Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005249.1 Hibiscus syriacus cultivar Beakdansim tig00011873_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: 335851
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:2845 original size:49 final size:50
Alignment explanation
Indices: 2733--2896 Score: 282
Period size: 49 Copynumber: 3.4 Consensus size: 50
2723 TGAGAACTAG
*
2733 ATAAACGAGCTTGTTCGTG---ATAAACGAAAGACTCAATAAACAAGCTT
1 ATAAACGAGCTTGTTCGTGAACATAAACGAATGACTCAATAAACAAGCTT
2780 ATAAACGAGCTTGTTCGTGAACATAAACGAATGACTCAATAAAC-AGCTT
1 ATAAACGAGCTTGTTCGTGAACATAAACGAATGACTCAATAAACAAGCTT
2829 ATAAACGAGCTTGTTCGTGAACATAAACGAATGACTCAATAAACAAGCTT
1 ATAAACGAGCTTGTTCGTGAACATAAACGAATGACTCAATAAACAAGCTT
*
2879 GTAAACGAGCTTGTTCGT
1 ATAAACGAGCTTGTTCGT
2897 CATAAACAAA
Statistics
Matches: 111, Mismatches: 2, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
47 19 0.17
49 49 0.44
50 43 0.39
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.25
Consensus pattern (50 bp):
ATAAACGAGCTTGTTCGTGAACATAAACGAATGACTCAATAAACAAGCTT
Found at i:5419 original size:35 final size:35
Alignment explanation
Indices: 5373--5446 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 35
5363 CAAAATTATT
*
5373 TTGAAGTATTTTAGAATTTTGGG-TTTAGAATGTAA
1 TTGAAGTATTTTAGAA-TTTGGGATTTAGAATGAAA
* *
5408 TTGAATTATTTTTGAATTTGGGATTTAGAATGAAA
1 TTGAAGTATTTTAGAATTTGGGATTTAGAATGAAA
5443 TTGA
1 TTGA
5447 GGACTGTTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
34 6 0.17
35 29 0.83
ACGTcount: A:0.32, C:0.00, G:0.22, T:0.46
Consensus pattern (35 bp):
TTGAAGTATTTTAGAATTTGGGATTTAGAATGAAA
Found at i:14459 original size:22 final size:22
Alignment explanation
Indices: 14434--14482 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
14424 GACTTTTTCT
14434 GTCAAAGTCAACGGTCAGATCA
1 GTCAAAGTCAACGGTCAGATCA
* * *
14456 GTCAAAGTCAATGGTCTGATCG
1 GTCAAAGTCAACGGTCAGATCA
14478 GTCAA
1 GTCAA
14483 CGATCAATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.22
Consensus pattern (22 bp):
GTCAAAGTCAACGGTCAGATCA
Found at i:18366 original size:2 final size:2
Alignment explanation
Indices: 18359--18383 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18349 ATGCCCATTC
18359 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 C
18384 ACTTCATTAT
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:20803 original size:25 final size:24
Alignment explanation
Indices: 20769--20819 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
20759 AAAACATGTC
*
20769 AAAAGATATA-ATTATCAAAAATTAA
1 AAAAGATATACAATAT-AAAAA-TAA
*
20794 AAAATATATACAATATAAAAATAA
1 AAAAGATATACAATATAAAAATAA
20818 AA
1 AA
20820 GAAAAAAACC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 5 0.22
25 14 0.61
26 4 0.17
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.25
Consensus pattern (24 bp):
AAAAGATATACAATATAAAAATAA
Found at i:29221 original size:74 final size:72
Alignment explanation
Indices: 29087--29228 Score: 196
Period size: 72 Copynumber: 1.9 Consensus size: 72
29077 AAAATGGGCC
* ** * * *
29087 CCCATTAAATTACTATATTTTTTAGTTTTTTAAATAAAAAATTATGTTTAAAATATTTTTTAATT
1 CCCACTAAATTACTATATTTTCAAGTATTTAAAATAAAAAAATATGTTTAAAATATTTTTTAATT
29152 ATTGAGG
66 ATTGAGG
29159 CCCACTAAATTA-TCATATTTTCAAGTATTTAAAATAAAAAAAATATGTTTAAAAATATTTTTTA
1 CCCACTAAATTACT-ATATTTTCAAGTATTTAAAAT-AAAAAAATATGTTT-AAAATATTTTTTA
29223 ATTATT
63 ATTATT
29229 AAACTTAAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
71 1 0.02
72 28 0.46
73 13 0.21
74 19 0.31
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (72 bp):
CCCACTAAATTACTATATTTTCAAGTATTTAAAATAAAAAAATATGTTTAAAATATTTTTTAATT
ATTGAGG
Found at i:31743 original size:36 final size:36
Alignment explanation
Indices: 31669--31740 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
31659 TAATATAGTG
* **
31669 TTTGAAGATTTAAATCTAATCTTTTTATTTTTAAAA
1 TTTGAAGATTTAAATCTAATCTTTATATGATTAAAA
31705 TTTGAAGATTTAAATCTAA-CTATTAATATGATTAAA
1 TTTGAAGATTTAAATCTAATCT-TT-ATATGATTAAA
31741 TTTAACTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
35 2 0.06
36 21 0.68
37 8 0.26
ACGTcount: A:0.40, C:0.06, G:0.07, T:0.47
Consensus pattern (36 bp):
TTTGAAGATTTAAATCTAATCTTTATATGATTAAAA
Found at i:32488 original size:20 final size:20
Alignment explanation
Indices: 32463--32509 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
32453 TTCGTGCATG
32463 GATGCACAACAGGATGAATC
1 GATGCACAACAGGATGAATC
*
32483 GATGCACAACAGGATGCATC
1 GATGCACAACAGGATGAATC
32503 GATGCAC
1 GATGCAC
32510 TAAGTGCATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.36, C:0.23, G:0.26, T:0.15
Consensus pattern (20 bp):
GATGCACAACAGGATGAATC
Found at i:32596 original size:21 final size:21
Alignment explanation
Indices: 32529--32628 Score: 121
Period size: 21 Copynumber: 4.7 Consensus size: 21
32519 TCAAAATGGA
*
32529 GTGCATGGATGCACTGCA-TG
1 GTGCATGGATGCACTGCAGAG
* **
32549 GTGCATCGATGCACTAGTGGCAG
1 GTGCATGGATGCACT-GCAG-AG
32572 GTGCATGGATGCACTGCAGAG
1 GTGCATGGATGCACTGCAGAG
*
32593 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGAG
*
32614 GTGCATTGATGCACT
1 GTGCATGGATGCACT
32629 TTGACACCCT
Statistics
Matches: 68, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
20 14 0.21
21 37 0.54
22 2 0.03
23 15 0.22
ACGTcount: A:0.21, C:0.20, G:0.36, T:0.23
Consensus pattern (21 bp):
GTGCATGGATGCACTGCAGAG
Found at i:33649 original size:2 final size:2
Alignment explanation
Indices: 33642--33675 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
33632 TGAGTGGATG
33642 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
33676 TGGGTCGGGT
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:34570 original size:31 final size:30
Alignment explanation
Indices: 34547--34636 Score: 94
Period size: 29 Copynumber: 3.0 Consensus size: 30
34537 AAATTATAAT
34547 TTATATTTTAAATTAATTTTTAAATT-TTC
1 TTATATTTTAAATTAATTTTTAAATTATTC
* * * * *
34576 TAAAATTTTATATTATTTTTTAAAATATGTC
1 TTATATTTTAAATTAATTTTTAAATTAT-TC
* *
34607 TTTTATTCTAAATTAATTTTTAAA-TATTC
1 TTATATTTTAAATTAATTTTTAAATTATTC
34636 T
1 T
34637 AATCTCTTCT
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
29 24 0.50
30 4 0.08
31 20 0.42
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (30 bp):
TTATATTTTAAATTAATTTTTAAATTATTC
Found at i:39086 original size:258 final size:258
Alignment explanation
Indices: 38629--39145 Score: 962
Period size: 258 Copynumber: 2.0 Consensus size: 258
38619 CCTTCTCTTG
*
38629 ACATGATTTTTGGAAGACTTGTTTAATTTATCAGAGTTAAATTTATTGTCAAACTGTCATATTCA
1 ACATGATTTTTGGAAGACTTGTTTAATTTATCAGAGTTAAATTTATTGTCAAACAGTCATATTCA
* * *
38694 TTCAACTTGTCAACCGACGAGTAGCAATCATGATCTTAAATCTGACACGAACACTAAGGATCACT
66 TTCAACTTATCAACCGACGAGTAACAATCATAATCTTAAATCTGACACGAACACTAAGGATCACT
38759 ATAAAATCCTTCAACCAATACTGAGGGAGGGGACTTTTAGACTGAGAATTTTCCTTCTTATGATG
131 ATAAAATCCTTCAACCAATACTGAGGGAGGGGACTTTTAGACTGAGAATTTTCCTTCTTATGATG
*
38824 AAATTCCACTTCATCTCAAAAAGTCTCCTTGACCAAATGATTTGAGTCGTCTGTAACTTCATT
196 AAATTCCACTTCATCTCAAAAAATCTCCTTGACCAAATGATTTGAGTCGTCTGTAACTTCATT
*
38887 ACATGATTTTTGGAAGATTTGTTTAATTTATCAGAGTTAAATTTATTGTCAAACAGTCATATTCA
1 ACATGATTTTTGGAAGACTTGTTTAATTTATCAGAGTTAAATTTATTGTCAAACAGTCATATTCA
38952 TTCAACTTATCAACCGACGAGTAACAATCATAATCTTAAATCTGACACGAACACTAAGGATCACT
66 TTCAACTTATCAACCGACGAGTAACAATCATAATCTTAAATCTGACACGAACACTAAGGATCACT
* *
39017 ATAAAATCCTTCAACCAATACTGAGGGAGGGGACTTTTTGACTGAGAATTTTCCTTTTTATGATG
131 ATAAAATCCTTCAACCAATACTGAGGGAGGGGACTTTTAGACTGAGAATTTTCCTTCTTATGATG
39082 AAATTCCACTTCATCTCAAAAAATCTCCTTGACCAAATGATTTGAGTCGTCTGTAACTTCATT
196 AAATTCCACTTCATCTCAAAAAATCTCCTTGACCAAATGATTTGAGTCGTCTGTAACTTCATT
39145 A
1 A
39146 GTTGAACCAT
Statistics
Matches: 251, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
258 251 1.00
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (258 bp):
ACATGATTTTTGGAAGACTTGTTTAATTTATCAGAGTTAAATTTATTGTCAAACAGTCATATTCA
TTCAACTTATCAACCGACGAGTAACAATCATAATCTTAAATCTGACACGAACACTAAGGATCACT
ATAAAATCCTTCAACCAATACTGAGGGAGGGGACTTTTAGACTGAGAATTTTCCTTCTTATGATG
AAATTCCACTTCATCTCAAAAAATCTCCTTGACCAAATGATTTGAGTCGTCTGTAACTTCATT
Found at i:40280 original size:19 final size:19
Alignment explanation
Indices: 40256--40298 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
40246 CCATAAGGCT
40256 TAACTACATAATCATAATC
1 TAACTACATAATCATAATC
40275 TAACTACATAATCATAATC
1 TAACTACATAATCATAATC
40294 TAACT
1 TAACT
40299 TATTCACAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.33
Consensus pattern (19 bp):
TAACTACATAATCATAATC
Found at i:41474 original size:41 final size:41
Alignment explanation
Indices: 41411--41581 Score: 132
Period size: 41 Copynumber: 4.2 Consensus size: 41
41401 TTAGTTGTAT
* * *
41411 TTTAGTGGCTTTTTTGAT-CAAACACCGATAAATACTCATAC
1 TTTAGTGACATTTTT-ATACAAACACCGATAAAGACTCATAC
* * * *
41452 TTTAGTGACGTTTTTATACAAACGCC-ACTAAATACTCATAT
1 TTTAGTGACATTTTTATACAAACACCGA-TAAAGACTCATAC
** * * * * *
41493 TTTAGTGGTATTTTTATATAAACGCCGCTAAAGATTCATAA
1 TTTAGTGACATTTTTATACAAACACCGATAAAGACTCATAC
* * * *
41534 TTTAGTGGA-ATTTTTATATAAACACCGCTAAAGATTCCTAC
1 TTTAGT-GACATTTTTATACAAACACCGATAAAGACTCATAC
41575 TTTAGTG
1 TTTAGTG
41582 GTGCTTTAAG
Statistics
Matches: 110, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
40 4 0.04
41 105 0.95
