Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008045.1 Hibiscus syriacus cultivar Beakdansim tig00110533_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: 243713
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:11314 original size:23 final size:23
Alignment explanation
Indices: 11287--11339 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
11277 TCCCAAAGAA
*
11287 CCACAT-AGATTTGCGCAGAAGTG
1 CCACATAAG-TTTGCACAGAAGTG
*
11310 CCACATAAGTTTGCACCGAAGTG
1 CCACATAAGTTTGCACAGAAGTG
11333 CCACATA
1 CCACATA
11340 TTTTTCCCGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 25 0.93
24 2 0.07
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CCACATAAGTTTGCACAGAAGTG
Found at i:12970 original size:26 final size:26
Alignment explanation
Indices: 12934--12988 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
12924 AGAAGAACAT
12934 GATGCTTATCTTCGAGTGGTTCTTCA
1 GATGCTTATCTTCGAGTGGTTCTTCA
12960 GATGCTTATCTTCGAGTGGTTCTTCA
1 GATGCTTATCTTCGAGTGGTTCTTCA
12986 GAT
1 GAT
12989 ACTTTGTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.42
Consensus pattern (26 bp):
GATGCTTATCTTCGAGTGGTTCTTCA
Found at i:14785 original size:18 final size:18
Alignment explanation
Indices: 14762--14808 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
14752 GCTGATTTAA
14762 GAAGAAGGTATCACCCTG
1 GAAGAAGGTATCACCCTG
*
14780 GAAGAAGGTATCGCCCTG
1 GAAGAAGGTATCACCCTG
14798 GAAGAAGGTAT
1 GAAGAAGGTAT
14809 TAGGTTTTGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.34, C:0.17, G:0.32, T:0.17
Consensus pattern (18 bp):
GAAGAAGGTATCACCCTG
Found at i:15715 original size:54 final size:54
Alignment explanation
Indices: 15647--15883 Score: 227
Period size: 54 Copynumber: 4.4 Consensus size: 54
15637 ACCAAATGGT
* *
15647 ACTATGTGTACAACTCACAGAATTCATCATATGTTGATGAACAACCGTTTC-AGC
1 ACTATGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAACCATTTCGA-C
** * * * * * * *
15701 ACTATACGTGCAACTCACGGAGTTCATCATATGTTGACGAAGAACCGTTTTGGC
1 ACTATGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAACCATTTCGAC
* ** *
15755 ACTTTGTGTGCTTCT-A-AGGAAATTCATGATATG-T--TGAACAACCATTTCGAC
1 ACTATGTGTGCAACTCACA-G-AATTCATCATATGTTGATGAACAACCATTTCGAC
*
15806 ACTATGTGTCCAACTCAC-GAAATTCATCATATGTTGATGAACAACCATTTCGAC
1 ACTATGTGTGCAACTCACAG-AATTCATCATATGTTGATGAACAACCATTTCGAC
* *
15860 ACTATGTGTGCAACCCACAAAATT
1 ACTATGTGTGCAACTCACAGAATT
15884 TATAATAGAT
Statistics
Matches: 144, Mismatches: 30, Indels: 18
0.75 0.16 0.09
Matches are distributed among these distances:
51 37 0.26
52 2 0.01
53 3 0.02
54 102 0.71
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (54 bp):
ACTATGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAACCATTTCGAC
Found at i:15883 original size:105 final size:107
Alignment explanation
Indices: 15647--15883 Score: 246
Period size: 105 Copynumber: 2.2 Consensus size: 107
15637 ACCAAATGGT
* * * *
15647 ACTATGTGTACAACTCACAGAATTCATCATATGTTGATGAACAACCGTTTCAGCACTATACGTGC
1 ACTATGTGTGCAACTCACAAAATTCATCATATGTT-ATGAACAACCATTTCAGCACTATACGTCC
* * * * * *
15712 AACTCACGGAGTTCATCATATGTTGACGAAGAACCGTTTTGGC
65 AACTCACGAAATTCATCATATGTTGACGAACAACCATTTCGAC
* ** * ** * **
15755 ACTTTGTGTGCTTCTAAGGAAATTCATGATATG-T-TGAACAACCATTTC-GACACTATGTGTCC
1 ACTATGTGTGCAACTCACAAAATTCATCATATGTTATGAACAACCATTTCAG-CACTATACGTCC
*
15817 AACTCACGAAATTCATCATATGTTGATGAACAACCATTTCGAC
65 AACTCACGAAATTCATCATATGTTGACGAACAACCATTTCGAC
*
15860 ACTATGTGTGCAACCCACAAAATT
1 ACTATGTGTGCAACTCACAAAATT
15884 TATAATAGAT
Statistics
Matches: 101, Mismatches: 27, Indels: 5
0.76 0.20 0.04
Matches are distributed among these distances:
104 1 0.01
105 75 0.74
107 1 0.01
108 24 0.24
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (107 bp):
ACTATGTGTGCAACTCACAAAATTCATCATATGTTATGAACAACCATTTCAGCACTATACGTCCA
ACTCACGAAATTCATCATATGTTGACGAACAACCATTTCGAC
Found at i:16650 original size:21 final size:21
Alignment explanation
Indices: 16626--16690 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
16616 ATGTGACTGA
*
16626 GATTTTTTCGGTTTACTGGTT
1 GATTTTTTCGGTTTACTAGTT
*
16647 GATTTTTTTGGTTTACTAGTT
1 GATTTTTTCGGTTTACTAGTT
16668 GATTGATTTT--GTTTACTAGTT
1 GATT--TTTTCGGTTTACTAGTT
16689 GA
1 GA
16691 ATTGGTATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
21 36 0.90
23 4 0.10
ACGTcount: A:0.15, C:0.06, G:0.22, T:0.57
Consensus pattern (21 bp):
GATTTTTTCGGTTTACTAGTT
Found at i:17391 original size:18 final size:18
Alignment explanation
Indices: 17365--17421 Score: 78
Period size: 18 Copynumber: 3.2 Consensus size: 18
17355 TTGAGGACAA
17365 GCCTGCAAATGTAGATGG
1 GCCTGCAAATGTAGATGG
*
17383 GCCTACAAATGTAGATGG
1 GCCTGCAAATGTAGATGG
* * *
17401 GTCTGCTAATATAGATGG
1 GCCTGCAAATGTAGATGG
17419 GCC
1 GCC
17422 AACTTTTAGG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.25
Consensus pattern (18 bp):
GCCTGCAAATGTAGATGG
Found at i:24010 original size:20 final size:19
Alignment explanation
Indices: 23983--24041 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 19
23973 CATTTTGGTG
23983 CAGAGGGAATCGATCCCCC
1 CAGAGGGAATCGATCCCCC
*
24002 CATGAGGGAACCGATTCCCCC
1 CA-GAGGGAATCGA-TCCCCC
*
24023 CACAGGGAATCGATACCCC
1 CAGAGGGAATCGAT-CCCC
24042 TTGGGGTTCT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
19 3 0.09
20 23 0.68
21 8 0.24
ACGTcount: A:0.27, C:0.37, G:0.24, T:0.12
Consensus pattern (19 bp):
CAGAGGGAATCGATCCCCC
Found at i:30935 original size:13 final size:13
Alignment explanation
Indices: 30917--30949 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
30907 TTTCGAGAAA
30917 AGAAAAAGAAAAC
1 AGAAAAAGAAAAC
*
30930 AGAAAAAGCAAAC
1 AGAAAAAGAAAAC
30943 AGAAAAA
1 AGAAAAA
30950 ACAAACATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.76, C:0.09, G:0.15, T:0.00
Consensus pattern (13 bp):
AGAAAAAGAAAAC
Found at i:30954 original size:13 final size:13
Alignment explanation
Indices: 30917--30956 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
30907 TTTCGAGAAA
30917 AGAAAAAGA-AAAC
1 AGAAAAA-ACAAAC
*
30930 AGAAAAAGCAAAC
1 AGAAAAAACAAAC
30943 AGAAAAAACAAAC
1 AGAAAAAACAAAC
30956 A
1 A
30957 TTTATGGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.75, C:0.12, G:0.12, T:0.00
Consensus pattern (13 bp):
AGAAAAAACAAAC
Found at i:38738 original size:405 final size:405
Alignment explanation
Indices: 37981--38795 Score: 1515
Period size: 405 Copynumber: 2.0 Consensus size: 405
37971 TTCCTTGTGC
* *
37981 GAGGAGTATCTTGGAGGTGTGCCGCCTAATTTCAATGGTGGTCGAATACCGTTAATTTGGTTGGA
