Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold81
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: 1151237
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.32
Warning! 79344 characters in sequence are not A, C, G, or T
File 9 of 9
Found at i:991906 original size:16 final size:16
Alignment explanation
Indices: 991866--991908 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
991856 TTATTTTGAG
*
991866 TTCAAATCATTCCAAA
1 TTCAAATTATTCCAAA
* * *
991882 TTTAGATTATTCTAAA
1 TTCAAATTATTCCAAA
991898 TTCAAATTATT
1 TTCAAATTATT
991909 TTTAAGATCA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.40, C:0.14, G:0.02, T:0.44
Consensus pattern (16 bp):
TTCAAATTATTCCAAA
Found at i:992990 original size:21 final size:21
Alignment explanation
Indices: 992966--993009 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
992956 ATAATTTAAA
992966 ACTCCTAATTATGATCTTTGC
1 ACTCCTAATTATGATCTTTGC
992987 ACTCCTAATTATGATCTTTGC
1 ACTCCTAATTATGATCTTTGC
993008 AC
1 AC
993010 GAAAGTGGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.25, G:0.09, T:0.41
Consensus pattern (21 bp):
ACTCCTAATTATGATCTTTGC
Found at i:994371 original size:99 final size:99
Alignment explanation
Indices: 994195--994394 Score: 391
Period size: 99 Copynumber: 2.0 Consensus size: 99
994185 GTTACTTATC
994195 CAATGGTTGGAAGCAACTTGCATATTCATGGATAATTTTAAAAGGAATACAAGTTTCCACCTTAT
1 CAATGGTTGGAAGCAACTTGCATATTCATGGATAATTTTAAAAGGAATACAAGTTTCCACCTTAT
*
994260 TTTGCACCACCCCTCGGTTCGTCGGAGTCGGAGT
66 TTTGCACAACCCCTCGGTTCGTCGGAGTCGGAGT
994294 CAATGGTTGGAAGCAACTTGCATATTCATGGATAATTTTAAAAGGAATACAAGTTTCCACCTTAT
1 CAATGGTTGGAAGCAACTTGCATATTCATGGATAATTTTAAAAGGAATACAAGTTTCCACCTTAT
994359 TTTGCACAACCCCTCGGTTCGTCGGAGTCGGAGT
66 TTTGCACAACCCCTCGGTTCGTCGGAGTCGGAGT
994393 CA
1 CA
994395 CTAGCAGTGT
Statistics
Matches: 100, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
99 100 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (99 bp):
CAATGGTTGGAAGCAACTTGCATATTCATGGATAATTTTAAAAGGAATACAAGTTTCCACCTTAT
TTTGCACAACCCCTCGGTTCGTCGGAGTCGGAGT
Found at i:994468 original size:2 final size:2
Alignment explanation
Indices: 994461--994491 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
994451 CCCTACTTTC
994461 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
994492 TTACCTGGGT
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:996511 original size:18 final size:17
Alignment explanation
Indices: 996461--996512 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
996451 TTTACACATG
996461 AAATAAATTTTATAGATTA
1 AAAT-AATTTTATA-ATTA
* *
996480 ATATAAATTT-TAATTA
1 AAATAATTTTATAATTA
996496 AAATATATTTTATAATT
1 AAATA-ATTTTATAATT
996513 TTATTTATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
16 8 0.30
17 6 0.22
18 10 0.37
19 3 0.11
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (17 bp):
AAATAATTTTATAATTA
Found at i:997116 original size:22 final size:23
Alignment explanation
Indices: 997075--997118 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
997065 ATTTTTTAAT
*
997075 TTTTTTTAAAAAATAATAATTAGA
1 TTTTATTAAAAAAT-ATAATTAGA
997099 TTTTATTAAAAAAT-TAATTA
1 TTTTATTAAAAAATATAATTA
997119 AATTAGTCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
24 13 0.68
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
TTTTATTAAAAAATATAATTAGA
Found at i:1001324 original size:20 final size:21
Alignment explanation
Indices: 1001274--1001324 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
1001264 ATTTTTTTAG
1001274 ATTTTTAATATATTTAATAAAT
1 ATTTTTAA-ATATTTAATAAAT
* *
1001296 ATTTATAAATA-TTAATTAAT
1 ATTTTTAAATATTTAATAAAT
*
1001316 TTTTTTAAA
1 ATTTTTAAA
1001325 ATAAAAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 15 0.60
21 3 0.12
22 7 0.28
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTTTTAAATATTTAATAAAT
Found at i:1001766 original size:2 final size:2
Alignment explanation
Indices: 1001759--1001797 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1001749 ATCTATGGAC
1001759 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1001798 AGATTAAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1002292 original size:2 final size:2
Alignment explanation
Indices: 1002285--1002311 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1002275 CTCTATCTTA
1002285 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
1002312 ATAAAGGGTT
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:1002872 original size:21 final size:20
Alignment explanation
Indices: 1002847--1002888 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
1002837 AATTTTATTC
1002847 TTGAAATACTAATTACAAAAA
1 TTGAAAT-CTAATTACAAAAA
*
1002868 TTGAACTCTAATTACAAAAA
1 TTGAAATCTAATTACAAAAA
1002888 T
1 T
1002889 AAAAACTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.52, C:0.12, G:0.05, T:0.31
Consensus pattern (20 bp):
TTGAAATCTAATTACAAAAA
Found at i:1002895 original size:21 final size:20
Alignment explanation
Indices: 1002855--1002892 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1002845 TCTTGAAATA
**
1002855 CTAATTACAAAAATTGAACT
1 CTAATTACAAAAATAAAACT
1002875 CTAATTACAAAAATAAAA
1 CTAATTACAAAAATAAAA
1002893 ACTACAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.58, C:0.13, G:0.03, T:0.26
Consensus pattern (20 bp):
CTAATTACAAAAATAAAACT
Found at i:1003392 original size:20 final size:20
Alignment explanation
Indices: 1003367--1003425 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 20
1003357 ACATGCTTTT
1003367 TGATATTTGAATATTATTTA
1 TGATATTTGAATATTATTTA
*
1003387 TGATATATATATATATATTATTTA
1 TGATAT-T-T-GA-ATATTATTTA
1003411 TGATATTTGAATATT
1 TGATATTTGAATATT
1003426 CTTAATTAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
20 11 0.33
21 2 0.06
22 2 0.06
23 2 0.06
24 16 0.48
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.54
Consensus pattern (20 bp):
TGATATTTGAATATTATTTA
Found at i:1003700 original size:19 final size:18
Alignment explanation
Indices: 1003678--1003713 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1003668 ATTAAAACTT
1003678 TTTTAATTATTTAATATTA
1 TTTTAATT-TTTAATATTA
*
1003697 TTTTAATTTTTTATATT
1 TTTTAATTTTTAATATT
1003714 TAATATATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTTAATTTTTAATATTA
Found at i:1004242 original size:16 final size:16
Alignment explanation
Indices: 1004208--1004241 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
1004198 TGATTAATAA
1004208 TTTTAATATTTAATTT
1 TTTTAATATTTAATTT
1004224 TTTTAATA-TT-ATTT
1 TTTTAATATTTAATTT
1004238 TTTT
1 TTTT
1004242 TCCGAGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
