Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004123.1 Hibiscus syriacus cultivar Beakdansim tig00009023_pilon, 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: 1596068
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 9
Found at i:374560 original size:36 final size:37
Alignment explanation
Indices: 374485--374577 Score: 125
Period size: 36 Copynumber: 2.5 Consensus size: 37
374475 GGATCATATC
* *
374485 TTTAGGAGTTTAAATCATAGATGAACTCTATCCTATT
1 TTTAGGAGTTTAAATCCTAGATAAACTCTATCCTATT
* * *
374522 TTTAGAAGTTTAAATCCTAGA-AAATTTTATCCTATT
1 TTTAGGAGTTTAAATCCTAGATAAACTCTATCCTATT
*
374558 TTTAGGAGTTTGAATCCTAG
1 TTTAGGAGTTTAAATCCTAG
374578 TAGGACGAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
36 30 0.61
37 19 0.39
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (37 bp):
TTTAGGAGTTTAAATCCTAGATAAACTCTATCCTATT
Found at i:375652 original size:106 final size:106
Alignment explanation
Indices: 375311--377102 Score: 2652
Period size: 106 Copynumber: 17.0 Consensus size: 106
375301 GCATTGTTCT
* * ** * *
375311 GAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
375376 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
375417 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-T--GAA-AT-TTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* ** * * *
375476 TCAGC-CACCTCTTCGTCGTGAAGTTGAGCTTGTGTTGCCTTG
66 CCAGCGGTCC-CTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * * * * * *
375518 G-GTTCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTATGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
375582 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * ** * * * *
375623 GAGTCCAATATCATACACTGTGAAATTGAAATTGGCTCTGAAATT-GGAAATTATTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
375687 CCAGCGATCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
375728 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTCGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
375793 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTATCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
375834 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
375899 CCAACGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
375940 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
376005 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
376046 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
376111 CCAGCGGTCCCTTCGTCGTGAAGTTAAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
376152 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
376217 CCAGTGGTCCCTTTGTTGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
376258 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGAAAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
376323 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
376364 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
376429 CTAGCGGCCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
376470 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
376535 CCAACGGTCCCTTCATTGTGAGGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
376576 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
376641 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
376682 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGAGAAGTTGTTTGCTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
376747 CCAGCGGT-CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * ** * *
376787 GAGTCCAATATCCTTCGCTATGAAGTTGAAATTGGCTATGAAATTGTAAAGTTATTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
376852 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
376893 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGATCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
376958 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * *
376999 GAGTCCAATATCCTTCGTTGTAAAGTTGAAATTGGTTCCGAAATTGGAAAATT-ATTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
377063 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
377103 TGATTGGCAT
Statistics
Matches: 1538, Mismatches: 136, Indels: 25
0.91 0.08 0.01
Matches are distributed among these distances:
99 2 0.00
100 73 0.05
101 5 0.00
102 4 0.00
104 3 0.00
105 243 0.16
106 1206 0.78
107 2 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:377956 original size:22 final size:22
Alignment explanation
Indices: 377930--377984 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
377920 TTGTGTTTGG
377930 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
377952 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
377974 TCAAAGGTTTG
1 TCAAAGGTTTG
377985 ATGGGGTAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.24, C:0.13, G:0.27, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:383250 original size:31 final size:30
Alignment explanation
Indices: 383201--383258 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
383191 ATAGTAAGTA
* *
383201 AAAAAACAAATAATAAAATATATATAAAAAAG
1 AAAAAACAAAGAAGAAAATA-A-ATAAAAAAG
383233 AAAAAA-AAAGAAGAAAATAAATAAAA
1 AAAAAACAAAGAAGAAAATAAATAAAA
383259 CAAATAAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 6 0.25
30 1 0.04
31 11 0.46
32 6 0.25
ACGTcount: A:0.79, C:0.02, G:0.05, T:0.14
Consensus pattern (30 bp):
AAAAAACAAAGAAGAAAATAAATAAAAAAG
Found at i:383409 original size:2 final size:2
Alignment explanation
Indices: 383402--383446 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
383392 GATAATTACA
383402 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
383442 AT AT A
1 AT AT A
383447 ATAAGTAGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:383656 original size:24 final size:23
Alignment explanation
Indices: 383621--383665 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
383611 TATAACAACA
383621 ATAATATCAATAAAAAAATATAAT
1 ATAATATCAAT-AAAAAATATAAT
383645 ATAATGAT-AATAAAAAATATA
1 ATAAT-ATCAATAAAAAATATA
383666 GAAAATTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 10 0.50
24 8 0.40
25 2 0.10
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (23 bp):
ATAATATCAATAAAAAATATAAT
Found at i:383833 original size:12 final size:11
Alignment explanation
Indices: 383805--383845 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
383795 TAACAAAATA
* *
383805 AATAATATAAA
1 AATAATACAAG
383816 AATAATACAAG
1 AATAATACAAG
383827 TAATAATACAAG
1 -AATAATACAAG
383839 AATAATA
1 AATAATA
383846 AAAAGAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (11 bp):
AATAATACAAG
Found at i:383891 original size:27 final size:28
Alignment explanation
Indices: 383864--383915 Score: 83
Period size: 25 Copynumber: 2.0 Consensus size: 28
383854 GAGAAAGTAA
383864 AAAAAATATA-ATA-ATAATA-AAATAT
1 AAAAAATATACATATATAATATAAATAT
383889 AAAAAATATACATATATAATATAAATA
1 AAAAAATATACATATATAATATAAATA
383916 AGTAGAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 10 0.42
26 3 0.12
27 6 0.25
28 5 0.21
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (28 bp):
AAAAAATATACATATATAATATAAATAT
Found at i:384577 original size:37 final size:37
Alignment explanation
Indices: 384527--384631 Score: 156
Period size: 37 Copynumber: 2.8 Consensus size: 37
384517 ATGTTTGTGG
* *
384527 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
* * *
384564 ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
*
384601 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAG
384632 GACGAAAAGG
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
Found at i:385202 original size:3 final size:3
Alignment explanation
Indices: 385194--385256 Score: 83
Period size: 3 Copynumber: 21.3 Consensus size: 3
385184 AAAATTATTT
* * *
385194 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATT ATA ATA ATT ATT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
385241 ATA ATA AAA ATA ATA A
1 ATA ATA ATA ATA ATA A
385257 AACCGGGATA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
2 2 0.04
3 51 0.96
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:385475 original size:42 final size:42
Alignment explanation
Indices: 385415--385541 Score: 110
Period size: 50 Copynumber: 2.8 Consensus size: 42
385405 TGAAACTTTG
* *
385415 AATTGCTCCTCCATCTTGAGACATTGAAACTTTTAGAAAGTA
1 AATTGCTCCTTCAACTTGAGACATTGAAACTTTTAGAAAGTA
* * * *
385457 AATTGCTCGTTCAACTTGAAGACTTGAGGCATTAAAACTTTTGGAAATTA
1 AATTGCTCCTTCAACTT---GA---GA--CATTGAAACTTTTAGAAAGTA
* *
385507 AATTGATCCTTCAACGTGAGACATTGAAACTTTTA
1 AATTGCTCCTTCAACTTGAGACATTGAAACTTTTA
385542 AAAATGTACA
Statistics
Matches: 66, Mismatches: 11, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
42 26 0.39
44 2 0.03
45 2 0.03
47 2 0.03
48 2 0.03
50 32 0.48
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Consensus pattern (42 bp):
AATTGCTCCTTCAACTTGAGACATTGAAACTTTTAGAAAGTA
Found at i:385877 original size:43 final size:43
Alignment explanation
Indices: 385830--385937 Score: 119
Period size: 43 Copynumber: 2.5 Consensus size: 43
385820 GAAACTTTTT
* * *
385830 GAAATTTAAATTGCTCCTCCAATTTAA-ACTATAAAAAAATTTG
1 GAAATTTAAATTGCTCCTCCAAATTAAGACAAT-AAAAAATTTA
* * * * *
385873 GAAATGTAAATTGCTCCTCTAAATTAAGGCAATTAAAATTTTA
1 GAAATTTAAATTGCTCCTCCAAATTAAGACAATAAAAAATTTA
*
385916 GAAATTTAAATTGTTCCTCCAA
1 GAAATTTAAATTGCTCCTCCAA
385938 CTTGAGGAAT
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
43 50 0.94
44 3 0.06
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (43 bp):
GAAATTTAAATTGCTCCTCCAAATTAAGACAATAAAAAATTTA
Found at i:385952 original size:43 final size:43
Alignment explanation
Indices: 385864--385986 Score: 135
Period size: 43 Copynumber: 2.9 Consensus size: 43
