Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002323.1 Hibiscus syriacus cultivar Beakdansim tig00004738_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: 155256
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:5682 original size:55 final size:55
Alignment explanation
Indices: 5582--5688 Score: 126
Period size: 55 Copynumber: 1.9 Consensus size: 55
5572 TTCTATCCCC
* * *
5582 GTATTCAATCATTCACTCTCCTATTATCTTGAAATAAAAAAAAAAAATCAATCAT
1 GTATTCAATCAATCACTCTCCTACTATCTTGAAATAAAAAAAAAAAAACAATCAT
* * * * *
5637 GTATTCAATCAATCACTCATCC-ACTGTCTTTAAATATATATAAAAAAACAAT
1 GTATTCAATCAATCACTC-TCCTACTATCTTGAAATAAAAAAAAAAAAACAAT
5689 TCATAACTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
55 40 0.93
56 3 0.07
ACGTcount: A:0.45, C:0.19, G:0.04, T:0.33
Consensus pattern (55 bp):
GTATTCAATCAATCACTCTCCTACTATCTTGAAATAAAAAAAAAAAAACAATCAT
Found at i:12066 original size:22 final size:21
Alignment explanation
Indices: 12033--12077 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
12023 ACTGATTACA
12033 AACTAACTAACTACAAGCTGAT
1 AACTAACTAACTACAAGCT-AT
*
12055 AACTAA-TCAACTATAAGCTAT
1 AACTAACT-AACTACAAGCTAT
12076 AA
1 AA
12078 AGATTACAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.49, C:0.20, G:0.07, T:0.24
Consensus pattern (21 bp):
AACTAACTAACTACAAGCTAT
Found at i:19506 original size:19 final size:19
Alignment explanation
Indices: 19455--19506 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
19445 AACACCCAAA
19455 TTTG-AATATAATCCATTTT
1 TTTGAAATATAAT-CATTTT
* *
19474 TTCTTAAA-ACAATCATTTT
1 TT-TGAAATATAATCATTTT
19493 TTTGAAATATAATC
1 TTTGAAATATAATC
19507 CATCACATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
18 4 0.15
19 15 0.58
20 5 0.19
21 2 0.08
ACGTcount: A:0.37, C:0.12, G:0.04, T:0.48
Consensus pattern (19 bp):
TTTGAAATATAATCATTTT
Found at i:29896 original size:15 final size:16
Alignment explanation
Indices: 29862--29896 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
29852 AGACTAAAAT
29862 AATGCGAAAATACTATA
1 AATGCGAAAATAC-ATA
29879 AATGCGAAAATA-ATA
1 AATGCGAAAATACATA
29894 AAT
1 AAT
29897 TGACTCTACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
17 12 0.67
ACGTcount: A:0.57, C:0.09, G:0.11, T:0.23
Consensus pattern (16 bp):
AATGCGAAAATACATA
Found at i:35052 original size:22 final size:22
Alignment explanation
Indices: 34996--35053 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 22
34986 CGCGATTCTG
34996 ACTATCGCATTGCGATTTTCCA
1 ACTATCGCATTGCGATTTTCCA
* * * *
35018 AAT-TCGCGTTGCGGTTTTCCT
1 ACTATCGCATTGCGATTTTCCA
*
35039 ACTATCGCAATGCGA
1 ACTATCGCATTGCGA
35054 ATATGTAAAT
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
21 17 0.63
22 10 0.37
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (22 bp):
ACTATCGCATTGCGATTTTCCA
Found at i:35067 original size:20 final size:20
Alignment explanation
Indices: 35042--35113 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
35032 TTTTCCTACT
35042 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
35062 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
* *
35082 ATCGCAATGCGATTATG-ACT
1 ATCGCAATGCGAATATGTA-A
35102 ATCGCAATGCGA
1 ATCGCAATGCGA
35114 TTCTGACTGT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
19 1 0.02
20 48 0.98
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:35114 original size:20 final size:20
Alignment explanation
Indices: 35083--35209 Score: 218
Period size: 20 Copynumber: 6.3 Consensus size: 20
35073 AATATGTAAA
* * *
35083 TCGCAATGCGATTATGACTA