15 2 0.11
16 8 0.44
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTAATATTTAATTT
Found at i:1005232 original size:15 final size:15
Alignment explanation
Indices: 1005212--1005245 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1005202 ATTTTAGATC
* *
1005212 AAATATGTATAATAT
1 AAATATATATAAAAT
1005227 AAATATATATAAAAT
1 AAATATATATAAAAT
1005242 AAAT
1 AAAT
1005246 TATTAATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (15 bp):
AAATATATATAAAAT
Found at i:1005276 original size:22 final size:21
Alignment explanation
Indices: 1005251--1005315 Score: 66
Period size: 20 Copynumber: 3.2 Consensus size: 21
1005241 TAAATTATTA
1005251 ATATATTAAATTTTATATAAAT
1 ATATATT-AATTTTATATAAAT
*
1005273 ATATAATAA-TTTA-A-AAAT
1 ATATATTAATTTTATATAAAT
* *
1005291 A-ATTTTAATATTATATAAAT
1 ATATATTAATTTTATATAAAT
1005311 ATATA
1 ATATA
1005316 AATTATTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 9
0.71 0.10 0.19
Matches are distributed among these distances:
17 5 0.15
18 8 0.24
19 2 0.06
20 9 0.26
21 4 0.12
22 6 0.18
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
ATATATTAATTTTATATAAAT
Found at i:1005322 original size:20 final size:20
Alignment explanation
Indices: 1005240--1005323 Score: 67
Period size: 19 Copynumber: 4.5 Consensus size: 20
1005230 TATATATAAA
1005240 ATAAATTATTA-AT--ATAT
1 ATAAATTATTATATAAATAT
1005257 -TAAATT-TTATATAAATAT
1 ATAAATTATTATATAAATAT
* *
1005275 AT-AATAATT-TAAAAATAAT
1 ATAAATTATTATATAAAT-AT
* *
1005294 TTTAA-TATTATATAAATAT
1 ATAAATTATTATATAAATAT
1005313 ATAAATTATTA
1 ATAAATTATTA
1005324 AATTTATGAA
Statistics
Matches: 51, Mismatches: 7, Indels: 15
0.70 0.10 0.21
Matches are distributed among these distances:
15 3 0.06
16 8 0.16
18 13 0.25
19 14 0.27
20 13 0.25
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATAAATTATTATATAAATAT
Found at i:1009191 original size:5 final size:5
Alignment explanation
Indices: 1009181--1009230 Score: 59
Period size: 5 Copynumber: 10.0 Consensus size: 5
1009171 TGTAATTTTA
*
1009181 AATAT AATAT AAT-T -ATAT AATAT AAATAT AATAT AAAAT ATATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT -AATAT AATAT AATAT A-ATAT AATAT
1009231 GAAAAATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
3 2 0.05
4 2 0.05
5 26 0.67
6 9 0.23
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:1009209 original size:11 final size:11
Alignment explanation
Indices: 1009179--1009258 Score: 71
Period size: 11 Copynumber: 7.5 Consensus size: 11
1009169 TTTGTAATTT
1009179 TAAATATAATA
1 TAAATATAATA
1009190 TAATTATATAATA
1 TAA--ATATAATA
1009203 TAAATATAATA
1 TAAATATAATA
1009214 TAAA-AT-ATA
1 TAAATATAATA
*
1009223 TATAATATGA-A
1 TA-AATATAATA
* *
1009234 -AAATTTTATA
1 TAAATATAATA
1009244 TAAATAT-ATA
1 TAAATATAATA
1009254 TAAAT
1 TAAAT
1009259 TATACGAATT
Statistics
Matches: 59, Mismatches: 3, Indels: 15
0.77 0.04 0.19
Matches are distributed among these distances:
9 10 0.17
10 14 0.24
11 23 0.39
12 1 0.02
13 11 0.19
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (11 bp):
TAAATATAATA
Found at i:1009577 original size:20 final size:19
Alignment explanation
Indices: 1009551--1009599 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
1009541 ACAGTTATTT
***
1009551 ATAAATTTTAATGTATAAA
1 ATAAATTTTAAAAAATAAA
*
1009570 ATTAAATTATAAAAAATAAA
1 A-TAAATTTTAAAAAATAAA
1009590 ATAAATTTTA
1 ATAAATTTTA
1009600 TTTTAAAAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
ATAAATTTTAAAAAATAAA
Found at i:1009861 original size:13 final size:14
Alignment explanation
Indices: 1009837--1010007 Score: 63
Period size: 16 Copynumber: 12.0 Consensus size: 14
1009827 ATTTAAATAT
*
1009837 TTATATTTTATTTA
1 TTATATTATATTTA
1009851 TT-TATTATATTATA
1 TTATATTATATT-TA
1009865 TTATAATTATATTTAAA
1 TTAT-ATTATATTT--A
* *
1009882 ATATTTTATATTTA
1 TTATATTATATTTA
*
1009896 -TATA-AAT-TTTA
1 TTATATTATATTTA
*
1009907 ATATATTAATAATTTA
1 TTATATT-AT-ATTTA
*
1009923 -TATTATATAAATTT-
1 TTA-TAT-TATATTTA
* * *
1009937 TAAAAATATATTTA
1 TTATATTATATTTA
1009951 TATAATATTATATTT-
1 T-T-ATATTATATTTA
* *
1009966 TAATTATTATATATA
1 TTA-TATTATATTTA
*
1009981 -TGTATTATATTTA
1 TTATATTATATTTA
1009994 -TATAATTATATTTA
1 TTAT-ATTATATTTA
1010008 AACTTTTCAT
Statistics
Matches: 118, Mismatches: 20, Indels: 38
0.67 0.11 0.22
Matches are distributed among these distances:
11 4 0.03
12 6 0.05
13 30 0.25
14 30 0.25
15 10 0.08
16 33 0.28
17 5 0.04
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (14 bp):
TTATATTATATTTA
Found at i:1009906 original size:27 final size:28
Alignment explanation
Indices: 1009876--1009953 Score: 88
Period size: 32 Copynumber: 2.6 Consensus size: 28
1009866 TATAATTATA
1009876 TTTAAAATAT-TTTATATTTATATAAAT
1 TTTAAAATATATTTATATTTATATAAAT
1009903 TTTAATATATTAATAATTTATA-TTATATAAAT
1 TTTAA-A-A-T-AT-ATTTATATTTATATAAAT
1009935 TTTAAAAATATATTTATAT
1 TTT-AAAATATATTTATAT
1009954 AATATTATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
27 5 0.12
28 8 0.19
29 3 0.07
30 2 0.05
31 3 0.07
32 14 0.33
33 8 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
TTTAAAATATATTTATATTTATATAAAT
Found at i:1009918 original size:18 final size:17
Alignment explanation
Indices: 1009871--1009938 Score: 67
Period size: 16 Copynumber: 4.2 Consensus size: 17
1009861 TATATTATAA
1009871 TTATATTTA-A-AATATT
1 TTATATTTATATAA-ATT
1009887 TTATATTTATATAAATT
1 TTATATTTATATAAATT
1009904 TTAATATATTA-AT-AA-T
1 TT-ATAT-TTATATAAATT
1009920 TTATA-TTATATAAATT
1 TTATATTTATATAAATT
1009936 TTA
1 TTA
1009939 AAAATATATT
Statistics
Matches: 45, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
13 3 0.07
14 2 0.04
15 5 0.11
16 16 0.36
17 8 0.18
18 8 0.18
19 3 0.07
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTATATTTATATAAATT
Found at i:1009924 original size:60 final size:61
Alignment explanation
Indices: 1009832--1009996 Score: 146
Period size: 60 Copynumber: 2.7 Consensus size: 61
1009822 TTATAATTTA
* *
1009832 AATATTTATATTTTATTTATT-TATTATATTATATTATAATTATATTT-AAAATAT-TTTATAT
1 AATA-TTAAATTTTAATTATTATA-TAT-TTATATTATAATTATATTTAAAAATATATTTATAT
* *
1009893 -TTATATAAATTTTAATATATTA-ATAATTTATATTAT-A-TAAATTTTAAAAATATATTTATAT
1 AATAT-TAAATTTTAAT-TATTATAT-ATTTATATTATAATTATA-TTTAAAAATATATTTATAT
* * * *
1009954 AATATTATATTTTAATTATTATATATATGTATTATATTTATAT
1 AATATTAAATTTTAATTATTATATATTTATATTATAATTATAT
1009997 AATTATATTT
Statistics
Matches: 83, Mismatches: 10, Indels: 22
0.72 0.09 0.19
Matches are distributed among these distances:
58 3 0.04
59 5 0.06
60 42 0.51
61 27 0.33
62 6 0.07
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (61 bp):