385854 TAAACTATAA
* * * *
385864 AAAAATTTGGAAATGTAAATTGCTCCTCTAAA-TTAAGGCAATT
1 AAAATTTTGGAAATTTAAATTGATCCTC-AAACTTGAGGCAATT
* * *
385907 AAAATTTTAGAAATTTAAATTGTTCCTCCAACTTGAGG-AATTT
1 AAAATTTTGGAAATTTAAATTGATCCTCAAACTTGAGGCAA-TT
*
385950 AAAATTTTGGAAA-TTAAATTAATCCTCAAACTTGAGG
1 AAAATTTTGGAAATTTAAATTGATCCTCAAACTTGAGG
385987 GACAAGTTCA
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
42 25 0.37
43 43 0.63
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (43 bp):
AAAATTTTGGAAATTTAAATTGATCCTCAAACTTGAGGCAATT
Found at i:387646 original size:43 final size:43
Alignment explanation
Indices: 387583--387671 Score: 169
Period size: 43 Copynumber: 2.1 Consensus size: 43
387573 AAATTTATTC
387583 AAATCACCTCATTCTATGAGTTTTATATCTTTGATTTGAAGAT
1 AAATCACCTCATTCTATGAGTTTTATATCTTTGATTTGAAGAT
*
387626 AAATCACCTCATTCTTTGAGTTTTATATCTTTGATTTGAAGAT
1 AAATCACCTCATTCTATGAGTTTTATATCTTTGATTTGAAGAT
387669 AAA
1 AAA
387672 ACTTTTTAAG
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:0.31, C:0.13, G:0.11, T:0.44
Consensus pattern (43 bp):
AAATCACCTCATTCTATGAGTTTTATATCTTTGATTTGAAGAT
Found at i:390035 original size:29 final size:29
Alignment explanation
Indices: 390003--390065 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
389993 AAATTAAATA
390003 AATATTTTAAAAATTAATAAAATATT-TTT
1 AATATTTTAAAAATTAA-AAAATATTATTT
*
390032 AATATTTTAAAAATTAAATAATATTATTT
1 AATATTTTAAAAATTAAAAAATATTATTT
*
390061 CATAT
1 AATAT
390066 AAATAATTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 7 0.23
29 24 0.77
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (29 bp):
AATATTTTAAAAATTAAAAAATATTATTT
Found at i:390036 original size:92 final size:92
Alignment explanation
Indices: 389940--390123 Score: 266
Period size: 92 Copynumber: 2.0 Consensus size: 92
389930 AAATTAAATA
* * *
389940 AATATTTTAAAACTTAAATAATATTATTTTAAAAAAATATTATATGATTTTAAAAATTAAATAAA
1 AATATTTTAAAAATTAAATAATATTATTTCAAAAAAATA--ATATGATTTAAAAAATTAAATAAA
390005 TATTTTAAAA-ATTAATAAA-AT-ATTTTT
64 TATTTTAAAATATT-ATAAATATAATTTTT
* * *
390032 AATATTTTAAAAATTAAATAATATTATTTCATATAAATAATTTGATTTAAAAAATTAAATAAATA
1 AATATTTTAAAAATTAAATAATATTATTTCAAAAAAATAATATGATTTAAAAAATTAAATAAATA
390097 TTTTAAAATATTATAAATATAATTTTT
66 TTTTAAAATATTATAAATATAATTTTT
390124 TAGAATTATT
Statistics
Matches: 83, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
90 37 0.45
91 5 0.06
92 41 0.49
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (92 bp):
AATATTTTAAAAATTAAATAATATTATTTCAAAAAAATAATATGATTTAAAAAATTAAATAAATA
TTTTAAAATATTATAAATATAATTTTT
Found at i:390054 original size:19 final size:19
Alignment explanation
Indices: 390031--390109 Score: 61
Period size: 19 Copynumber: 3.9 Consensus size: 19
390021 AAAATATTTT
390031 TAATATTTTAAAAATTAAA
1 TAATATTTTAAAAATTAAA
** *
390050 TAATATTATTTCATA-TAAA
1 TAATATT-TTAAAAATTAAA
*
390069 TAATTTGATTTAAAAAATTAAA
1 TAA--T-ATTTTAAAAATTAAA
390091 TAAATATTTTAAAATATTA
1 T-AATATTTTAAAA-ATTA
390110 TAAATATAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 12
0.69 0.12 0.18
Matches are distributed among these distances:
19 14 0.31
20 12 0.27
21 9 0.20
22 8 0.18
23 2 0.04
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (19 bp):
TAATATTTTAAAAATTAAA
Found at i:390103 original size:21 final size:19
Alignment explanation
Indices: 390077--390116 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
390067 AATAATTTGA
390077 TTTAAAAAATTAAATAAATAT
1 TTTAAAAAATT--ATAAATAT
*
390098 TTTAAAATATTATAAATAT
1 TTTAAAAAATTATAAATAT
390117 AATTTTTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
21 10 0.56
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TTTAAAAAATTATAAATAT
Found at i:390104 original size:20 final size:20
Alignment explanation
Indices: 389927--390030 Score: 115
Period size: 20 Copynumber: 5.0 Consensus size: 20
389917 TTTAGTATAA
389927 TAAAAATTAAATAAATATTT
1 TAAAAATTAAATAAATATTT
*
389947 TAAAACTTAAATAATATTATTT
1 TAAAAATTAAATAA-A-TATTT
*
389969 TAAAAA--AATATTATATGATTT
1 TAAAAATTAA-A-TAAAT-ATTT
389990 TAAAAATTAAATAAATATTT
1 TAAAAATTAAATAAATATTT
390010 TAAAAATT-AATAAAATATTT
1 TAAAAATTAAAT-AAATATTT
390030 T
1 T
390031 TAATATTTTA
Statistics
Matches: 72, Mismatches: 4, Indels: 16
0.78 0.04 0.17
Matches are distributed among these distances:
19 3 0.04
20 37 0.51
21 17 0.24
22 13 0.18
23 2 0.03
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (20 bp):
TAAAAATTAAATAAATATTT
Found at i:390144 original size:24 final size:22
Alignment explanation
Indices: 390077--390152 Score: 73
Period size: 24 Copynumber: 3.3 Consensus size: 22
390067 AATAATTTGA
* *
390077 TTTAAAA-AATTAAATAAATAT
1 TTTAAAATATTTAAATAAATTT
390098 TTTAAAATATTATAAATATAATTT
1 TTTAAAATATT-TAAATA-AATTT
*
390122 TTTAGAATTATTTAATATAAATTT
1 TTTA-AAATATTTAA-ATAAATTT
*
390146 TATAAAA
1 TTTAAAA
390153 GTATAAAAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
21 7 0.16
22 2 0.04
23 8 0.18
24 19 0.42
25 9 0.20
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (22 bp):
TTTAAAATATTTAAATAAATTT
Found at i:397659 original size:21 final size:23
Alignment explanation
Indices: 397609--397671 Score: 76
Period size: 24 Copynumber: 2.8 Consensus size: 23
397599 ATACCCCCAT
397609 AAGGGAACCGATTCCCCCCTTTG
1 AAGGGAACCGATTCCCCCCTTTG
*
397632 AATGGGAACCGATTCCCTCC-TTG
1 AA-GGGAACCGATTCCCCCCTTTG
* *
397655 -AGGGAATCGATACCCCC
1 AAGGGAACCGATTCCCCC
397672 AGTGGGTTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
21 13 0.37
22 1 0.03
23 5 0.14
24 16 0.46
ACGTcount: A:0.24, C:0.33, G:0.22, T:0.21
Consensus pattern (23 bp):
AAGGGAACCGATTCCCCCCTTTG
Found at i:401754 original size:23 final size:22
Alignment explanation
Indices: 401715--401772 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
401705 AGAAAAGAGA
401715 ATAATTTT-A-TTTTTAATATAT
1 ATAATTTTAATTTTTTAATA-AT
* *
401736 ATATTTTTAGTTTTTTAATAAT
1 ATAATTTTAATTTTTTAATAAT
*
401758 TTAATTTTAATTTTT
1 ATAATTTTAATTTTT
401773 GGTATTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 7 0.23
22 14 0.47
23 9 0.30
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (22 bp):
ATAATTTTAATTTTTTAATAAT
Found at i:401765 original size:22 final size:22
Alignment explanation
Indices: 401715--401772 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
401705 AGAAAAGAGA
401715 ATAATTTTA-TTTTTAATATAT
1 ATAATTTTATTTTTTAATATAT
*
401736 ATATTTTTAGTTTTTTAATA-AT
1 ATAATTTTA-TTTTTTAATATAT
* *
401758 TTAATTTTAATTTTT
1 ATAATTTTATTTTTT
401773 GGTATTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 13 0.42
22 9 0.29
23 9 0.29
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (22 bp):
ATAATTTTATTTTTTAATATAT
Found at i:412169 original size:18 final size:19
Alignment explanation
Indices: 412137--412173 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
412127 TTTATACAAT
*
412137 GAAATATGGGGGGGGAGAG
1 GAAATATGGGAGGGGAGAG
412156 GAAA-ATGGGAGGGGAGAG
1 GAAATATGGGAGGGGAGAG
412174 TTGAGAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.35, C:0.00, G:0.57, T:0.08
Consensus pattern (19 bp):
GAAATATGGGAGGGGAGAG
Found at i:412208 original size:32 final size:33
Alignment explanation
Indices: 412162--412230 Score: 113
Period size: 32 Copynumber: 2.1 Consensus size: 33
412152 AGAGGAAAAT
*
412162 GGGAGGGGAGAGTTGAGAGTAAAAGAAAGATCG
1 GGGAGGGGAGAGTTGAGAATAAAAGAAAGATCG
*
412195 GGGATGGGA-AGTTGAGAATAAAAGAAAGATCG
1 GGGAGGGGAGAGTTGAGAATAAAAGAAAGATCG
412227 GGGA
1 GGGA
412231 AGAGGGGAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 26 0.76
33 8 0.24
ACGTcount: A:0.41, C:0.03, G:0.43, T:0.13
Consensus pattern (33 bp):
GGGAGGGGAGAGTTGAGAATAAAAGAAAGATCG
Found at i:412400 original size:15 final size:14
Alignment explanation
Indices: 412380--412413 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
412370 ATTTAGTCTT
412380 AATTTCAATAATCTA
1 AATTTCAA-AATCTA
*
412395 AATTTCTAAATCTA
1 AATTTCAAAATCTA
412409 AATTT
1 AATTT
412414 TACAATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (14 bp):
AATTTCAAAATCTA
Found at i:417104 original size:36 final size:37
Alignment explanation
Indices: 417026--417126 Score: 161
Period size: 36 Copynumber: 2.8 Consensus size: 37
417016 GGTTTTGAAA
417026 ATATTTTTGAAAACGTATAATATATAATTATAAAAAC
1 ATATTTTTGAAAACGTATAATATATAATTATAAAAAC
* *
417063 ATATTTTTGAAAACGTATAATATAGT-TTTA-AAAAAT
1 ATATTTTTGAAAACGTATAATATA-TAATTATAAAAAC
417099 ATATTTTTGAAAACGTATAATATATAAT
1 ATATTTTTGAAAACGTATAATATATAAT
417127 ATTTTTAAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
35 1 0.02
36 30 0.51
37 27 0.46
38 1 0.02
ACGTcount: A:0.49, C:0.04, G:0.07, T:0.41
Consensus pattern (37 bp):
ATATTTTTGAAAACGTATAATATATAATTATAAAAAC
Found at i:417146 original size:99 final size:97
Alignment explanation
Indices: 417025--417237 Score: 227
Period size: 99 Copynumber: 2.2 Consensus size: 97
417015 TGGTTTTGAA
* *
417025 AATATTTTTGAAAACGTATAATATATA-ATTATAAAAACATATTTTTGAAAACGTATA-ATATA-
1 AATATTTTTAAAAACGTATAATATATAGATTATAAAAA-A-ACTTTTGAAAACGTATATATATAG
* *
417087 GTTTTAAAAAATATATTTTTGAAAACGTATAATATAT
64 GTTTT--AAAA-ATACTTTTGAAAACGCATAATATAT
** * * * *
417124 AATATTTTTAAAAATTTATAATATTTAGTTTTTTTAAAAAACTTTTGAAAACGTATATTATATAG
1 AATATTTTTAAAAACGTATAATATATAG-ATTATAAAAAAACTTTTGAAAACGTATA-TATATAG
417189 GTTTTAAAAATACTTTTGAAAACGCATAATATAT
64 GTTTTAAAAATACTTTTGAAAACGCATAATATAT
* *
417223 AGT-TTTTAAAAAACG
1 AATATTTTTAAAAACG
417238 ACTTTGAAAA
Statistics
Matches: 95, Mismatches: 14, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
98 9 0.09
99 64 0.67
100 5 0.05
101 12 0.13
102 5 0.05
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.42
Consensus pattern (97 bp):