1 GAGGTGTATCTTGGAGGTGTCCCGCCTAATTTCAATGGTGGTCGAATACCGTTAATTTGGTTGGA
38046 TACAACTTTTAAACATTTGAGTCACGATGCCTCCAAGGAACATGTTAAAATGTATGCACGAGCTT
66 TACAACTTTTAAACATTTGAGTCACGATGCCTCCAAGGAACATGTTAAAATGTATGCACGAGCTT
38111 GTATATTACAACTCATAGGAAGGATCATAATGCCTGACAAATCGCGTAACCAAGTTCATTATATG
131 GTATATTACAACTCATAGGAAGGATCATAATGCCTGACAAATCGCGTAACCAAGTTCATTATATG
* *
38176 TGGTTGCGTCACCTCACATATTTTCATGTTATTGGCACACTAATTTGGGGCTTTACAGTTTTGGC
196 TGGTTGCGTCACCTCACATATTTTCATGTTACTGGCACACTAATTTGGGGCTCTACAGTTTTGGC
* *
38241 ATTTTTTATAGGGAAATGTGTCGAGCAACTGATTATCAAAAAAAATGCTATCGGCAAATGTCTCC
261 ATTTTTTATAGGGAAATGTGTAGAGCAACTGATTATCAAAAAAAATGCTATCGGCAAATGTATCC
38306 TTTTTCTCTAGTCTTGGGTGTGGTATCACATGCCTTTTTTATGACCGATCGTGAAAACTCGTTGG
326 TTTTTCTCTAGTCTTGGGTGTGGTATCACATG-CTTTTTTATGACCGATCGTGAAAACTCGTTGG
38371 TCTTCTTGCGATTGTT
390 TCTTCTTGCGATTGTT
*
38387 GAGGTGTATCTTGGAGGTGTCCCGCCTAATTTCAATGGTGGTTGAATACCGTTAATTTGGTTGGA
1 GAGGTGTATCTTGGAGGTGTCCCGCCTAATTTCAATGGTGGTCGAATACCGTTAATTTGGTTGGA
38452 TACAACTTTTAAACATTTGAGTCACGATGCCTCCAA-GAACATGTTAAAATGTATGCACGAGCTT
66 TACAACTTTTAAACATTTGAGTCACGATGCCTCCAAGGAACATGTTAAAATGTATGCACGAGCTT
*
38516 GTATATTACAACTCATAGGAAGGATCATAATGCCTGACAAATCGCGTAACCAAGTTCATTGTATG
131 GTATATTACAACTCATAGGAAGGATCATAATGCCTGACAAATCGCGTAACCAAGTTCATTATATG
*
38581 TGGTTGCGTCACCTCACATATTTTCATGTTACTGGCACACTCATTTGGGGCTCTACAGTTTTGGC
196 TGGTTGCGTCACCTCACATATTTTCATGTTACTGGCACACTAATTTGGGGCTCTACAGTTTTGGC
*
38646 ATTTTTTATAGGGAAATGTGTAGAGCAACTGATTATCGAAAAAAATGCTATCGGCAAATGTATCC
261 ATTTTTTATAGGGAAATGTGTAGAGCAACTGATTATCAAAAAAAATGCTATCGGCAAATGTATCC
*
38711 TTTTTCTCTAGTCTTGGGTGTGGTATCATATGCTTTTTTATGACCGATCGTGAAAACTCGTTGGT
326 TTTTTCTCTAGTCTTGGGTGTGGTATCACATGCTTTTTTATGACCGATCGTGAAAACTCGTTGGT
38776 CTTCTTGCGATTGTT
391 CTTCTTGCGATTGTT
38791 GAGGT
1 GAGGT
38796 AATTTCAATA
Statistics
Matches: 398, Mismatches: 11, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
404 53 0.13
405 247 0.62
406 98 0.25
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.35
Consensus pattern (405 bp):
GAGGTGTATCTTGGAGGTGTCCCGCCTAATTTCAATGGTGGTCGAATACCGTTAATTTGGTTGGA
TACAACTTTTAAACATTTGAGTCACGATGCCTCCAAGGAACATGTTAAAATGTATGCACGAGCTT
GTATATTACAACTCATAGGAAGGATCATAATGCCTGACAAATCGCGTAACCAAGTTCATTATATG
TGGTTGCGTCACCTCACATATTTTCATGTTACTGGCACACTAATTTGGGGCTCTACAGTTTTGGC
ATTTTTTATAGGGAAATGTGTAGAGCAACTGATTATCAAAAAAAATGCTATCGGCAAATGTATCC
TTTTTCTCTAGTCTTGGGTGTGGTATCACATGCTTTTTTATGACCGATCGTGAAAACTCGTTGGT
CTTCTTGCGATTGTT
Found at i:48519 original size:24 final size:24
Alignment explanation
Indices: 48484--48533 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
48474 GTCACGGTAA
48484 CTCATTTATTTCAATCAACAATCT
1 CTCATTTATTTCAATCAACAATCT
*
48508 CTCATTTGTTTCAATCAACAATCT
1 CTCATTTATTTCAATCAACAATCT
48532 CT
1 CT
48534 AATGATACTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.30, C:0.26, G:0.02, T:0.42
Consensus pattern (24 bp):
CTCATTTATTTCAATCAACAATCT
Found at i:56588 original size:19 final size:19
Alignment explanation
Indices: 56566--56602 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
56556 ATAAATTAGA
56566 AATAAAAAAAAATAATAAT
1 AATAAAAAAAAATAATAAT
* *
56585 AATAATAATAAATAATAA
1 AATAAAAAAAAATAATAA
56603 AAGCCTAGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (19 bp):
AATAAAAAAAAATAATAAT
Found at i:56590 original size:9 final size:10
Alignment explanation
Indices: 56565--56602 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
56555 AATAAATTAG
* *
56565 AAATAAAAAA
1 AAATAATAAT
56575 AAATAATAAT
1 AAATAATAAT
56585 -AATAATAAT
1 AAATAATAAT
56594 AAATAATAA
1 AAATAATAA
56603 AAGCCTAGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 9 0.36
10 16 0.64
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (10 bp):
AAATAATAAT
Found at i:64252 original size:21 final size:21
Alignment explanation
Indices: 64226--64283 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
64216 AGTAATATGT
64226 ATGAATTTAAAATTCATAGAA
1 ATGAATTTAAAATTCATAGAA
*
64247 ATGAATTTAAAATTCATAGCA
1 ATGAATTTAAAATTCATAGAA
64268 ATGAATTTAAAATTCA
1 ATGAATTTAAAATTCA
64284 AGTATAGCGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.50, C:0.07, G:0.09, T:0.34
Consensus pattern (21 bp):
ATGAATTTAAAATTCATAGAA
Found at i:69439 original size:182 final size:181
Alignment explanation
Indices: 69094--69456 Score: 692
Period size: 182 Copynumber: 2.0 Consensus size: 181
69084 GTGCTAAAGA
69094 ATTAATAATCAATCCCATTGATTTATGCCTAAACCCCAAAACTCAAACTACATCAAGTTTATGGA
1 ATTAATAATCAATCCCATTGATTTATGCCTAAACCCCAAAACTCAAACTACATCAAGTTTATGGA
69159 GGAAATTCTCTCCAAGAAAAGAAGGTTTGGCGAATTCGAGACTATTGTACTCATTGAGGGATGCA
66 GGAAATTCTCTCCAAGAAAAGAAGGTTTGGCGAATTCGAGACTATTGTACTCATTGAGGGATGCA
*
69224 GTGTTATGGTTCCAAGTTGATTGCCACCAAAACTAAAAGATCCAGGGAGTT
131 GTGTTATGGTTCCAAGTTGATTACCACCAAAACTAAAAGATCCAGGGAGTT
69275 ATTAATAATCAATATCCCATTGATTTATGCCTAAACCCCAAAACTCAAACTACATCAAGTTTATG
1 ATTAATAATC-A-ATCCCATTGATTTATGCCTAAACCCCAAAACTCAAACTACATCAAGTTTATG
69340 GAGGAAATTCTCTCCAAGAAAAG-AGGTTTGGCGAATTCGAGACTATTGTACTCATTGAGGGATG
64 GAGGAAATTCTCTCCAAGAAAAGAAGGTTTGGCGAATTCGAGACTATTGTACTCATTGAGGGATG
69404 CAGTGTTATGGTTCCAAGTTGATTACCACCAAAACTAAAAGATCCAGGGAGTT
129 CAGTGTTATGGTTCCAAGTTGATTACCACCAAAACTAAAAGATCCAGGGAGTT
69457 TCATTATTCC
Statistics
Matches: 179, Mismatches: 1, Indels: 3
0.98 0.01 0.02
Matches are distributed among these distances:
181 10 0.06
182 94 0.53
183 75 0.42
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (181 bp):
ATTAATAATCAATCCCATTGATTTATGCCTAAACCCCAAAACTCAAACTACATCAAGTTTATGGA
GGAAATTCTCTCCAAGAAAAGAAGGTTTGGCGAATTCGAGACTATTGTACTCATTGAGGGATGCA
GTGTTATGGTTCCAAGTTGATTACCACCAAAACTAAAAGATCCAGGGAGTT
Found at i:73342 original size:16 final size:16
Alignment explanation
Indices: 73318--73349 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
73308 TTCATTGAAG
73318 ATTTCCATGACATTTA
1 ATTTCCATGACATTTA
*
73334 ATTTTCATGACATTTA
1 ATTTCCATGACATTTA
73350 GATAGATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.16, G:0.06, T:0.47
Consensus pattern (16 bp):
ATTTCCATGACATTTA
Found at i:74053 original size:95 final size:95
Alignment explanation
Indices: 73890--74079 Score: 380
Period size: 95 Copynumber: 2.0 Consensus size: 95
73880 TTTTGTTTCT
73890 TTAATTACTTTGATAATTATGATATTTTCTAGAAATACCTATGATGGTGAACCTCATCGACTAAG
1 TTAATTACTTTGATAATTATGATATTTTCTAGAAATACCTATGATGGTGAACCTCATCGACTAAG
73955 AGCACACACATACATGAGTATCATAAGTTG
66 AGCACACACATACATGAGTATCATAAGTTG
73985 TTAATTACTTTGATAATTATGATATTTTCTAGAAATACCTATGATGGTGAACCTCATCGACTAAG