42 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (41 bp):
TTTAGTGACATTTTTATACAAACACCGATAAAGACTCATAC
Found at i:41582 original size:41 final size:41
Alignment explanation
Indices: 41430--41582 Score: 164
Period size: 41 Copynumber: 3.7 Consensus size: 41
41420 TTTTTTGATC
* * * *
41430 AAACACCGATAAATACTCATACTTTAGT-GACGTTTTTATAC
1 AAACACCGCTAAAGACTCATACTTTAGTGGA-ATTTTTATAT
* * * * *
41471 AAACGCCACTAAATACTCATATTTTAGTGGTATTTTTATAT
1 AAACACCGCTAAAGACTCATACTTTAGTGGAATTTTTATAT
* * *
41512 AAACGCCGCTAAAGATTCATAATTTAGTGGAATTTTTATAT
1 AAACACCGCTAAAGACTCATACTTTAGTGGAATTTTTATAT
* *
41553 AAACACCGCTAAAGATTCCTACTTTAGTGG
1 AAACACCGCTAAAGACTCATACTTTAGTGG
41583 TGCTTTAAGC
Statistics
Matches: 96, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
41 95 0.99
42 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35
Consensus pattern (41 bp):
AAACACCGCTAAAGACTCATACTTTAGTGGAATTTTTATAT
Found at i:50425 original size:21 final size:21
Alignment explanation
Indices: 50401--50459 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
50391 TGATTTATTA
*
50401 TTATGGATTTCAATTTTCTTG
1 TTATGGATTTCAAGTTTCTTG
* *
50422 TTATGGATTTGAAGTTTGTTG
1 TTATGGATTTCAAGTTTCTTG
50443 TTAT-GATTGTCAAGTTT
1 TTATGGATT-TCAAGTTT
50460 ATTGGTTAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.12
21 29 0.88
ACGTcount: A:0.20, C:0.05, G:0.20, T:0.54
Consensus pattern (21 bp):
TTATGGATTTCAAGTTTCTTG
Found at i:50721 original size:44 final size:43
Alignment explanation
Indices: 50652--50743 Score: 125
Period size: 44 Copynumber: 2.1 Consensus size: 43
50642 TTCTAAATTC
*
50652 ACAAACGACACTATATGATATAACATTTAGCGGCATTTTTGGG
1 ACAAACGACACTATATGATAGAACATTTAGCGGCATTTTTGGG
*
50695 AACAAACG-CAACTATATG-TCAGAACATTTAGTGGCATTTTTGGG
1 -ACAAACGAC-ACTATATGAT-AGAACATTTAGCGGCATTTTTGGG
50739 ACAAA
1 ACAAA
50744 ACGCCACAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
43 7 0.16
44 37 0.84
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.28
Consensus pattern (43 bp):
ACAAACGACACTATATGATAGAACATTTAGCGGCATTTTTGGG
Found at i:51390 original size:2 final size:2
Alignment explanation
Indices: 51385--51410 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
51375 ATTGTTTTTA
51385 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
51411 TTAAAATAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53104 original size:32 final size:32
Alignment explanation
Indices: 53068--53129 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
53058 ACTTATCGCG
*
53068 TCATCATCTTAGGTGATGTAACACATGTCACA
1 TCATCATCTTAAGTGATGTAACACATGTCACA
*
53100 TCATCATCTTAATTGATGTAACACATGTCA
1 TCATCATCTTAAGTGATGTAACACATGTCA
53130 TGTCATAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (32 bp):
TCATCATCTTAAGTGATGTAACACATGTCACA
Found at i:53149 original size:32 final size:32
Alignment explanation
Indices: 53068--53152 Score: 93
Period size: 32 Copynumber: 2.7 Consensus size: 32
53058 ACTTATCGCG
* *
53068 TCATCATCTTAGGTGATGTAACACATGTCACA
1 TCATCAACTTAGATGATGTAACACATGTCACA
* **
53100 TCATCATCTTA-ATTGATGTAACACATGTCATG
1 TCATCAACTTAGA-TGATGTAACACATGTCACA
53132 TCAT-AACATTAGATGATGTAA
1 TCATCAAC-TTAGATGATGTAA
53153 TATATCAATA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
31 2 0.04
32 43 0.93
33 1 0.02
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (32 bp):
TCATCAACTTAGATGATGTAACACATGTCACA
Found at i:58164 original size:23 final size:23
Alignment explanation
Indices: 58118--58164 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
58108 AACCATATAG
** **
58118 ATGAACATGTTGGCGAACGTTAA
1 ATGAACATGTTCCCGAACACTAA
58141 ATGAACATGTTCCCGAACACTAA
1 ATGAACATGTTCCCGAACACTAA
58164 A
1 A
58165 CAAACCAACA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (23 bp):
ATGAACATGTTCCCGAACACTAA
Found at i:69998 original size:29 final size:29
Alignment explanation
Indices: 69955--70110 Score: 132
Period size: 29 Copynumber: 5.6 Consensus size: 29
69945 CCTTTTTAAG
*
69955 AAATATTTACCAAAATATCATCATTTTCA
1 AAATAATTACCAAAATATCATCATTTTCA
* *
69984 AAATAATTACTAAAATATCAT--TTTTTA
1 AAATAATTACCAAAATATCATCATTTTCA
* *
70011 AAGAAAATTA-CTAAAT-T-ATCA-TTT-A
1 AA-ATAATTACCAAAATATCATCATTTTCA
* * *
70036 TAAA-AATTACAAAAATAGCA-CTATTTTTA
1 -AAATAATTACCAAAATATCATC-ATTTTCA
* *
70065 AAATAATTACCAGAATATCACCATTTTCA
1 AAATAATTACCAAAATATCATCATTTTCA
70094 AAATAATTACCAAAATA
1 AAATAATTACCAAAATA
70111 CCACTCGATT
Statistics
Matches: 101, Mismatches: 14, Indels: 24
0.73 0.10 0.17
Matches are distributed among these distances:
24 5 0.05
25 8 0.08
26 7 0.07
27 13 0.13
28 12 0.12
29 55 0.54
30 1 0.01
ACGTcount: A:0.50, C:0.13, G:0.02, T:0.35
Consensus pattern (29 bp):
AAATAATTACCAAAATATCATCATTTTCA
Found at i:70020 original size:28 final size:28
Alignment explanation
Indices: 69947--70034 Score: 90
Period size: 28 Copynumber: 3.1 Consensus size: 28
69937 GTTATCACCC
*
69947 TTTTT-AAGAAATATTTACCAAAATATCAT
1 TTTTTAAAGAAA-A-TTACTAAAATATCAT
* *
69976 CATTTTCAAA-ATAATTACTAAAATATCAT
1 --TTTTTAAAGAAAATTACTAAAATATCAT
*
70005 TTTTTAAAGAAAATTACTAAATTATCAT
1 TTTTTAAAGAAAATTACTAAAATATCAT
70033 TT
1 TT
70035 ATAAAAATTA
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
27 7 0.14
28 19 0.39
29 14 0.29
30 1 0.02
31 6 0.12
32 2 0.04
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.42
Consensus pattern (28 bp):
TTTTTAAAGAAAATTACTAAAATATCAT
Found at i:70898 original size:2 final size:2
Alignment explanation
Indices: 70891--70931 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
70881 AAATTTCAAT
70891 TA 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 TA T
70932 TCCCAATTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:75039 original size:22 final size:22
Alignment explanation
Indices: 75011--75055 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
75001 GGGGTTGAGG
75011 CCTGATTGTGTTACATTCAATA
1 CCTGATTGTGTTACATTCAATA
75033 CCTGATTGTGTTACATTCAATA
1 CCTGATTGTGTTACATTCAATA
75055 C
1 C
75056 TTTGATAGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (22 bp):
CCTGATTGTGTTACATTCAATA
Found at i:75620 original size:7 final size:8
Alignment explanation
Indices: 75599--75626 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
75589 CATGATCAAG
75599 GGAAAAAT
1 GGAAAAAT
75607 GGAAAAAT
1 GGAAAAAT
75615 GGAAAAAT
1 GGAAAAAT
75623 GGAA
1 GGAA
75627 GTTTTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.61, C:0.00, G:0.29, T:0.11
Consensus pattern (8 bp):
GGAAAAAT
Found at i:78870 original size:46 final size:46
Alignment explanation
Indices: 78751--78894 Score: 209
Period size: 46 Copynumber: 3.1 Consensus size: 46
78741 TTTATTTTCA
*
78751 TTTTTTGAATAAATGCTTGCGAACTAGATATCATGCGGTTAGGTTTA-
1 TTTTTTGAAT-AA-GCATGCGAACTAGATATCATGCGGTTAGGTTTAT
* *
78798 TTTTTCGAACAAGCATGCGAACTAGATATCATGCGGTTAGGTTTAT
1 TTTTTTGAATAAGCATGCGAACTAGATATCATGCGGTTAGGTTTAT
* *
78844 TTTTTTGAATAAGCATGCGAATTAGATATCATGCGGTTAGGATTTCT
1 TTTTTTGAATAAGCATGCGAACTAGATATCATGCGGTTAGG-TTTAT
78891 TTTT
1 TTTT
78895 GTGGATAACA
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
45 32 0.36
46 40 0.45
47 16 0.18
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.40
Consensus pattern (46 bp):
TTTTTTGAATAAGCATGCGAACTAGATATCATGCGGTTAGGTTTAT
Found at i:88405 original size:18 final size:18
Alignment explanation
Indices: 88371--88514 Score: 60
Period size: 18 Copynumber: 7.5 Consensus size: 18
88361 TTGCTTGAAG
*
88371 AAGAAATAAAAGA-GAAAA
1 AAGAAA-AAAAAATGAAAA
88389 AAGAAAAAAAAATGAAAA
1 AAGAAAAAAAAATGAAAA
* *
88407 ATA-ATAATAAAAATGAGAAG
1 A-AGA-AAAAAAAATGA-AAA
*
88427 AAGAAAAAGGAAAAGGAAAA
1 AAGAAAAA--AAAATGAAAA
* *
88447 AATG-AGAAAAAACGAAAA
1 AA-GAAAAAAAAATGAAAA
* *
88465 TGATGGAAAAAACGAAAAGAAAA
1 --A-AGAAAAAA--AAATGAAAA
* *
88488 AAGAAGAAAAAATGGAAA
1 AAGAAAAAAAAATGAAAA
*
88506 ATGAAAAAA
1 AAGAAAAAA
88515 GAGAAAAAAT
Statistics
Matches: 95, Mismatches: 17, Indels: 28
0.68 0.12 0.20
Matches are distributed among these distances:
17 5 0.05
18 36 0.38
19 15 0.16
20 19 0.20
21 12 0.13
23 8 0.08
ACGTcount: A:0.73, C:0.01, G:0.18, T:0.08
Consensus pattern (18 bp):
AAGAAAAAAAAATGAAAA
Found at i:88499 original size:42 final size:42
Alignment explanation
Indices: 88430--88509 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
88420 TGAGAAGAAG
*
88430 AAAAAGGAAAAGGAAAAAATGAGAAAAAACGAAAATGATGGA
1 AAAAACGAAAAGGAAAAAATGAGAAAAAACGAAAATGATGGA
*
88472 AAAAACGAAAA-GAAAAAA-GAAGAAAAAATGGAAAATGA
1 AAAAACGAAAAGGAAAAAATG-AGAAAAAA-CGAAAATGA
88510 AAAAAGAGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 1 0.03
41 15 0.44
42 18 0.53
ACGTcount: A:0.70, C:0.03, G:0.21, T:0.06
Consensus pattern (42 bp):
AAAAACGAAAAGGAAAAAATGAGAAAAAACGAAAATGATGGA
Found at i:88524 original size:24 final size:24
Alignment explanation
Indices: 88470--88524 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
88460 GAAAATGATG
88470 GAAAAAA-CGAAAAGAAAAAAGAA
1 GAAAAAATCGAAAAGAAAAAAGAA
*
88493 GAAAAAATGGAAAATGAAAAAAG-A
1 GAAAAAATCGAAAA-GAAAAAAGAA
88517 GAAAAAAT
1 GAAAAAAT
88525 AAAAAATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 7 0.24
24 14 0.48
25 8 0.28
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.05
Consensus pattern (24 bp):
GAAAAAATCGAAAAGAAAAAAGAA
Found at i:88530 original size:24 final size:25
Alignment explanation
