA
1 T-AAAGGAAGA
266417 TCTACGACTC
Statistics
Matches: 186, Mismatches: 27, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
39 2 0.01
40 9 0.05
41 149 0.80
42 26 0.14
ACGTcount: A:0.39, C:0.10, G:0.25, T:0.26
Consensus pattern (41 bp):
TAAAGGAAGACTCATGACTCGGGATGAGCATGAGATTATAT
Found at i:266402 original size:123 final size:124
Alignment explanation
Indices: 266160--266385 Score: 355
Period size: 123 Copynumber: 1.8 Consensus size: 124
266150 ACTTGAAGTA
*
266160 TAAATGGAAGACTCATGTCTCGGGATGAGCATGAGATTATATTAAAGGAAGACTCGTGACTCAAA
1 TAAATGGAAGACTCATGTCTCGGGATGAGCATAAGATTATATTAAAGGAAGACTCGTGACTCAAA
* *
266225 ATGAGCATGAGATTATATTAAAGGAAGACTCGTGACTAAAAATGAGCATGAGATTAAAT
66 ATGAGCATGAGATTATATTAAAGGAAGACTCATGACTAAAAATGAGCATAAGATTAAAT
* ***
266284 TAAA-GGAAGACTTATGTCTCGGGATGAGCATAAGATTATATTAAAGGAAGACTCGTGACTCGGG
1 TAAATGGAAGACTCATGTCTCGGGATGAGCATAAGATTATATTAAAGGAAGACTCGTGACTCAAA
* *
266348 ATGAGTATGAGATTATATTTAAAGGAAGACTTATGACT
66 ATGAGCATGAGATTATA-TTAAAGGAAGACTCATGACT
266386 CGGTAGAGCA
Statistics
Matches: 93, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
123 71 0.76
124 22 0.24
ACGTcount: A:0.38, C:0.11, G:0.24, T:0.27
Consensus pattern (124 bp):
TAAATGGAAGACTCATGTCTCGGGATGAGCATAAGATTATATTAAAGGAAGACTCGTGACTCAAA
ATGAGCATGAGATTATATTAAAGGAAGACTCATGACTAAAAATGAGCATAAGATTAAAT
Found at i:266498 original size:16 final size:16
Alignment explanation
Indices: 266477--266509 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
266467 ATACAATGAT
266477 TGCGAACTTACTAAGC
1 TGCGAACTTACTAAGC
266493 TGCGAACTTACTAAGC
1 TGCGAACTTACTAAGC
266509 T
1 T
266510 TAGAAAGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.27
Consensus pattern (16 bp):
TGCGAACTTACTAAGC
Found at i:274010 original size:17 final size:17
Alignment explanation
Indices: 273988--274021 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
273978 ATAATATATA
273988 TATATATATTATAAATG
1 TATATATATTATAAATG
274005 TATATATATTATAAATG
1 TATATATATTATAAATG
274022 AGACTGAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (17 bp):
TATATATATTATAAATG
Found at i:274643 original size:17 final size:17
Alignment explanation
Indices: 274598--274648 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 17
274588 ACTACAATGG
* * *
274598 AAATGTGATAACAAGTA
1 AAATGTAATGACAACTA
* *
274615 AAATGCAGTGACAACTA
1 AAATGTAATGACAACTA
274632 AAATGTAATGACAACTA
1 AAATGTAATGACAACTA
274649 GATGAAATGT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.22
Consensus pattern (17 bp):
AAATGTAATGACAACTA
Found at i:275055 original size:3 final size:3
Alignment explanation
Indices: 275047--275114 Score: 60
Period size: 3 Copynumber: 24.3 Consensus size: 3
275037 GTTGGAACAA
*
275047 CTT CTT CTT CTT TTT CTT -TT CCTT C-T CTT C-T CTT C-T CTT CCTT
1 CTT CTT CTT CTT CTT CTT CTT -CTT CTT CTT CTT CTT CTT CTT -CTT
275090 CTT CTT C-T CTT -TT C-T CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
275115 AACATCCTCA
Statistics
Matches: 54, Mismatches: 2, Indels: 18
0.73 0.03 0.24
Matches are distributed among these distances:
2 14 0.26
3 35 0.65
4 5 0.09