AATATTAAATTTTAATTATTATATATTTATATTATAATTATATTTAAAAATATATTTATAT
Found at i:1009929 original size:65 final size:68
Alignment explanation
Indices: 1009823--1010009 Score: 177
Period size: 61 Copynumber: 2.9 Consensus size: 68
1009813 TTTATTTTTT
* *
1009823 TATAAT-TTAAATATTTATATT-TTATTTAT-TTATTATATTATATTATAATTATATTTAAAATA
1 TATAATATTAAAT-TTTA-ATTATTATATATAGTATTATATTATA-TATAATTATATTTAAAATA
1009885 T-TTTA
63 TATTTA
* *
1009890 TAT-TTATATAAATTTTAATATATTA-ATA-A-T-TTATATTATATA-AA-T-T-TTAAAAATAT
1 TATAATAT-TAAATTTTAAT-TATTATATATAGTATTATATTATATATAATTATATTTAAAATAT
1009946 ATTTA
64 ATTTA
*
1009951 TATAATATTATATTTTAATTATTATATATATGTATTATATT-TATATAATTATATTTAAA
1 TATAATATTAAATTTTAATTATTATATATA-GTATTATATTATATATAATTATATTTAAA
1010010 CTTTTCATTT
Statistics
Matches: 98, Mismatches: 6, Indels: 31
0.73 0.04 0.23
Matches are distributed among these distances:
60 14 0.14
61 21 0.21
62 5 0.05
63 2 0.02
64 7 0.07
65 19 0.19
66 5 0.05
67 12 0.12
68 13 0.13
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (68 bp):
TATAATATTAAATTTTAATTATTATATATAGTATTATATTATATATAATTATATTTAAAATATAT
TTA
Found at i:1010344 original size:6 final size:6
Alignment explanation
Indices: 1010330--1010383 Score: 58
Period size: 6 Copynumber: 9.3 Consensus size: 6
1010320 TAATTTAATT
* **
1010330 TTTATA TTTAAA TTTAAA TTTAAA TTT--A TTTATG TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
1010376 TTAAAA TT
1 TTTAAA TT
1010384 AATTTTTTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
4 4 0.10
6 37 0.90
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:1010359 original size:22 final size:22
Alignment explanation
Indices: 1010334--1010377 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1010324 TTAATTTTTA
1010334 TATTTAAATTTAAATTTAAATT
1 TATTTAAATTTAAATTTAAATT
**
1010356 TATTTATGTTTAAATTTAAATT
1 TATTTAAATTTAAATTTAAATT
1010378 AAAATTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
TATTTAAATTTAAATTTAAATT
Found at i:1010362 original size:28 final size:28
Alignment explanation
Indices: 1010330--1010388 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
1010320 TAATTTAATT
* *
1010330 TTTATATTTAAATTTAAATTTAAATTTA
1 TTTATATTTAAATTTAAATTAAAATTAA
*
1010358 TTTATGTTTAAATTTAAATTAAAATTAA
1 TTTATATTTAAATTTAAATTAAAATTAA
1010386 TTT
1 TTT
1010389 TTTTATAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (28 bp):
TTTATATTTAAATTTAAATTAAAATTAA
Found at i:1010986 original size:10 final size:10
Alignment explanation
Indices: 1010971--1010995 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1010961 TGTAAATAAT
1010971 AATTAATTTA
1 AATTAATTTA
1010981 AATTAATTTA
1 AATTAATTTA
1010991 AATTA
1 AATTA
1010996 TTAAAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
AATTAATTTA
Found at i:1011253 original size:19 final size:19
Alignment explanation
Indices: 1011231--1011277 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
1011221 AAAAATATAT
1011231 TAATATTAATTAAATTTTA
1 TAATATTAATTAAATTTTA
* *
1011250 TAATATTTTATTATATTTTA
1 TAATA-TTAATTAAATTTTA
1011270 -AATATTAA
1 TAATATTAA
1011278 ATCAAAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 3 0.12
19 9 0.38
20 12 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TAATATTAATTAAATTTTA
Found at i:1012740 original size:13 final size:13
Alignment explanation
Indices: 1012722--1012747 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1012712 CAATTTTTTG
1012722 TGTATCGATACAT
1 TGTATCGATACAT
1012735 TGTATCGATACAT
1 TGTATCGATACAT
1012748 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1012832 original size:20 final size:20
Alignment explanation
Indices: 1012807--1012879 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1012797 CATCCTTTTT
1012807 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
1012827 ATGTATCGATACATTTTTTTC
1 ATGTATCGATACA-TTGCAAC
1012848 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1012868 ATGTATCGATAC
1 ATGTATCGATAC
1012880 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:1012852 original size:21 final size:21
Alignment explanation
Indices: 1012786--1012862 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
1012776 CTGCCAAGAA
*
1012786 ATGTATCGATACATCCTTTTT-
1 ATGTATCGATACAT-TTTTTTC
****
1012807 ATGTATCGATACA-TTGCAAC
1 ATGTATCGATACATTTTTTTC
1012827 ATGTATCGATACATTTTTTTC
1 ATGTATCGATACATTTTTTTC
1012848 ATGTATCGATACATT
1 ATGTATCGATACATT
1012863 GCAACATGTA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
19 1 0.02
20 13 0.29
21 31 0.69
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.43
Consensus pattern (21 bp):
ATGTATCGATACATTTTTTTC
Found at i:1012852 original size:41 final size:41
Alignment explanation
Indices: 1012786--1012879 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
1012776 CTGCCAAGAA
1012786 ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
*
1012827 ATGTATCGATACAT-TTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCCTTTTT-ATGTATCGATACATTGCAAC
1012868 ATGTATCGATAC
1 ATGTATCGATAC
1012880 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 5 0.10
41 46 0.90
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
Found at i:1013487 original size:48 final size:48
Alignment explanation
Indices: 1013432--1013527 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
1013422 AAATTTTACG
1013432 AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
1 AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
1013480 AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
1 AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
1013528 TTATCTCCCC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.25, C:0.29, G:0.08, T:0.38
Consensus pattern (48 bp):
AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
Found at i:1015009 original size:13 final size:13
Alignment explanation
Indices: 1014991--1015029 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1014981 ATAATCACCC
*
1014991 TGTATCGATACAG
1 TGTATCGATACAA
1015004 TGTATCGATACAA
1 TGTATCGATACAA
1015017 TGTATCGATACAA
1 TGTATCGATACAA
1015030 GGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1017128 original size:15 final size:15
Alignment explanation
Indices: 1017108--1017138 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1017098 ATTTCGTTTG
*
1017108 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1017123 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1017138 G
1 G
1017139 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1021218 original size:13 final size:13
Alignment explanation
Indices: 1021200--1021225 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1021190 CAATTTTTTG