Indices: 88479--88535 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 25
88469 GGAAAAAACG
**
88479 AAAA-GAAAAAAGAAGAAAAAATGG
1 AAAATGAAAAAAGAAGAAAAAATAA
88503 AAAATGAAAAAAG-AGAAAAAATAA
1 AAAATGAAAAAAGAAGAAAAAATAA
88527 AAAAT-AAAA
1 AAAATGAAAA
88536 GATAAAAGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
23 4 0.13
24 18 0.60
25 8 0.27
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.07
Consensus pattern (25 bp):
AAAATGAAAAAAGAAGAAAAAATAA
Found at i:89929 original size:51 final size:51
Alignment explanation
Indices: 89855--90057 Score: 298
Period size: 51 Copynumber: 3.9 Consensus size: 51
89845 AAACTCGTTT
89855 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
*
89906 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGAACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* * *
89957 GTTGAAGATTGTTTGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACACGTTT
1 GTTGAAGA----TTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* * *
90012 ATTGAAGATCGAGTCTTTATACTCTCTGAAGGAATAGGGAGCGGAC
1 GTTGAAGATTGAGTC-CTATACTCTCTGAAGGAATAGGGAGCGGAC
90058 CCGTTTTATG
Statistics
Matches: 138, Mismatches: 9, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
51 64 0.46
52 28 0.20
55 46 0.33
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.27
Consensus pattern (51 bp):
GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
Found at i:90002 original size:55 final size:55
Alignment explanation
Indices: 89865--90247 Score: 385
Period size: 55 Copynumber: 7.1 Consensus size: 55
89855 GTTGAAGATT
* *
89865 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGA---TT-
1 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTCATTGAAGATTGTTC
* * * *
89916 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGAACAAGTTCGTTGAAGATTGTTT
1 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTCATTGAAGATTGTTC
* *
89971 GAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTATTGAAGA----TC
1 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTCATTGAAGATTGTTC
* * *
90022 GAGTCTTTATACTCTCTGAAGGAATAGGGAGCGGACCCGTT-TTATGAAGATTGTTC
1 GAGTC-CTATACTCTCTGAAGGAATAGGGAGCGGACACGTTCAT-TGAAGATTGTTC
* * ** *
90078 GAGTTCTATACTCCCTGAACGG-ATAGGGAGCAAACTCGTTC-TATGAAGATTGTTC
1 GAGTCCTATACTCTCTGAA-GGAATAGGGAGCGGACACGTTCAT-TGAAGATTGTTC
* * * * *
90133 GAGTTCTATACTCCCTGAATGAATAGGGAGCGGACCCGTTTATTGAAGATTGTTC
1 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTCATTGAAGATTGTTC
* * * * * *
90188 GAGTCTTATACTCCCTGAATGAATAGGGAGCAGACACG-CCATTTGAAGATTTTTC
1 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTCA-TTGAAGATTGTTC
*
90243 AAGTC
1 GAGTC
90248 TCACTTATTA
Statistics
Matches: 287, Mismatches: 30, Indels: 26
0.84 0.09 0.08
Matches are distributed among these distances:
51 55 0.19
52 38 0.13
54 4 0.01
55 181 0.63
56 9 0.03
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (55 bp):
GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTCATTGAAGATTGTTC
Found at i:90166 original size:162 final size:157
Alignment explanation
Indices: 89850--90223 Score: 439
Period size: 162 Copynumber: 2.3 Consensus size: 157
89840 GAAGCAAACT
* * *
89850 CGTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGAT
1 CGTTTATTGAAGATCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGAT
* * *
89915 TGAGTCCTATACTCTCTGAAGGAATAGGGAGCGAACAAGTTCGTTGAAGATTGTTTGAGTCCTAT
66 TGAGTCCTATACTCCCTGAAGGAATAGGGAGCAAACAAGTTCGTTGAAGATTGTTCGAGTCCTAT
*
89980 ACTCTCTGAAGGAATAGAGAGCGGACA
131 ACTCCCTGAAGGAATAGAGAGCGGACA
** *
90007 CGTTTATTGAAGATCGAGTCTTTATACTCTCTGAAGGAATAGGGAGCGGACCCGTT-TTATGAAG
1 CGTTTATTGAAGATCGAGTC-TTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGT-TGAAG
* **
90071 ATTGTTCGAGTTCTATACTCCCTGAACGG-ATAGGGAGCAAACTCGTTC-TATGAAGATTGTTCG
64 A---TT-GAGTCCTATACTCCCTGAA-GGAATAGGGAGCAAACAAGTTCGT-TGAAGATTGTTCG
* * * *
90134 AGTTCTATACTCCCTGAATGAATAGGGAGCGGACC
123 AGTCCTATACTCCCTGAAGGAATAGAGAGCGGACA
* * *
90169 CGTTTATTGAAGATTGTTCGAGTCTTATACTCCCTGAATGAATAGGGAGCAGACA
1 CGTTTATTGAAGA----TCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACA
90224 CGCCATTTGA
Statistics
Matches: 184, Mismatches: 21, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
157 19 0.10
158 38 0.21
161 3 0.02
162 88 0.48
163 2 0.01
165 27 0.15
166 7 0.04
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (157 bp):
CGTTTATTGAAGATCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGAT
TGAGTCCTATACTCCCTGAAGGAATAGGGAGCAAACAAGTTCGTTGAAGATTGTTCGAGTCCTAT
ACTCCCTGAAGGAATAGAGAGCGGACA
Found at i:93520 original size:27 final size:27
Alignment explanation
Indices: 93489--93583 Score: 176
Period size: 27 Copynumber: 3.6 Consensus size: 27
93479 TCTATTTACA
93489 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
93516 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
93543 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
93570 AAATC--ATCTCTATA
1 AAATCATATCTCTATA
93584 ATTCCTACAC
Statistics
Matches: 68, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
25 9 0.13
27 59 0.87
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.31
Consensus pattern (27 bp):
AAATCATATCTCTATAGGAATGGTAAC
Found at i:101889 original size:3 final size:3
Alignment explanation
Indices: 101881--101984 Score: 156
Period size: 3 Copynumber: 35.0 Consensus size: 3
101871 ATACCATCCT
*
101881 TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TCA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
101928 TTA TTA TTA TTA TAA ATA TTA TTA TTA TTA TTA TTA TTA TTA TTA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
101976 ATA TTA TTA
1 TTA TTA TTA
101985 AGGTAAACTA
Statistics
Matches: 90, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
2 2 0.02
3 88 0.98
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:111148 original size:19 final size:19
Alignment explanation
Indices: 111124--111179 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
111114 GAACGCTGGA
111124 AACCGGTTTTGACCGGTTT
1 AACCGGTTTTGACCGGTTT
111143 AACCGGTTTTGAACCGGTTTT
1 AACCGGTTTTG-ACCGG-TTT
*
111164 GACCGG-TTTGACCGGT
1 AACCGGTTTTGACCGGT
111180 CACGACCCGT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
18 1 0.03
19 16 0.47
20 9 0.26
21 8 0.24
ACGTcount: A:0.16, C:0.21, G:0.29, T:0.34
Consensus pattern (19 bp):
AACCGGTTTTGACCGGTTT
Found at i:111159 original size:11 final size:11
Alignment explanation
Indices: 111124--111172 Score: 70
Period size: 10 Copynumber: 4.8 Consensus size: 11
111114 GAACGCTGGA
111124 AACCGGTTTTG
1 AACCGGTTTTG
111135 -ACCGG-TTT-
1 AACCGGTTTTG
111143 AACCGGTTTTG
1 AACCGGTTTTG
111154 AACCGGTTTTG
1 AACCGGTTTTG
111165 -ACCGGTTT
1 AACCGGTTT
111173 GACCGGTCAC
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
9 8 0.23
10 16 0.46
11 11 0.31
ACGTcount: A:0.16, C:0.20, G:0.27, T:0.37
Consensus pattern (11 bp):
AACCGGTTTTG
Found at i:111175 original size:9 final size:10
Alignment explanation
Indices: 111125--111179 Score: 78
Period size: 9 Copynumber: 5.6 Consensus size: 10
111115 AACGCTGGAA
111125 ACCGGTTTTG
1 ACCGGTTTTG
*
111135 ACCGG-TTTA
1 ACCGGTTTTG
111144 ACCGGTTTTG
1 ACCGGTTTTG
111154 AACCGGTTTTG
1 -ACCGGTTTTG
111165 ACCGG-TTTG
1 ACCGGTTTTG
111174 ACCGGT
1 ACCGGT
111180 CACGACCCGT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
9 17 0.43
10 13 0.32
11 10 0.25
ACGTcount: A:0.15, C:0.22, G:0.29, T:0.35
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:111223 original size:18 final size:18
Alignment explanation
Indices: 111200--111251 Score: 95
Period size: 18 Copynumber: 2.9 Consensus size: 18
111190 TTACCCGTTT
*
111200 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCA
111218 ACCCGACCCGTTGACCCA
1 ACCCGACCCGTTGACCCA
111236 ACCCGACCCGTTGACC
1 ACCCGACCCGTTGACC
111252 GTTGACCGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.19, C:0.50, G:0.19, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGTTGACCCA
Found at i:111234 original size:13 final size:13
Alignment explanation
Indices: 111192--111222 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
111182 CGACCCGTTT
*
111192 ACCCGTTTACCCG
1 ACCCGTTGACCCG
111205 ACCCGTTGACCCG
1 ACCCGTTGACCCG
111218 ACCCG
1 ACCCG
111223 ACCCGTTGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.48, G:0.19, T:0.16
Consensus pattern (13 bp):
ACCCGTTGACCCG
Found at i:111320 original size:29 final size:29
Alignment explanation
Indices: 111259--111325 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
111249 ACCGTTGACC
*****
111259 GGTGCTATTATGGGAATTAATTCAGTTTT
1 GGTGCTATTATGGGAATTAATTCAAAAAG
*
111288 GGTGCTATTCTGGGAATTAATTCAAAAAG
1 GGTGCTATTATGGGAATTAATTCAAAAAG
111317 GGTGCTATT
1 GGTGCTATT
111326 TGTGTAAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.27, C:0.09, G:0.25, T:0.39
Consensus pattern (29 bp):
GGTGCTATTATGGGAATTAATTCAAAAAG
Found at i:119653 original size:14 final size:15
Alignment explanation
Indices: 119617--119654 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
119607 ATATTTAATT
119617 TAAATTAT-TAACTAA
1 TAAATTATAT-ACTAA
119632 TAAATTATATACTAA
1 TAAATTATATACTAA
119647 T-AATTATA
1 TAAATTATA
119655 GAAATAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.32
15 14 0.64
16 1 0.05
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (15 bp):