AATATTTTTAAAAACGTATAATATATAGATTATAAAAAAACTTTTGAAAACGTATATATATAGGT
TTTAAAAATACTTTTGAAAACGCATAATATAT
Found at i:417157 original size:26 final size:26
Alignment explanation
Indices: 417099--417163 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
417089 TTTAAAAAAT
* **
417099 ATATTTTTGAAAACGTATAATATATA
1 ATATTTTTAAAAATTTATAATATATA
*
417125 ATATTTTTAAAAATTTATAATATTTA
1 ATATTTTTAAAAATTTATAATATATA
* *
417151 GTTTTTTTAAAAA
1 ATATTTTTAAAAA
417164 ACTTTTGAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.49
Consensus pattern (26 bp):
ATATTTTTAAAAATTTATAATATATA
Found at i:417209 original size:36 final size:35
Alignment explanation
Indices: 417155--417260 Score: 131
Period size: 36 Copynumber: 2.9 Consensus size: 35
417145 TATTTAGTTT
417155 TTTTAAAAAACTTTTGAAAACGTATATTATATAGG
1 TTTTAAAAAACTTTTGAAAACGTATATTATATAGG
* * *
417190 TTTTAAAAATACTTTTGAAAACGCATAATATATAGT
1 TTTTAAAAA-ACTTTTGAAAACGTATATTATATAGG
* * *
417226 TTTTAAAAAACGACTTTGAAAACATATATAATATA
1 TTTTAAAAAAC--TTTTGAAAACGTATATTATATA
417261 ATGGTTTTGA
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
35 11 0.18
36 32 0.53
37 17 0.28
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (35 bp):
TTTTAAAAAACTTTTGAAAACGTATATTATATAGG
Found at i:417338 original size:20 final size:20
Alignment explanation
Indices: 417313--417360 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
417303 TTGTTATTTA
417313 TATTATTTCTATT-TTTTATT
1 TATTATTTCT-TTATTTTATT
* *
417333 TATTATGTATTTATTTTATT
1 TATTATTTCTTTATTTTATT
417353 TATT-TTTC
1 TATTATTTC
417361 GTGTCCATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.73
Consensus pattern (20 bp):
TATTATTTCTTTATTTTATT
Found at i:417356 original size:9 final size:9
Alignment explanation
Indices: 417309--417358 Score: 50
Period size: 9 Copynumber: 5.3 Consensus size: 9
417299 AACATTGTTA
417309 TTTATATTAT
1 TTTAT-TTAT
417319 TTCTA-TT-T
1 TT-TATTTAT
417327 TTTATTTAT
1 TTTATTTAT
417336 TATGTATTTAT
1 T-T-TATTTAT
417347 TTTATTTAT
1 TTTATTTAT
417356 TTT
1 TTT
417359 TCGTGTCCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
7 2 0.06
8 5 0.14
9 14 0.40
10 4 0.11
11 10 0.29
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (9 bp):
TTTATTTAT
Found at i:420930 original size:59 final size:59
Alignment explanation
Indices: 420807--420930 Score: 151
Period size: 60 Copynumber: 2.1 Consensus size: 59
420797 TATCGTCCCT
* * * * **
420807 GACTATAGGGTGATGCTTGTTGAGTCTCTCAACAATTAAAAGTTACAAAATAGTTCTTC
1 GACTATAGGGTGATGCTTGTTGAGTCCCCCAACAATTAAAAGCTACAAAATAGATCACC
* * *
420866 TACTATAGGGTGTTGCTTTGTTGAGTCCCCCAACTATTAAAAGCTACAAAAT-GATCACC
1 GACTATAGGGTGATGC-TTGTTGAGTCCCCCAACAATTAAAAGCTACAAAATAGATCACC
420925 GACTAT
1 GACTAT
420931 TTAGTATGTT
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
59 23 0.43
60 31 0.57
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (59 bp):
GACTATAGGGTGATGCTTGTTGAGTCCCCCAACAATTAAAAGCTACAAAATAGATCACC
Found at i:425247 original size:29 final size:29
Alignment explanation
Indices: 425205--425286 Score: 146
Period size: 29 Copynumber: 2.8 Consensus size: 29
425195 AAACTAAATT
425205 GATGTCATTGCTTACATCATTTAAGTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
425234 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
425263 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
425287 GTTAGGTGAG
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
29 46 0.90
30 5 0.10
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:428703 original size:36 final size:36
Alignment explanation
Indices: 428614--428714 Score: 121
Period size: 36 Copynumber: 2.8 Consensus size: 36
428604 CCTTTTCATC
*
428614 CTACTAGGATTCAAACTCCTAAAAATAAGATATAATT
1 CTACTAGGATTCAAACTCCTAAAAAT-AGATAGAATT
* * *
428651 TTGCTAGGATTCAAACTCCTAAAAATAGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGATAGAATT
** * *
428687 CTACTATTATTTAAACTCCTAAAGATAG
1 CTACTAGGATTCAAACTCCTAAAAATAG
428715 GATCCACAAG
Statistics
Matches: 54, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
36 30 0.56
37 24 0.44
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.32
Consensus pattern (36 bp):
CTACTAGGATTCAAACTCCTAAAAATAGATAGAATT
Found at i:429152 original size:10 final size:11
Alignment explanation
Indices: 429107--429152 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
429097 AATTTAACCC
429107 TTATTATATAT
1 TTATTATATAT
*
429118 GTATATATATAT
1 TTAT-TATATAT
429130 TTATT-TATTAT
1 TTATTATA-TAT
429141 TTATTATA-AT
1 TTATTATATAT
429151 TT
1 TT
429153 TTTTCATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
10 6 0.20
11 12 0.40
12 12 0.40
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (11 bp):
TTATTATATAT
Found at i:429433 original size:4 final size:4
Alignment explanation
Indices: 429418--429460 Score: 50
Period size: 4 Copynumber: 10.2 Consensus size: 4
429408 ATTATACATA
* *
429418 TATT TTTT TATT TATT TATTT TATT TATAC TATT TATT TATT T
1 TATT TATT TATT TATT TA-TT TATT TAT-T TATT TATT TATT T
429461 TCATTATGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
4 26 0.79
5 7 0.21
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:429441 original size:13 final size:13
Alignment explanation
Indices: 429418--429460 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
429408 ATTATACATA
429418 TATTT-TTTTATT
1 TATTTATTTTATT
429430 TATTTATTTTATT
1 TATTTATTTTATT
*
429443 TATACTA-TTTATT
1 TAT-TTATTTTATT
429456 TATTT
1 TATTT
429461 TCATTATGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 6 0.22
13 19 0.70
14 2 0.07
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (13 bp):
TATTTATTTTATT
Found at i:429572 original size:18 final size:19
Alignment explanation
Indices: 429548--429593 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
429538 TGTATATATA
*
429548 TTTTTTTCTTC-ATTT-AT
1 TTTTTTTATTCAATTTCAT
429565 TTTATTTTATTCAATTTCAT
1 TTT-TTTTATTCAATTTCAT
429585 TTTTTTTAT
1 TTTTTTTAT
429594 ATTTGTTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 3 0.12
18 7 0.28
19 10 0.40
20 5 0.20
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTTTTATTCAATTTCAT
Found at i:435147 original size:22 final size:22
Alignment explanation
Indices: 435075--435150 Score: 125
Period size: 22 Copynumber: 3.5 Consensus size: 22
435065 CTACCCCATA
*
435075 AAACCGTTGAGCATCAAATGCC
1 AAACCTTTGAGCATCAAATGCC
*
435097 AAACCTATGAGCATCAAATGCC
1 AAACCTTTGAGCATCAAATGCC
*
435119 AAACCTTTGAGCAACAAATGCC
1 AAACCTTTGAGCATCAAATGCC
435141 AAACCTTTGA
1 AAACCTTTGA
435151 CCAAACATAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.39, C:0.26, G:0.14, T:0.20
Consensus pattern (22 bp):
AAACCTTTGAGCATCAAATGCC
Found at i:436217 original size:106 final size:106
Alignment explanation
Indices: 436090--437043 Score: 1470
Period size: 106 Copynumber: 9.0 Consensus size: 106
436080 ATATCGTACC
* * * *
436090 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
436155 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGAATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
436196 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAA--T--A
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
436257 AATTTCAGAGCCAATTTCAACTTCAC-GACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
* * *
436298 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
436363 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
436404 ACTCAAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
436469 AATTTCAGAGCCAATTTCAATTTCACAGCGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
436510 ACTCAAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
436575 AATTTCAGAGCCAATTACAACTTTACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
436616 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
436681 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
436722 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
436787 AATTTCAGAGCCAATTTAAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
436828 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * *
436893 AATTTCGGAGCTAATTTCAACTTCACAACAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * * *
436934 ACTCGAGGCAACACAAGTTCAACTTCACAATGAAGGGACGGCTGGTTGTCAACAAACAATTTCCT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * *
436999 GATTCCAGATCCAATTTCAACTTCAC-GACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
437040 ACTC
1 ACTC
437044 GGAACAATGC
Statistics
Matches: 790, Mismatches: 51, Indels: 14
0.92 0.06 0.02
Matches are distributed among these distances:
101 1 0.00
102 96 0.12
104 2 0.00
106 691 0.87
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:437882 original size:37 final size:37
Alignment explanation
Indices: 437796--437896 Score: 112
Period size: 37 Copynumber: 2.7 Consensus size: 37
437786 TTCATCCTAC
* * *
437796 TAGGATTCAAACTCCTAAAAATAGGATATAATTTTAA
1 TAGGACTCAAACTCCTAAAAATAGGATAGAATTCTAA
* *
437833 TAGGACTCAAACTCCTAAAAATAGGATAGAGTTCTAC
1 TAGGACTCAAACTCCTAAAAATAGGATAGAATTCTAA
** * * *
437870 TATTATTTAAACTCCTAAAGATAGGAT
1 TAGGACTCAAACTCCTAAAAATAGGAT
437897 CCACAAGCAT
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 54 1.00
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.31
Consensus pattern (37 bp):
TAGGACTCAAACTCCTAAAAATAGGATAGAATTCTAA
Found at i:438304 original size:2 final size:2
Alignment explanation
Indices: 438291--438346 Score: 73
Period size: 2 Copynumber: 29.5 Consensus size: 2
438281 CCTTATTATT
*
438291 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
438332 TA T- TA TT TA T- TA TA T
1 TA TA TA TA TA TA TA TA T
438347 TATTTTTTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