1021200 TGTATCGATACAT
1 TGTATCGATACAT
1021213 TGTATCGATACAT
1 TGTATCGATACAT
1021226 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1021310 original size:20 final size:20
Alignment explanation
Indices: 1021285--1021357 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1021275 CATCCTTTTT
1021285 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
1021305 ATGTATCGATACATTTTTTTC
1 ATGTATCGATACA-TTGCAAC
1021326 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1021346 ATGTATCGATAC
1 ATGTATCGATAC
1021358 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:1021330 original size:21 final size:21
Alignment explanation
Indices: 1021264--1021340 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
1021254 CTGCCAAGAA
*
1021264 ATGTATCGATACATCCTTTTT-
1 ATGTATCGATACAT-TTTTTTC
****
1021285 ATGTATCGATACA-TTGCAAC
1 ATGTATCGATACATTTTTTTC
1021305 ATGTATCGATACATTTTTTTC
1 ATGTATCGATACATTTTTTTC
1021326 ATGTATCGATACATT
1 ATGTATCGATACATT
1021341 GCAACATGTA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
19 1 0.02
20 13 0.29
21 31 0.69
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.43
Consensus pattern (21 bp):
ATGTATCGATACATTTTTTTC
Found at i:1021330 original size:41 final size:41
Alignment explanation
Indices: 1021264--1021357 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
1021254 CTGCCAAGAA
1021264 ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
*
1021305 ATGTATCGATACAT-TTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCCTTTTT-ATGTATCGATACATTGCAAC
1021346 ATGTATCGATAC
1 ATGTATCGATAC
1021358 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 5 0.10
41 46 0.90
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
Found at i:1021811 original size:31 final size:32
Alignment explanation
Indices: 1021775--1021842 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 32
1021765 AACTCAAATG
* * *
1021775 TTAAATTCAATTAATTCAAACTC-AGAATAAT
1 TTAAATCCAATTAACTCAAACTCAAAAATAAT
* *
1021806 TTAAATCCGATTAACTCGAACTCAAAAATAAT
1 TTAAATCCAATTAACTCAAACTCAAAAATAAT
1021838 TTAAA
1 TTAAA
1021843 AATTTAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
31 19 0.61
32 12 0.39
ACGTcount: A:0.49, C:0.15, G:0.04, T:0.32
Consensus pattern (32 bp):
TTAAATCCAATTAACTCAAACTCAAAAATAAT
Found at i:1022278 original size:2 final size:2
Alignment explanation
Indices: 1022265--1022294 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1022255 CCGATGATAA
*
1022265 AT AT AA 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
1022295 GAAAAATGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1023282 original size:37 final size:37
Alignment explanation
Indices: 1023241--1023319 Score: 133
Period size: 37 Copynumber: 2.2 Consensus size: 37
1023231 AGGCCATATT
*
1023241 TCTTTCCTTAAAGGTCAAAGAGTCTAGGGATAATGGC
1 TCTTTCCTTAAAGGTCAAAGAGTCTAGGGACAATGGC
*
1023278 TCTTTCCTTAAAGGTCAAAGAGTCTGGGGACAATGGC
1 TCTTTCCTTAAAGGTCAAAGAGTCTAGGGACAATGGC
1023315 T-TTTC
1 TCTTTC
1023320 GGGCACTTTG
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
36 4 0.10
37 36 0.90
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.32
Consensus pattern (37 bp):
TCTTTCCTTAAAGGTCAAAGAGTCTAGGGACAATGGC
Found at i:1024535 original size:34 final size:34
Alignment explanation
Indices: 1024492--1024591 Score: 173
Period size: 34 Copynumber: 2.9 Consensus size: 34
1024482 GTAAAAACCA
1024492 CCATTTAATCAACAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAAGCTACCAAATCTC
*
1024526 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAAGCTACCAAATCTC
* *
1024560 CCATTTAGTCAACAATGGTAAACTACCAAATC
1 CCATTTAATCAACAATGGTAAGCTACCAAATC
1024592 ACCAAGTTTG
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 62 1.00
ACGTcount: A:0.39, C:0.25, G:0.09, T:0.27
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAAGCTACCAAATCTC
Found at i:1024793 original size:34 final size:34
Alignment explanation
Indices: 1024749--1024887 Score: 188
Period size: 34 Copynumber: 4.1 Consensus size: 34
1024739 AGTTTACCAT
* *
1024749 TGGGAAATTTGATAGCTTACCATTGTTGATTAAA
1 TGGGAGATTTGGTAGCTTACCATTGTTGATTAAA
*
1024783 TGGGAGATTTGGTAGCTTACCATTATTGATTAAA
1 TGGGAGATTTGGTAGCTTACCATTGTTGATTAAA
* * * *
1024817 TGGGTGATTTGGTGGTTTACCATTGTTGACTAAA
1 TGGGAGATTTGGTAGCTTACCATTGTTGATTAAA
* * *
1024851 TGAGAGATTTGGTAGGTTGCCATTGTTGATTAAA
1 TGGGAGATTTGGTAGCTTACCATTGTTGATTAAA
1024885 TGG
1 TGG
1024888 TGGTTTTTAC
Statistics
Matches: 90, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 90 1.00
ACGTcount: A:0.27, C:0.08, G:0.27, T:0.39
Consensus pattern (34 bp):
TGGGAGATTTGGTAGCTTACCATTGTTGATTAAA
Found at i:1025248 original size:19 final size:19
Alignment explanation
Indices: 1025192--1025254 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
1025182 TGGTTGTCGA
**
1025192 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
1025211 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
1025230 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
1025249 GTTACT
1 GGTACT
1025255 GTACACGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:1029386 original size:34 final size:34
Alignment explanation
Indices: 1029320--1029504 Score: 246
Period size: 34 Copynumber: 5.5 Consensus size: 34
1029310 AAGTGGGAGA
* *
1029320 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
1029353 ATTGTTGACTAAATGGGAAATTTGATAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1029387 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
1029421 ATTATTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
1029455 ATTGTTGACTAAATGAGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1029489 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1029505 TGGTTTTTAC
Statistics
Matches: 130, Mismatches: 21, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
33 13 0.10
34 117 0.90
ACGTcount: A:0.27, C:0.08, G:0.25, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:1033851 original size:19 final size:19
Alignment explanation
Indices: 1033837--1033873 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
1033827 ACAGTAGCCG
1033837 TATACGTGAATAGTACCTA
1 TATACGTGAATAGTACCTA
1033856 TATACGTGAATAGTACCT
1 TATACGTGAATAGTACCT
1033874 CGACAACCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (19 bp):
TATACGTGAATAGTACCTA
Found at i:1034225 original size:34 final size:34
Alignment explanation
Indices: 1034179--1034535 Score: 459
Period size: 34 Copynumber: 10.5 Consensus size: 34
1034169 GTAAAAACCA
*
1034179 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
1034213 CCATTTAGTCAACAATAGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