TAAATTATATACTAA
Found at i:126787 original size:29 final size:29
Alignment explanation
Indices: 126745--126812 Score: 127
Period size: 29 Copynumber: 2.3 Consensus size: 29
126735 TTTATACACT
126745 ACCCTAAACCATAATCCCATAACCTTTTA
1 ACCCTAAACCATAATCCCATAACCTTTTA
*
126774 ACCCTAAACCATAATCTCATAACCTTTTA
1 ACCCTAAACCATAATCCCATAACCTTTTA
126803 ACCCTAAACC
1 ACCCTAAACC
126813 CTAAACTCTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.38, C:0.35, G:0.00, T:0.26
Consensus pattern (29 bp):
ACCCTAAACCATAATCCCATAACCTTTTA
Found at i:130408 original size:19 final size:19
Alignment explanation
Indices: 130384--130421 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
130374 AAGAAACTAT
130384 TTTTTAACTTTTAATAGTC
1 TTTTTAACTTTTAATAGTC
130403 TTTTTAACTTTTAATAGTC
1 TTTTTAACTTTTAATAGTC
130422 GAGAGATTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.05, T:0.58
Consensus pattern (19 bp):
TTTTTAACTTTTAATAGTC
Found at i:146763 original size:2 final size:2
Alignment explanation
Indices: 146756--146789 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
146746 ACCAAATTAC
146756 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
146790 CAACACTTTA
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:147484 original size:243 final size:241
Alignment explanation
Indices: 147056--147534 Score: 805
Period size: 243 Copynumber: 2.0 Consensus size: 241
147046 AGAGTGACAT
* * *
147056 AATTACAGCTAAACATAAACGTCAGTATTAAAATTGATAAAATTGAAACGTCAGTGACATAAACG
1 AATTACAGCTAAACATAAACGTCAGTATTAAAATTGACAAAATTGAAACGGCAATGACATAAACG
*
147121 AGCCCACAATTAAAGGTGAGTGGTACTTGAAGTAGTTAACCCTAAAATTTATATTATCTAAATCA
66 AGCCCACAATTAAAGGTGAGTGATACTTGAAGTAGTTAACCCTAAAATTTATATTATCTAAATCA
*
147186 ATACAGGTTACATACTTGATCTGGTGGGTGAGCCTTCTAGTAGAGACATTTTACATATACAAATA
131 ATACAGGTTACATACTTGATCTGGTGGGCGAGCCTTCTAGTAGAGACATTTTAC--ATACAAATA
*
147251 CTCAAATTTGATATATACTTAAATGATATCATATTATTTACTAGTTCA
194 ATCAAATTTGATATATACTTAAATGATATCATATTATTTACTAGTTCA
*
147299 AATTACAGCTAAACATAAACGTCAGTGTTAAAATTGACAAAATTGAAACGGCAATGACATAAACG
1 AATTACAGCTAAACATAAACGTCAGTATTAAAATTGACAAAATTGAAACGGCAATGACATAAACG
** * * * *
147364 AGCCCACGCTTAAAGGTGAGTGATATTTGAAGTAGTTAACCCTAAAATTTGTATTATCTAATTCG
66 AGCCCACAATTAAAGGTGAGTGATACTTGAAGTAGTTAACCCTAAAATTTATATTATCTAAATCA
*
147429 ATTCAGGTTACATACTTGATCTGGTGGGCGAGCCTTCTAGTAGAGACATTTTACATACAAATAAT
131 ATACAGGTTACATACTTGATCTGGTGGGCGAGCCTTCTAGTAGAGACATTTTACATACAAATAAT
*
147494 CAAATTTGATATATACTTAAATTATATCATATTATTTACTA
196 CAAATTTGATATATACTTAAATGATATCATATTATTTACTA
147535 CTTAAACTAA
Statistics
Matches: 221, Mismatches: 15, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
241 50 0.23
243 171 0.77
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (241 bp):
AATTACAGCTAAACATAAACGTCAGTATTAAAATTGACAAAATTGAAACGGCAATGACATAAACG
AGCCCACAATTAAAGGTGAGTGATACTTGAAGTAGTTAACCCTAAAATTTATATTATCTAAATCA
ATACAGGTTACATACTTGATCTGGTGGGCGAGCCTTCTAGTAGAGACATTTTACATACAAATAAT
CAAATTTGATATATACTTAAATGATATCATATTATTTACTAGTTCA
Found at i:147628 original size:18 final size:17
Alignment explanation
Indices: 147592--147633 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
147582 ATTTTTGGTC
147592 TTTTATGATTAAATATT
1 TTTTATGATTAAATATT
* *
147609 TTTTATTATTACAGTA-T
1 TTTTATGATTA-AATATT
147626 TTTTATGA
1 TTTTATGA
147634 ATTTTAAGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.31, C:0.02, G:0.07, T:0.60
Consensus pattern (17 bp):
TTTTATGATTAAATATT
Found at i:157100 original size:2 final size:2
Alignment explanation
Indices: 157093--157120 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
157083 TAACTATCAA
157093 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
157121 CCCCCTCCTC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:169507 original size:29 final size:29
Alignment explanation
Indices: 169475--169569 Score: 70
Period size: 29 Copynumber: 3.2 Consensus size: 29
169465 AATTAGTTCT
169475 TAAACTTTTAACTATTTCAATTTCATCCC
1 TAAACTTTTAACTATTTCAATTTCATCCC
* * * *
169504 TAAAC-TATGACTATCATTCTAAATTAAT-CC
1 TAAACTTTTAACTAT--TTC-AATTTCATCCC
*
169534 TCAAAATTTTAAAC-ATTTCAATTTCATCCC
1 T-AAACTTTT-AACTATTTCAATTTCATCCC
*
169564 CAAACT
1 TAAACT
169570 ATGCATTTAT
Statistics
Matches: 48, Mismatches: 11, Indels: 14
0.66 0.15 0.19
Matches are distributed among these distances:
28 7 0.15
29 15 0.31
30 11 0.23
31 9 0.19
32 4 0.08
33 2 0.04
ACGTcount: A:0.37, C:0.23, G:0.01, T:0.39
Consensus pattern (29 bp):
TAAACTTTTAACTATTTCAATTTCATCCC
Found at i:170750 original size:32 final size:31
Alignment explanation
Indices: 170689--170755 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 31
170679 TAACCGAATT
**
170689 AACCAAACTTTTTTTCTTTAACCGTTAACCG
1 AACCAAACTTTTTTTCTTTAACAATTAACCG
*
170720 AACCAAACTTTTTTTTTTTAA-AATACTAACCG
1 AACCAAACTTTTTTTCTTTAACAAT--TAACCG
170752 AACC
1 AACC
170756 GAATACATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 1 0.03
31 20 0.65
32 10 0.32
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.37
Consensus pattern (31 bp):
AACCAAACTTTTTTTCTTTAACAATTAACCG
Found at i:183831 original size:2 final size:2
Alignment explanation
Indices: 183824--183859 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
183814 CATAAAGTGA
183824 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
183860 GGAAATGGGG
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:185784 original size:24 final size:26
Alignment explanation
Indices: 185724--185787 Score: 71
Period size: 24 Copynumber: 2.5 Consensus size: 26
185714 AAAAGTAGAA
185724 TTTGATATTTTTCTTTATGTTATCATTC
1 TTTGAT-TTTTT-TTTATGTTATCATTC
185752 TTTGATTTTTTTTTAT-TTA-CATT-
1 TTTGATTTTTTTTTATGTTATCATTC
*
185775 TTATGGTTTTTTT
1 TT-TGATTTTTTT
185788 GAAAAGAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
23 2 0.06
24 13 0.38
25 3 0.09
26 5 0.15
27 5 0.15
28 6 0.18
ACGTcount: A:0.16, C:0.06, G:0.08, T:0.70
Consensus pattern (26 bp):
TTTGATTTTTTTTTATGTTATCATTC
Found at i:188366 original size:4 final size:4
Alignment explanation
Indices: 188357--188404 Score: 51
Period size: 4 Copynumber: 12.0 Consensus size: 4
188347 TATTATACAA
* * * * *
188357 ATAT ATAT ATAT ATAT ATAT ATAT GTAT GTAT GTAT GTAT GTAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
188405 GTATGTATGT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (4 bp):
ATAT
Found at i:188405 original size:8 final size:8
Alignment explanation
Indices: 188358--188438 Score: 81
Period size: 8 Copynumber: 9.6 Consensus size: 8
188348 ATTATACAAA
*
188358 TATATATA
1 TATATATG
*
188366 TATATATA
1 TATATATG
188374 TATATATG
1 TATATATG
*
188382 TATGTATG
1 TATATATG
*
188390 TATGTATG
1 TATATATG
188398 TATATATG
1 TATATATG
*
188406 TATGTATG
1 TATATATG
188414 TACGTATGTATG
1 TA--TA--TATG
188426 TATATATG
1 TATATATG
188434 TATAT
1 TATAT
188439 GGGCCACGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
8 55 0.86
10 3 0.05
12 6 0.09
ACGTcount: A:0.35, C:0.01, G:0.15, T:0.49
Consensus pattern (8 bp):
TATATATG
Found at i:188405 original size:12 final size:12
Alignment explanation
Indices: 188362--188438 Score: 91
Period size: 12 Copynumber: 6.4 Consensus size: 12
188352 TACAAATATA
* *
188362 TATATATATATA
1 TATATATGTATG
188374 TATATATGTATG
1 TATATATGTATG
*
188386 TATGTATGTATG
1 TATATATGTATG
188398 TATATATGTATG
1 TATATATGTATG
* *
188410 TATGTACGTATG
1 TATATATGTATG
* *
188422 TATGTATATATG
1 TATATATGTATG
188434 TATAT
1 TATAT
188439 GGGCCACGTC
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 56 1.00
ACGTcount: A:0.34, C:0.01, G:0.16, T:0.49
Consensus pattern (12 bp):
TATATATGTATG
Found at i:188409 original size:4 final size:4
Alignment explanation
Indices: 188378--188436 Score: 91
Period size: 4 Copynumber: 14.8 Consensus size: 4
188368 TATATATATA
* *
188378 TATG TATG TATG TATG TATG TATA TATG TATG TATG TACG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
188426 TATA TATG TAT
1 TATG TATG TAT
188437 ATGGGCCACG
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 49 1.00
ACGTcount: A:0.29, C:0.02, G:0.20, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:193270 original size:18 final size:18
Alignment explanation
Indices: 193247--193318 Score: 108
Period size: 18 Copynumber: 4.0 Consensus size: 18
193237 TCGGAATAAT
*
193247 TAGTGGTCCTTCGAGACA
1 TAGTGGTCCTTCGGGACA
*
193265 TAGTGGTCATTCGGGACA
1 TAGTGGTCCTTCGGGACA
*
193283 TAATGGTCCTTCGGGACA
1 TAGTGGTCCTTCGGGACA
*
193301 TAGTGGTCTTTCGGGACA
1 TAGTGGTCCTTCGGGACA
193319 AATATTCAGT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 48 1.00
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.29
Consensus pattern (18 bp):
TAGTGGTCCTTCGGGACA
Found at i:193301 original size:36 final size:37
Alignment explanation
Indices: 193227--193318 Score: 123
Period size: 36 Copynumber: 2.5 Consensus size: 37
193217 GATGGATTAT
* * *
193227 TAGTGGTCATTCGGAATAATTAGTGGTCCTTCGAGACA
1 TAGTGGTCATTCGGGA-CATTAATGGTCCTTCGAGACA
*
193265 TAGTGGTCATTCGGGACA-TAATGGTCCTTCGGGACA
1 TAGTGGTCATTCGGGACATTAATGGTCCTTCGAGACA
*
193301 TAGTGGTCTTTCGGGACA
1 TAGTGGTCATTCGGGACA
193319 AATATTCAGT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
36 33 0.67
37 1 0.02
38 15 0.31
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.30
Consensus pattern (37 bp):