1 TTAATTACTTTGATAATTATGATATTTTCTAGAAATACCTATGATGGTGAACCTCATCGACTAAG
74050 AGCACACACATACATGAGTATCATAAGTTG
66 AGCACACACATACATGAGTATCATAAGTTG
74080 ATTTGAGTTG
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 95 1.00
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.34
Consensus pattern (95 bp):
TTAATTACTTTGATAATTATGATATTTTCTAGAAATACCTATGATGGTGAACCTCATCGACTAAG
AGCACACACATACATGAGTATCATAAGTTG
Found at i:83567 original size:15 final size:16
Alignment explanation
Indices: 83547--83576 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
83537 TGTTTTTCTA
83547 TAATTTATAT-TTATT
1 TAATTTATATATTATT
83562 TAATTTATATATTAT
1 TAATTTATATATTAT
83577 CTTCCAACCG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TAATTTATATATTATT
Found at i:85657 original size:90 final size:89
Alignment explanation
Indices: 85500--85673 Score: 294
Period size: 90 Copynumber: 1.9 Consensus size: 89
85490 CTAACACACT
* *
85500 CTTTTATAGACAAGTTACCCTAATCATATTAGGGTTTTTATTATTTCAAATTAATTAAATCTCTA
1 CTTTTATAGACAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATA
*
85565 TTTAATTAATTAGAATTTAATAATC
66 TTTAATTAATT-GAAATTAATAATC
**
85590 CTTTTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATA
1 CTTTTATAGACAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATA
85655 TTTAATTAATTGAAATTAA
66 TTTAATTAATTGAAATTAA
85674 ATATTCGGGA
Statistics
Matches: 79, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
89 7 0.09
90 72 0.91
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.45
Consensus pattern (89 bp):
CTTTTATAGACAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATA
TTTAATTAATTGAAATTAATAATC
Found at i:87134 original size:37 final size:37
Alignment explanation
Indices: 87084--87161 Score: 156
Period size: 37 Copynumber: 2.1 Consensus size: 37
87074 GGAAGTTATG
87084 TTGCGACGATGCTCCATGAACTGCTCAAGCTACCAAC
1 TTGCGACGATGCTCCATGAACTGCTCAAGCTACCAAC
87121 TTGCGACGATGCTCCATGAACTGCTCAAGCTACCAAC
1 TTGCGACGATGCTCCATGAACTGCTCAAGCTACCAAC
87158 TTGC
1 TTGC
87162 CCACAGAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.26, C:0.32, G:0.19, T:0.23
Consensus pattern (37 bp):
TTGCGACGATGCTCCATGAACTGCTCAAGCTACCAAC
Found at i:94227 original size:20 final size:20
Alignment explanation
Indices: 94202--94241 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
94192 ATGCTGAGAT
94202 CGAGCATCCAGTCTCAATAC
1 CGAGCATCCAGTCTCAATAC
* *
94222 CGAGCATCTAGTCTTAATAC
1 CGAGCATCCAGTCTCAATAC
94242 TACCACCCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.25
Consensus pattern (20 bp):
CGAGCATCCAGTCTCAATAC
Found at i:101689 original size:19 final size:18
Alignment explanation
Indices: 101661--101696 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
101651 TTAACAACAT
*
101661 ATTTAATAAACATATTAA
1 ATTTAATAAAAATATTAA
101679 ATTTAAATAAAAATATTA
1 ATTT-AATAAAAATATTA
101697 GGCATAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
ATTTAATAAAAATATTAA
Found at i:107791 original size:2 final size:2
Alignment explanation
Indices: 107747--107774 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
107737 AAATAACATC
107747 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
107775 GCATAACATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:108401 original size:68 final size:68
Alignment explanation
Indices: 108321--108456 Score: 272
Period size: 68 Copynumber: 2.0 Consensus size: 68
108311 ATTTTATCGA
108321 ATTTTAACACTTTTTAGCTTTTAACATAAATTTCGGATAAAAAATTGTTTCTCACTAAACGTTAT
1 ATTTTAACACTTTTTAGCTTTTAACATAAATTTCGGATAAAAAATTGTTTCTCACTAAACGTTAT
108386 TTT
66 TTT
108389 ATTTTAACACTTTTTAGCTTTTAACATAAATTTCGGATAAAAAATTGTTTCTCACTAAACGTTAT
1 ATTTTAACACTTTTTAGCTTTTAACATAAATTTCGGATAAAAAATTGTTTCTCACTAAACGTTAT
108454 TTT
66 TTT
108457 GGGTATGAAC
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.34, C:0.13, G:0.07, T:0.46
Consensus pattern (68 bp):
ATTTTAACACTTTTTAGCTTTTAACATAAATTTCGGATAAAAAATTGTTTCTCACTAAACGTTAT
TTT
Found at i:112406 original size:81 final size:83
Alignment explanation
Indices: 112307--112471 Score: 300
Period size: 81 Copynumber: 2.0 Consensus size: 83
112297 CCAAATGATT
112307 TCTAAGTATATTCAATAGAATTA-TCGAATATCAAAAACATTACTCCAAA-CATTCAAAGATCAT
1 TCTAAGTATATTCAATAGAATTATTCGAATATC-AAAACATTACTCCAAATCATTCAAAGATCAT
112370 TTTTAATCCTTA-TCAAAG
65 TTTTAATCCTTACTCAAAG
112388 TCTAAGTATATTCAATAGAATTATTCGAATATCAAAACATTACTCCAAATCATTCAAAGATCATT
1 TCTAAGTATATTCAATAGAATTATTCGAATATCAAAACATTACTCCAAATCATTCAAAGATCATT
112453 TTTAATCCTTACTCAAAG
66 TTTAATCCTTACTCAAAG
112471 T
1 T
112472 GTAAAATAAA
Statistics
Matches: 81, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
81 39 0.48
82 35 0.43
83 7 0.09
ACGTcount: A:0.42, C:0.18, G:0.06, T:0.35
Consensus pattern (83 bp):
TCTAAGTATATTCAATAGAATTATTCGAATATCAAAACATTACTCCAAATCATTCAAAGATCATT
TTTAATCCTTACTCAAAG
Found at i:112605 original size:21 final size:21
Alignment explanation
Indices: 112564--112623 Score: 95
Period size: 21 Copynumber: 2.9 Consensus size: 21
112554 ATTGCTCAGA
112564 GGGA-ACCGATTCCCACCTAAG
1 GGGATACCGATTCCC-CCTAAG
*
112585 GGGGTACCGATTCCCCCTAAG
1 GGGATACCGATTCCCCCTAAG
112606 GGGATACCGATTCCCCCT
1 GGGATACCGATTCCCCCT
112624 GAATGGTTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 26 0.72
22 10 0.28
ACGTcount: A:0.22, C:0.35, G:0.25, T:0.18
Consensus pattern (21 bp):
GGGATACCGATTCCCCCTAAG
Found at i:114449 original size:21 final size:23
Alignment explanation
Indices: 114425--114475 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
114415 AGTGAATCGA
114425 TCCCCCCTTG-A-GGGAGCCGAT
1 TCCCCCCTTGAAGGGGAGCCGAT
* *
114446 TCCCCCTTTGAAGGGGATCCGAT
1 TCCCCCCTTGAAGGGGAGCCGAT
114469 TCCCCCC
1 TCCCCCC
114476 ACAGGGGAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 9 0.36
22 1 0.04
23 15 0.60
ACGTcount: A:0.14, C:0.41, G:0.24, T:0.22
Consensus pattern (23 bp):
TCCCCCCTTGAAGGGGAGCCGAT
Found at i:114501 original size:20 final size:21
Alignment explanation
Indices: 114457--114496 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
114447 CCCCCTTTGA
* *
114457 AGGGGATCCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
114478 AGGGGAACCGATACCCCCC
1 AGGGGAACCGATACCCCCC
114497 TAGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.42, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:114932 original size:19 final size:18
Alignment explanation
Indices: 114908--114954 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
114898 TTGATTTTCA
*
114908 AATTATTGTGTTTTGATTG
1 AATTATTGT-TGTTGATTG