1 3 0.06
2 44 0.94
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (2 bp):
TA
Found at i:438347 original size:12 final size:13
Alignment explanation
Indices: 438283--438351 Score: 68
Period size: 14 Copynumber: 5.2 Consensus size: 13
438273 AATTTAACCC
*
438283 TTATTATTTATAT
1 TTATTATATATAT
*
438296 GTATATATATATAT
1 TTAT-TATATATAT
*
438310 ATATATATATATAT
1 TTAT-TATATATAT
*
438324 ATATTATATATTAT
1 TTATTATATA-TAT
438338 TTATTATAT-TAT
1 TTATTATATATAT
438350 TT
1 TT
438352 TTTTTTTTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
12 5 0.10
13 9 0.18
14 36 0.72
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (13 bp):
TTATTATATATAT
Found at i:438616 original size:12 final size:11
Alignment explanation
Indices: 438599--438656 Score: 50
Period size: 12 Copynumber: 5.3 Consensus size: 11
438589 TTTATTATTA
438599 TATATATATTTT
1 TATATAT-TTTT
438611 TATATATTTTT
1 TATATATTTTT
*
438622 TTTA-ATTTTT
1 TATATATTTTT
*
438632 TAT-T-TTATT
1 TATATATTTTT
438641 TATACTATTTATT
1 TATA-TATTT-TT
438654 TAT
1 TAT
438657 TTTCATTATG
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
9 7 0.19
10 8 0.22
11 8 0.22
12 9 0.24
13 5 0.14
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.71
Consensus pattern (11 bp):
TATATATTTTT
Found at i:438811 original size:29 final size:29
Alignment explanation
Indices: 438754--438812 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
438744 TATTTTTTTC
* *
438754 TTCATTTATTTTATTTTATTTTATTCAAT
1 TTCATTTATTTTATTTTATTTCATCCAAT
*
438783 TTCATTT-TTTTATATTTGTTTCATCCAAT
1 TTCATTTATTTTAT-TTTATTTCATCCAAT
438812 T
1 T
438813 ATTTTATGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 6 0.23
29 20 0.77
ACGTcount: A:0.22, C:0.10, G:0.02, T:0.66
Consensus pattern (29 bp):
TTCATTTATTTTATTTTATTTCATCCAAT
Found at i:440606 original size:29 final size:28
Alignment explanation
Indices: 440564--440673 Score: 166
Period size: 29 Copynumber: 3.8 Consensus size: 28
440554 AACTAAATTA
440564 ATGTCATTGCTTACATCATTTAAGTGAAT
1 ATGTCATTGCTTACATCATTTAAGT-AAT
*
440593 ATGTCATTACTTACATCATTTAAGTAAAT
1 ATGTCATTGCTTACATCATTTAAGT-AAT
*
440622 ATGTCATTGTTTACATCATTTAAGTAAT
1 ATGTCATTGCTTACATCATTTAAGTAAT
440650 GATGTCATTGCTTACATCAATTTA
1 -ATGTCATTGCTTACATC-ATTTA
440674 GTTAGGTGAG
Statistics
Matches: 74, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
28 3 0.04
29 66 0.89
30 5 0.07
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.43
Consensus pattern (28 bp):
ATGTCATTGCTTACATCATTTAAGTAAT
Found at i:443298 original size:393 final size:388
Alignment explanation
Indices: 442576--443362 Score: 1247
Period size: 393 Copynumber: 2.0 Consensus size: 388
442566 TTATATTTAA
*
442576 TTTAGTCATTTTAGGGTAACTTGTGTGACATTTAAAAAAATTCACAACCACGATACCCGCAATAA
1 TTTAGTCATTTTAGGGTAACTTGTGTGACATTTAAAAAAATTCACAACCACAATACCCGCAATAA
** * * * * *
442641 CTGCAATGACATTCGTTATGTCCGCAACTGTGATAATCGCGACGCGACCGAAAATGTGACTGCGA
66 CCACAATGACATCCATTACGTCCGCAACTGTGATAAACGCGACGCGACCGAAAATGT-ACCGCGA
* *
442706 ACGCTATTTAAAACCCTAGCCACACATGCAAGTTCTGCAACTTGATCTCAGTCATTGCCCAGAAA
130 ACGCTATTTAAAACCCTAGCCACACATGCAAGTTATGCAACTTGATCTCAGCCATTGCCCAGAAA
* *
442771 AAACCAAGTACATCAGGGAAATTTTAGGAAGATGATGGATTGATGTTGGTTATTTTGTTCTTGGG
195 AAACCAAGTACATAAGGGAAATTTTAGGAAGATGATGGATTGATGTTGGTTATTTTGCTCTTGGG
* *
442836 GATTCATCTCGACTTATTCCTTCCCATCAGGAGGTTTCCCTCGCTCACCGCTTTAATTATTATAA
260 GATTCATCTCGACTTATTCCTTCCCATCAAGAGGTTTCCATCGCTCACCGCTTTAATTATTATAA
*
442901 GTAACATTTGGTTTATGGAGACTATAGCG-AATTTTTTATTTGGGTGGAGAACTGCAATCGATGA
325 GTAACATTTGGTTTATGGAGACTATAG-GTAA-TTTTTATTTGGGTGGAGAACTGCAATCAATGA
442965 T
388 T
* *
442966 TTTAGTCATTTTAGGGTAACTTGTGTGACATTTAAAAAAATTCACGACCACAATACCCGCAATGA
1 TTTAGTCATTTTAGGGTAACTTGTGTGACATTTAAAAAAATTCACAACCACAATACCCGCAATAA
*
443031 CCACAATGACATCCATTACGTCCGCAACTGTGATAAACGCGATGCGACACGACCGAAATCGT-CC
66 CCACAATGACATCCATTACGTCCGCAACTGTGATAAACGCGACGCGAC-CGA---AAAT-GTACC
* * * *
443095 GCGAACGCTATTTAAAACCCTGGCCACACATGCAAGTTATGTAGCTTGATCTCAGCCATTGGCCA
126 GCGAACGCTATTTAAAACCCTAGCCACACATGCAAGTTATGCAACTTGATCTCAGCCATTGCCCA
443160 GAAAAAACCAAGTACATAAGGGAAATTTTAGGAAGATGATGGATTGATGTTGGTTATTTTGCTCT
191 GAAAAAACCAAGTACATAAGGGAAATTTTAGGAAGATGATGGATTGATGTTGGTTATTTTGCTCT
443225 TGGGGATTCATCTCGACTTATTCCTTCCCATCAAGAGGTGTTCCAT-GCTCACCGCTTTAATTAT
256 TGGGGATTCATCTCGACTTATTCCTTCCCATCAAGAGGT-TTCCATCGCTCACCGCTTTAATTAT
* * *
443289 TATAAGTAACATTTGGTTTATTGAGACTATAGGTGATTTTTATTTGGGTGGAGAGCTGCAATCAA
320 TATAAGTAACATTTGGTTTATGGAGACTATAGGTAATTTTTATTTGGGTGGAGAACTGCAATCAA
443354 TGAT
385 TGAT
443358 TTTAG
1 TTTAG
443363 AAGGAGAAAT
Statistics
Matches: 365, Mismatches: 25, Indels: 12
0.91 0.06 0.03
Matches are distributed among these distances:
390 103 0.28
391 3 0.01
392 37 0.10
393 211 0.58
394 9 0.02
395 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (388 bp):
TTTAGTCATTTTAGGGTAACTTGTGTGACATTTAAAAAAATTCACAACCACAATACCCGCAATAA
CCACAATGACATCCATTACGTCCGCAACTGTGATAAACGCGACGCGACCGAAAATGTACCGCGAA
CGCTATTTAAAACCCTAGCCACACATGCAAGTTATGCAACTTGATCTCAGCCATTGCCCAGAAAA
AACCAAGTACATAAGGGAAATTTTAGGAAGATGATGGATTGATGTTGGTTATTTTGCTCTTGGGG
ATTCATCTCGACTTATTCCTTCCCATCAAGAGGTTTCCATCGCTCACCGCTTTAATTATTATAAG
TAACATTTGGTTTATGGAGACTATAGGTAATTTTTATTTGGGTGGAGAACTGCAATCAATGAT
Found at i:460382 original size:22 final size:22
Alignment explanation
Indices: 460354--460405 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
460344 CTAGAGACTT
*
460354 TTTTCTCTAG-TTTTTGGGTGAA
1 TTTTCTCT-GTTTTTTGGGCGAA
460376 TTTTCTCTGTTTTTTGGGCGAA
1 TTTTCTCTGTTTTTTGGGCGAA
460398 TTTTCTCT
1 TTTTCTCT
460406 TGTGAATCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 1 0.04
22 27 0.96
ACGTcount: A:0.10, C:0.13, G:0.19, T:0.58
Consensus pattern (22 bp):
TTTTCTCTGTTTTTTGGGCGAA
Found at i:463350 original size:107 final size:109
Alignment explanation
Indices: 463233--463427 Score: 245
Period size: 109 Copynumber: 1.8 Consensus size: 109
463223 CAAACAGAGG
* *
463233 ACAACCCAAAAAATA-AAAAGCA-TGCAAG-AGAAGGGAAATTA-AAATTTTAAACCATACAGGT
1 ACAACCCAAAAAATACAAAA-CACT-CAAGAAAAAGGGAAAATAGAAATTTTAAACCATACAGGT
*
463294 AACCAGAATGCAAAAACACGCTAAAATTAGAGGGACTAAAACACGA
64 AACCAAAATGCAAAAACACGCTAAAATTAGAGGGACTAAAACACGA
* * *** * *
463340 ACAACCCAAAAATTACAAAACACTCAAGAAAAAGGGAAAATAGCAATTTTGGTCCCTACAGGTGA
1 ACAACCCAAAAAATACAAAACACTCAAGAAAAAGGGAAAATAGAAATTTTAAACCATACAGGTAA
*
463405 CCAAAATGTAAAAACACGCTAAA
66 CCAAAATGCAAAAACACGCTAAA
463428 CCTAGGGGAC
Statistics
Matches: 73, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
107 20 0.27
108 16 0.22
109 37 0.51
ACGTcount: A:0.52, C:0.18, G:0.15, T:0.15
Consensus pattern (109 bp):
ACAACCCAAAAAATACAAAACACTCAAGAAAAAGGGAAAATAGAAATTTTAAACCATACAGGTAA
CCAAAATGCAAAAACACGCTAAAATTAGAGGGACTAAAACACGA
Found at i:471648 original size:14 final size:14
Alignment explanation
Indices: 471610--471648 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
471600 GTATTACTCT
471610 ATAATCTCTAAACC
1 ATAATCTCTAAACC
* *
471624 ATAAGCCCTAAACC
1 ATAATCTCTAAACC
*
471638 TTAATCTCTAA
1 ATAATCTCTAA
471649 CTTAAAATCC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.41, C:0.28, G:0.03, T:0.28
Consensus pattern (14 bp):
ATAATCTCTAAACC
Found at i:472661 original size:2 final size:2
Alignment explanation
Indices: 472654--472697 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
472644 ATACTTTCTT
*
472654 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
472695 TA T
1 TA T
472698 TTAAAATAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:479345 original size:12 final size:11
Alignment explanation
Indices: 479328--479384 Score: 64
Period size: 12 Copynumber: 5.2 Consensus size: 11
479318 TCATTTACAA
479328 TTTTTGATTTTT
1 TTTTTG-TTTTT
*
479340 TTTTTG--ATT
1 TTTTTGTTTTT
479349 TTTTTGTTTTT
1 TTTTTGTTTTT
*
479360 TATTTTGTTTTG
1 T-TTTTGTTTTT
479372 TTTTTGTTTTT
1 TTTTTGTTTTT
479383 TT
1 TT
479385 ATGAAAAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
9 8 0.21
11 14 0.37
12 16 0.42
ACGTcount: A:0.05, C:0.00, G:0.11, T:0.84
Consensus pattern (11 bp):
TTTTTGTTTTT
Found at i:479350 original size:11 final size:10
Alignment explanation
Indices: 479336--479384 Score: 55
Period size: 11 Copynumber: 4.7 Consensus size: 10
479326 AATTTTTGAT
479336 TTTTTTTTTG
1 TTTTTTTTTG
479346 ATTTTTTTGTT-
1 -TTTTTTT-TTG
*
479357 TTTTATTTTG
1 TTTTTTTTTG
479367 TTTTGTTTTTG
1 TTTT-TTTTTG
479378 TTTTTTT
1 TTTTTTT
479385 ATGAAAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
9 2 0.06
10 13 0.39
11 16 0.48
12 2 0.06
ACGTcount: A:0.04, C:0.00, G:0.10, T:0.86
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:479360 original size:17 final size:16
Alignment explanation
Indices: 479335--479384 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
479325 CAATTTTTGA
479335 TTTTTTTTTTGATTTT
1 TTTTTTTTTTGATTTT
*
479351 TTTGTTTTTT-ATTTT
1 TTTTTTTTTTGATTTT
*
479366 GTTTTGTTTTTG-TTTT
1 -TTTTTTTTTTGATTTT
479382 TTT
1 TTT
479385 ATGAAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 8 0.28
16 21 0.72
ACGTcount: A:0.04, C:0.00, G:0.10, T:0.86
Consensus pattern (16 bp):
TTTTTTTTTTGATTTT
Found at i:483898 original size:23 final size:24
Alignment explanation
Indices: 483872--483922 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
483862 CTATGCGGTT
* *
483872 CTTCAGGA-CAATTCTATACGATC
1 CTTCAGGATAAATTCTACACGATC
* *
483895 CTTCGGGATAAATTCTACACGGTC
1 CTTCAGGATAAATTCTACACGATC
483919 CTTC
1 CTTC
483923 GGGAATTTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.31
Consensus pattern (24 bp):
CTTCAGGATAAATTCTACACGATC
Found at i:483911 original size:24 final size:24
Alignment explanation