TAGTGGTCATTCGGGACATTAATGGTCCTTCGAGACA
Found at i:200153 original size:18 final size:18
Alignment explanation
Indices: 200082--200154 Score: 85
Period size: 18 Copynumber: 3.9 Consensus size: 18
200072 AGGGATTATC
* *
200082 AGTGGTCCTTCGGGATAT
1 AGTGGTCATTCGGGACAT
*
200100 AGTGGTTC-TTCGGAACAATT
1 AGTGG-TCATTCGGGAC-A-T
200120 AGTGGTCATTCGGGACAT
1 AGTGGTCATTCGGGACAT
200138 AGTGGTCATTCGGGACA
1 AGTGGTCATTCGGGACA
200155 AATATTCAGT
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
18 29 0.60
19 6 0.12
20 13 0.27
ACGTcount: A:0.22, C:0.16, G:0.32, T:0.30
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:212738 original size:311 final size:311
Alignment explanation
Indices: 212175--212797 Score: 1237
Period size: 311 Copynumber: 2.0 Consensus size: 311
212165 CATGAATATC
212175 TACCACACTGCCCCATCTACCAGCCAACTTCTCGAAGAAAGATTCATTCTAGCATAACAAAGGAA
1 TACCACACTGCCCCATCTACCAGCCAACTTCTCGAAGAAAGATTCATTCTAGCATAACAAAGGAA
*
212240 CCCCTTTTAATTCTGCCATGTAGAAGGCCATTGGGACCCTGGTTTCATTCAGTAAAGGTTCCACT
66 CCCCTTTTAATTCTGCCATGCAGAAGGCCATTGGGACCCTGGTTTCATTCAGTAAAGGTTCCACT
212305 CGCTCAAACCACTGTTTTAAAACCTCTTCCTTGTTGCTCCATAACTCCAATATCTCCTAATGAGA
131 CGCTCAAACCACTGTTTTAAAACCTCTTCCTTGTTGCTCCATAACTCCAATATCTCCTAATGAGA
212370 TTTAAGAACTATCACACAAGAATTCCAGACATAGCCCCATCTAGCAATTTGAACATCATAGCCTT
196 TTTAAGAACTATCACACAAGAATTCCAGACATAGCCCCATCTAGCAATTTGAACATCATAGCCTT
212435 CTTTTAATAAAGCATTCCGAATGAACTCAACTTGAAAAGAGTATTTGATAA
261 CTTTTAATAAAGCATTCCGAATGAACTCAACTTGAAAAGAGTATTTGATAA
212486 TACCACACTGCCCCATCTACCAGCCAACTTCTCGAAGAAAGATTCATTCTAGCATAACAAAGGAA
1 TACCACACTGCCCCATCTACCAGCCAACTTCTCGAAGAAAGATTCATTCTAGCATAACAAAGGAA
212551 CCCCTTTTAATTCTGCCATGCAGAAGGCCATTGGGACCCTGGTTTCATTCAGTAAAGGTTCCACT
66 CCCCTTTTAATTCTGCCATGCAGAAGGCCATTGGGACCCTGGTTTCATTCAGTAAAGGTTCCACT
212616 CGCTCAAACCACTGTTTTAAAACCTCTTCCTTGTTGCTCCATAACTCCAATATCTCCTAATGAGA
131 CGCTCAAACCACTGTTTTAAAACCTCTTCCTTGTTGCTCCATAACTCCAATATCTCCTAATGAGA
212681 TTTAAGAACTATCACACAAGAATTCCAGACATAGCCCCATCTAGCAATTTGAACATCATAGCCTT
196 TTTAAGAACTATCACACAAGAATTCCAGACATAGCCCCATCTAGCAATTTGAACATCATAGCCTT
212746 CTTTTAATAAAGCATTCCGAATGAACTCAACTTGAAAAGAGTATTTGATAA
261 CTTTTAATAAAGCATTCCGAATGAACTCAACTTGAAAAGAGTATTTGATAA
212797 T
1 T
212798 CCCTGTTAAT
Statistics
Matches: 311, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
311 311 1.00
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.28
Consensus pattern (311 bp):
TACCACACTGCCCCATCTACCAGCCAACTTCTCGAAGAAAGATTCATTCTAGCATAACAAAGGAA
CCCCTTTTAATTCTGCCATGCAGAAGGCCATTGGGACCCTGGTTTCATTCAGTAAAGGTTCCACT
CGCTCAAACCACTGTTTTAAAACCTCTTCCTTGTTGCTCCATAACTCCAATATCTCCTAATGAGA
TTTAAGAACTATCACACAAGAATTCCAGACATAGCCCCATCTAGCAATTTGAACATCATAGCCTT
CTTTTAATAAAGCATTCCGAATGAACTCAACTTGAAAAGAGTATTTGATAA
Found at i:217543 original size:13 final size:13
Alignment explanation
Indices: 217516--217557 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
217506 ATATATGTTA
*
217516 TTTTACAATTTGT
1 TTTTCCAATTTGT
*
217529 TTATTCTAA-TTGT
1 TT-TTCCAATTTGT
217542 TTTTCCAATTTGT
1 TTTTCCAATTTGT
217555 TTT
1 TTT
217558 ATAACATCAG
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
12 5 0.21
13 15 0.62
14 4 0.17
ACGTcount: A:0.19, C:0.10, G:0.07, T:0.64
Consensus pattern (13 bp):
TTTTCCAATTTGT
Found at i:219378 original size:6 final size:6
Alignment explanation
Indices: 219369--219398 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
219359 GGGTTGGGAA
*
219369 TTGGAC TTGGAC TTGGAC TTGGAC ATGGAC
1 TTGGAC TTGGAC TTGGAC TTGGAC TTGGAC
219399 GTAGCCGTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.20, C:0.17, G:0.33, T:0.30
Consensus pattern (6 bp):
TTGGAC
Found at i:238216 original size:21 final size:20
Alignment explanation
Indices: 238190--238233 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
238180 GATTTCTGGG
* *
238190 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCC-TT
238211 CAAGGGGAACCGATACCCTT
1 CAAGGGGAACCGATACCCTT
238231 CAA
1 CAA
238234 CGAACAACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.32, C:0.27, G:0.25, T:0.16
Consensus pattern (20 bp):
CAAGGGGAACCGATACCCTT
Found at i:239946 original size:144 final size:146
Alignment explanation
Indices: 239764--240072 Score: 509
Period size: 146 Copynumber: 2.1 Consensus size: 146
239754 GAGTCGAGGG
* * *
239764 TCTACGCGATCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTC-TGAAAGACACAT
1 TCTACGCGGTCCTTCGGGA-ATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
239828 ACTTGATCCCTAGTATATG-TATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTAT
65 ACTTGATCCCTAGTATATGATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTAT
239892 ATGGCACTACGGTGCAAT
130 AT-GCACTACGGTGCAAT
239910 TCTACGCGGTCCTTCGGG-ATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACATA
1 TCTACGCGGTCCTTCGGGAATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACATA
*
239974 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTGTTAT
66 CTTGATCCCTAGTATATG-ATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTAT
*
240039 ATGCACTACGGTGTAAT
130 ATGCACTACGGTGCAAT
240056 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
240073 TGCAATTATA
Statistics
Matches: 154, Mismatches: 5, Indels: 8
0.92 0.03 0.05
Matches are distributed among these distances:
144 30 0.19
145 32 0.21
146 46 0.30
147 46 0.30
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (146 bp):
TCTACGCGGTCCTTCGGGAATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACATA
CTTGATCCCTAGTATATGATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTATA
TGCACTACGGTGCAAT
Found at i:240073 original size:23 final size:23
Alignment explanation
Indices: 240041--240084 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
240031 ATTGTTATAT
* *
240041 GCACTACGGTGTAATTCTACGCG
1 GCACTACGGTGCAATTATACGCG
*
240064 GCACTTCGGTGCAATTATACG
1 GCACTACGGTGCAATTATACG
240085 AGCTGTGGTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.27
Consensus pattern (23 bp):
GCACTACGGTGCAATTATACGCG
Found at i:241509 original size:30 final size:28
Alignment explanation
Indices: 241474--241545 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
241464 AAATATTTGA
* **
241474 AATATTTGTTATTATGGTTTTACTTTTTTT
1 AATATTTATTATTATGGGCTTA--TTTTTT
*
241504 AATATTTATTATTTTGGGCTTATTTTTT
1 AATATTTATTATTATGGGCTTATTTTTT
241532 AATATTTATTATTA
1 AATATTTATTATTA
241546 GGACCTATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 19 0.51
30 18 0.49
ACGTcount: A:0.25, C:0.03, G:0.08, T:0.64
Consensus pattern (28 bp):
AATATTTATTATTATGGGCTTATTTTTT
Found at i:241562 original size:28 final size:28
Alignment explanation
Indices: 241498--241562 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
241488 TGGTTTTACT
* * * *
241498 TTTTTTAATATTTATTATTTTGGGCTTA
1 TTTTATAATATTTATTATTTAGGACCTA
*
241526 TTTTTTAATATTTATTA-TTAGGACCTA
1 TTTTATAATATTTATTATTTAGGACCTA
241553 TTTTCATAAT
1 TTTT-ATAAT
241563 TTATTTTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 11 0.34
28 21 0.66
ACGTcount: A:0.26, C:0.06, G:0.08, T:0.60
Consensus pattern (28 bp):
TTTTATAATATTTATTATTTAGGACCTA
Found at i:242260 original size:14 final size:14
Alignment explanation
Indices: 242241--242267 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
242231 GTATGCATCT
242241 AAATCAAACCCAAG
1 AAATCAAACCCAAG
242255 AAATCAAACCCAA
1 AAATCAAACCCAA
242268 CATAGTTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.30, G:0.04, T:0.07
Consensus pattern (14 bp):
AAATCAAACCCAAG
Found at i:243053 original size:149 final size:146
Alignment explanation
Indices: 242878--243264 Score: 572
Period size: 149 Copynumber: 2.7 Consensus size: 146
242868 CAACAACTTT
*
242878 TTTATCCTCGGCCTTCTTTTCCTCTACATTTTCATCAACCTTCTTCTCCTCAATTCGATCCACAA
1 TTTATCCTCGGCCTTCTTTTCCTCTACATTTTCATCAACCTTCTTCACCTCAATTCGATCCACAA
*
242943 CCTTGTCATCTTGAGCTTCACTGATCTTCTTGGTTTCTCTTTGACAACTTTCGAAGTTTGTGATG
66 CCTTGTCATCTTGAGCTTCACTGATCTTCTT-G-TTCTCTTTGACAACTTTCGAAGTTCGTGATG
*
243008 CACTTGGTGGTTCAACACA
129 C-CTTGGTCGTTCAACACA
* *
243027 TTTATCCTCAGCCTTCTTTTCCTCTACATTTTCATCAACCTTCTTCACCTCGATTCGATCCACAA
1 TTTATCCTCGGCCTTCTTTTCCTCTACATTTTCATCAACCTTCTTCACCTCAATTCGATCCACAA
243092 CCTTGTCATCTTGAGCTTCACTGATCTTC---TTCTCTTTGACAACTTTCGAAGTTCGTGATGCC
66 CCTTGTCATCTTGAGCTTCACTGATCTTCTTGTTCTCTTTGACAACTTTCGAAGTTCGTGATGCC
*
243154 TTGGTCGTTCAACATA
131 TTGGTCGTTCAACACA
* * * * * *
243170 TTTATCCTCGGCC-TCTTATCTTCTACGTTTTCGTCAA-C--CTTCACCTCAATTTGGTCCACAA
1 TTTATCCTCGGCCTTCTTTTCCTCTACATTTTCATCAACCTTCTTCACCTCAATTCGATCCACAA
* *
243231 CCTTGTTATCTAGAGCTTCACTGATCTTCTTGTT
66 CCTTGTCATCTTGAGCTTCACTGATCTTCTTGTT
243265 ATTGTTCTTC
Statistics
Matches: 219, Mismatches: 16, Indels: 13
0.88 0.06 0.05
Matches are distributed among these distances:
139 47 0.21
141 1 0.00
142 22 0.10
143 27 0.12
144 31 0.14
149 91 0.42
ACGTcount: A:0.18, C:0.29, G:0.12, T:0.41
Consensus pattern (146 bp):
TTTATCCTCGGCCTTCTTTTCCTCTACATTTTCATCAACCTTCTTCACCTCAATTCGATCCACAA
CCTTGTCATCTTGAGCTTCACTGATCTTCTTGTTCTCTTTGACAACTTTCGAAGTTCGTGATGCC
TTGGTCGTTCAACACA
Found at i:243077 original size:27 final size:28
Alignment explanation
Indices: 243024--243077 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 28
243014 GTGGTTCAAC
* * **
243024 ACATTTATCCTCAGCCTTCTTTTCCTCT