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:275076 original size:5 final size:5
Alignment explanation
Indices: 275068--275114 Score: 51
Period size: 5 Copynumber: 8.8 Consensus size: 5
275058 TTTTCTTTTC
275068 CTTCT CTTCT CTTCT CTTC- CTTCTT CTTCT CTTTTCT CTTCTT CTTC
1 CTTCT CTTCT CTTCT CTTCT CTTC-T CTTCT C--TTCT CTTC-T CTTC
275115 AACATCCTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
4 4 0.11
5 19 0.51
6 9 0.24
7 5 0.14
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (5 bp):
CTTCT
Found at i:275082 original size:25 final size:25
Alignment explanation
Indices: 275047--275110 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 25
275037 GTTGGAACAA
275047 CTTCTTCTTCTT-T-TTCTTTTCCTT
1 CTTCTTC-TCTTCTCTTCTTTTCCTT
*
275071 C-TCTTCTCTTCTCTTC-CTT-CTT
1 CTTCTTCTCTTCTCTTCTTTTCCTT
*
275093 CTTC-TCTTTTCTCTTCTT
1 CTTCTTCTCTTCTCTTCTT
275111 CTTCAACATC
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
22 19 0.58
23 10 0.30
24 4 0.12
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (25 bp):
CTTCTTCTCTTCTCTTCTTTTCCTT
Found at i:275086 original size:15 final size:16
Alignment explanation
Indices: 275047--275114 Score: 67
Period size: 15 Copynumber: 4.4 Consensus size: 16
275037 GTTGGAACAA
275047 CTTCTTCTTCTT-T-TT
1 CTTCTTC-TCTTCTCTT
275062 CTT-TTC-CTTCTCTT
1 CTTCTTCTCTTCTCTT
275076 C-TCTTCTCTTC-CTT
1 CTTCTTCTCTTCTCTT
275090 CTTCTTCTCTTTTCTCTT
1 CTTCTTCTC--TTCTCTT
275108 CTTCTTC
1 CTTCTTC
275115 AACATCCTCA
Statistics
Matches: 45, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
12 3 0.07
13 2 0.04
14 13 0.29
15 14 0.31
17 3 0.07
18 10 0.22
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (16 bp):
CTTCTTCTCTTCTCTT
Found at i:286358 original size:21 final size:20
Alignment explanation
Indices: 286332--286390 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 20
286322 GATTCTGCAT
*
286332 ACTTGTTTCAGTAGAAGAGTC
1 ACTTGTATC-GTAGAAGAGTC
**
286353 ACTTGTATCGATAGAATTGTC
1 ACTTGTATCG-TAGAAGAGTC
286374 ACTTGTATCGGTAGAAG
1 ACTTGTATC-GTAGAAG
286391 TCTGCATTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.34
Consensus pattern (20 bp):
ACTTGTATCGTAGAAGAGTC
Found at i:287923 original size:49 final size:49
Alignment explanation
Indices: 287850--287988 Score: 188
Period size: 49 Copynumber: 2.8 Consensus size: 49
287840 ATCTATTTAT
* * * * * *
287850 AGGTTGAAAAAACCTTATTCTAATCAAAGTCAAATAGATGAAGTGTAGTA
1 AGGTTG-AAAAACCTTATTCTAATCAAAATAAAATAAAAGAAATGTAATA
*
287900 AGGTTGAAAAACCATATTCTAATCAAAATAAAATAAAAGAAATGTAATA
1 AGGTTGAAAAACCTTATTCTAATCAAAATAAAATAAAAGAAATGTAATA
* *
287949 AGGTTGAAAAACTTTATCCTAATCAAAATAAAATAAAAGA
1 AGGTTGAAAAACCTTATTCTAATCAAAATAAAATAAAAGA
287989 TGTAATTTTA
Statistics
Matches: 79, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
49 73 0.92
50 6 0.08
ACGTcount: A:0.52, C:0.09, G:0.13, T:0.26
Consensus pattern (49 bp):
AGGTTGAAAAACCTTATTCTAATCAAAATAAAATAAAAGAAATGTAATA
Found at i:292057 original size:8 final size:8
Alignment explanation
Indices: 292044--292070 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
292034 AAAAATAATT