Indices: 483881--483926 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
483871 TCTTCAGGAC
*
483881 AATTCTATACGATCCTTCGGGATA
1 AATTCTACACGATCCTTCGGGATA
*
483905 AATTCTACACGGTCCTTCGGGA
1 AATTCTACACGATCCTTCGGGA
483927 ATTTCTACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (24 bp):
AATTCTACACGATCCTTCGGGATA
Found at i:483935 original size:22 final size:22
Alignment explanation
Indices: 483883--483956 Score: 67
Period size: 22 Copynumber: 3.2 Consensus size: 22
483873 TTCAGGACAA
* * *
483883 TTCTATACGATCCTTCGGGATAAA
1 TTCTACACGGTCCTTCGGG--AAT
483907 TTCTACACGGTCCTTCGGGAAT
1 TTCTACACGGTCCTTCGGGAAT
** *
483929 TTCTACATTGTCTTTCGGGACAT
1 TTCTACACGGTCCTTCGGGA-AT
483952 TTCTA
1 TTCTA
483957 TATGTCACTT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
22 19 0.44
23 7 0.16
24 17 0.40
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.38
Consensus pattern (22 bp):
TTCTACACGGTCCTTCGGGAAT
Found at i:483968 original size:23 final size:22
Alignment explanation
Indices: 483893--483969 Score: 66
Period size: 22 Copynumber: 3.4 Consensus size: 22
483883 TTCTATACGA
* **
483893 TCCTTCGGGATAAATTCTACACGG
1 TCCTTCGGG--AATTTCTACATTG
483917 TCCTTCGGGAATTTCTACATTG
1 TCCTTCGGGAATTTCTACATTG
* *
483939 TCTTTCGGGACATTTCTATA-TG
1 TCCTTCGGGA-ATTTCTACATTG
483961 TCACTTCGG
1 TC-CTTCGG
483970 TGCATATTCT
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
22 23 0.51
23 13 0.29
24 9 0.20
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.38
Consensus pattern (22 bp):
TCCTTCGGGAATTTCTACATTG
Found at i:486635 original size:21 final size:20
Alignment explanation
Indices: 486595--486635 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
486585 GTTGTGGTTG
*
486595 TTTCTAGCCGTTGGGGATGA
1 TTTCTAGCCGTTGAGGATGA
*
486615 TTTCTAGCCATTTGAGGATGA
1 TTTCTAGCC-GTTGAGGATGA
486636 AATCTCTGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.20, C:0.15, G:0.29, T:0.37
Consensus pattern (20 bp):
TTTCTAGCCGTTGAGGATGA
Found at i:486782 original size:20 final size:21
Alignment explanation
Indices: 486745--486784 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
486735 AGCCTTTGGG
*
486745 GCCTGATGGTATTAATACTAT
1 GCCTGATGGTATCAATACTAT
*
486766 GCCT-ATGGTATCGATACTA
1 GCCTGATGGTATCAATACTA
486785 CTATGTAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (21 bp):
GCCTGATGGTATCAATACTAT
Found at i:491654 original size:23 final size:23
Alignment explanation
Indices: 491620--491704 Score: 98
Period size: 23 Copynumber: 3.7 Consensus size: 23
491610 GAGTCAAGGG
*
491620 TTCTACGCGGTCCTTCGGGACAA
1 TTCTACGTGGTCCTTCGGGACAA
* * *
491643 TTCTATGTGGTCATTCGAGACAAA
1 TTCTACGTGGTCCTTCGGGAC-AA
** *
491667 TTCTACACGGTCCTTCGGGACAT
1 TTCTACGTGGTCCTTCGGGACAA
491690 TTCTACGTGGTCCTT
1 TTCTACGTGGTCCTT
491705 TGGAACATTT
Statistics
Matches: 49, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
23 31 0.63
24 18 0.37
ACGTcount: A:0.19, C:0.26, G:0.22, T:0.33
Consensus pattern (23 bp):
TTCTACGTGGTCCTTCGGGACAA
Found at i:491749 original size:24 final size:23
Alignment explanation
Indices: 491713--491764 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 23
491703 TTTGGAACAT
* *
491713 TTCTATGCGGCACTTCGGTGCATA
1 TTCTACGCAGCACTTCGGTGCA-A
491737 TTCTACGCAGCACTTCGGTGCAA
1 TTCTACGCAGCACTTCGGTGCAA
491760 TTCTA
1 TTCTA
491765 TGTGGCAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 6 0.23
24 20 0.77
ACGTcount: A:0.19, C:0.27, G:0.21, T:0.33
Consensus pattern (23 bp):
TTCTACGCAGCACTTCGGTGCAA
Found at i:504886 original size:21 final size:21
Alignment explanation
Indices: 504862--504902 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
504852 ACGTTTTCAC
*
504862 CTTTCACTTTCTATCTTTTTA
1 CTTTCACTTTCTATCATTTTA
*
504883 CTTTTACTTTCTATCATTTT
1 CTTTCACTTTCTATCATTTT
504903 CTTCTCCCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.22, G:0.00, T:0.63
Consensus pattern (21 bp):
CTTTCACTTTCTATCATTTTA
Found at i:519747 original size:20 final size:20
Alignment explanation
Indices: 519715--519752 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
519705 TTTATTTTCT
*
519715 TAAAATGATATATGATATTA
1 TAAAATGATATATCATATTA
519735 TAAAAT-ATCATATCATAT
1 TAAAATGAT-ATATCATAT
519753 GAATTATGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.39
Consensus pattern (20 bp):
TAAAATGATATATCATATTA
Found at i:520364 original size:44 final size:44
Alignment explanation
Indices: 520301--520435 Score: 189
Period size: 44 Copynumber: 3.0 Consensus size: 44
520291 ATAAATAAAT
* *
520301 TTACCATTTATCCCATAAGCTCGTAAGCTTATTTTATCAATATAC
1 TTACCA-TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
*
520346 TTACCATTATTCCATAAGCTCGTATGCTTATTTTACCAATATAC
1 TTACCATTATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
* * * **
520390 TTGCCATGATTACATAAGCTCGTAATTTTATTTTACCAATATAC
1 TTACCATTATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
520434 TT
1 TT
520436 GTCATTAACC
Statistics
Matches: 81, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
44 75 0.93
45 6 0.07
ACGTcount: A:0.30, C:0.21, G:0.07, T:0.41
Consensus pattern (44 bp):
TTACCATTATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
Found at i:520638 original size:59 final size:59
Alignment explanation
Indices: 520575--520686 Score: 163
Period size: 59 Copynumber: 1.9 Consensus size: 59
520565 CTTCCCCTTT
* * *
520575 CATTTTAGCACATGGAGTGCCCTAT-TCAAAAATTCATACCATTAGTATGATTTTGTTAC
1 CATTTTAGCACATGAAATGCCCTATGT-AAAAATCCATACCATTAGTATGATTTTGTTAC
* *
520634 CATTTTAGCATATGAAATGCCCTATGTGAAAATCCATACCATTAGTATGATTT
1 CATTTTAGCACATGAAATGCCCTATGTAAAAATCCATACCATTAGTATGATTT
520687 CCTTATCTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
59 46 0.98
60 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (59 bp):
CATTTTAGCACATGAAATGCCCTATGTAAAAATCCATACCATTAGTATGATTTTGTTAC
Found at i:520879 original size:59 final size:59
Alignment explanation
Indices: 520710--520930 Score: 272
Period size: 58 Copynumber: 3.8 Consensus size: 59
520700 GCACTTTATC
* * * * *
520710 TGGAAATCTATACACTCAATATGATTCCCTTACCATTTTAGCACA-TAAATGC-CCTATC
1 TGGAAATCTATACACTCAATATGATTTCCTTACTATTTTAGCACACTCAGTGCTCC-ATA
* *** *
520768 TGGAAATCCATATTTTCAATATGATTTCCTTATTA-TTTAGCACACTCAGTGCTCCAT-
1 TGGAAATCTATACACTCAATATGATTTCCTTACTATTTTAGCACACTCAGTGCTCCATA
*
520825 TGGAAATCTATACACTCAGTATGATTTCCCTTACTATTTTAGCACACTCAGTGCTCCATA
1 TGGAAATCTATACACTCAATATGATTT-CCTTACTATTTTAGCACACTCAGTGCTCCATA
*
520885 TGGAAATCTATACACTCAGTATGATTTCCTTA-TCATTTTAGCACAC
1 TGGAAATCTATACACTCAATATGATTTCCTTACT-ATTTTAGCACAC
520931 AAAGTGCCAT
Statistics
Matches: 142, Mismatches: 15, Indels: 11
0.85 0.09 0.07
Matches are distributed among these distances:
57 31 0.22
58 43 0.30
59 41 0.29
60 27 0.19
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.36
Consensus pattern (59 bp):
TGGAAATCTATACACTCAATATGATTTCCTTACTATTTTAGCACACTCAGTGCTCCATA
Found at i:520937 original size:59 final size:58
Alignment explanation
Indices: 520710--520937 Score: 257
Period size: 59 Copynumber: 3.9 Consensus size: 58
520700 GCACTTTATC
* * *
520710 TGGAAATCTATACACTCAATATGATTCCCTTACCATTTTAGCACATAAA-TGC-CCTAT
1 TGGAAATCTATACACTCAATATGATTTCCTTATCATTTTAGCACACAAAGTGCTCC-AT
* *** * **
520767 CTGGAAATCCATATTTTCAATATGATTTCCTTATTA-TTTAGCACACTCAGTGCTCCAT
1 -TGGAAATCTATACACTCAATATGATTTCCTTATCATTTTAGCACACAAAGTGCTCCAT
* **
520825 TGGAAATCTATACACTCAGTATGATTTCCCTTA-CTATTTTAGCACACTCAGTGCTCCAT
1 TGGAAATCTATACACTCAATATGATTT-CCTTATC-ATTTTAGCACACAAAGTGCTCCAT
*
520884 ATGGAAATCTATACACTCAGTATGATTTCCTTATCATTTTAGCACACAAAGTGC
1 -TGGAAATCTATACACTCAATATGATTTCCTTATCATTTTAGCACACAAAGTGC
520938 CATTCGGTAA
Statistics
Matches: 145, Mismatches: 18, Indels: 13
0.82 0.10 0.07
Matches are distributed among these distances:
57 32 0.22
58 39 0.27
59 46 0.32
60 28 0.19
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (58 bp):
TGGAAATCTATACACTCAATATGATTTCCTTATCATTTTAGCACACAAAGTGCTCCAT
Found at i:526022 original size:7 final size:7
Alignment explanation
Indices: 526010--526040 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
526000 AATCATTATT
526010 TCTCAAA
1 TCTCAAA
526017 TCTCAAA
1 TCTCAAA
526024 TCTCAAA
1 TCTCAAA
526031 TCTCAAA
1 TCTCAAA
526038 TCT
1 TCT
526041 GTTCAACAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.39, C:0.29, G:0.00, T:0.32
Consensus pattern (7 bp):
TCTCAAA
Found at i:533066 original size:113 final size:113
Alignment explanation
Indices: 532863--533100 Score: 431
Period size: 113 Copynumber: 2.1 Consensus size: 113
532853 ATATTATCAG
*
532863 AAATGGAAATATGACGTGCGACACATTTTTATTAATATCATACATTTTTGGGGTAAATATGAAAA
1 AAATTGAAATATGACGTGCGACACATTTTTATTAATATCATACATTTTTGGGGTAAATATGAAAA
* *
532928 AACCAATAATTTAGATATATGAGGAAAGAACCTGAATGACTAGTTTAA
66 AACCAATAATTTAGATATATGAGGAAAGAACCTGAAGGACTAATTTAA
532976 AAATTGAAATATGACGTGCGACACATTTTTATTAATATCATACATTTTTGGGGTAAATATGAAAA
1 AAATTGAAATATGACGTGCGACACATTTTTATTAATATCATACATTTTTGGGGTAAATATGAAAA
*
533041 AACCAATAATTTAGATATATGAGGAAAGAACCTGAAGGACTAATTTAG
66 AACCAATAATTTAGATATATGAGGAAAGAACCTGAAGGACTAATTTAA
*
533089 AAGTTGAAATAT
1 AAATTGAAATAT
533101 AGTTGAAGGT
Statistics
Matches: 120, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
113 120 1.00
ACGTcount: A:0.43, C:0.09, G:0.17, T:0.31
Consensus pattern (113 bp):
AAATTGAAATATGACGTGCGACACATTTTTATTAATATCATACATTTTTGGGGTAAATATGAAAA
AACCAATAATTTAGATATATGAGGAAAGAACCTGAAGGACTAATTTAA
Found at i:537007 original size:21 final size:18
Alignment explanation
Indices: 536981--537025 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 18
536971 GCTTATATGA
*
536981 GTATATGTGATATATGTTATT
1 GTATATGT--TATATGAT-TT
537002 GTATATGTTATATGATTT