1 ACATTTATCATCAACCTTCTTCACCTCT
243052 ACATTT-TCATCAACCTTCTTCACCTC
1 ACATTTATCATCAACCTTCTTCACCTC
243078 GATTCGATCC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
27 16 0.73
28 6 0.27
ACGTcount: A:0.19, C:0.37, G:0.02, T:0.43
Consensus pattern (28 bp):
ACATTTATCATCAACCTTCTTCACCTCT
Found at i:244747 original size:15 final size:15
Alignment explanation
Indices: 244727--244768 Score: 66
Period size: 17 Copynumber: 2.7 Consensus size: 15
244717 AAATTTAAGT
244727 TATAAAATTAACGAG
1 TATAAAATTAACGAG
244742 TATAAAATATTAACGAG
1 TAT-AAA-ATTAACGAG
244759 TATAAAATTA
1 TATAAAATTA
244769 TCTTCGGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.28
16 6 0.24
17 12 0.48
ACGTcount: A:0.55, C:0.05, G:0.10, T:0.31
Consensus pattern (15 bp):
TATAAAATTAACGAG
Found at i:244755 original size:17 final size:17
Alignment explanation
Indices: 244733--244766 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
244723 AAGTTATAAA
244733 ATTAACGAGTATAAAAT
1 ATTAACGAGTATAAAAT
244750 ATTAACGAGTATAAAAT
1 ATTAACGAGTATAAAAT
244767 TATCTTCGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.12, T:0.29
Consensus pattern (17 bp):
ATTAACGAGTATAAAAT
Found at i:246187 original size:19 final size:18
Alignment explanation
Indices: 246146--246191 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 18
246136 ATTGATTAAA
246146 AATATTATTTTTAAAAAAT
1 AATATT-TTTTTAAAAAAT
246165 AATAATTTTTTT-AAAAAT
1 AAT-ATTTTTTTAAAAAAT
246183 AAATATTTT
1 -AATATTTT
246192 AAACTCTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 11 0.44
19 11 0.44
20 3 0.12
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AATATTTTTTTAAAAAAT
Found at i:246190 original size:18 final size:17
Alignment explanation
Indices: 246143--246191 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 17
246133 AGAATTGATT
246143 AAAAATATTATTTTTAAA
1 AAAAATATT-TTTTTAAA
246161 AAATAATAATTTTTTTAAA
1 AAA-AAT-ATTTTTTTAAA
246180 AATAAATATTTT
1 AA-AAATATTTT
246192 AAACTCTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 8 0.29
19 16 0.57
20 4 0.14
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AAAAATATTTTTTTAAA
Found at i:252132 original size:15 final size:15
Alignment explanation
Indices: 252099--252142 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
252089 CCTAAGGTTT
* * *
252099 ATTTATATTAAATTT
1 ATTTTTATTATATTA
*
252114 ATTTTTATTTTATTA
1 ATTTTTATTATATTA
252129 ATTTTTATTATATT
1 ATTTTTATTATATT
252143 CAATCATTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
ATTTTTATTATATTA
Found at i:253717 original size:27 final size:27
Alignment explanation
Indices: 253679--253732 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
253669 AGGGCAGGGA
*
253679 GATGTCCTATATGGGTATCACAATGTC
1 GATGTCCCATATGGGTATCACAATGTC
*
253706 GATGTCCCATATGGGTATCTCAATGTC
1 GATGTCCCATATGGGTATCACAATGTC
253733 TCTTTATTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.33
Consensus pattern (27 bp):
GATGTCCCATATGGGTATCACAATGTC
Found at i:254396 original size:161 final size:162
Alignment explanation
Indices: 254131--254455 Score: 643
Period size: 161 Copynumber: 2.0 Consensus size: 162
254121 GAACTTTAAG
254131 TAATATATCATTGAACTTTGATTTTCACTTCAATTATATCATTAAATTGTTAACGATTTTGTTAT
1 TAATATATCATTGAACTTTGATTTTCACTTCAATTATATCATTAAATTGTTAACGATTTTGTTAT
254196 ATGGTTGACGATTGTCATGAACGCCAATCGAAACGATATCG-TTTAGATCATGTTGTTTTGATAC
66 ATGGTTGACGATTGTCATGAACGCCAATCGAAACGATATCGTTTTAGATCATGTTGTTTTGATAC
254260 CCAAAAGACCTAAATGACATCGTTTTGCTGAA
131 CCAAAAGACCTAAATGACATCGTTTTGCTGAA
254292 TAATATATCATTGAACTTTGATTTTCACTTCAATTATATCATTAAATTGTTAACGATTTTGTTAT
1 TAATATATCATTGAACTTTGATTTTCACTTCAATTATATCATTAAATTGTTAACGATTTTGTTAT
254357 ATGGTTGACGATTGTCATGAACGCCAATCGAAACGATATCGTTTTAGATCATGTTGTTTTGATAC
66 ATGGTTGACGATTGTCATGAACGCCAATCGAAACGATATCGTTTTAGATCATGTTGTTTTGATAC
254422 CCAAAAGACCTAAATGACATCGTTTTGCTGAA
131 CCAAAAGACCTAAATGACATCGTTTTGCTGAA
254454 TA
1 TA
254456 TTTTTTTTAT
Statistics
Matches: 163, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
161 106 0.65
162 57 0.35
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.39
Consensus pattern (162 bp):
TAATATATCATTGAACTTTGATTTTCACTTCAATTATATCATTAAATTGTTAACGATTTTGTTAT
ATGGTTGACGATTGTCATGAACGCCAATCGAAACGATATCGTTTTAGATCATGTTGTTTTGATAC
CCAAAAGACCTAAATGACATCGTTTTGCTGAA
Found at i:255055 original size:16 final size:16
Alignment explanation
Indices: 255042--255073 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
255032 TTTTATTTTT
255042 AAGATCTTGGATTTAG
1 AAGATCTTGGATTTAG
255058 AAGATCTTGGATTTAG
1 AAGATCTTGGATTTAG
255074 GCGGCAATGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.38
Consensus pattern (16 bp):
AAGATCTTGGATTTAG
Found at i:257022 original size:2 final size:2
Alignment explanation
Indices: 257015--257047 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
257005 AAAGGTATGA
257015 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
257048 CCGAAGGAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:261445 original size:29 final size:30
Alignment explanation
Indices: 261400--261471 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 30
261390 TTTTTTCATT
*
261400 TAAGTACCTAAAGTATC-TTTTGATCAAAA
1 TAAGTACCTAAACTATCTTTTTGATCAAAA
*
261429 TAAGTACCTAAACTATCTTTTTTGGTCAAAA
1 TAAGTACCTAAACTATC-TTTTTGATCAAAA
*
261460 TAGGTACCTAAA
1 TAAGTACCTAAA
261472 GTATTCAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 16 0.42
31 22 0.58
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (30 bp):
TAAGTACCTAAACTATCTTTTTGATCAAAA
Found at i:266176 original size:29 final size:30
Alignment explanation
Indices: 266129--266200 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 30
266119 TTTTTTCATT
* *
266129 TAAGTACCTAAAGTGTC-TTTTGGTCAAAA
1 TAAGTACCTAAACTATCTTTTTGGTCAAAA
*
266158 TAAGTATCTAAACTATCTTTTTTGGTCAAAA
1 TAAGTACCTAAACTATC-TTTTTGGTCAAAA
*
266189 TAGGTACCTAAA
1 TAAGTACCTAAA
266201 GTATTTAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
29 14 0.39
31 22 0.61
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (30 bp):
TAAGTACCTAAACTATCTTTTTGGTCAAAA
Found at i:266334 original size:29 final size:29
Alignment explanation
Indices: 266287--266384 Score: 106
Period size: 29 Copynumber: 3.3 Consensus size: 29
266277 GAAAAAATTG
*
266287 AATACTTCAGGTACTTATTTTGATAAAAA
1 AATACTTTAGGTACTTATTTTGATAAAAA
* * *
266316 AATACTTTAGGCACCTATTTTGACCAAAAA
1 AATACTTTAGGTACTTATTTTGA-TAAAAA
* * * *
266346 GATAAGTTTAGATACTTATTTTGATCAAAA
1 AAT-ACTTTAGGTACTTATTTTGATAAAAA
266376 AATACTTTA
1 AATACTTTA
266385 AGTAATTCAA
Statistics
Matches: 54, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
29 25 0.46
30 13 0.24
31 16 0.30
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (29 bp):
AATACTTTAGGTACTTATTTTGATAAAAA
Found at i:269689 original size:17 final size:17
Alignment explanation
Indices: 269655--269706 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
269645 ACCGGACAAA
* *
269655 TTTATTATTTTAGAGAG
1 TTTATTAATTTACAGAG
*
269672 TTTATTAATTTACCGAG
1 TTTATTAATTTACAGAG
*
269689 --TATTAATTTAAAGAG
1 TTTATTAATTTACAGAG
269704 TTT
1 TTT
269707 CTACTGTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 13 0.46
17 15 0.54
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.50
Consensus pattern (17 bp):
TTTATTAATTTACAGAG
Found at i:271570 original size:31 final size:31
Alignment explanation
Indices: 271535--271607 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
271525 GTCATATTAC
*
271535 CACTTTCGACATGTGAAATGTGTCACATCAT
1 CACTTTCGACATGTGAAATATGTCACATCAT
* * * *
271566 CACTTTCGAAATGTGAAATATGTTATATCGT
1 CACTTTCGACATGTGAAATATGTCACATCAT
271597 CACTTTCGACA
1 CACTTTCGACA
271608 CATGACACGT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (31 bp):
CACTTTCGACATGTGAAATATGTCACATCAT
Found at i:271964 original size:34 final size:34
Alignment explanation
Indices: 271905--271971 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 34
271895 TTCTTGATAT
*
271905 TTGTTTTCTCCTTTTTATCAAGAGAGAA-TTGTTA
1 TTGTTTTCTCCTTTTGATC-AGAGAGAAGTTGTTA
271939 TTGTTTTCTCCTTGTTAGATC-GAGAGAAGTTGT
1 TTGTTTTCTCCTT-TT-GATCAGAGAGAAGTTGT
271972 AATTTCTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 20 0.69
35 6 0.21
36 3 0.10
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.48
Consensus pattern (34 bp):
TTGTTTTCTCCTTTTGATCAGAGAGAAGTTGTTA
Found at i:272896 original size:22 final size:22
Alignment explanation
Indices: 272865--272915 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
272855 CTGAGTGGCA
272865 TATGAAATTTGTCCCGAAAGACC
1 TATG-AATTTGTCCCGAAAGACC
* *
272888 TGTGAATTTGTCCCGAAGGACC
1 TATGAATTTGTCCCGAAAGACC
272910 TATGAA
1 TATGAA
272916 ACCCTCGACT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 22 0.88
23 3 0.12
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (22 bp):
TATGAATTTGTCCCGAAAGACC
Found at i:273490 original size:64 final size:63
Alignment explanation
Indices: 273357--273513 Score: 158
Period size: 64 Copynumber: 2.4 Consensus size: 63
273347 TAATGAAGGT
* * * ** *
273357 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATGTTGTATTATTACTGGG
1 ATGCATCGATGCA-TACTAATGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAAAGAG
* *
273421 ATGCATCGATGCATGACTCATGCATCGATGCACT-AATTGCATTCGATGTTTCTATT-TTAAA-A