114927 AATTA-TGTTGTTGATTG
1 AATTATTGTTGTTGATTG
114944 AATTA-TGTTGT
1 AATTATTGTTGT
114955 GTTATGAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 19 0.70
18 3 0.11
19 5 0.19
ACGTcount: A:0.23, C:0.00, G:0.21, T:0.55
Consensus pattern (18 bp):
AATTATTGTTGTTGATTG
Found at i:114962 original size:17 final size:17
Alignment explanation
Indices: 114916--114954 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
114906 CAAATTATTG
114916 TGTT-TTGATTGAATTA
1 TGTTGTTGATTGAATTA
114932 TGTTGTTGATTGAATTA
1 TGTTGTTGATTGAATTA
114949 TGTTGT
1 TGTTGT
114955 GTTATGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.21, C:0.00, G:0.23, T:0.56
Consensus pattern (17 bp):
TGTTGTTGATTGAATTA
Found at i:118856 original size:15 final size:16
Alignment explanation
Indices: 118819--118851 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
118809 ATTTTTGGAA
118819 AATGAAAATA-AAAAT
1 AATGAAAATAGAAAAT
118834 AATGAAAATATGAAAAT
1 AATGAAAATA-GAAAAT
118851 A
1 A
118852 TAAAAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.62
17 6 0.38
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (16 bp):
AATGAAAATAGAAAAT
Found at i:119154 original size:26 final size:27
Alignment explanation
Indices: 119114--119170 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 27
119104 TATTGAATAT
* *
119114 ATAATAATTTTATATTTT-AAATTTAA
1 ATAATAATTTAATATTTTAAAAATTAA
*
119140 ATAATACTTTAATATTTTAAAAATTAA
1 ATAATAATTTAATATTTTAAAAATTAA
119167 ATAA
1 ATAA
119171 GTTCTCAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 16 0.59
27 11 0.41
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (27 bp):
ATAATAATTTAATATTTTAAAAATTAA
Found at i:119880 original size:18 final size:19
Alignment explanation
Indices: 119845--119881 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
119835 CACGGAATGT
119845 AAGATTACCAGTAGGAATAA
1 AAGATTACCAG-AGGAATAA
119865 AAGATTACCA-AGGAATA
1 AAGATTACCAGAGGAATA
119882 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.51, C:0.11, G:0.19, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGAGGAATAA
Found at i:120755 original size:31 final size:31
Alignment explanation
Indices: 120720--120797 Score: 111
Period size: 31 Copynumber: 2.5 Consensus size: 31
120710 CCAAAAAACA
* *
120720 TAAGTTTTGGTCATTTACATTATTGTTTTAT
1 TAAGTTTTGGTCACTTACATTAATGTTTTAT
**
120751 TAAGTTTTGGTCACTTATGTTAATGTTTTAT
1 TAAGTTTTGGTCACTTACATTAATGTTTTAT
*
120782 TATGTTTTGGTCACTT
1 TAAGTTTTGGTCACTT
120798 GGACGTTGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.21, C:0.08, G:0.15, T:0.56
Consensus pattern (31 bp):
TAAGTTTTGGTCACTTACATTAATGTTTTAT
Found at i:128929 original size:20 final size:21
Alignment explanation
Indices: 128890--128950 Score: 72
Period size: 23 Copynumber: 2.9 Consensus size: 21
128880 TTTTGGTGCA
*
128890 GAGGGAATCGA-TCCCTCC-TT
1 GAGGGAACCGATTCCC-CCTTT
128910 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCTTT
128931 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATTCCCCC
128951 CCACAGGGGA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
20 12 0.33
21 7 0.19
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.33, G:0.26, T:0.20
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCTTT
Found at i:130620 original size:12 final size:12
Alignment explanation
Indices: 130603--130631 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
130593 AGATGAGCCT
130603 GAGCAGCCCGAG
1 GAGCAGCCCGAG
130615 GAGCAGCCCGAG
1 GAGCAGCCCGAG
130627 GAGCA
1 GAGCA
130632 AGCACAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.28, C:0.31, G:0.41, T:0.00
Consensus pattern (12 bp):
GAGCAGCCCGAG
Found at i:135438 original size:18 final size:18
Alignment explanation
Indices: 135415--135450 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
135405 TAACCTCAAA
135415 ATGGTACCGATACCATGT
1 ATGGTACCGATACCATGT
**
135433 ATGGTATTGATACCATGT
1 ATGGTACCGATACCATGT
135451 TAATATAGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (18 bp):
ATGGTACCGATACCATGT
Found at i:136997 original size:24 final size:24
Alignment explanation
Indices: 136949--136994 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
136939 AATGATGGTA
136949 AAAGAAGAAGAATATCAAGAAAAG
1 AAAGAAGAAGAATATCAAGAAAAG
* *
136973 AAAGATGAAGAA-ATGAAGAAAA
1 AAAGAAGAAGAATATCAAGAAAA
136995 AGATTGGGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.67, C:0.02, G:0.22, T:0.09
Consensus pattern (24 bp):
AAAGAAGAAGAATATCAAGAAAAG
Found at i:141249 original size:20 final size:22
Alignment explanation
Indices: 141222--141283 Score: 74
Period size: 20 Copynumber: 2.9 Consensus size: 22
141212 ATTCTGTGCA
141222 CTTAGTATCGATAATGTTCAT-
1 CTTAGTATCGATAATGTTCATG
* *
141243 C-TAGTATCGATATTGTTCTTG
1 CTTAGTATCGATAATGTTCATG
* *
141264 CTTAGTATTGATACTGTTCA
1 CTTAGTATCGATAATGTTCA
141284 ACAGTACCGA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 15 0.44
ACGTcount: A:0.24, C:0.15, G:0.16, T:0.45
Consensus pattern (22 bp):
CTTAGTATCGATAATGTTCATG
Found at i:141352 original size:18 final size:19
Alignment explanation
Indices: 141329--141367 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
141319 CTCAAGATTT
*
141329 TCCTTGA-AGTATCGATAC
1 TCCTTGAGAGTACCGATAC
141347 TCCTTGAGGAGTACCGATAC
1 TCCTTGA-GAGTACCGATAC
141367 T
1 T
141368 ACTCGTCGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
20 11 0.61
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.31
Consensus pattern (19 bp):
TCCTTGAGAGTACCGATAC
Found at i:143652 original size:20 final size:20
Alignment explanation
Indices: 143627--143682 Score: 112
Period size: 20 Copynumber: 2.8 Consensus size: 20
143617 ATTTTAATAT
143627 GGTAGTACCGATACTGCTAA
1 GGTAGTACCGATACTGCTAA
143647 GGTAGTACCGATACTGCTAA
1 GGTAGTACCGATACTGCTAA
143667 GGTAGTACCGATACTG
1 GGTAGTACCGATACTG
143683 TGCTTATAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.25
Consensus pattern (20 bp):
GGTAGTACCGATACTGCTAA
Found at i:144897 original size:14 final size:13
Alignment explanation
Indices: 144877--144919 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
144867 TGAGAGATAC
144877 AAAAAATGAGGAA
1 AAAAAATGAGGAA
144890 AGAAAAATGAGAGAA
1 A-AAAAATGAG-GAA
*
144905 AAAAGA-GAGGAA
1 AAAAAATGAGGAA
144917 AAA
1 AAA
144920 GAAAAGGTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 6 0.22
13 4 0.15
14 13 0.48
15 4 0.15
ACGTcount: A:0.70, C:0.00, G:0.26, T:0.05
Consensus pattern (13 bp):
AAAAAATGAGGAA
Found at i:156549 original size:17 final size:18
Alignment explanation