292044 TTCTCTTC
1 TTCTCTTC
292052 TTCTCTTC
1 TTCTCTTC
292060 TTCTCTTC
1 TTCTCTTC
292068 TTC
1 TTC
292071 ATCCACTCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (8 bp):
TTCTCTTC
Found at i:292880 original size:26 final size:26
Alignment explanation
Indices: 292850--292948 Score: 87
Period size: 26 Copynumber: 3.9 Consensus size: 26
292840 GCAAGCTAGT
292850 AAGCGTAAACACATAAATAAGCTGA-
1 AAGCGTAAACACATAAATAAGCTGAC
** ** *
292875 AGAGCGT-AA-ATGTGTACAAGCTGAC
1 A-AGCGTAAACACATAAATAAGCTGAC
* **
292900 AAGCGTAAACGCATAAATAAATTGAC
1 AAGCGTAAACACATAAATAAGCTGAC
*
292926 AAGCGTAAACGCATAAATAAGCT
1 AAGCGTAAACACATAAATAAGCT
292949 AATAATTATA
Statistics
Matches: 55, Mismatches: 15, Indels: 7
0.71 0.19 0.09
Matches are distributed among these distances:
24 15 0.27
25 6 0.11
26 34 0.62
ACGTcount: A:0.46, C:0.16, G:0.19, T:0.18
Consensus pattern (26 bp):
AAGCGTAAACACATAAATAAGCTGAC
Found at i:292916 original size:50 final size:50
Alignment explanation
Indices: 292761--292919 Score: 180
Period size: 50 Copynumber: 3.2 Consensus size: 50
292751 CATACATATA
* * * *
292761 ATAATATAAGCTGACGAGCGTAAACATGTGT--AAGTTAGCGAGCGTAAATGC
1 ATAA-ATAAGCTGAAGAGCGT-AA-ATGTGTACAAGCTAGCAAGCGTAAACGC
* * * * *
292812 ATAATTAAGCTGATGAGCGTAAATGTGTGCAAGCTAGTAAGCGTAAACAC
1 ATAAATAAGCTGAAGAGCGTAAATGTGTACAAGCTAGCAAGCGTAAACGC
292862 ATAAATAAGCTGAAGAGCGTAAATGTGTACAAGCT-GACAAGCGTAAACGC
1 ATAAATAAGCTGAAGAGCGTAAATGTGTACAAGCTAG-CAAGCGTAAACGC
292912 ATAAATAA
1 ATAAATAA
292920 ATTGACAAGC
Statistics
Matches: 93, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
48 6 0.06
49 3 0.03
50 80 0.86
51 4 0.04
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.22
Consensus pattern (50 bp):
ATAAATAAGCTGAAGAGCGTAAATGTGTACAAGCTAGCAAGCGTAAACGC
Found at i:294048 original size:11 final size:11
Alignment explanation
Indices: 294032--294056 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
294022 AATTGATTTC
294032 AAATGATTTTA
1 AAATGATTTTA
294043 AAATGATTTTA
1 AAATGATTTTA
294054 AAA
1 AAA
294057 CCTCTAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATGATTTTA
Found at i:296299 original size:20 final size:20
Alignment explanation
Indices: 296274--296329 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
296264 AAAATTACAA
296274 AAAAATAATTTTAAAAAATT
1 AAAAATAATTTTAAAAAATT
*
296294 AAAAATAATTTT-TAAAATT
1 AAAAATAATTTTAAAAAATT
*
296313 CAAAAT-ATTTATAAAAA
1 AAAAATAATTT-TAAAAA
296330 TTCTAAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
18 4 0.13
19 12 0.39
20 15 0.48
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAAATAATTTTAAAAAATT
Found at i:296329 original size:19 final size:19
Alignment explanation
Indices: 296283--296340 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
296273 AAAAAATAAT
*
296283 TTTA-AAAAATTAAAAATAA
1 TTTATAAAAATTCAAAAT-A
*
296302 TTT-TTAAAATTCAAAATA
1 TTTATAAAAATTCAAAATA
296320 TTTATAAAAATTCTAAAATA
1 TTTATAAAAATTC-AAAATA
296340 T
1 T
296341 GTATTTTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
18 4 0.12
19 22 0.67
20 7 0.21
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (19 bp):