1 TCGCAACGCGATTCTGACTG
*
35103 TCGCAATGCGATTCTGACTG
1 TCGCAACGCGATTCTGACTG
35123 TCGCAACGCGATTCTGACTG
1 TCGCAACGCGATTCTGACTG
35143 TCGCAACGCGATTCTGACTG
1 TCGCAACGCGATTCTGACTG
35163 TCGCAACGCGATTCTGACTG
1 TCGCAACGCGATTCTGACTG
35183 TCGCAACGCGATTCTGACTG
1 TCGCAACGCGATTCTGACTG
35203 TCGCAAC
1 TCGCAAC
35210 ACTGAATTTC
Statistics
Matches: 104, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 104 1.00
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTG
Found at i:35127 original size:60 final size:60
Alignment explanation
Indices: 35063--35193 Score: 165
Period size: 60 Copynumber: 2.2 Consensus size: 60
35053 AATATGTAAA
* * *
35063 TCGCAATGCGAATATGTA-AATCGCAATGCGATTATGACTATCGCAATGCGATTCTGACTG
1 TCGCAACGCGAATATG-ACAATCGCAACGCGATTATGACTATCGCAACGCGATTCTGACTG
* * ** * *
35123 TCGCAACGCGATTCTGACTGTCGCAACGCGATTCTGACTGTCGCAACGCGATTCTGACTG
1 TCGCAACGCGAATATGACAATCGCAACGCGATTATGACTATCGCAACGCGATTCTGACTG
35183 TCGCAACGCGA
1 TCGCAACGCGA
35194 TTCTGACTGT
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
59 1 0.02
60 60 0.98
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (60 bp):
TCGCAACGCGAATATGACAATCGCAACGCGATTATGACTATCGCAACGCGATTCTGACTG
Found at i:36064 original size:24 final size:24
Alignment explanation
Indices: 36028--36081 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
36018 GTATTCGAAA
36028 TTTGATCTCGGTCAATACCCGGAC
1 TTTGATCTCGGTCAATACCCGGAC
* * *
36052 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTCGGTCAATACCCGGAC
36076 TTTGAT
1 TTTGAT
36082 GATGTTTCAG
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:0.20, C:0.20, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATCTCGGTCAATACCCGGAC
Found at i:36289 original size:15 final size:15
Alignment explanation
Indices: 36271--36307 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
36261 AGAAAACGAA
36271 GAAGAAAAAATCCCC
1 GAAGAAAAAATCCCC
*
36286 GAAG-AAAAGTCCCC
1 GAAGAAAAAATCCCC
36300 GAAGAAAA
1 GAAGAAAA
36308 TGCCACGGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.54, C:0.22, G:0.19, T:0.05
Consensus pattern (15 bp):
GAAGAAAAAATCCCC
Found at i:38347 original size:12 final size:12
Alignment explanation
Indices: 38332--38374 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
38322 CAAGAAAAAA
38332 GCAATCAAAATC
1 GCAATCAAAATC
38344 GCAATCAAAATC
1 GCAATCAAAATC
**
38356 AAAATCAAAATC
1 GCAATCAAAATC
*
38368 CCAATCA
1 GCAATCA
38375 CAACCGGCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.53, C:0.26, G:0.05, T:0.16
Consensus pattern (12 bp):
GCAATCAAAATC
Found at i:38355 original size:6 final size:6
Alignment explanation
Indices: 38334--38367 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
38324 AGAAAAAAGC
**
38334 AATCAA AATCGC AATCAA AATCAA AATCAA AATC
1 AATCAA AATCAA AATCAA AATCAA AATCAA AATC
38368 CCAATCACAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.59, C:0.21, G:0.03, T:0.18
Consensus pattern (6 bp):
AATCAA
Found at i:38690 original size:140 final size:140
Alignment explanation
Indices: 38434--38703 Score: 513
Period size: 140 Copynumber: 1.9 Consensus size: 140
38424 AAACGTTGTA
38434 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
* * *
38499 TGATTTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTAAATATCACAACGCGAATTTGACTAT
38564 TATGTGTATT
131 TATGTGTATT
38574 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
38639 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTAAATATCACAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTAAATATCACAACGCGAATTTGACTAT