Indices: 156509--156552 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
156499 TTGAAACATA
156509 TGATAATTGTATAATTTT
1 TGATAATTGTATAATTTT
156527 TGATAATTGTATAATTTT
1 TGATAATTGTATAATTTT
156545 T-ATAATTG
1 TGATAATTG
156553 AGTGACTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 7 0.27
18 19 0.73
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.55
Consensus pattern (18 bp):
TGATAATTGTATAATTTT
Found at i:157043 original size:47 final size:47
Alignment explanation
Indices: 156974--157066 Score: 161
Period size: 47 Copynumber: 2.0 Consensus size: 47
156964 TACATTCATG
*
156974 CCGTTTCACGTGTTGCAGAATAGCTTTTGCTTATCCACCAGCTCTTT
1 CCGTTTCACGTGTTGCAGAATAGCTTTCGCTTATCCACCAGCTCTTT
157021 CCGTTTCACGTGTTG-AGGAATAGCTTTCGCTTATCCACCAGCTCTT
1 CCGTTTCACGTGTTGCA-GAATAGCTTTCGCTTATCCACCAGCTCTT
157067 CTGTGTCAAG
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
46 1 0.02
47 43 0.98
ACGTcount: A:0.17, C:0.28, G:0.18, T:0.37
Consensus pattern (47 bp):
CCGTTTCACGTGTTGCAGAATAGCTTTCGCTTATCCACCAGCTCTTT
Found at i:168418 original size:49 final size:50
Alignment explanation
Indices: 168336--168447 Score: 172
Period size: 49 Copynumber: 2.2 Consensus size: 50
168326 AAGCTAATAC
* * *
168336 AAAGAGTGTACACAAATTTCAACAAGTGCAGAAAAGT-CAAAAAAATTAA
1 AAAGGGTGTACACAAATTTCAACAAGTGCAGAAAAGTAAAAAAAAATAAA
*
168385 AAAGGGTGTGCACAAATTTCAACAAGTGCAGAAAAGTAAAAAAAAAATAAA
1 AAAGGGTGTACACAAATTTCAACAAGTGCAGAAAAGT-AAAAAAAAATAAA
168436 AAAGGGTGTACA
1 AAAGGGTGTACA
168448 GAATTTTTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
49 35 0.62
51 21 0.38
ACGTcount: A:0.54, C:0.11, G:0.18, T:0.17
Consensus pattern (50 bp):
AAAGGGTGTACACAAATTTCAACAAGTGCAGAAAAGTAAAAAAAAATAAA
Found at i:169703 original size:75 final size:71
Alignment explanation
Indices: 169597--169744 Score: 233
Period size: 75 Copynumber: 2.0 Consensus size: 71
169587 GTAACCTAGC
*
169597 TGTCAATGAATCTTTCAGGTTCGAGTGTCAGCTGTACTTACTAATGAACCTTTCTTGTTGAATCC
1 TGTCAATGAATCTTTCAGGTTCGAGTGTCAGCTGTACTTACTAATGAACCTCTCTTGTTGAATCC
169662 TGATTG
66 TGATTG
*
169668 TGTCAATGAATCTTTCTCTCAGGTTCGAGTGTCAGCTGTACTTACTAATGGACCTCTCTTGTTGA
1 TGTCAATGAATC--T-T-TCAGGTTCGAGTGTCAGCTGTACTTACTAATGAACCTCTCTTGTTGA
*
169733 ATCTTGATTG
62 ATCCTGATTG
169743 TG
1 TG
169745 ATCGCTACAT
Statistics
Matches: 70, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
71 12 0.17
73 1 0.01
74 1 0.01
75 56 0.80
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (71 bp):
TGTCAATGAATCTTTCAGGTTCGAGTGTCAGCTGTACTTACTAATGAACCTCTCTTGTTGAATCC
TGATTG
Found at i:176353 original size:24 final size:24
Alignment explanation
Indices: 176296--176356 Score: 95
Period size: 24 Copynumber: 2.5 Consensus size: 24
176286 GGGTCTATAC
* *
176296 GGTCTTTCGAGACAAATTCTACGT
1 GGTCCTTCGGGACAAATTCTACGT
*
176320 GGTCCTTCGGGACAAATTCTATGT
1 GGTCCTTCGGGACAAATTCTACGT
176344 GGTCCTTCGGGAC
1 GGTCCTTCGGGAC
176357 TTATATGTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.20, C:0.23, G:0.26, T:0.31
Consensus pattern (24 bp):
GGTCCTTCGGGACAAATTCTACGT
Found at i:176540 original size:24 final size:24
Alignment explanation
Indices: 176470--176540 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 24
176460 CAATCTTATA
*
176470 TGGCACTACGGTGC-ATTTCTACG
1 TGGCACTTCGGTGCAATTTCTACG
* *
176493 CGGCACTTCGGTGCAAATTCTACG
1 TGGCACTTCGGTGCAATTTCTACG
* *
176517 TGGCACTTTGGTGCAATTTATACG
1 TGGCACTTCGGTGCAATTTCTACG
176541 AGCTGTGGTG
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 12 0.30
24 28 0.70
ACGTcount: A:0.20, C:0.24, G:0.25, T:0.31
Consensus pattern (24 bp):
TGGCACTTCGGTGCAATTTCTACG
Found at i:176855 original size:18 final size:17
Alignment explanation
Indices: 176819--176857 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
176809 TAAAAGGTAT
* *
176819 TAATGATAATAATACGA
1 TAATGATAAGAATAAGA
176836 TAATGATAAGGAATAAGA
1 TAATGATAA-GAATAAGA
176854 TAAT
1 TAAT
176858 CATATATGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.54, C:0.03, G:0.15, T:0.28
Consensus pattern (17 bp):
TAATGATAAGAATAAGA
Found at i:191099 original size:24 final size:23
Alignment explanation
Indices: 191054--191165 Score: 133
Period size: 23 Copynumber: 4.9 Consensus size: 23
191044 TCGGAAAAAA
*
191054 TATGTGGCACTTCGGTGCAAACC
1 TATGTGGCACTTTGGTGCAAACC
191077 TATGTGGCACTTTTGGTGCAAACC
1 TATGTGGCAC-TTTGGTGCAAACC
*
191101 TATGTGACACTTTGGTGCAAACC
1 TATGTGGCACTTTGGTGCAAACC
*
191124 TATGTGGTC-CTTTGG-G-ACAA-T
1 TATGTGG-CACTTTGGTGCA-AACC
*
191145 TATGTGGCACTTTAGTGCAAA
1 TATGTGGCACTTTGGTGCAAA
191166 TTACGAGCAG
Statistics
Matches: 78, Mismatches: 5, Indels: 13
0.81 0.05 0.14
Matches are distributed among these distances:
20 1 0.01
21 13 0.17
22 6 0.08
23 36 0.46
24 22 0.28
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (23 bp):
TATGTGGCACTTTGGTGCAAACC
Found at i:197949 original size:23 final size:23
Alignment explanation
Indices: 197918--197970 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
197908 AATATATGGC
197918 ACTTCGGTGCAAACCTATGTGGT
1 ACTTCGGTGCAAACCTATGTGGT
* *
197941 ACTTTGGTGCAAACTTATGTGGT
1 ACTTCGGTGCAAACCTATGTGGT
*
197964 CCTTCGG
1 ACTTCGG
197971 GACAATTATG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.34
Consensus pattern (23 bp):
ACTTCGGTGCAAACCTATGTGGT
Found at i:198651 original size:24 final size:25
Alignment explanation
Indices: 198608--198658 Score: 79
Period size: 24 Copynumber: 2.1 Consensus size: 25
198598 TTTAAAGGTT
198608 AATGAACATGTTCTTTGGAATTTCA
1 AATGAACATGTTCTTTGGAATTTCA
198633 AATGACACATG-T-TTTGGAATTTCA
1 AATGA-ACATGTTCTTTGGAATTTCA
198657 AA
1 AA
198659 AGAAATGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 14 0.56
25 6 0.24
26 5 0.20
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (25 bp):
AATGAACATGTTCTTTGGAATTTCA
Found at i:210709 original size:46 final size:46
Alignment explanation
Indices: 210638--210825 Score: 232
Period size: 46 Copynumber: 4.1 Consensus size: 46
210628 TATGGTCTCT
* * * * * *
210638 TTTCATGCATTAATACTTCCGTTCATGCATTTTAATCATGGCATCC
1 TTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGACATCC
* * *
210684 TTTCATGCCCTAATGCATCATTTCATGCATTTTAGTTATGACATCC
1 TTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGACATCC
* * **
210730 TTTCATGCCTTAATGCATCCGTTCATGCATTTTTATTATGGTATCC
1 TTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGACATCC
* * *
210776 TCTCCTGCCTTAATGCATCCTTTCATGCATTTTAGTTATGACATCC
1 TTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGACATCC
210822 TTTC
1 TTTC