1 ATGCATCGATGCAT-ACTAATGCATCGATGCA-TAAAATGCATTCGATG-TTCTATTATTAAAGA
273483 G
63 G
*
273484 AGTGCATCGATGCATTACAAATGCATCGAT
1 A-TGCATCGATGCA-TACTAATGCATCGAT
273514 ACACCTTCAA
Statistics
Matches: 79, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
63 3 0.04
64 68 0.86
65 8 0.10
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.32
Consensus pattern (63 bp):
ATGCATCGATGCATACTAATGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAAAGAG
Found at i:279695 original size:23 final size:23
Alignment explanation
Indices: 279667--279718 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
279657 CTGAGTGGCA
*
279667 TATGAAATTTGTCCTGAAGGACC
1 TATGAAATTTGTCCCGAAGGACC
*
279690 TGTG-AATTTGTCCCGAAGGACC
1 TATGAAATTTGTCCCGAAGGACC
279712 TATGAAA
1 TATGAAA
279719 CCCTCGACTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (23 bp):
TATGAAATTTGTCCCGAAGGACC
Found at i:281343 original size:21 final size:21
Alignment explanation
Indices: 281319--281379 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
281309 CCAACTTTGA
281319 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
281340 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
281354 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
281375 AAATG
1 AAATG
281380 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:281352 original size:35 final size:35
Alignment explanation
Indices: 281313--281427 Score: 178
Period size: 35 Copynumber: 3.3 Consensus size: 35
281303 TGGCAACCAA
281313 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
281348 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
** *
281383 CTTTGAAAAATATTTTTCAAAGTTTGGTAGATGTTT
1 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
281419 -GTTGAAAAT
1 CTTTGAAAAT
281428 AGGAATGGGT
Statistics
Matches: 75, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
34 5 0.07
35 43 0.57
36 27 0.36
ACGTcount: A:0.30, C:0.05, G:0.19, T:0.45
Consensus pattern (35 bp):
CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:285940 original size:21 final size:21
Alignment explanation
Indices: 285916--285976 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
285906 CCAACTTTGA
285916 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
285937 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
285951 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
285972 AAATG
1 AAATG
285977 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:285997 original size:36 final size:35
Alignment explanation
Indices: 285910--286014 Score: 176
Period size: 35 Copynumber: 3.0 Consensus size: 35
285900 TGGCAACCAA
285910 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
285945 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
285980 CTTTGAAAAATGTTTTTCAAAGTTTGG-AAAAGTTT
1 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
286015 GGTAGATGTT
Statistics
Matches: 67, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
35 47 0.70
36 20 0.30
ACGTcount: A:0.30, C:0.06, G:0.19, T:0.45
Consensus pattern (35 bp):
CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:287968 original size:26 final size:26
Alignment explanation
Indices: 287938--288005 Score: 118
Period size: 26 Copynumber: 2.6 Consensus size: 26
287928 TATTTTCTCT
*
287938 TTTAAAATTTTATAAATTTATATTTC
1 TTTAAAATTTTATAAATTTACATTTC
*
287964 TTTAAAATTTTATAAATTTGCATTTC
1 TTTAAAATTTTATAAATTTACATTTC
287990 TTTAAAATTTTATAAA
1 TTTAAAATTTTATAAA
288006 AATACAAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.54
Consensus pattern (26 bp):
TTTAAAATTTTATAAATTTACATTTC
Found at i:290006 original size:19 final size:19
Alignment explanation
Indices: 289982--290021 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
289972 TATTTAAAAT
289982 ATAAATATAATA-AATTATA
1 ATAAATAT-ATACAATTATA
*
290001 ATAAATATTTACAATTATA
1 ATAAATATATACAATTATA
290020 AT
1 AT
290022 CATATATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 2 0.11
19 17 0.89
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (19 bp):
ATAAATATATACAATTATA
Found at i:292082 original size:36 final size:36
Alignment explanation
Indices: 292006--292256 Score: 382
Period size: 36 Copynumber: 7.0 Consensus size: 36
291996 ACACTAGAAC
*
292006 CGGAAGTGTCGATGCTT-CCTCCCGTTC-ACTTGAAT
1 CGGAAGTGCCGATGCTTCCCT-CCGTTCGACTTGAAT
* * * *
292041 CGGAAGTGCCGATGCTTTCTTTCGTTCGATTTGAAT
1 CGGAAGTGCCGATGCTTCCCTCCGTTCGACTTGAAT
* *
292077 CGGAAGTGCTGATGCTTCCCTCCGTTCGATTTGAAT
1 CGGAAGTGCCGATGCTTCCCTCCGTTCGACTTGAAT
292113 CGGAAGTGCCGATGCTTCCCTCCGTTCGACTTGAAT
1 CGGAAGTGCCGATGCTTCCCTCCGTTCGACTTGAAT
*
292149 CGGAAGTGCCGATGCTTCCCTCCGTTCGATTTGAAT
1 CGGAAGTGCCGATGCTTCCCTCCGTTCGACTTGAAT
*
292185 CGGAAGTGCCGATGCTTTCCTCCGTTCGACTTGAAT
1 CGGAAGTGCCGATGCTTCCCTCCGTTCGACTTGAAT
*
292221 CGGAAGTGCCGATGCTT-ACTCCGTTCGACTTGAAT
1 CGGAAGTGCCGATGCTTCCCTCCGTTCGACTTGAAT
292256 C
1 C
292257 AATGCAAACT
Statistics
Matches: 200, Mismatches: 14, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
35 39 0.19
36 161 0.81
ACGTcount: A:0.17, C:0.27, G:0.25, T:0.31
Consensus pattern (36 bp):
CGGAAGTGCCGATGCTTCCCTCCGTTCGACTTGAAT
Found at i:300229 original size:19 final size:18
Alignment explanation
Indices: 300202--300239 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
300192 CAAAATTATA
300202 AAATTTTAA-AGAAAAAAT
1 AAATTTTAATA-AAAAAAT
300220 AAATTCTTAATAAAAAAAT
1 AAATT-TTAATAAAAAAAT
300239 A
1 A
300240 TAAAATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
19 12 0.67
20 1 0.06
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (18 bp):
AAATTTTAATAAAAAAAT
Found at i:300768 original size:5 final size:5
Alignment explanation
Indices: 300758--300782 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
300748 GGGAGTTTGA
300758 TTTAT TTTAT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT
300783 ATATTAGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTAT
Found at i:301870 original size:26 final size:26
Alignment explanation
Indices: 301836--301886 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
301826 TTTGATAAAC
301836 TCAATTAATTTAAATATATTTTTATA
1 TCAATTAATTTAAATATATTTTTATA
301862 TCAATTAATTTAAATATATTTTTAT
1 TCAATTAATTTAAATATATTTTTAT
301887 TTAATTTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (26 bp):
TCAATTAATTTAAATATATTTTTATA
Found at i:307982 original size:38 final size:38
Alignment explanation
Indices: 307931--308008 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
307921 TTTTTGCCAA
307931 CACGCATTACCATTTCAGCAAAACCAATATCCGCCGCC
1 CACGCATTACCATTTCAGCAAAACCAATATCCGCCGCC
* *
307969 CACGCCTTACCATTTCAGCAAAACCACTATCCGCCGCC
1 CACGCATTACCATTTCAGCAAAACCAATATCCGCCGCC
308007 CA
1 CA
308009 ATGAGTGAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.29, C:0.42, G:0.10, T:0.18
Consensus pattern (38 bp):
CACGCATTACCATTTCAGCAAAACCAATATCCGCCGCC
Found at i:309712 original size:7 final size:7
Alignment explanation
Indices: 309702--309745 Score: 88
Period size: 7 Copynumber: 6.3 Consensus size: 7
309692 CACACTTCAC
309702 ACTTGAT
1 ACTTGAT
309709 ACTTGAT
1 ACTTGAT
309716 ACTTGAT
1 ACTTGAT
309723 ACTTGAT
1 ACTTGAT
309730 ACTTGAT
1 ACTTGAT
309737 ACTTGAT
1 ACTTGAT
309744 AC
1 AC
309746 ATATGCTTAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.41
Consensus pattern (7 bp):
ACTTGAT
Found at i:309719 original size:21 final size:21
Alignment explanation
Indices: 309695--309740 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
309685 TACACTTCAC
309695 ACTTCACACTTGATACTTGAT
1 ACTTCACACTTGATACTTGAT
* *
309716 ACTTGATACTTGATACTTGAT
1 ACTTCACACTTGATACTTGAT
309737 ACTT
1 ACTT
309741 GATACATATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.28, C:0.20, G:0.11, T:0.41
Consensus pattern (21 bp):
ACTTCACACTTGATACTTGAT
Found at i:316195 original size:29 final size:29
Alignment explanation
Indices: 316153--316226 Score: 148
Period size: 29 Copynumber: 2.6 Consensus size: 29
316143 AGCAGGAGGG
316153 AGTGCATGGCGACCTACAAGGTCGCCCGA
1 AGTGCATGGCGACCTACAAGGTCGCCCGA
316182 AGTGCATGGCGACCTACAAGGTCGCCCGA
1 AGTGCATGGCGACCTACAAGGTCGCCCGA
316211 AGTGCATGGCGACCTA
1 AGTGCATGGCGACCTA
316227 TGTTTGGGGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.24, C:0.30, G:0.31, T:0.15
Consensus pattern (29 bp):
AGTGCATGGCGACCTACAAGGTCGCCCGA
Found at i:320688 original size:37 final size:37
Alignment explanation
Indices: 320646--320720 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
320636 TTCATTAAAC
*
320646 ATTTTTAT-ATTTTCAA-TTTTGTAAAAAAAATTATATA
1 ATTTTTATGAATTT-AATTTTTGTAAAAAAAA-TATATA
* *
320683 ATTTTTATGAATTTAATTTTTTTAAAGAAAATATATA
1 ATTTTTATGAATTTAATTTTTGTAAAAAAAATATATA
320720 A
1 A
320721 ATATTTGTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 17 0.52
38 16 0.48
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (37 bp):
ATTTTTATGAATTTAATTTTTGTAAAAAAAATATATA
Found at i:321211 original size:21 final size:21
Alignment explanation
Indices: 321182--321234 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
321172 ATTCTGACTA
321182 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
321203 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
321224 TCGCAATGCGA
1 TCGCATTGCGA
321235 ATACGTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:321249 original size:20 final size:20