38704 CGCAATACGA
Statistics
Matches: 127, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 127 1.00
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.43
Consensus pattern (140 bp):
TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTAAATATCACAACGCGAATTTGACTAT
TATGTGTATT
Found at i:38704 original size:20 final size:20
Alignment explanation
Indices: 38681--38954 Score: 303
Period size: 20 Copynumber: 14.1 Consensus size: 20
38671 TTCATTTAAA
*
38681 TATCACAACGCGAATTTGAC
1 TATCGCAACGCGAATTTGAC
** *
38701 TATCGCAATACGAATTTGAT
1 TATCGCAACGCGAATTTGAC
*
38721 TATCGCAATGCGAATTTGAC
1 TATCGCAACGCGAATTTGAC
* *
38741 TATCGCAACCCGAATATGAC
1 TATCGCAACGCGAATTTGAC
*
38761 TATCGCAACGCGAATATGAC
1 TATCGCAACGCGAATTTGAC
*
38781 TATCGCAACGCGAATTTGTC
1 TATCGCAACGCGAATTTGAC
*
38801 TATCGCAACG-GCTATTTGAC
1 TATCGCAACGCG-AATTTGAC
38821 TATCGCAACGCGAATTTGAC
1 TATCGCAACGCGAATTTGAC
* *
38841 TATCGCAATGCGAATTTGAT
1 TATCGCAACGCGAATTTGAC
* *
38861 TATCGCAATGCGAATTTGAT
1 TATCGCAACGCGAATTTGAC
* *
38881 TATCGCAACGGGTATTTGAC
1 TATCGCAACGCGAATTTGAC
*
38901 TATCGCAACGAGAA----A-
1 TATCGCAACGCGAATTTGAC
* * *
38916 -ATCGCAAAGCGTATTAGAC
1 TATCGCAACGCGAATTTGAC
38935 TATCGCAACGCGAA-TTGAC
1 TATCGCAACGCGAATTTGAC
38954 T
1 T
38955 TTTGCGTTGC
Statistics
Matches: 217, Mismatches: 29, Indels: 17
0.83 0.11 0.06
Matches are distributed among these distances:
14 10 0.05
16 1 0.00
18 1 0.00
19 6 0.03
20 198 0.91
21 1 0.00
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (20 bp):
TATCGCAACGCGAATTTGAC
Found at i:39004 original size:20 final size:20
Alignment explanation
Indices: 38949--39004 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
38939 GCAACGCGAA
*
38949 TTGACTTTTGCGTTGCGATT
1 TTGACTTTAGCGTTGCGATT
* * *
38969 TTGTCTTTCGCATTGCGATT
1 TTGACTTTAGCGTTGCGATT
*
38989 TTGAGTTTAGCGTTGC
1 TTGACTTTAGCGTTGC
39005 AAAAGTGTAC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.11, C:0.16, G:0.25, T:0.48
Consensus pattern (20 bp):
TTGACTTTAGCGTTGCGATT
Found at i:39165 original size:14 final size:14
Alignment explanation
Indices: 39105--39166 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
39095 CACAAATAAG
*
39105 AATTATTTACACATC
1 AATT-TTTACAAATC
**
39120 AATATTAAACAAATC
1 AAT-TTTTACAAATC
*
39135 AACTTTTACAAATC
1 AATTTTTACAAATC
*
39149 AATTTTTATAAATC
1 AATTTTTACAAATC
39163 AATT
1 AATT
39167 AAACAAGAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 12 0.32
16 1 0.03
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.39
Consensus pattern (14 bp):
AATTTTTACAAATC
Found at i:40657 original size:42 final size:41
Alignment explanation
Indices: 40553--40661 Score: 105
Period size: 42 Copynumber: 2.6 Consensus size: 41
40543 AGAATGTTGG
* * * *
40553 GAGGGACCTCTTCAACGATGACAGTGGCCTCTTGAACGGTGT
1 GAGGGGCCTCTTGAACGATGAAAG-GGCCTCTTGAACGATGT
* **
40595 GAGGGGACTCTTGAGGGATGATAAGGGCCTCTTGAACGATAG-
1 GAGGGGCCTCTTGAACGATGA-AAGGGCCTCTTGAACGAT-GT
40637 G-GGAGGCCTCTTGAACGATGAAAGG
1 GAGG-GGCCTCTTGAACGATGAAAGG
40662 TGAGTCGGGC
Statistics
Matches: 54, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
41 6 0.11
42 45 0.83
43 3 0.06
ACGTcount: A:0.25, C:0.18, G:0.36, T:0.21
Consensus pattern (41 bp):
GAGGGGCCTCTTGAACGATGAAAGGGCCTCTTGAACGATGT
Found at i:41183 original size:20 final size:20
Alignment explanation
Indices: 41158--41233 Score: 116
Period size: 20 Copynumber: 3.8 Consensus size: 20
41148 TCGCAACACG
*
41158 AATGACTATCACAACGCGAA
1 AATGACTATCGCAACGCGAA
*