210826 TTGCATTTTA
Statistics
Matches: 118, Mismatches: 24, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
46 118 1.00
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.43
Consensus pattern (46 bp):
TTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGACATCC
Found at i:210735 original size:26 final size:26
Alignment explanation
Indices: 210659--210965 Score: 254
Period size: 26 Copynumber: 12.8 Consensus size: 26
210649 AATACTTCCG
* *
210659 TTCATGCATTTTAATCATGGCATCCT
1 TTCATGCATTTTAGTTATGGCATCCT
** *
210685 TTCATGC--CCTA---AT-GCATCAT
1 TTCATGCATTTTAGTTATGGCATCCT
*
210705 TTCATGCATTTTAGTTATGACATCCT
1 TTCATGCATTTTAGTTATGGCATCCT
* *
210731 TTCATGC--CTTA---AT-GCATCCG
1 TTCATGCATTTTAGTTATGGCATCCT
*
210751 TTCATGCATTTTTA-TTATGGTATCCT
1 TTCATGCA-TTTTAGTTATGGCATCCT
* * *
210777 CTCCTGC--CTTA---AT-GCATCCT
1 TTCATGCATTTTAGTTATGGCATCCT
*
210797 TTCATGCATTTTAGTTATGACATCCT
1 TTCATGCATTTTAGTTATGGCATCCT
*
210823 TTCTTGCATTTTAGTTATGGCATCCT
1 TTCATGCATTTTAGTTATGGCATCCT
*
210849 TTCAT---TTCTTA---AT-GCATCCA
1 TTCATGCATT-TTAGTTATGGCATCCT
*
210869 TTCATGCATTTTAATTATGGCATCCT
1 TTCATGCATTTTAGTTATGGCATCCT
*
210895 ATCATGCATTTTAGTTATGGCATCCT
1 TTCATGCATTTTAGTTATGGCATCCT
210921 TTCATGCATTTTAGTTATGGCAT-CT
1 TTCATGCATTTTAGTTATGGCATCCT
210946 TTCATGCATTTTAGTTATGG
1 TTCATGCATTTTAGTTATGG
210966 ATTCGGTTTA
Statistics
Matches: 226, Mismatches: 29, Indels: 53
0.73 0.09 0.17
Matches are distributed among these distances:
20 47 0.21
21 8 0.04
22 8 0.04
23 10 0.04
24 8 0.04
25 30 0.13
26 115 0.51
ACGTcount: A:0.21, C:0.21, G:0.13, T:0.45
Consensus pattern (26 bp):
TTCATGCATTTTAGTTATGGCATCCT
Found at i:210790 original size:92 final size:92
Alignment explanation
Indices: 210638--210832 Score: 291
Period size: 92 Copynumber: 2.1 Consensus size: 92
210628 TATGGTCTCT
* *
210638 TTTCATGCATTAATACTTCCGTTCATGCATTTTAATCATGGCATCCTTTCATGCCCTAATGCATC
1 TTTCATGCATTAATACATCCGTTCATGCATTTTAATCATGGCATCCTCTCATGCCCTAATGCATC
210703 ATTTCATGCATTTTAGTTATGACATCC
66 ATTTCATGCATTTTAGTTATGACATCC
* * * * * * *
210730 TTTCATGCCTTAATGCATCCGTTCATGCATTTTTATTATGGTATCCTCTCCTGCCTTAATGCATC
1 TTTCATGCATTAATACATCCGTTCATGCATTTTAATCATGGCATCCTCTCATGCCCTAATGCATC
*
210795 CTTTCATGCATTTTAGTTATGACATCC
66 ATTTCATGCATTTTAGTTATGACATCC
*
210822 TTTCTTGCATT
1 TTTCATGCATT
210833 TTAGTTATGG
Statistics
Matches: 91, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
92 91 1.00
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.44
Consensus pattern (92 bp):
TTTCATGCATTAATACATCCGTTCATGCATTTTAATCATGGCATCCTCTCATGCCCTAATGCATC
ATTTCATGCATTTTAGTTATGACATCC
Found at i:210841 original size:72 final size:72
Alignment explanation
Indices: 210745--210964 Score: 255
Period size: 72 Copynumber: 3.0 Consensus size: 72
210735 TGCCTTAATG
* * * *
210745 CATCCGTTCATGCATTTTTA-TTATGGTATCCTCTCCTGCCTTAATGCATCCTTTCATGCATTTT
1 CATCCTTTCATGCA-TTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTT
210809 AGTTATGA
65 AGTTATGA
* ** *
210817 CATCCTTTCTTGCATTTTAGTTATGGCATCCTTTCATTTCTTAATGCATCCATTCATGCATTTTA
1 CATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTA
* *
210882 ATTATGG
66 GTTATGA
* *
210889 CATCCTATCATGCATTTTAGTTATGGCATCCTTTCATGCATTTTAGTTATGGCAT-CTTTCATGC
1 CATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGC--CTTA---AT-GCATCCTTTCATGC
210953 ATTTTAGTTATG
60 ATTTTAGTTATG
210965 GATTCGGTTT
Statistics
Matches: 124, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
71 5 0.04
72 91 0.73
74 3 0.02
77 21 0.17
78 4 0.03
ACGTcount: A:0.20, C:0.21, G:0.13, T:0.46
Consensus pattern (72 bp):
CATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTA
GTTATGA
Found at i:211462 original size:14 final size:14
Alignment explanation
Indices: 211443--211469 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
211433 CTGTGTTGCC
211443 TGGTATCGATACCA
1 TGGTATCGATACCA
211457 TGGTATCGATACC
1 TGGTATCGATACC
211470 CTTCTCTCAG
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:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (14 bp):
TGGTATCGATACCA
Found at i:217852 original size:54 final size:51
Alignment explanation
Indices: 217770--217968 Score: 185
Period size: 46 Copynumber: 4.1 Consensus size: 51
217760 AATACTTCCG
* * *
217770 TTCATGCATTTTAATCATGGCATCCTTTCATTTCCTAATGCCATAATGCATCCT
1 TTCATGCATTTTAGTTATGGCATCCTTTCATTT-C--ATGCCTTAATGCATCCT
217824 TTCATGCATTTTAGTTATGGCAT-C---C-TTTCATGCCTTAATGCATCCT
1 TTCATGCATTTTAGTTATGGCATCCTTTCATTTCATGCCTTAATGCATCCT
* * *
217870 TTCATGCATTTAAGTTATGTCATCCTTTCA---C--GCCTTAATGCATCAT
1 TTCATGCATTTTAGTTATGGCATCCTTTCATTTCATGCCTTAATGCATCCT
* * *
217916 TTCATGTATTTTAGTTATGGCA-----TCATTTCATGCCTTAGTGCATCCA
1 TTCATGCATTTTAGTTATGGCATCCTTTCATTTCATGCCTTAATGCATCCT
217962 TTCATGC
1 TTCATGC
217969 CTTAGTGCAT
Statistics
Matches: 122, Mismatches: 13, Indels: 28
0.75 0.08 0.17
Matches are distributed among these distances:
41 3 0.02
44 1 0.01
46 88 0.72
47 1 0.01
48 2 0.02
49 3 0.02
50 2 0.02
53 1 0.01
54 21 0.17
ACGTcount: A:0.22, C:0.24, G:0.12, T:0.42
Consensus pattern (51 bp):
TTCATGCATTTTAGTTATGGCATCCTTTCATTTCATGCCTTAATGCATCCT
Found at i:217874 original size:46 final size:46
Alignment explanation
Indices: 217807--217968 Score: 243
Period size: 46 Copynumber: 3.5 Consensus size: 46
217797 TCATTTCCTA
*
217807 ATGCCATAATGCATCCTTTCATGCATTTTAGTTATGGCATCCTTTC
1 ATGCCTTAATGCATCCTTTCATGCATTTTAGTTATGGCATCCTTTC
* *
217853 ATGCCTTAATGCATCCTTTCATGCATTTAAGTTATGTCATCCTTTC
1 ATGCCTTAATGCATCCTTTCATGCATTTTAGTTATGGCATCCTTTC
* * * *
217899 ACGCCTTAATGCATCATTTCATGTATTTTAGTTATGGCATCATTTC
1 ATGCCTTAATGCATCCTTTCATGCATTTTAGTTATGGCATCCTTTC
* *
217945 ATGCCTTAGTGCATCCATTCATGC
1 ATGCCTTAATGCATCCTTTCATGC
217969 CTTAGTGCAT
Statistics
Matches: 102, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 102 1.00
ACGTcount: A:0.22, C:0.23, G:0.13, T:0.41
Consensus pattern (46 bp):
ATGCCTTAATGCATCCTTTCATGCATTTTAGTTATGGCATCCTTTC
Found at i:217960 original size:66 final size:66
Alignment explanation
Indices: 217890--218028 Score: 190
Period size: 66 Copynumber: 2.1 Consensus size: 66
217880 TAAGTTATGT
* * * *
217890 CATCCTTTCACGCCTTAATGCAT-CATTTCATGTATTTTAGTTATGGCATCATTTCATGCCTTAG
1 CATCCTTTCACGCCTTAATGCATCCA-TTCATGCATTTTAATTATGGAATCATTTCATGCCTTAA
217954 TG
65 TG
* * * *
217956 CATCCATTCATGCCTTAGTGCATCCATTCATGCATTTTAATTATGGAATCCTTTCATGCCTTAAT
1 CATCCTTTCACGCCTTAATGCATCCATTCATGCATTTTAATTATGGAATCATTTCATGCCTTAAT
218021 G
66 G
218022 CATCCTT
1 CATCCTT
218029 CCATGCATTT