Alignment explanation
Indices: 321224--321276 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
321214 TTTTCCTAAT
321224 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
321244 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
321264 TCGCAACGCGAAT
1 TCGCAATGCGAAT
321277 CTGACTATCG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:321499 original size:22 final size:22
Alignment explanation
Indices: 321473--321538 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
321463 GGCGACATCC
* *
321473 GTCCCCATCTCTGATGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
321495 GTCCCCATCTCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
*
321517 GTCTCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
321539 TTCACGGTCA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.26, C:0.36, G:0.14, T:0.24
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:321951 original size:20 final size:20
Alignment explanation
Indices: 321875--321944 Score: 97
Period size: 20 Copynumber: 3.5 Consensus size: 20
321865 CGATTCTGTC
* *
321875 GTTGCGATTTTTA-TTTCGC
1 GTTGCGATTTTCATTTTCGT
**
321894 GTTGCGATAGTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
321914 GTTGCGATTTTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
321934 GTTGCGATTTT
1 GTTGCGATTTT
321945 AAGTTTCAGA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 10 0.23
20 34 0.77
ACGTcount: A:0.11, C:0.14, G:0.23, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGT
Found at i:323852 original size:20 final size:20
Alignment explanation
Indices: 323827--323984 Score: 130
Period size: 20 Copynumber: 8.6 Consensus size: 20
323817 AGAATAGTTT
*
323827 ACTATCGCAATGCGAAAATG
1 ACTATCGCAACGCGAAAATG
323847 ACTATCGCAACGCGAAAATG
1 ACTATCGCAACGCGAAAATG
*
323867 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAACGCGAAAATG
*
323883 A--ATCGCAATGCG-AAATG
1 ACTATCGCAACGCGAAAATG
**
323900 AAAATCGCAA--C-AACAA--
1 ACTATCGCAACGCGAA-AATG
323916 A--ATCGCAACGCGAAAATG
1 ACTATCGCAACGCGAAAATG
323934 ACTATCGCAACGCG-AAATG
1 ACTATCGCAACGCGAAAATG
* **
323953 ACTATCGCAATGCGAATTTG
1 ACTATCGCAACGCGAAAATG
323973 ACTATCGCAACG
1 ACTATCGCAACG
323985 AAAGAATCGC
Statistics
Matches: 116, Mismatches: 7, Indels: 30
0.76 0.05 0.20
Matches are distributed among these distances:
14 14 0.12
16 10 0.09
17 8 0.07
18 5 0.04
19 25 0.22
20 54 0.47
ACGTcount: A:0.41, C:0.23, G:0.20, T:0.16
Consensus pattern (20 bp):
ACTATCGCAACGCGAAAATG
Found at i:323907 original size:19 final size:19
Alignment explanation
Indices: 323883--324013 Score: 75
Period size: 19 Copynumber: 7.3 Consensus size: 19
323873 GCAACGAGAG
323883 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
323902 AATCGCAA--C--AA-CAA
1 AATCGCAATGCGAAATGAA
* *
323916 AATCGCAACGCGAAAATGAC
1 AATCGCAATGCG-AAATGAA
* * *
323936 TATCGCAACGCGAAATGAC
1 AATCGCAATGCGAAATGAA
* * *
323955 TATCGCAATGCGAATTTGAC
1 AATCGCAATGCGAA-ATGAA
*
323975 TATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
*
323989 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
324008 AATCGC
1 AATCGC
324014 TTTGGGATTC
Statistics
Matches: 92, Mismatches: 8, Indels: 24
0.74 0.06 0.19
Matches are distributed among these distances:
14 17 0.18
15 2 0.02
16 7 0.08
17 2 0.02
18 4 0.04
19 36 0.39
20 24 0.26
ACGTcount: A:0.44, C:0.22, G:0.18, T:0.16
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:323918 original size:53 final size:53
Alignment explanation
Indices: 323830--324013 Score: 160
Period size: 53 Copynumber: 3.5 Consensus size: 53
323820 ATAGTTTACT
**
323830 ATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAGAGA
1 ATCGCAATGCG-AAATGAAAATCGCAACGCGAAAATGACTATCGCAACGAGAGA
* * * **
323884 ATCGCAATGCGAAATGAAAATCGCAACAAC-AAAATCG-C-AACGCGAA-AATGACT
1 ATCGCAATGCGAAATGAAAATCGCAAC-GCGAAAAT-GACTATCGC-AACGA-GAGA
* ** * ** *
323937 ATCGCAACGCGAAATGACTATCGCAATGCGAATTTGACTATCGCAACGAAAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGCGAAAATGACTATCGCAACGAGAGA
*
323990 ATCGCAATACGAAATGAAAATCGC
1 ATCGCAATGCGAAATGAAAATCGC
324014 TTTGGGATTC
Statistics
Matches: 99, Mismatches: 23, Indels: 17
0.71 0.17 0.12
Matches are distributed among these distances:
52 7 0.07
53 74 0.75
54 18 0.18
ACGTcount: A:0.42, C:0.22, G:0.20, T:0.16
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAACGCGAAAATGACTATCGCAACGAGAGA
Found at i:324109 original size:20 final size:20
Alignment explanation
Indices: 324027--324115 Score: 106
Period size: 20 Copynumber: 4.5 Consensus size: 20
324017 GGGATTCTCT
* **
324027 CGTTGTGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
*
324047 CATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* *
324067 CATTGCGATAGTCATTTTTG
1 CGTTGCGATAGTCATTTTCG
*
324087 CGTTGTGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
324107 CGTTACGAT
1 CGTTGCGAT
324116 TTTAAGTTTC
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 59 1.00
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.40
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:324640 original size:18 final size:19
Alignment explanation
Indices: 324601--324642 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
324591 CTCACCTGTC
324601 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
324622 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
324640 ATC
1 ATC
324643 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:324705 original size:42 final size:42
Alignment explanation
Indices: 324596--324706 Score: 109
Period size: 42 Copynumber: 2.6 Consensus size: 42
324586 CCTGACTCAC
* * * *
324596 CTGTCATCGTTCAAGAGGCCTC-CCCTATCGTTCAAGAGGCCC
1 CTGTCATCATTCAAGAGGTCTCTCCC-ACCGTTCAAGAGGCCA
* ** *
324638 CTATCATCCCTCAAGA-GTCACCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCATTCAAGAGGTC-TCTCCCACCGTTCAAGAGGCCA
*
324680 CTGTCATCATTGAAGAGGTCTCTCCCA
1 CTGTCATCATTCAAGAGGTCTCTCCCA
324707 ACATTCTAGA
Statistics
Matches: 54, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
41 2 0.04
42 46 0.85
43 6 0.11
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
CTGTCATCATTCAAGAGGTCTCTCCCACCGTTCAAGAGGCCA
Found at i:326264 original size:14 final size:14
Alignment explanation
Indices: 326245--326298 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
326235 GGAAATGACT
326245 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
326259 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
326278 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
326292 ATCGCAA
1 ATCGCAA
326299 TGCGAAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:326275 original size:33 final size:33
Alignment explanation
Indices: 326225--326313 Score: 133
Period size: 33 Copynumber: 2.6 Consensus size: 33
326215 AAAACAGACT
* **
326225 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
326259 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
326292 ATCGCAATGCGAAAATGAAAAT
1 ATCGCAATGCG-AAATGAAAAT
326314 TTGCGATTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
33 32 0.63
34 19 0.37
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:326357 original size:34 final size:34
Alignment explanation
Indices: 326314--326407 Score: 136
Period size: 33 Copynumber: 2.8 Consensus size: 34
326304 AAATGAAAAT
326314 TTGCGATTTTCATTTTCGCATTGCGATTCACTCG
1 TTGCGATTTTCATTTTCGCATTGCGATTCACTCG
*
326348 TTGCGATTTTCA-TTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTTCGCATTGCGATTCACTCG
** * *
326381 TTGCGATAGTCATTTCCGCGTTGCGAT
1 TTGCGATTTTCATTTTCGCATTGCGAT
326408 AGTCATTTCC
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 30 0.56
34 24 0.44
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.43
Consensus pattern (34 bp):
TTGCGATTTTCATTTTCGCATTGCGATTCACTCG
Found at i:326404 original size:20 final size:20
Alignment explanation
Indices: 326379--326483 Score: 167
Period size: 20 Copynumber: 5.2 Consensus size: 20
326369 GCGATTCTCT
326379 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
326399 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* *
326419 CATTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
326439 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
326459 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
326479 CGTTG
1 CGTTG
326484 TGATTTCCGC
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
20 76 0.97
21 2 0.03
ACGTcount: A:0.17, C:0.23, G:0.25, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:328932 original size:24 final size:24
Alignment explanation
Indices: 328898--328951 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
328888 CTGAAACATC
*
328898 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
328922 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
328946 ATCAAA
1 ATCAAA
328952 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:329821 original size:20 final size:20
Alignment explanation
Indices: 329793--329839 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
329783 AAATTCAGTA
* *
329793 TTGCAATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCACG
*
329813 TTGCGATAGTCAGATTCACG
1 TTGCGATAGTCAGAATCACG
329833 TTGCGAT
1 TTGCGAT
329840 TTACGTATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCACG
Done.