1034247 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
1034281 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
1034315 CCATTTAGTCAACAATGGTAAACTACCAAATCAC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
1034349 CATTATTTAATCAACAATGGCAACCTACCAAATCTC
1 C--CATTTAATCAACAATGGTAACCTACCAAATCTC
* *
1034385 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
1034419 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
1034453 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
1034487 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
1034520 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
1034536 TCTCCCACTT
Statistics
Matches: 282, Mismatches: 35, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
33 21 0.07
34 224 0.79
35 8 0.03
36 29 0.10
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:1034467 original size:172 final size:169
Alignment explanation
Indices: 1034177--1034535 Score: 682
Period size: 172 Copynumber: 2.1 Consensus size: 169
1034167 TGGTAAAAAC
1034177 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATAGTAAACCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATAGTAAACCACCAA
1034242 ATCACCCATTTAATCAATAATGGTAAGCTACCAAATCTCCCATTTAATCAACAATGGTAAGCTAC
66 ATCACCCATTTAATCAATAATGGTAAGCTACCAAATCTCCCATTTAATCAACAATGGTAAGCTAC
1034307 CAAATTTCCCATTTAGTCAACAATGGTAAACTACCAAAT
131 CAAATTTCCCATTTAGTCAACAATGGTAAACTACCAAAT
*
1034346 CACCATTATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCAC
1 CACC---ATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATAGTAAACCAC
1034411 CAAATCACCCATTTAATCAATAATGGTAAGCTACCAAATCTCCCATTTAATCAACAATGGTAAGC
63 CAAATCACCCATTTAATCAATAATGGTAAGCTACCAAATCTCCCATTTAATCAACAATGGTAAGC
1034476 TACCAAATTTCCCATTTAGTCAACAATGGTAAACTACCAAAT
128 TACCAAATTTCCCATTTAGTCAACAATGGTAAACTACCAAAT
1034518 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
1034536 TCTCCCACTT
Statistics
Matches: 186, Mismatches: 1, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
169 18 0.10
172 168 0.90
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (169 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATAGTAAACCACCAA
ATCACCCATTTAATCAATAATGGTAAGCTACCAAATCTCCCATTTAATCAACAATGGTAAGCTAC
CAAATTTCCCATTTAGTCAACAATGGTAAACTACCAAAT
Found at i:1038631 original size:19 final size:19
Alignment explanation
Indices: 1038609--1038665 Score: 96
Period size: 19 Copynumber: 3.0 Consensus size: 19
1038599 TACAGTAACC
*
1038609 GTATACTTGAATAGTACCT
1 GTATACGTGAATAGTACCT
1038628 GTATACGTGAATAGTACCT
1 GTATACGTGAATAGTACCT
*
1038647 ATATACGTGAATAGTACCT
1 GTATACGTGAATAGTACCT
1038666 CGACAACCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (19 bp):
GTATACGTGAATAGTACCT
Found at i:1039015 original size:34 final size:34
Alignment explanation
Indices: 1038969--1039153 Score: 257
Period size: 34 Copynumber: 5.5 Consensus size: 34
1038959 GTAAAAACCA
*
1038969 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
1039003 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
1039037 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
1039071 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
1039105 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
1039138 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
1039154 ATCATGCAAT
Statistics
Matches: 135, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
33 18 0.13
34 113 0.84
35 4 0.03
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:1041016 original size:14 final size:15
Alignment explanation
Indices: 1040999--1041027 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1040989 CTTTAATAAA
1040999 TAAATTTTAA-ATTT
1 TAAATTTTAATATTT
1041013 TAAATTTTAATATTT
1 TAAATTTTAATATTT
1041028 ATATTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TAAATTTTAATATTT
Found at i:1044824 original size:2 final size:2
Alignment explanation
Indices: 1044817--1044841 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1044807 AAAATCATCA
1044817 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1044842 AAGGGCAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1048371 original size:15 final size:15
Alignment explanation
Indices: 1048362--1048413 Score: 68
Period size: 15 Copynumber: 3.3 Consensus size: 15
1048352 TATTTATTTT
1048362 TTATAAATTTAAATA
1 TTATAAATTTAAATA
*
1048377 TTATAAATTTAAAAA
1 TTATAAATTTAAATA
*
1048392 TTTTAAAATTTAAAATA
1 TTAT-AAATTT-AAATA
1048409 TTATA
1 TTATA
1048414 TTTACTATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
15 17 0.55
16 7 0.23
17 7 0.23
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
TTATAAATTTAAATA
Found at i:1048818 original size:16 final size:16
Alignment explanation
Indices: 1048790--1048831 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
1048780 AATTATTATT
* *
1048790 TTATAATT-TTATTTT
1 TTATAATTAATATTTA
*
1048805 TTATTATTAATATTTA
1 TTATAATTAATATTTA
1048821 TTATAATTAAT
1 TTATAATTAAT
1048832 TGTAATAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTATAATTAATATTTA
Found at i:1048875 original size:27 final size:26
Alignment explanation
Indices: 1048812--1048890 Score: 65
Period size: 27 Copynumber: 3.0 Consensus size: 26
1048802 TTTTTATTAT
* *
1048812 TAATATTTATT-A-TAATTAATTGTAA
1 TAATATTAATTAATTAA-TAATTTTAA
* **
1048837 TAATATTTATTATATTCGTAATTTTAA
1 TAATATTAATTA-ATTAATAATTTTAA
1048864 TAA-ATATAATTAATTAATAATTTTAA
1 TAATAT-TAATTAATTAATAATTTTAA
1048890 T
1 T
1048891 TATAATTTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
25 11 0.25
26 15 0.34
27 17 0.39
28 1 0.02
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (26 bp):
TAATATTAATTAATTAATAATTTTAA
Found at i:1058655 original size:14 final size:15
Alignment explanation
Indices: 1058629--1058657 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1058619 AAATTTAGAT
1058629 TATAAAAAGAAGAAA
1 TATAAAAAGAAGAAA
1058644 TATAAAAA-AAGAAA
1 TATAAAAAGAAGAAA
1058658 AAAGGACCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.14
Consensus pattern (15 bp):
TATAAAAAGAAGAAA
Found at i:1062704 original size:17 final size:16
Alignment explanation
Indices: 1062684--1062743 Score: 59
Period size: 17 Copynumber: 3.6 Consensus size: 16
1062674 TATTAACATA
*
1062684 TAAAAATTTATATAAAT
1 TAAAAATATATA-AAAT
1062701 TAAAAATATATAAAAT
1 TAAAAATATATAAAAT
*
1062717 T-ATAATATAATAAAAT
1 TAAAAATAT-ATAAAAT
*
1062733 ATATAAATATA
1 -TAAAAATATA
1062744 GATTATTGAG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
15 6 0.17
16 12 0.33
17 13 0.36
18 5 0.14
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TAAAAATATATAAAAT