TTTATAAAAATTCAAAATA
Found at i:296610 original size:23 final size:23
Alignment explanation
Indices: 296566--296612 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
296556 TGTAACAAGA
**
296566 TTTTAATTTAACATTATTAATTT
1 TTTTAATTTAACATTAACAATTT
296589 TTTTAATTTAAC-TTGAACAATTT
1 TTTTAATTTAACATT-AACAATTT
296612 T
1 T
296613 ATTCGATTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 2 0.10
23 19 0.90
ACGTcount: A:0.34, C:0.06, G:0.02, T:0.57
Consensus pattern (23 bp):
TTTTAATTTAACATTAACAATTT
Found at i:298985 original size:24 final size:24
Alignment explanation
Indices: 298932--298985 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
298922 AATTTGTAGG
*
298932 TTAAATAAATTATACTAATAAATG
1 TTAAATAAATTATACTAATAAATA
* *
298956 TAAAATATATTATACTAATAAATA
1 TTAAATAAATTATACTAATAAATA
298980 TTAAAT
1 TTAAAT
298986 TTTCTAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.39
Consensus pattern (24 bp):
TTAAATAAATTATACTAATAAATA
Found at i:305174 original size:17 final size:17
Alignment explanation
Indices: 305141--305185 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
305131 CATTAAATTA
*
305141 CAATGACAAATGGAAATG
1 CAATGAC-AATGCAAATG
305159 CAATGACAATGCAAATG
1 CAATGACAATGCAAATG
* *
305176 TAGTGACAAT
1 CAATGACAAT
305186 TAAAATGTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 17 0.71
18 7 0.29
ACGTcount: A:0.47, C:0.13, G:0.20, T:0.20
Consensus pattern (17 bp):
CAATGACAATGCAAATG
Found at i:311733 original size:18 final size:18
Alignment explanation
Indices: 311691--311725 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
311681 AACTTGTGGC
* *
311691 TGCATCTAGTTGTATGAA
1 TGCATCTAGTTCTACGAA
311709 TGCATCTAGTTCTACGA
1 TGCATCTAGTTCTACGA
311726 TAGCATCTGA
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:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (18 bp):
TGCATCTAGTTCTACGAA
Found at i:313381 original size:24 final size:23
Alignment explanation
Indices: 313349--313395 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
313339 AATTAATCTA
*
313349 TCAATGCAAACGTAAAATAAATTG
1 TCAAAGCAAA-GTAAAATAAATTG
* *
313373 TCAAAGCAAATTAAGATAAATTG
1 TCAAAGCAAAGTAAAATAAATTG
313396 AATAATTGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.51, C:0.11, G:0.13, T:0.26
Consensus pattern (23 bp):
TCAAAGCAAAGTAAAATAAATTG
Found at i:318273 original size:49 final size:49
Alignment explanation
Indices: 318216--318312 Score: 185
Period size: 49 Copynumber: 2.0 Consensus size: 49
318206 GTCACGACAC
318216 AGGACCTGGTGTGTCGCGACATCGACCCTTGGATAAGGATCTCACACTA
1 AGGACCTGGTGTGTCGCGACATCGACCCTTGGATAAGGATCTCACACTA
*
318265 AGGACCTGGTGTGTCGTGACATCGACCCTTGGATAAGGATCTCACACT
1 AGGACCTGGTGTGTCGCGACATCGACCCTTGGATAAGGATCTCACACT
318313 TAATGAAGGG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.24, C:0.26, G:0.27, T:0.24
Consensus pattern (49 bp):
AGGACCTGGTGTGTCGCGACATCGACCCTTGGATAAGGATCTCACACTA
Found at i:318325 original size:49 final size:49
Alignment explanation
Indices: 318223--318325 Score: 154
Period size: 49 Copynumber: 2.1 Consensus size: 49