1 GTATATGTTATATGATTT
537020 GTATAT
1 GTATAT
537026 ATTCATGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 8 0.35
19 7 0.30
21 8 0.35
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.53
Consensus pattern (18 bp):
GTATATGTTATATGATTT
Found at i:537518 original size:23 final size:23
Alignment explanation
Indices: 537413--537516 Score: 127
Period size: 23 Copynumber: 4.5 Consensus size: 23
537403 GGTTCTACGC
537413 GGTCCTTCGGGACAATTCTACAT
1 GGTCCTTCGGGACAATTCTACAT
* * *
537436 GGTCATTCGGGAAAATTCTAAAT
1 GGTCCTTCGGGACAATTCTACAT
* *
537459 GGTCATTCTGGACAATTCTACAT
1 GGTCCTTCGGGACAATTCTACAT
* * **
537482 GGTCCTTCGGGATATTTCTACGC
1 GGTCCTTCGGGACAATTCTACAT
537505 GGTCCTTCGGGA
1 GGTCCTTCGGGA
537517 TAAATTCATA
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 69 1.00
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.32
Consensus pattern (23 bp):
GGTCCTTCGGGACAATTCTACAT
Found at i:539572 original size:10 final size:10
Alignment explanation
Indices: 539544--539611 Score: 95
Period size: 10 Copynumber: 6.7 Consensus size: 10
539534 TTTCTTACCA
539544 TTTATTT-TT
1 TTTATTTATT
539553 TTT-TTTATT
1 TTTATTTATT
539562 ATTTATTATTATT
1 -TTTA-T-TTATT
539575 TTTATTTATT
1 TTTATTTATT
539585 TTTATTTATT
1 TTTATTTATT
539595 TTTATTTATT
1 TTTATTTATT
539605 TTTATTT
1 TTTATTT
539612 TACTAACTGT
Statistics
Matches: 54, Mismatches: 0, Indels: 9
0.86 0.00 0.14
Matches are distributed among these distances:
8 3 0.06
9 5 0.09
10 35 0.65
11 1 0.02
12 5 0.09
13 5 0.09
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTATTTATT
Found at i:539581 original size:16 final size:16
Alignment explanation
Indices: 539560--539611 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
539550 TTTTTTTTTA
539560 TTATTTATTATTATTT
1 TTATTTATTATTATTT
*
539576 TTATTTATT-TT-TAT
1 TTATTTATTATTATTT
539590 TTATTT-TTATTTATTT
1 TTATTTATTA-TTATTT
539606 TTATTT
1 TTATTT
539612 TACTAACTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
13 2 0.06
14 8 0.26
15 4 0.13
16 17 0.55
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (16 bp):
TTATTTATTATTATTT
Found at i:539611 original size:6 final size:6
Alignment explanation
Indices: 539544--539612 Score: 70
Period size: 6 Copynumber: 11.3 Consensus size: 6
539534 TTTCTTACCA
* *
539544 TTTATT TTTTTT TTTATT ATTTATT ATTATT TTTA-- TTTATT TTTATT
1 TTTATT TTTATT TTTATT -TTTATT TTTATT TTTATT TTTATT TTTATT
*
539591 TATTTTT ATTTATT TTTATT TT
1 T-TTATT -TTTATT TTTATT TT
539613 ACTAACTGTT
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
4 4 0.08
6 33 0.63
7 14 0.27
8 1 0.02
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTATT
Found at i:544207 original size:17 final size:18
Alignment explanation
Indices: 544179--544213 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
544169 TCAACATCAA
*
544179 ATATTGGGGCATTTTTGG
1 ATATTGGGGCATCTTTGG
544197 ATATT-GGGCATCTTTGG
1 ATATTGGGGCATCTTTGG
544214 GGATTCAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.17, C:0.09, G:0.31, T:0.43
Consensus pattern (18 bp):
ATATTGGGGCATCTTTGG
Found at i:544775 original size:38 final size:38
Alignment explanation
Indices: 544694--544775 Score: 125
Period size: 36 Copynumber: 2.2 Consensus size: 38
544684 GAATCGTGCT
*
544694 CACCATTGTCTCTCTTGAGACAGTTTCCCTTGAAACAA
1 CACCTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAA
544732 -A-CTTTGTCTCTCTTGAGACAGTTTCCCTTGGAAA-AA
1 CACCTTTGTCTCTCTTGAGACAGTTTCCCTT-GAAACAA
544768 CACCTTTG
1 CACCTTTG
544776 AAATTGTTTC
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
36 29 0.73
37 6 0.15
38 5 0.12
ACGTcount: A:0.24, C:0.27, G:0.15, T:0.34
Consensus pattern (38 bp):
CACCTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAA
Found at i:544998 original size:37 final size:37
Alignment explanation
Indices: 544947--545018 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
544937 TGGAACTAAG
* * * *
544947 TTTTGTCTCTCTTGAGACAGTTTTTCTTAAAACAAAA
1 TTTTATCTCCCTTGAGACAGTTTCTCATAAAACAAAA
*
544984 TTTTATCTCCCTTGAGACCGTTTCTCATAAAACAA
1 TTTTATCTCCCTTGAGACAGTTTCTCATAAAACAA
545019 CAAATATCTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (37 bp):
TTTTATCTCCCTTGAGACAGTTTCTCATAAAACAAAA
Found at i:545829 original size:106 final size:106
Alignment explanation
Indices: 545637--546054 Score: 573
Period size: 106 Copynumber: 4.0 Consensus size: 106
545627 TCGCGCCACC
* * *
545637 CGAGACTACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCTCAAT
1 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
* *
545702 TTCAGAGCAAATTTCAACTTCACAGCGAAGGATATTGGACT
66 TTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACT
* ** *
545743 CAAGACAACACAAGTTCAACTTCACAACGAAGGGACAACTGGTTGTCAACAAATAATTTCCCAAT
1 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
* * * **
545808 TTTAGAGCTAATTTCAACTTCACAGCGAAGGGCATTGGACT
66 TTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACT
* * * *
545849 CGAGATAGCACAAGTTCAACTTCACAACAAAGGGACGGTTGGTTGTCAAC-AA-AA------AAT
1 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
* *
545906 TTCAGAACCAATTTCAACTTCACAGTGAAGGATATTGGATT
66 TTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACT
*
545947 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAGT
1 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
* *
546012 TCCAGAACCAATTTCAACTTCACAGCGGAGGATATTGGACT
66 TTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACT
546053 CG
1 CG
546055 GAACAATACA
Statistics
Matches: 270, Mismatches: 34, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
98 83 0.31
99 2 0.01
100 2 0.01
104 2 0.01
105 2 0.01
106 179 0.66
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.23
Consensus pattern (106 bp):
CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
TTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACT
Found at i:546007 original size:204 final size:207
Alignment explanation
Indices: 545637--546054 Score: 592
Period size: 204 Copynumber: 2.0 Consensus size: 207
545627 TCGCGCCACC
*
545637 CGAGACTACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCTCAAT
1 CGAGACTACACAAGTTCAACTTCACAACAAAGGGACGGCTGGTTGTCAACAAACAA-----CAAT
*
545702 TTCAGAGCAAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCA
61 TTCAGAACAAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCA
* ** * *
545767 CAACGAAGGGACAACTGGTTGTCAACAAATAATTTCCCAATTTTAGAGCTAATTTCAACTTCACA
126 CAACGAAGGGACAACTGGTTGTCAACAAACAATTTCCCAATTCCAGAACCAATTTCAACTTCACA
*
545832 GCGAAGGGCATTGGACT
191 GCGAAGGACATTGGACT
*
545849 CGAGA-TAGCACAAGTTCAACTTCACAACAAAGGGACGGTTGGTTGTCAAC-AA-AA-AATTTCA
1 CGAGACTA-CACAAGTTCAACTTCACAACAAAGGGACGGCTGGTTGTCAACAAACAACAATTTCA
* * * *
545910 GAACCAATTTCAACTTCACAGTGAAGGATATTGGATTCGAGACAACACAAGTTCAACTTCACAAC
65 GAACAAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAAC
** * *
545975 GAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAGTTCCAGAACCAATTTCAACTTCACAGCGG
130 GAAGGGACAACTGGTTGTCAACAAACAATTTCCCAATTCCAGAACCAATTTCAACTTCACAGCGA
*
546040 AGGATATTGGACT
195 AGGACATTGGACT
546053 CG
1 CG
546055 GAACAATACA
Statistics
Matches: 187, Mismatches: 18, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
204 136 0.73
210 2 0.01
211 4 0.02
212 45 0.24
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.23
Consensus pattern (207 bp):
CGAGACTACACAAGTTCAACTTCACAACAAAGGGACGGCTGGTTGTCAACAAACAACAATTTCAG
AACAAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACG
AAGGGACAACTGGTTGTCAACAAACAATTTCCCAATTCCAGAACCAATTTCAACTTCACAGCGAA
GGACATTGGACT
Found at i:547517 original size:2 final size:2
Alignment explanation
Indices: 547506--547537 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
547496 ATTTATATGT
547506 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
547538 TTTACGTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:549712 original size:23 final size:23
Alignment explanation
Indices: 549679--549784 Score: 113
Period size: 23 Copynumber: 4.6 Consensus size: 23
549669 GTTCTACGCA
* *
549679 GTCCTTCGGGATAATTTTACATG
1 GTCCTTCGGGACAATTATACATG
*
549702 GTCCTTTGGGACAATTATACATG
1 GTCCTTCGGGACAATTATACATG
* *
549725 GTCCTTCAGGACAATTCTACATG
1 GTCCTTCGGGACAATTATACATG
* * * * *
549748 GTTCTTCAGGACATTTCTACGTG
1 GTCCTTCGGGACAATTATACATG
*
549771 GTCATTCGGGACAA
1 GTCCTTCGGGACAA
549785 ATTCATATGC
Statistics
Matches: 70, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 70 1.00
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.34
Consensus pattern (23 bp):
GTCCTTCGGGACAATTATACATG
Found at i:549864 original size:16 final size:17
Alignment explanation
Indices: 549843--549875 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
549833 TGTGCACAAA
549843 ATCTAT-GTACTCACAT
1 ATCTATAGTACTCACAT
*
549859 ATCTATAGTTCTCACAT
1 ATCTATAGTACTCACAT
549876 GTGTACATGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.30, C:0.24, G:0.06, T:0.39
Consensus pattern (17 bp):
ATCTATAGTACTCACAT
Found at i:552552 original size:81 final size:81
Alignment explanation
Indices: 552417--552580 Score: 328
Period size: 81 Copynumber: 2.0 Consensus size: 81
552407 TATAAGAGAA
552417 GTAACCATGTGGATAAAGGAAGGAAAGAAAACTTTGGAGTTATCTTCTTCCTCCCGTGGGTTCTT
1 GTAACCATGTGGATAAAGGAAGGAAAGAAAACTTTGGAGTTATCTTCTTCCTCCCGTGGGTTCTT
552482 GGCTAAAGGTGAGTTG
66 GGCTAAAGGTGAGTTG
552498 GTAACCATGTGGATAAAGGAAGGAAAGAAAACTTTGGAGTTATCTTCTTCCTCCCGTGGGTTCTT
1 GTAACCATGTGGATAAAGGAAGGAAAGAAAACTTTGGAGTTATCTTCTTCCTCCCGTGGGTTCTT
552563 GGCTAAAGGTGAGTTG
66 GGCTAAAGGTGAGTTG
552579 GT
1 GT
552581 CTTTAGCTGG
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 83 1.00
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.30