Found at i:1062711 original size:27 final size:27
Alignment explanation
Indices: 1062661--1062739 Score: 76
Period size: 27 Copynumber: 3.0 Consensus size: 27
1062651 TTTAAAATTT
** *
1062661 ATTTAATATAAATTATTAACATATAAAA
1 ATTT-ATATAAATTAAAAATATATAAAA
1062689 ATTTATATAAATTAAAAATATAT-AAA
1 ATTTATATAAATTAAAAATATATAAAA
1062715 A-TTATAATATAA-T-AAAATATATAAA
1 ATTTAT-ATA-AATTAAAAATATATAAA
1062740 TATAGATTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
25 13 0.29
26 10 0.22
27 18 0.40
28 4 0.09
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (27 bp):
ATTTATATAAATTAAAAATATATAAAA
Found at i:1062714 original size:10 final size:9
Alignment explanation
Indices: 1062603--1062743 Score: 72
Period size: 8 Copynumber: 16.4 Consensus size: 9
1062593 TTTATATGAT
1062603 TATAT-AAA
1 TATATAAAA
1062611 TATAATAAAA
1 TAT-ATAAAA
*
1062621 AAT-TAAAA
1 TATATAAAA
1062629 TATAATATAAA
1 TAT-ATA-AAA
1062640 TATAT-AAA
1 TATATAAAA
*
1062648 TATTTTAAAA
1 TA-TATAAAA
* **
1062658 TTTAT-TTA
1 TATATAAAA
*
1062666 -ATATAAAT
1 TATATAAAA
*
1062674 TAT-TAACA
1 TATATAAAA
1062682 TATA-AAAA
1 TATATAAAA
*
1062690 TTTATATAAA
1 TATATA-AAA
1062700 T-TA-AAAA
1 TATATAAAA
1062707 TATATAAAA
1 TATATAAAA
*
1062716 T-TATAATA
1 TATATAAAA
1062724 TA-ATAAAA
1 TATATAAAA
1062732 TATAT-AAA
1 TATATAAAA
1062740 TATA
1 TATA
1062744 GATTATTGAG
Statistics
Matches: 100, Mismatches: 17, Indels: 32
0.67 0.11 0.21
Matches are distributed among these distances:
7 7 0.07
8 52 0.52
9 18 0.18
10 17 0.17
11 6 0.06
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (9 bp):
TATATAAAA
Found at i:1062723 original size:15 final size:15
Alignment explanation
Indices: 1062692--1062743 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
1062682 TATAAAAATT
*
1062692 TATAT-AAATTAAAAA
1 TATATAAAATT-ATAA
1062707 TATATAAAATTATAA
1 TATATAAAATTATAA
1062722 TATAATAAAATATATAA
1 TAT-ATAAAAT-TATAA
1062739 -ATATA
1 TATATA
1062744 GATTATTGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
15 14 0.42
16 14 0.42
17 5 0.15
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TATATAAAATTATAA
Found at i:1064268 original size:2 final size:2
Alignment explanation
Indices: 1064261--1064289 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1064251 TAATTTTTCG
1064261 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1064290 TCCCATCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1065287 original size:25 final size:25
Alignment explanation
Indices: 1065249--1065320 Score: 72
Period size: 25 Copynumber: 2.8 Consensus size: 25
1065239 AAATATCGAT
1065249 TTAAATTTTAATTTAAAAAATAAATAA
1 TTAAA-TTT-ATTTAAAAAATAAATAA
** * *
1065276 TTAAATTTATTTTTATATTAAATAA
1 TTAAATTTATTTAAAAAATAAATAA
*
1065301 ATAAATTTATTTAAATAAAT
1 TTAAATTTATTTAAA-AAAT
1065321 TCAAAATTTT
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
25 25 0.71
26 5 0.14
27 5 0.14
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
TTAAATTTATTTAAAAAATAAATAA
Found at i:1070206 original size:2 final size:2
Alignment explanation
Indices: 1070199--1070235 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1070189 AAAGGAAAAG
1070199 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1070236 AAAAGGAACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1070981 original size:17 final size:17
Alignment explanation
Indices: 1070959--1070993 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1070949 ATAACAAAAA
1070959 TTAGGTACTATTAAGAG
1 TTAGGTACTATTAAGAG
1070976 TTAGGTACTATTAAGAG
1 TTAGGTACTATTAAGAG
1070993 T
1 T
1070994 ACCCTCGCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.06, G:0.23, T:0.37
Consensus pattern (17 bp):
TTAGGTACTATTAAGAG
Found at i:1079580 original size:22 final size:23
Alignment explanation
Indices: 1079541--1079588 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
1079531 TAAATTAATA
*
1079541 ATTTATTTATGTTTTTATAAAAT
1 ATTTATTTATATTTTTATAAAAT
*
1079564 ATTTATTT-TATTTTTATAATAT
1 ATTTATTTATATTTTTATAAAAT
1079586 ATT
1 ATT
1079589 ACATTTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (23 bp):
ATTTATTTATATTTTTATAAAAT
Found at i:1080108 original size:65 final size:65
Alignment explanation
Indices: 1080004--1080132 Score: 204
Period size: 65 Copynumber: 2.0 Consensus size: 65
1079994 ACCATGAATG
* * *
1080004 CATCATTATAATTGCACTAGATCTGCTGTTTTCGTATTTAAATTTTAAATTTATTAAATAATATT
1 CATCATTATAATTGCACTAAATCTACTGTTTTCGTATTTAAATTTTAAACTTATTAAATAATATT
* * *
1080069 CATCATTATAATTGCACTAAATCTATTTTTTTTGTATTTAAATTTTAAACTTATTAAATAATAT
1 CATCATTATAATTGCACTAAATCTACTGTTTTCGTATTTAAATTTTAAACTTATTAAATAATAT
1080133 CCGTATTTTA
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
65 58 1.00
ACGTcount: A:0.36, C:0.10, G:0.05, T:0.49
Consensus pattern (65 bp):
CATCATTATAATTGCACTAAATCTACTGTTTTCGTATTTAAATTTTAAACTTATTAAATAATATT
Found at i:1083682 original size:28 final size:29
Alignment explanation
Indices: 1083649--1083708 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
1083639 AAAGAAAAGG
1083649 ATAGCAAGTAG-AAAAAAAAATAAAAGCC
1 ATAGCAAGTAGAAAAAAAAAATAAAAGCC
1083677 ATAGCAAGTAGAAAAAAAAAATAAAAGCC
1 ATAGCAAGTAGAAAAAAAAAATAAAAGCC
1083706 ATA
1 ATA
1083709 ACAGGACAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 11 0.35
29 20 0.65
ACGTcount: A:0.65, C:0.10, G:0.13, T:0.12
Consensus pattern (29 bp):
ATAGCAAGTAGAAAAAAAAAATAAAAGCC
Found at i:1093610 original size:52 final size:52
Alignment explanation
Indices: 1093529--1093761 Score: 268
Period size: 52 Copynumber: 4.5 Consensus size: 52
1093519 ATGTCGCTGA
* * * *
1093529 TGGTGTCACTGATTCTGATGATGTCATGGTGGTGATTAGAATTAGAGTGACT
1 TGGTGTCACTGATACTGATGACGCCATAGTGGTGATTAGAATTAGAGTGACT
* * * * ** *
1093581 TGGTGCCACTAATTCTGATGATGTTATGGTGGTGATTAGAATTAGAGTGACT
1 TGGTGTCACTGATACTGATGACGCCATAGTGGTGATTAGAATTAGAGTGACT
* * * **
1093633 TTGTGTCACTGATAATTATGACGCCATAGTGGTGATTACTATTAGAGTGACT
1 TGGTGTCACTGATACTGATGACGCCATAGTGGTGATTAGAATTAGAGTGACT
* * *
1093685 TGGTGTCACTAATACTTATGACGCCATAGTGGCGATTAGAATTAGAGTGACT
1 TGGTGTCACTGATACTGATGACGCCATAGTGGTGATTAGAATTAGAGTGACT
* **
1093737 TAGTACCACTGATACTGATGACGCC
1 TGGTGTCACTGATACTGATGACGCC
1093762 TTGGTGGCGA
Statistics
Matches: 155, Mismatches: 26, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
52 155 1.00
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.34
Consensus pattern (52 bp):
TGGTGTCACTGATACTGATGACGCCATAGTGGTGATTAGAATTAGAGTGACT
Found at i:1093769 original size:52 final size:52
Alignment explanation
Indices: 1093535--1093791 Score: 253
Period size: 52 Copynumber: 4.9 Consensus size: 52
1093525 CTGATGGTGT
* * * *