318213 CACAGGACCT
**
318223 GGTGTGTCGCGACATCGACCCTTGGATAAGGATCTCACACTAAGGACCT
1 GGTGTGTCGCGACATCGACCCTTGGATAAGGATCTCACACTAAGGACAG
* *
318272 GGTGTGTCGTGACATCGACCCTTGGATAAGGATCTCACACTTAATGA-AG
1 GGTGTGTCGCGACATCGACCCTTGGATAAGGATCTCACAC-TAAGGACAG
318321 GGTGT
1 GGTGT
318326 TTTGGTCTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
49 44 0.90
50 5 0.10
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (49 bp):
GGTGTGTCGCGACATCGACCCTTGGATAAGGATCTCACACTAAGGACAG
Found at i:333917 original size:43 final size:43
Alignment explanation
Indices: 333867--333955 Score: 169
Period size: 43 Copynumber: 2.1 Consensus size: 43
333857 ATAGAAAAGG
333867 CCACTCTTTTTGCCTTAGTGCACCATTGCATTTCTCGAAAGAT
1 CCACTCTTTTTGCCTTAGTGCACCATTGCATTTCTCGAAAGAT
*
333910 CCACTCTTTTTGCCTTAGTGCACCGTTGCATTTCTCGAAAGAT
1 CCACTCTTTTTGCCTTAGTGCACCATTGCATTTCTCGAAAGAT
333953 CCA
1 CCA
333956 AGCAACTACA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.20, C:0.29, G:0.15, T:0.36
Consensus pattern (43 bp):
CCACTCTTTTTGCCTTAGTGCACCATTGCATTTCTCGAAAGAT
Found at i:342470 original size:16 final size:15
Alignment explanation
Indices: 342451--342494 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
342441 AATTTAAAAT
*
342451 AAATTAAAAAGTTAA
1 AAATTAAAAAATTAA
342466 CAAATTAAATAAATTAA
1 -AAATTAAA-AAATTAA
*
342483 AAATTAGAAAAT
1 AAATTAAAAAAT
342495 AATTTTCTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 4 0.16
16 15 0.60
17 6 0.24
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (15 bp):
AAATTAAAAAATTAA
Found at i:342481 original size:25 final size:25
Alignment explanation
Indices: 342428--342488 Score: 88
Period size: 25 Copynumber: 2.4 Consensus size: 25
342418 ATTAATTAGT
*
342428 TTAAAATATTAACAATTTAAAATAAA
1 TTAAAA-ATTAACAAATTAAAATAAA
342454 TTAAAAAGTTAACAAATT-AAATAAA
1 TTAAAAA-TTAACAAATTAAAATAAA
342479 TTAAAAATTA
1 TTAAAAATTA
342489 GAAAATAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
24 3 0.09
25 15 0.45
26 15 0.45
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (25 bp):
TTAAAAATTAACAAATTAAAATAAA
Found at i:352411 original size:21 final size:21
Alignment explanation
Indices: 352387--352446 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 21
352377 TAGTTGCATG
352387 ACTTGTATTGATAGAAATTAC
1 ACTTGTATTGATAGAAATTAC
* * * *
352408 ACTTGTACTGGTAGAACTTGC
1 ACTTGTATTGATAGAAATTAC
** *
352429 ACAGGTATCGATAGAAAT
1 ACTTGTATTGATAGAAAT
352447 CTGTAGTGCT
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32
Consensus pattern (21 bp):
ACTTGTATTGATAGAAATTAC
Found at i:357054 original size:13 final size:13
Alignment explanation
Indices: 357038--357100 Score: 60
Period size: 13 Copynumber: 4.8 Consensus size: 13
357028 TAGTAAACAT
357038 TTTTTTTTTCTTC
1 TTTTTTTTTCTTC
*
357051 TTTTCTTTTC-TC
1 TTTTTTTTTCTTC
357063 TTTTATTTTT-TTC
1 TTTT-TTTTTCTTC
*
357076 TTTCTTTTTC-TC
1 TTTTTTTTTCTTC
357088 ATTTTCTTTTTCT
1 -TTTT-TTTTTCT
357101 AAGTGACTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
12 13 0.32
13 21 0.52
14 6 0.15
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTTTTTTCTTC
Done.