Consensus pattern (81 bp):
GTAACCATGTGGATAAAGGAAGGAAAGAAAACTTTGGAGTTATCTTCTTCCTCCCGTGGGTTCTT
GGCTAAAGGTGAGTTG
Found at i:553841 original size:19 final size:19
Alignment explanation
Indices: 553813--553857 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
553803 TATTGAATGG
*
553813 AAATAGGCTTGAATAGCTC
1 AAATAAGCTTGAATAGCTC
553832 AAATAAGCTTGAATAGCTC
1 AAATAAGCTTGAATAGCTC
553851 AAATAAG
1 AAATAAG
553858 TTTAAGGCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.44, C:0.13, G:0.18, T:0.24
Consensus pattern (19 bp):
AAATAAGCTTGAATAGCTC
Found at i:554451 original size:19 final size:19
Alignment explanation
Indices: 554427--554466 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
554417 CGAATAATTG
* *
554427 AATCGAATATATAATTTTA
1 AATCGAATATAAAATCTTA
554446 AATCGAATATAAAATCTTA
1 AATCGAATATAAAATCTTA
554465 AA
1 AA
554467 ATTCAATCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.35
Consensus pattern (19 bp):
AATCGAATATAAAATCTTA
Found at i:554611 original size:12 final size:13
Alignment explanation
Indices: 554579--554613 Score: 54
Period size: 12 Copynumber: 2.7 Consensus size: 13
554569 AAAGATTTTC
554579 TTTTTGAAAATCAA
1 TTTTTG-AAATCAA
554593 TTTTTGAAATCAA
1 TTTTTGAAATCAA
554606 -TTTTGAAA
1 TTTTTGAAA
554614 AATTACTCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 8 0.38
13 7 0.33
14 6 0.29
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.46
Consensus pattern (13 bp):
TTTTTGAAATCAA
Found at i:554616 original size:14 final size:14
Alignment explanation
Indices: 554579--554614 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
554569 AAAGATTTTC
554579 TTTTTGAAAATCAA
1 TTTTTGAAAATCAA
554593 TTTTTG-AAATCAA
1 TTTTTGAAAATCAA
554606 -TTTTGAAAA
1 TTTTTGAAAA
554615 ATTACTCCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 5 0.24
13 10 0.48
14 6 0.29
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (14 bp):
TTTTTGAAAATCAA
Found at i:554953 original size:25 final size:25
Alignment explanation
Indices: 554916--554966 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
554906 AAGCAAATCC
*
554916 AAACACCATAATA-TAAAACATTCA
1 AAACACCACAATATTAAAACATTCA
*
554940 AAACAACCACAATATTCAAACATTCA
1 AAAC-ACCACAATATTAAAACATTCA
554966 A
1 A
554967 GTTAACCATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 4 0.17
25 8 0.35
26 11 0.48
ACGTcount: A:0.57, C:0.24, G:0.00, T:0.20
Consensus pattern (25 bp):
AAACACCACAATATTAAAACATTCA
Found at i:556321 original size:19 final size:18
Alignment explanation
Indices: 556297--556343 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
556287 TATATAGTTT
556297 TCAAAACAACATAATTAAA
1 TCAAAACAACA-AATTAAA
*
556316 TCAAAAACAACAATTTAAA
1 TC-AAAACAACAAATTAAA
*
556335 ACAAAACAA
1 TCAAAACAA
556344 TTTTTTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 7 0.28
19 9 0.36
20 9 0.36
ACGTcount: A:0.66, C:0.17, G:0.00, T:0.17
Consensus pattern (18 bp):
TCAAAACAACAAATTAAA
Found at i:561140 original size:18 final size:18
Alignment explanation
Indices: 561099--561141 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
561089 AACTCCAACA
*
561099 TTCTTCTTTTTCTCTGTC
1 TTCTTCTTTGTCTCTGTC
*
561117 TCCTTCTTTGTCTC-GTCC
1 TTCTTCTTTGTCTCTGT-C
561135 TTCTTCT
1 TTCTTCT
561142 CGAGGTCTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.00, C:0.33, G:0.07, T:0.60
Consensus pattern (18 bp):
TTCTTCTTTGTCTCTGTC
Found at i:563621 original size:21 final size:22
Alignment explanation
Indices: 563575--563635 Score: 54
Period size: 21 Copynumber: 2.8 Consensus size: 22
563565 TGCTTATATG
*
563575 AGTATATGTGATAT-ATGTTAT
1 AGTATATGTTATATGATGTTAT
* *
563596 TGTATATGTTATATGAT-TTGT
1 AGTATATGTTATATGATGTTAT
*
563617 AGTATTCATGTTATGTGAT
1 AGTA-T-ATGTTATATGAT
563636 AATAAACTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
21 18 0.56
22 3 0.09
23 11 0.34
ACGTcount: A:0.28, C:0.02, G:0.20, T:0.51
Consensus pattern (22 bp):
AGTATATGTTATATGATGTTAT
Found at i:572802 original size:14 final size:13
Alignment explanation
Indices: 572771--572806 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
572761 GAGTCAACCC
*
572771 GTTGACTTTGACT
1 GTTGACTTTAACT
572784 GTTGACTTTAACTT
1 GTTGACTTTAAC-T
572798 GTTGACTTT
1 GTTGACTTT
572807 GACCAAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.17, C:0.14, G:0.19, T:0.50
Consensus pattern (13 bp):
GTTGACTTTAACT
Found at i:576265 original size:49 final size:49
Alignment explanation
Indices: 576193--576290 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
576183 TACCCCGAGG
576193 ATATTGCTTAATTATTCATCAAGCTAATGGACAAAAAGTCATTAAAAAA
1 ATATTGCTTAATTATTCATCAAGCTAATGGACAAAAAGTCATTAAAAAA
576242 ATATTGCTTAATTATTCATCAAGCTAATGGACAAAAAGTCATTAAAAAA
1 ATATTGCTTAATTATTCATCAAGCTAATGGACAAAAAGTCATTAAAAAA
576291 CTAAAAGGCA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.31
Consensus pattern (49 bp):
ATATTGCTTAATTATTCATCAAGCTAATGGACAAAAAGTCATTAAAAAA
Found at i:577782 original size:3 final size:3
Alignment explanation
Indices: 577774--577828 Score: 74
Period size: 3 Copynumber: 18.0 Consensus size: 3
577764 GCCTATAAAT
* * *
577774 ATA ATA ATA ATA TTA ATA ATA ATA ATA ATA ATA ATTT TTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA
577820 ATA ATA ATA
1 ATA ATA ATA
577829 TACTATTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
3 44 0.98
4 1 0.02
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
ATA
Found at i:577837 original size:25 final size:25
Alignment explanation
Indices: 577774--577828 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
577764 GCCTATAAAT
*
577774 ATAATAATAA-TATTAATAATAATA
1 ATAATAATAATTTTTAATAATAATA
577798 ATAATAATAATTTTTAATAATAATA
1 ATAATAATAATTTTTAATAATAATA
577823 ATAATA
1 ATAATA
577829 TACTATTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 10 0.34
25 19 0.66
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
ATAATAATAATTTTTAATAATAATA
Found at i:579631 original size:31 final size:31
Alignment explanation
Indices: 579583--579662 Score: 142
Period size: 31 Copynumber: 2.6 Consensus size: 31
579573 ATAATTATGA
* *
579583 AAAATATATATTAATTTATATATTTATAAAT
1 AAAATATTTATTTATTTATATATTTATAAAT
579614 AAAATATTTATTTATTTATATATTTATAAAT
1 AAAATATTTATTTATTTATATATTTATAAAT
579645 AAAATATTTATTTATTTA
1 AAAATATTTATTTATTTA
579663 GAAATATCAG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (31 bp):
AAAATATTTATTTATTTATATATTTATAAAT
Found at i:579922 original size:16 final size:16
Alignment explanation
Indices: 579901--579931 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
579891 ATTTTAACGA
579901 ATATATTATTATATAT
1 ATATATTATTATATAT
579917 ATATATTATTATATA
1 ATATATTATTATATA
579932 AATAATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATATATTATTATATAT
Found at i:581289 original size:12 final size:12
Alignment explanation
Indices: 581260--581299 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
581250 GGTATTGGGC
*
581260 AATATAAATAAT
1 AATATTAATAAT
* *
581272 ATTATTAATAAA
1 AATATTAATAAT
581284 AATATTAATAAT
1 AATATTAATAAT
581296 AATA
1 AATA
581300 ATATAAATAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AATATTAATAAT
Found at i:581289 original size:15 final size:15
Alignment explanation
Indices: 581263--581309 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
581253 ATTGGGCAAT
*
581263 ATAAATAATATTATTA
1 ATAAA-AATATTAATA
581279 ATAAAAATATTAATA
1 ATAAAAATATTAATA
* *
581294 ATAATAATATAAATA
1 ATAAAAATATTAATA
581309 A
1 A
581310 AACTGGGACA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
15 23 0.82
16 5 0.18
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
ATAAAAATATTAATA
Found at i:583269 original size:14 final size:14
Alignment explanation
Indices: 583250--583278 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
583240 TTAAACTACA
583250 GAACATTTGATCAT
1 GAACATTTGATCAT
583264 GAACATTTGATCAT
1 GAACATTTGATCAT
583278 G
1 G
583279 GCGTTTGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (14 bp):
GAACATTTGATCAT
Found at i:584560 original size:17 final size:18
Alignment explanation
Indices: 584522--584563 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
584512 AGAAATCATT
584522 AAGAAG-AAAAGAAGTGG
1 AAGAAGAAAAAGAAGTGG
584539 AAGAAGAAAAATGAAG-GG
1 AAGAAGAAAAA-GAAGTGG
584557 -AGAAGAA
1 AAGAAGAA
584564 TTTCAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 13 0.57
18 6 0.26
19 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.33, T:0.05
Consensus pattern (18 bp):
AAGAAGAAAAAGAAGTGG
Found at i:585995 original size:2 final size:2
Alignment explanation
Indices: 585988--586034 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
585978 AACCTAAATA
585988 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
586030 AT AT A
1 AT AT A
586035 GTTAAAACAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:586436 original size:18 final size:18
Alignment explanation
Indices: 586415--586464 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 18
586405 ATAATATATG
*
586415 TATATCATATATAAAATA
1 TATATAATATATAAAATA
* *
586433 TATAGAATATAT-ATATA
1 TATATAATATATAAAATA
*
586450 TATATGAT-TATAAAA
1 TATATAATATATAAAA
586465 AATCATTTAA
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
16 3 0.12
17 12 0.48
18 10 0.40
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (18 bp):
TATATAATATATAAAATA
Found at i:586714 original size:15 final size:15
Alignment explanation
Indices: 586694--586727 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
586684 TTAAAAATAA
*
586694 ATTTAAAATAAAAAT
1 ATTTAAAAGAAAAAT
*
586709 ATTTAAAAGAAACAT
1 ATTTAAAAGAAAAAT
586724 ATTT
1 ATTT
586728 TTTAAAGAAA