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
66 61 0.97
67 2 0.03
ACGTcount: A:0.22, C:0.24, G:0.12, T:0.41
Consensus pattern (66 bp):
CATCCTTTCACGCCTTAATGCATCCATTCATGCATTTTAATTATGGAATCATTTCATGCCTTAAT
G
Found at i:218012 original size:46 final size:45
Alignment explanation
Indices: 217957--218094 Score: 188
Period size: 46 Copynumber: 3.0 Consensus size: 45
217947 GCCTTAGTGC
* * *
217957 ATCCATTCATGCCTTAGTGCATCCATTCATGCATTTTAATTATGGA
1 ATCCTTTCATGCCTTAATGCATCC-TTCATGCATTTTAGTTATGGA
*
218003 ATCCTTTCATGCCTTAATGCATCCTTCCATGCATTTTAGTTATGGC
1 ATCCTTTCATGCCTTAATGCATCCTT-CATGCATTTTAGTTATGGA
*
218049 A-CCATTTCATGCCTTAATGCATCTTTTCATGCATTTTAGTTATGGA
1 ATCC-TTTCATGCCTTAATGCATC-CTTCATGCATTTTAGTTATGGA
218095 TTCGGTTTAG
Statistics
Matches: 83, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
45 4 0.05
46 77 0.93
47 2 0.02
ACGTcount: A:0.23, C:0.22, G:0.13, T:0.41
Consensus pattern (45 bp):
ATCCTTTCATGCCTTAATGCATCCTTCATGCATTTTAGTTATGGA
Found at i:218040 original size:112 final size:112
Alignment explanation
Indices: 217843--218080 Score: 352
Period size: 112 Copynumber: 2.1 Consensus size: 112
217833 TTTAGTTATG
* **
217843 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTAAGTTATGTCATCCTTTCACGCCTTAA
1 GCATCCTTTCATGCCTTAATGCATCCATTCATGCATTTAAGTTATGGAATCCTTTCACGCCTTAA
* * * *
217908 TGCATCATTTCATGTATTTTAGTTATGGCATCATTTCATGCCTTAGT
66 TGCATCATTCCATGCATTTTAGTTATGGCACCATTTCATGCCTTAAT
* * *
217955 GCATCCATTCATGCCTTAGTGCATCCATTCATGCATTTTAA-TTATGGAATCCTTTCATGCCTTA
1 GCATCCTTTCATGCCTTAATGCATCCATTCATGCA-TTTAAGTTATGGAATCCTTTCACGCCTTA
*
218019 ATGCATCCTTCCATGCATTTTAGTTATGGCACCATTTCATGCCTTAAT
65 ATGCATCATTCCATGCATTTTAGTTATGGCACCATTTCATGCCTTAAT
*
218067 GCATCTTTTCATGC
1 GCATCCTTTCATGC
218081 ATTTTAGTTA
Statistics
Matches: 112, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
112 107 0.96
113 5 0.04
ACGTcount: A:0.22, C:0.24, G:0.13, T:0.41
Consensus pattern (112 bp):
GCATCCTTTCATGCCTTAATGCATCCATTCATGCATTTAAGTTATGGAATCCTTTCACGCCTTAA
TGCATCATTCCATGCATTTTAGTTATGGCACCATTTCATGCCTTAAT
Found at i:220912 original size:55 final size:55
Alignment explanation
Indices: 220845--221297 Score: 591
Period size: 55 Copynumber: 8.2 Consensus size: 55
220835 TTCTTTGAGG
* * * ***
220845 TGCACACATAGTGCCTATACGATCATTCATAAACATATTATGAATTATATGGTTT
1 TGCACACTTAGTGCCGATACGGTCATTCATAAACATATTATGAATTCCGTGGTTT
* *
220900 TACACACTTAGTGCCGATACGGTCATTCATAAACATAATATGAATTCCGTGGTTT
1 TGCACACTTAGTGCCGATACGGTCATTCATAAACATATTATGAATTCCGTGGTTT
* ** * * * *
220955 TGCACACTTAGTGTCGATATAGCCGTTCATAAACATATTATGAATTACATGGTTT
1 TGCACACTTAGTGCCGATACGGTCATTCATAAACATATTATGAATTCCGTGGTTT
* * *
221010 TACACACTTAGTGTCGATACGGTCATTCATAAACATATTATGAATTCCATGGTTT
1 TGCACACTTAGTGCCGATACGGTCATTCATAAACATATTATGAATTCCGTGGTTT
* * * ** * * *
221065 TGCACAGTTAGTGCTGATATGGTTGTTCATAAACAAATTATGAATTTCGTGATTT
1 TGCACACTTAGTGCCGATACGGTCATTCATAAACATATTATGAATTCCGTGGTTT
* * *
221120 TGCACACTTAGTGTCGATACGATCATTCATAAACATATTATAAATTCCGTGGTTT
1 TGCACACTTAGTGCCGATACGGTCATTCATAAACATATTATGAATTCCGTGGTTT
* * * *
221175 TGCACACTTAGTGCAGACACAGTCATTCATAAACATATTATGAATTCCGTTGTTT
1 TGCACACTTAGTGCCGATACGGTCATTCATAAACATATTATGAATTCCGTGGTTT
* *
221230 TGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTTCGTGGTTT
1 TGCACACTTAGTGCCGATACGGTCATTCATAAACATATTATGAATTCCGTGGTTT
221285 TGCACACTTAGTG
1 TGCACACTTAGTG
221298 TTGATAGTAC
Statistics
Matches: 340, Mismatches: 58, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
55 340 1.00
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.36
Consensus pattern (55 bp):
TGCACACTTAGTGCCGATACGGTCATTCATAAACATATTATGAATTCCGTGGTTT
Found at i:222538 original size:30 final size:30
Alignment explanation
Indices: 222504--222571 Score: 127
Period size: 30 Copynumber: 2.3 Consensus size: 30
222494 ATACTTTACC
222504 ATTTATTTAATTTAATCCTCCCGATTTTTA
1 ATTTATTTAATTTAATCCTCCCGATTTTTA
*
222534 ATTTATTTAATTTAATTCTCCCGATTTTTA
1 ATTTATTTAATTTAATCCTCCCGATTTTTA
222564 ATTTATTT
1 ATTTATTT
222572 CAATGTAGTC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.26, C:0.13, G:0.03, T:0.57
Consensus pattern (30 bp):
ATTTATTTAATTTAATCCTCCCGATTTTTA
Found at i:226672 original size:45 final size:45
Alignment explanation
Indices: 226622--226722 Score: 150
Period size: 45 Copynumber: 2.2 Consensus size: 45
226612 TATTCATTAT
*
226622 TTTCATTTATGGCATCCTTTCATG-CTATTAATGCACAATTGTGCA
1 TTTCATTTATGGCATCCTTTCATGCCT-TTAATGCACAATTATGCA
** *
226667 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGGA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACAATTATGCA
226712 TTTCATTTATG
1 TTTCATTTATG
226723 TAATGAAAAC
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
45 49 0.96
46 2 0.04
ACGTcount: A:0.22, C:0.20, G:0.14, T:0.45
Consensus pattern (45 bp):
TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACAATTATGCA
Found at i:227260 original size:95 final size:96
Alignment explanation
Indices: 227094--227294 Score: 255
Period size: 95 Copynumber: 2.1 Consensus size: 96
227084 CCCTACCATG
* * *
227094 GTATCGATACTTCTATACTATGGTATTGATACACCCTTGTAGTATCGATACCATTTCTATATTTT
1 GTATCGATACTTCTATACTATGGTACTGATACACCCTTGTAGTATCGATACCATTTCTACATTCT
* *
227159 GTAATT-CATGGCATCGATAACTTTCTCTTA
66 GGAATTCCATAGCATCGATAACTTTCTCTTA
* * *
227189 GTATCGATACTTCTATACTATGGTACTGATACTCCCTT-TCAGTTTCTATACCATTT-TGACATT
1 GTATCGATACTTCTATACTATGGTACTGATACACCCTTGT-AGTATCGATACCATTTCT-ACATT
* * * *
227252 CTGGAATTCCCTAGTATCGATACCTTTCTCTTG
64 CTGGAATTCCATAGCATCGATAACTTTCTCTTA
227285 GTATCGATAC
1 GTATCGATAC
227295 CCACAGCAGT
Statistics
Matches: 91, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
94 2 0.02
95 60 0.66
96 29 0.32
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.41
Consensus pattern (96 bp):
GTATCGATACTTCTATACTATGGTACTGATACACCCTTGTAGTATCGATACCATTTCTACATTCT
GGAATTCCATAGCATCGATAACTTTCTCTTA
Found at i:230589 original size:55 final size:55
Alignment explanation
Indices: 230502--230842 Score: 362
Period size: 55 Copynumber: 6.2 Consensus size: 55
230492 TTCTTTGAGG
* * * * * **
230502 TGCACACGTAGTGCCTATACAGTCGTTGATAAACATATTATGAATTCCGTGGTTT
1 TGCACACTTAGAGCCGATACGGTCGTTCATAAACATATTATGAATTATGTGGTTT
* * * * * * *
230557 TCCACACATACAGTCGATACGGTTGTTCATAAACAAATTATGAATTTTGTGGTTT
1 TGCACACTTAGAGCCGATACGGTCGTTCATAAACATATTATGAATTATGTGGTTT
* *
230612 TGCACACTTAGTGCCGATATGGTCGTTCATAAACATATTATGAATTATGTGGTTT
1 TGCACACTTAGAGCCGATACGGTCGTTCATAAACATATTATGAATTATGTGGTTT
* * * * *
230667 TGCACACTTAGTGCTGATATGGTCGTTCTTAAACATATTATGAATTATGTTGTTT