1093535 CACTGATTCTGATGATGTCATGGTGGTGATTAGAATTAGAGTGACTTGGTGC
1 CACTGATACTGATGACGCCATGGTGGTGATTAGAATTAGAGTGACTTAGTGC
* * * ** * *
1093587 CACTAATTCTGATGATGTTATGGTGGTGATTAGAATTAGAGTGACTTTGTGT
1 CACTGATACTGATGACGCCATGGTGGTGATTAGAATTAGAGTGACTTAGTGC
* * * ** * *
1093639 CACTGATAATTATGACGCCATAGTGGTGATTACTATTAGAGTGACTTGGTGT
1 CACTGATACTGATGACGCCATGGTGGTGATTAGAATTAGAGTGACTTAGTGC
* * * * *
1093691 CACTAATACTTATGACGCCATAGTGGCGATTAGAATTAGAGTGACTTAGTAC
1 CACTGATACTGATGACGCCATGGTGGTGATTAGAATTAGAGTGACTTAGTGC
* * * ** *
1093743 CACTGATACTGATGACGCCTTGGTGGCGATCAGGGTTGGAGTGACTTAG
1 CACTGATACTGATGACGCCATGGTGGTGATTAGAATTAGAGTGACTTAG
1093792 AATCACTAAT
Statistics
Matches: 174, Mismatches: 31, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
52 174 1.00
ACGTcount: A:0.26, C:0.14, G:0.28, T:0.33
Consensus pattern (52 bp):
CACTGATACTGATGACGCCATGGTGGTGATTAGAATTAGAGTGACTTAGTGC
Found at i:1106056 original size:17 final size:17
Alignment explanation
Indices: 1106034--1106070 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
1106024 AACTAAGCTG
1106034 TTTATTTTTTATAAATA
1 TTTATTTTTTATAAATA
*
1106051 TTTATTTTTTATATATA
1 TTTATTTTTTATAAATA
1106068 TTT
1 TTT
1106071 TTATATATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTATTTTTTATAAATA
Found at i:1111152 original size:2 final size:2
Alignment explanation
Indices: 1111145--1111185 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1111135 ATATAAATTG
*
1111145 TA TA TA TA AA 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 TA TA TA T
1111186 GCAAACAAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1113730 original size:2 final size:2
Alignment explanation
Indices: 1113723--1113751 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1113713 TTGCGTCTTT
1113723 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
1113752 TCTAATAATG
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
Found at i:1114124 original size:24 final size:22
Alignment explanation
Indices: 1114081--1114131 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 22
1114071 GTCAAATGAC
* *
1114081 TTTTTATTTTTATATCTATAAA
1 TTTTTATTTTTAAATATATAAA
*
1114103 TTTTTATTAATTTAAATATATATA
1 TTTTTATT--TTTAAATATATAAA
1114127 TTTTT
1 TTTTT
1114132 GACATTTCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 8 0.33
24 16 0.67
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTTTATTTTTAAATATATAAA
Found at i:1114342 original size:19 final size:20
Alignment explanation
Indices: 1114318--1114355 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1114308 TACCATGTAA
1114318 ATATATATTCA-ATATAAAG
1 ATATATATTCATATATAAAG
*
1114337 ATATATATTTATATATAAA
1 ATATATATTCATATATAAA
1114356 TATAAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (20 bp):
ATATATATTCATATATAAAG
Found at i:1114384 original size:16 final size:16
Alignment explanation
Indices: 1114356--1114398 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
1114346 TATATATAAA
*
1114356 TATAAAT-TTTAATTT
1 TATAAATATTTAATAT
1114371 TATAAATATTTAATAT
1 TATAAATATTTAATAT
1114387 TATCAAA-ATTTA
1 TAT-AAATATTTA
1114399 CATCAAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 7 0.28
16 15 0.60
17 3 0.12
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (16 bp):
TATAAATATTTAATAT
Found at i:1115703 original size:2 final size:2
Alignment explanation
Indices: 1115696--1115723 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1115686 TTGAAAACAA
1115696 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
1115724 CTCAATTACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1119037 original size:14 final size:14
Alignment explanation
Indices: 1119018--1119045 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1119008 TGGAACTACA
1119018 ACTCATGATAAGAT
1 ACTCATGATAAGAT
1119032 ACTCATGATAAGAT
1 ACTCATGATAAGAT
1119046 TCTAAGGAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (14 bp):
ACTCATGATAAGAT
Found at i:1120814 original size:15 final size:15
Alignment explanation
Indices: 1120794--1120826 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1120784 TGGGTTTGGG
1120794 TCATTTAGATTTAGA
1 TCATTTAGATTTAGA
*
1120809 TCATTTGGATTTAGA
1 TCATTTAGATTTAGA
1120824 TCA
1 TCA
1120827 ATCGGTTTTG
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:0.30, C:0.09, G:0.15, T:0.45
Consensus pattern (15 bp):
TCATTTAGATTTAGA
Found at i:1125103 original size:20 final size:18
Alignment explanation
Indices: 1125078--1125182 Score: 52
Period size: 18 Copynumber: 5.3 Consensus size: 18
1125068 GCCCAGCATG
1125078 ATAATAAAAAATAATATAAA
1 ATAAT-AAAAAT-ATATAAA
*
1125098 ATAATACAAATATAT-AA
1 ATAATAAAAATATATAAA
*
1125115 ATATATAACATTTTAA-ATATAATT
1 ATA-ATAA-A----AATATATAA-A
1125139 ATAATAAATATATATATAAAA
1 ATAATAAA-A-ATATAT-AAA
*
1125160 ATAATACAAATATATAAA
1 ATAATAAAAATATATAAA
*
1125178 TTAAT
1 ATAAT
1125183 TATTAAATTT
Statistics
Matches: 68, Mismatches: 6, Indels: 24
0.69 0.06 0.24
Matches are distributed among these distances:
17 5 0.07
18 14 0.21
19 14 0.21
20 7 0.10
21 11 0.16
22 7 0.10
23 7 0.10
24 3 0.04
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (18 bp):
ATAATAAAAATATATAAA
Found at i:1125118 original size:8 final size:8
Alignment explanation
Indices: 1125090--1125178 Score: 55
Period size: 8 Copynumber: 11.4 Consensus size: 8
1125080 AATAAAAAAT
1125090 AATATA-A
1 AATATATA
*
1125097 AATAATACA
1 AAT-ATATA
1125106 AATATATA
1 AATATATA
1125114 AATATATA
1 AATATATA
*
1125122 ACAT-T-TT
1 A-ATATATA
1125129 AA-ATATA
1 AATATATA
*
1125136 ATTATAATA
1 AATAT-ATA
1125145 AATATAT-
1 AATATATA
*
1125152 -ATATAAA
1 AATATATA
*
1125159 AATAATACA
1 AAT-ATATA
1125168 AATATATA
1 AATATATA
1125176 AAT
1 AAT
1125179 TAATTATTAA
Statistics
Matches: 64, Mismatches: 8, Indels: 19
0.70 0.09 0.21
Matches are distributed among these distances:
6 7 0.11
7 7 0.11
8 30 0.47
9 20 0.31
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (8 bp):
AATATATA
Found at i:1125157 original size:21 final size:21
Alignment explanation
Indices: 1125086--1125180 Score: 60
Period size: 21 Copynumber: 4.7 Consensus size: 21
1125076 TGATAATAAA
*
1125086 AAATA-ATATAA-AATAATAC
1 AAATATATATAATTATAATAC
1125105 AAATATATA-AA-TAT-ATAAC
1 AAATATATATAATTATAAT-AC
** *
1125124 ATTTTAAATATAATTATAATA-
1 A-AATATATATAATTATAATAC
**
1125145 AATATATATATAAAAATAATAC
1 AA-ATATATATAATTATAATAC
1125167 AAATATATA-AATTA
1 AAATATATATAATTA
1125181 ATTATTAAAT
Statistics
Matches: 57, Mismatches: 11, Indels: 15
0.69 0.13 0.18
Matches are distributed among these distances:
18 2 0.04
19 12 0.21
20 11 0.19
21 24 0.42
22 6 0.11
23 2 0.04