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:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (15 bp):
ATTTAAAAGAAAAAT
Found at i:587741 original size:26 final size:26
Alignment explanation
Indices: 587710--587775 Score: 132
Period size: 26 Copynumber: 2.5 Consensus size: 26
587700 GCATGGTCTT
587710 GTGCATCGATGCATCAAATGCACTGA
1 GTGCATCGATGCATCAAATGCACTGA
587736 GTGCATCGATGCATCAAATGCACTGA
1 GTGCATCGATGCATCAAATGCACTGA
587762 GTGCATCGATGCAT
1 GTGCATCGATGCAT
587776 AGTATGTGCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.24
Consensus pattern (26 bp):
GTGCATCGATGCATCAAATGCACTGA
Found at i:590333 original size:23 final size:23
Alignment explanation
Indices: 590304--590380 Score: 79
Period size: 23 Copynumber: 3.4 Consensus size: 23
590294 CATGACCCTG
*
590304 TGCATCGATGCACATTCAAGGCG
1 TGCATCGATGCACATTCAAGGCA
* *
590327 TGCATCGGTGCATCA-GCAA-G-A
1 TGCATCGATGCA-CATTCAAGGCA
*
590348 TGAATCGATGCACATTCAAAGGCA
1 TGCATCGATGCACATTC-AAGGCA
590372 TGCATCGAT
1 TGCATCGAT
590381 TCACTGTTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
20 2 0.05
21 11 0.26
22 3 0.07
23 15 0.36
24 11 0.26
ACGTcount: A:0.30, C:0.23, G:0.25, T:0.22
Consensus pattern (23 bp):
TGCATCGATGCACATTCAAGGCA
Found at i:592256 original size:15 final size:15
Alignment explanation
Indices: 592236--592265 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
592226 TACCTATATC
592236 ATCATTCAAACAAGA
1 ATCATTCAAACAAGA
592251 ATCATTCAAACAAGA
1 ATCATTCAAACAAGA
592266 TTATCATCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.20, G:0.07, T:0.20
Consensus pattern (15 bp):
ATCATTCAAACAAGA
Found at i:596059 original size:45 final size:46
Alignment explanation
Indices: 595974--596061 Score: 151
Period size: 45 Copynumber: 1.9 Consensus size: 46
595964 AAATAGCCTG
* *
595974 AGTGCATCGATGCATGGTCTTGTGCATCGATGCATCAAATGCACTA
1 AGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCACTA
596020 AGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 AGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
596062 TTCAATGTTC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 22 0.55
46 18 0.45
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.27
Consensus pattern (46 bp):
AGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCACTA
Found at i:597891 original size:24 final size:25
Alignment explanation
Indices: 597864--597930 Score: 66
Period size: 24 Copynumber: 2.7 Consensus size: 25
597854 TCATTTTATA
597864 TTATTAAAAAATTAAAAA-TTAAAG
1 TTATTAAAAAATTAAAAAGTTAAAG
* *
597888 TTATAAAAAAATAAGAAAAAGTTAAAG
1 TTATTAAAAAAT--TAAAAAGTTAAAG
* *
597915 -GATTAAAATATTAAAA
1 TTATTAAAAAATTAAAA
597931 GTTTGAAGGT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
24 15 0.44
26 13 0.38
27 6 0.18
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.28
Consensus pattern (25 bp):
TTATTAAAAAATTAAAAAGTTAAAG
Found at i:597943 original size:23 final size:24
Alignment explanation
Indices: 597904--597949 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
597894 AAAAATAAGA
597904 AAAAGTTAAAGGATTAAA-ATATT
1 AAAAGTTAAAGGATTAAATATATT
*
597927 AAAAGTTTGAAGG-TTAAATATAT
1 AAAAG-TTAAAGGATTAAATATAT
597950 AGTCAGACCG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.52, C:0.00, G:0.15, T:0.33
Consensus pattern (24 bp):
AAAAGTTAAAGGATTAAATATATT
Found at i:600738 original size:3 final size:3
Alignment explanation
Indices: 600732--600883 Score: 111
Period size: 3 Copynumber: 51.7 Consensus size: 3
600722 ATTATGTGTA
* *
600732 TAT TAT TA- TAC TA- TAT TA- TAT TAT TAT TAC TAT TAT ATAGT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TA-T TAT
* * * * *
600775 TAC TA- TAT ATAT TAG TAT TAT TAG TAT TAT TAG CAT TAT TAT TA-
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
600819 TAC TAT TAT TAC TAT TA- TAT TGT TAG TAT TAT TACT AAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT
600864 TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
600884 AAGTAAAATT
Statistics
Matches: 119, Mismatches: 19, Indels: 22
0.74 0.12 0.14
Matches are distributed among these distances:
2 14 0.12
3 95 0.80
4 9 0.08
5 1 0.01
ACGTcount: A:0.36, C:0.05, G:0.04, T:0.56
Consensus pattern (3 bp):
TAT
Found at i:610818 original size:2 final size:2
Alignment explanation
Indices: 610811--610856 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
610801 ATTTCATTCA
610811 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
610853 AT AT
1 AT AT
610857 GCATACATAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:611782 original size:41 final size:41
Alignment explanation
Indices: 611717--611804 Score: 115
Period size: 41 Copynumber: 2.1 Consensus size: 41
611707 AAGTTTAGTA
* *
611717 GGTAGTGGGCGGGTGTGGACGTAAAAAGTTATATATGTCGTG
1 GGTAGTGGGCGGGTGTGGACGTAAAAAGTCATAT-CGTCGTG
* * *
611759 GGTAGTGGG-TGGTGTGGATGTAAAAAGTCATATCGTTGTG
1 GGTAGTGGGCGGGTGTGGACGTAAAAAGTCATATCGTCGTG
611799 GGTAGT
1 GGTAGT
611805 TGGTAGATGA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
40 11 0.27
41 21 0.51
42 9 0.22
ACGTcount: A:0.23, C:0.06, G:0.41, T:0.31
Consensus pattern (41 bp):
GGTAGTGGGCGGGTGTGGACGTAAAAAGTCATATCGTCGTG
Found at i:618624 original size:13 final size:13
Alignment explanation
Indices: 618608--618633 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
618598 AGACTATTGG
618608 TAAAATTTTAAAT
1 TAAAATTTTAAAT
618621 TAAAATTTTAAAT
1 TAAAATTTTAAAT
618634 AAATAAAAAT
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TAAAATTTTAAAT
Found at i:623474 original size:128 final size:128
Alignment explanation
Indices: 623247--623744 Score: 934
Period size: 128 Copynumber: 3.9 Consensus size: 128
623237 CTATAATCGG
623247 TTCACTATTCACATGAAGGCGCGTTCCC-GGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
*
623311 TATCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
623374 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
623439 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAG--ATAT-A-TACCTATTAT
66 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
*
623498 TTCACTATTTACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
623563 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
*
623626 TTCACTATTTACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
623691 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGT
66 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGT
623745 TTGAATAACT
Statistics
Matches: 364, Mismatches: 2, Indels: 9
0.97 0.01 0.02
Matches are distributed among these distances:
124 118 0.32
125 1 0.00
126 8 0.02
127 29 0.08
128 208 0.57
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.33
Consensus pattern (128 bp):
TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
Found at i:623691 original size:252 final size:251
Alignment explanation
Indices: 623247--623740 Score: 952
Period size: 252 Copynumber: 2.0 Consensus size: 251
623237 CTATAATCGG
623247 TTCACTATTCACATGAAGGCGCGTTCCCGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTT
*
623312 ATCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 ATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
623377 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
131 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
623442 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATACCTATTAT
196 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATACCTATTAT
*
623498 TTCACTATTTACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCC-GGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
623563 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTT
65 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTT
*
623628 CACTATTTACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTA
130 CACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTA
623693 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATAT
195 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATAT
623741 CAGTTTGAAT
Statistics
Matches: 239, Mismatches: 3, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
251 27 0.11
252 212 0.89
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.33
Consensus pattern (251 bp):
TTCACTATTCACATGAAGGCGCGTTCCCGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTT
ATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATACCTATTAT
Found at i:624227 original size:33 final size:33
Alignment explanation
Indices: 624127--624229 Score: 129
Period size: 33 Copynumber: 3.2 Consensus size: 33
624117 TAAGTTGAAA
*
624127 TTTAATGTTAAATTTCGAATACTATAATTTATAT
1 TTTAAT-TTAAATTTCGAATAATATAATTTATAT
* * *
624161 TTAAATTTAAA-TT-GAATAATATTATTTTTAT
1 TTTAATTTAAATTTCGAATAATATAATTTATAT
* *
624192 TTTATTTTAAATTTCGAATAATATAATTTGTAT
1 TTTAATTTAAATTTCGAATAATATAATTTATAT
624225 TTTAA
1 TTTAA
624230 AAACATTATC
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
31 24 0.41
32 4 0.07
33 25 0.43
34 5 0.09
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (33 bp):
TTTAATTTAAATTTCGAATAATATAATTTATAT
Found at i:624815 original size:21 final size:21
Alignment explanation
Indices: 624748--624817 Score: 106
Period size: 21 Copynumber: 3.3 Consensus size: 21
624738 ATATGGTATA
*
624748 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
624769 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
624790 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
624811 AACCCTG
1 AACCCTG
624818 TGGAGATGGC
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
20 3 0.07
21 39 0.87
22 3 0.07
ACGTcount: A:0.21, C:0.27, G:0.33, T:0.19
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Done.