1 TGCACACTTAGAGCCGATACGGTCGTTCATAAACATATTATGAATTATGTGGTTT
* * * * * *
230722 TGCACACTTAGTGCCGATACGGTCGTGCATAAATATATTATAAATTTTATGGTTT
1 TGCACACTTAGAGCCGATACGGTCGTTCATAAACATATTATGAATTATGTGGTTT
* * * * *
230777 TACACACTTA-ATGCCGATACGATCATTCATAAACATATTATGAATT-TCGCGATTT
1 TGCACACTTAGA-GCCGATACGGTCGTTCATAAACATATTATGAATTAT-GTGGTTT
230832 TGCACACTTAG
1 TGCACACTTAG
230843 TGCTGATAGT
Statistics
Matches: 239, Mismatches: 44, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
54 1 0.00
55 238 1.00
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.37
Consensus pattern (55 bp):
TGCACACTTAGAGCCGATACGGTCGTTCATAAACATATTATGAATTATGTGGTTT
Found at i:230700 original size:110 final size:109
Alignment explanation
Indices: 230502--230850 Score: 403
Period size: 110 Copynumber: 3.2 Consensus size: 109
230492 TTCTTTGAGG
* * * * ** *
230502 TGCACACGTAGTGCCTATACAGTCGTTGATAAACATATTATGAATTCCGTGGTTTTCCACACATA
1 TGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTATGTGGTTTTACACAC-T-
* * *
230567 CAGT-CGATACGGTTGTTCATAAACAAATTATGAATTTTGTGGTTT
64 TAGTGCGATACGGTCGTTCATAAACATATTATGAATTTTGTGGTTT
* *
230612 TGCACACTTAGTGCCGATATGGTCGTTCATAAACATATTATGAATTATGTGGTTTTGCACACTTA
1 TGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTATGTGGTTTTACACACTTA
* * * *
230677 GTGCTGATATGGTCGTTCTTAAACATATTATGAATTATGTTGTTT
66 GTGC-GATACGGTCGTTCATAAACATATTATGAATTTTGTGGTTT
* * * * *
230722 TGCACACTTAGTGCCGATACGGTCGTGCATAAATATATTATAAATTTTATGGTTTTACACACTTA
1 TGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTATGTGGTTTTACACACTTA
* * * * * *
230787 ATGCCGATACGATCATTCATAAACATATTATGAATTTCGCGATTT
66 GTG-CGATACGGTCGTTCATAAACATATTATGAATTTTGTGGTTT
*
230832 TGCACACTTAGTGCTGATA
1 TGCACACTTAGTGCCGATA
230851 GTACACATAA
Statistics
Matches: 203, Mismatches: 33, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
108 3 0.01
109 2 0.01
110 197 0.97
111 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.37
Consensus pattern (109 bp):
TGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTATGTGGTTTTACACACTTA
GTGCGATACGGTCGTTCATAAACATATTATGAATTTTGTGGTTT
Found at i:230777 original size:165 final size:165
Alignment explanation
Indices: 230531--230850 Score: 435
Period size: 165 Copynumber: 1.9 Consensus size: 165
230521 CAGTCGTTGA
* * * *
230531 TAAACATATTATGAATTCCGTGGTTTTCCACACATACAGTCGATACGGTTGTTCATAAACAAATT
1 TAAACATATTATGAATTACGTGGTTTTCCACACATACAGCCGATACGGTCGTGCATAAACAAATT
* * * * * * *
230596 ATGAATTTTGTGGTTTTGCACACTTAGTGCCGATATGGTCGTTCATAAACATATTATGAATTAT-
66 ATAAATTTTATGGTTTTACACACTTAATGCCGATACGATCATTCATAAACATATTATGAATT-TC
* *
230660 GTGGTTTTGCACACTTAGTGCTGATATGGTCGTTCT
130 GCGATTTTGCACACTTAGTGCTGATATGGTCGTTCT
* * * * ** * *
230696 TAAACATATTATGAATTATGTTGTTTTGCACACTTAGTGCCGATACGGTCGTGCATAAATATATT
1 TAAACATATTATGAATTACGTGGTTTTCCACACATACAGCCGATACGGTCGTGCATAAACAAATT
230761 ATAAATTTTATGGTTTTACACACTTAATGCCGATACGATCATTCATAAACATATTATGAATTTCG
66 ATAAATTTTATGGTTTTACACACTTAATGCCGATACGATCATTCATAAACATATTATGAATTTCG
230826 CGATTTTGCACACTTAGTGCTGATA
131 CGATTTTGCACACTTAGTGCTGATA
230851 GTACACATAA
Statistics
Matches: 133, Mismatches: 21, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
164 1 0.01
165 132 0.99
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (165 bp):
TAAACATATTATGAATTACGTGGTTTTCCACACATACAGCCGATACGGTCGTGCATAAACAAATT
ATAAATTTTATGGTTTTACACACTTAATGCCGATACGATCATTCATAAACATATTATGAATTTCG
CGATTTTGCACACTTAGTGCTGATATGGTCGTTCT
Found at i:232990 original size:21 final size:21
Alignment explanation
Indices: 232942--232996 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
232932 CCCATATTCA
* **
232942 GAGTATCGATAGTCTACCCTC
1 GAGTATCGATACTCTACCAAC
*
232963 G-GTATCGATACTCTACGAAC
1 GAGTATCGATACTCTACCAAC
232983 GAGTATCGATACTC
1 GAGTATCGATACTC
232997 GCTTTCCCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.27
Consensus pattern (21 bp):
GAGTATCGATACTCTACCAAC
Found at i:234037 original size:20 final size:20
Alignment explanation
Indices: 234008--234045 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
233998 CAGTACCTAC
*
234008 CCTTGAGTATTGATACTCCA
1 CCTTGAGTATCGATACTCCA
*
234028 CCTTGGGTATCGATACTC
1 CCTTGAGTATCGATACTC
234046 TATAGTAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.34
Consensus pattern (20 bp):
CCTTGAGTATCGATACTCCA
Found at i:235931 original size:20 final size:20
Alignment explanation
Indices: 235908--235945 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
235898 TAAGGATACC
*
235908 AACACTCCGGTATGGATAGT
1 AACACTCCGATATGGATAGT
*
235928 AACACTCTGATATGGATA
1 AACACTCCGATATGGATA
235946 CAAAATTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.26
Consensus pattern (20 bp):
AACACTCCGATATGGATAGT
Found at i:236022 original size:20 final size:20
Alignment explanation
Indices: 235955--236028 Score: 103
Period size: 20 Copynumber: 3.7 Consensus size: 20
235945 ACAAAATTCA
*
235955 TCCAGTATGGATACCAACAC
1 TCCAGTATCGATACCAACAC
* *
235975 TCCGGTATCAATACCAACAC
1 TCCAGTATCGATACCAACAC
*
235995 TCCGGTATCGATACCAACAC
1 TCCAGTATCGATACCAACAC
*
236015 TCTAGTATCGATAC
1 TCCAGTATCGATAC
236029 AAAACCTTCG
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.32, C:0.31, G:0.14, T:0.23
Consensus pattern (20 bp):
TCCAGTATCGATACCAACAC
Found at i:236023 original size:40 final size:40
Alignment explanation
Indices: 235959--236051 Score: 107
Period size: 40 Copynumber: 2.3 Consensus size: 40
235949 AATTCATCCA
* * *
235959 GTATGGATACCAACACTCCGGTATCAATAC-CAACACTCCG
1 GTATCGATACCAACACTCCAGTATCAATACAAAAC-CTCCG
* * *
235999 GTATCGATACCAACACTCTAGTATCGATACAAAACCTTCG
1 GTATCGATACCAACACTCCAGTATCAATACAAAACCTCCG
*
236039 GTATTGATACCAA
1 GTATCGATACCAA
236052 GGGATCGTTA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
40 42 0.93
41 3 0.07
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (40 bp):
GTATCGATACCAACACTCCAGTATCAATACAAAACCTCCG
Found at i:241871 original size:20 final size:20
Alignment explanation
Indices: 241842--241916 Score: 78
Period size: 20 Copynumber: 3.7 Consensus size: 20
241832 CAGTTCATTC
*
241842 GGTATGGATACCAACACTCT
1 GGTATCGATACCAACACTCT
*
241862 GGTATTGATACCAACACTCT
1 GGTATCGATACCAACACTCT
* ** * *
241882 AGTATCGATATTAAAACCTTT
1 GGTATCGATACCAACA-CTCT
241903 GGTATCGATACCAA
1 GGTATCGATACCAA
241917 GGGCCGCCGA
Statistics
Matches: 44, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
20 30 0.68
21 14 0.32
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.29
Consensus pattern (20 bp):
GGTATCGATACCAACACTCT
Done.