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (21 bp):
AAATATATATAATTATAATAC
Found at i:1126671 original size:2 final size:2
Alignment explanation
Indices: 1126664--1126702 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1126654 CTACAAGTTT
1126664 TA TA 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 TA TA T
1126703 TTATGCTATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1126798 original size:2 final size:2
Alignment explanation
Indices: 1126793--1126826 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1126783 ACACACACAC
1126793 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
1126827 TCTCAGCATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1126953 original size:2 final size:2
Alignment explanation
Indices: 1126941--1126984 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
1126931 AATACTACTC
1126941 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1126981 AT AT
1 AT AT
1126985 CGTTGCAGGC
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1128089 original size:14 final size:14
Alignment explanation
Indices: 1128050--1128091 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
1128040 TAAAAAATTT
* *
1128050 TAATTTAATTTTTT
1 TAATTTAATTTATA
*
1128064 TAATTAAATTTATA
1 TAATTTAATTTATA
1128078 TAATTTAATTTATA
1 TAATTTAATTTATA
1128092 ATATTAATTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TAATTTAATTTATA
Found at i:1128193 original size:26 final size:26
Alignment explanation
Indices: 1128157--1128221 Score: 89
Period size: 26 Copynumber: 2.5 Consensus size: 26
1128147 AAATAAATAA
1128157 TTTATATTATATTAT-TTTA-ATATT
1 TTTATATTATATTATATTTATATATT
*
1128181 TTTATAAATTATATTGTATTTATATATT
1 TTTAT--ATTATATTATATTTATATATT
1128209 TTTATATTATATT
1 TTTATATTATATT
1128222 TACAAATTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
24 5 0.14
26 17 0.47
27 4 0.11
28 10 0.28
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.65
Consensus pattern (26 bp):
TTTATATTATATTATATTTATATATT
Found at i:1128215 original size:21 final size:21
Alignment explanation
Indices: 1128189--1128253 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
1128179 TTTTTATAAA
* *
1128189 TTATATTGTATTTATATATTT
1 TTATATTGTATTTACAAATTT
*
1128210 TTATATTATATTTACAAATTT
1 TTATATTGTATTTACAAATTT
*
1128231 TTATTATATGTATGTTTCAAATT
1 TTA-TAT-TGTAT-TTACAAATT
1128254 ATTAAAATAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
21 21 0.58
22 3 0.08
23 4 0.11
24 8 0.22
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.60
Consensus pattern (21 bp):
TTATATTGTATTTACAAATTT
Found at i:1131130 original size:75 final size:75
Alignment explanation
Indices: 1130988--1131132 Score: 184
Period size: 75 Copynumber: 1.9 Consensus size: 75
1130978 TTTAGTCATT
* * ** * ** * *
1130988 GTTATATTGAATATCAAGATGATATGATGTGTGCTGAATGTCGTGCATTCAACCTTTGTTCTTAA
1 GTTATATTGAATATCAAGATGATATGATGTGTGCTAAATATCGTGCAGACAACCATAATGCTAAA
1131053 AGATACTGTC
66 AGATACTGTC
*
1131063 GTTATATTGAATATCTAGATGATATGATGTGTGCTAAATATCGTGCAGACAACCATAATAGC-AA
1 GTTATATTGAATATCAAGATGATATGATGTGTGCTAAATATCGTGCAGACAACCATAAT-GCTAA
1131127 AAGATA
65 AAGATA
1131133 GTGTTCTTAA
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
75 58 0.98
76 1 0.02
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.34
Consensus pattern (75 bp):
GTTATATTGAATATCAAGATGATATGATGTGTGCTAAATATCGTGCAGACAACCATAATGCTAAA
AGATACTGTC
Found at i:1131773 original size:2 final size:2
Alignment explanation
Indices: 1131766--1131794 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1131756 AGCTACCCTG
1131766 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1131795 ACACACACAC
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1131799 original size:2 final size:2
Alignment explanation
Indices: 1131794--1131821 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1131784 CTCTCTCTCT
1131794 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
1131822 TTGCACAGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1132579 original size:18 final size:18
Alignment explanation
Indices: 1132556--1132593 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1132546 TACAGCAGCA
1132556 ATTAAATAAGCTATAATC
1 ATTAAATAAGCTATAATC
1132574 ATTAAATAAGCTATAATC
1 ATTAAATAAGCTATAATC
1132592 AT
1 AT
1132594 ATAGCTTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.11, G:0.05, T:0.34
Consensus pattern (18 bp):
ATTAAATAAGCTATAATC
Found at i:1132629 original size:2 final size:2
Alignment explanation
Indices: 1132619--1132652 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1132609 GAGGTGATAA
*
1132619 AT AT TT 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
1132653 TTGAAATGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1132912 original size:5 final size:5
Alignment explanation
Indices: 1132902--1132927 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1132892 CGACACGCAT
1132902 AATGG AATGG AATGG AATGG AATGG A
1 AATGG AATGG AATGG AATGG AATGG A
1132928 TTTTTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.19
Consensus pattern (5 bp):
AATGG
Found at i:1133043 original size:2 final size:2
Alignment explanation
Indices: 1133036--1133071 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1133026 ATTTGGCACG
1133036 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1133072 TGTCTCTGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1138465 original size:15 final size:15
Alignment explanation
Indices: 1138445--1138477 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1138435 GAACGAAAGG
1138445 TTTCATTTTTAGTAT
1 TTTCATTTTTAGTAT
1138460 TTTCATTTTTAGTAT
1 TTTCATTTTTAGTAT
1138475 TTT
1 TTT
1138478 TGTATAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.70
Consensus pattern (15 bp):
TTTCATTTTTAGTAT
Found at i:1145141 original size:2 final size:2
Alignment explanation
Indices: 1145134--1145196 Score: 72
Period size: 2 Copynumber: 31.5 Consensus size: 2
1145124 AGTCAAGCTT
* * *
1145134 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TT TT TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * *
1145176 TT TC TA TA TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC T
1145197 AGCAACTCTC
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.03, C:0.40, G:0.00, T:0.57
Consensus pattern (2 bp):
TC
Found at i:1149661 original size:13 final size:13
Alignment explanation
Indices: 1149643--1149668 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1149633 TACAGCAAGT
1149643 ATGTATCGATACA
1 ATGTATCGATACA
1149656 ATGTATCGATACA
1 ATGTATCGATACA
1149669 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Done.