41178 AATGACTATCTCAACGCGAA
1 AATGACTATCGCAACGCGAA
41198 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
**
41218 TTTGACTATCGCAACG
1 AATGACTATCGCAACG
41234 AGAGAATCGC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:43240 original size:20 final size:20
Alignment explanation
Indices: 43217--43272 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
43207 TCTGAAACTT
43217 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
43237 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** *
43257 ACTATCGCAACGCGAA
1 AAAATCGCAACACGAA
43273 TTTGACTATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.50, C:0.23, G:0.16, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:43278 original size:20 final size:20
Alignment explanation
Indices: 43240--43312 Score: 119
Period size: 20 Copynumber: 3.6 Consensus size: 20
43230 GAAAATGAAA
* **
43240 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAATTTGACT
43260 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
43280 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
43300 ATCGCAACGCGAA
1 ATCGCAACGCGAA
43313 ACTAAAATCG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAATTTGACT
Found at i:43927 original size:20 final size:20
Alignment explanation
Indices: 43902--44008 Score: 133
Period size: 20 Copynumber: 5.3 Consensus size: 20
43892 GAAAATTGTA
* *
43902 TTGCGATTGTCAGCATCGCG
1 TTGCGATAGTCAGAATCGCG
*
43922 TTGCGACAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCG
* *
43942 TTGCGACAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
43962 TTGCGATTGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCG
* * *
43982 TTGCGATAGTCATACTCGCA
1 TTGCGATAGTCAGAATCGCG
44002 TTGCGAT
1 TTGCGAT
44009 TTACATATTC
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 76 1.00
ACGTcount: A:0.21, C:0.23, G:0.27, T:0.28
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:49549 original size:14 final size:14
Alignment explanation
Indices: 49530--49562 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
49520 TCTAGTGAAA
49530 CCAACTTTGCAATT
1 CCAACTTTGCAATT
49544 CCAACTTTGCAATT
1 CCAACTTTGCAATT
49558 CCAAC
1 CCAAC
49563 AGGCAGTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.30, C:0.33, G:0.06, T:0.30
Consensus pattern (14 bp):
CCAACTTTGCAATT
Found at i:60514 original size:24 final size:24
Alignment explanation
Indices: 60485--60535 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
60475 ATTAGAACCG
* *
60485 AGAGTGCACAAATGCACTAATTCA
1 AGAGTGCACAAATACACTAATACA
* *
60509 AGAGTGCATAATTACACTAATACA
1 AGAGTGCACAAATACACTAATACA
60533 AGA
1 AGA
60536 TCGATCTATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.45, C:0.18, G:0.16, T:0.22
Consensus pattern (24 bp):
AGAGTGCACAAATACACTAATACA
Found at i:65728 original size:41 final size:41
Alignment explanation
Indices: 65671--65758 Score: 176
Period size: 41 Copynumber: 2.1 Consensus size: 41
65661 AATAAAGCTT
65671 AAGCAATAATTGGATCCATTCTCTTCAAACTGCACAATCAA
1 AAGCAATAATTGGATCCATTCTCTTCAAACTGCACAATCAA
65712 AAGCAATAATTGGATCCATTCTCTTCAAACTGCACAATCAA
1 AAGCAATAATTGGATCCATTCTCTTCAAACTGCACAATCAA
65753 AAGCAA
1 AAGCAA
65759 GTTAACAAAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.41, C:0.24, G:0.10, T:0.25
Consensus pattern (41 bp):
AAGCAATAATTGGATCCATTCTCTTCAAACTGCACAATCAA
Found at i:84019 original size:43 final size:43
Alignment explanation
Indices: 83958--84041 Score: 123
Period size: 43 Copynumber: 2.0 Consensus size: 43
83948 TGGATCATAC
* *
83958 ATCGTAGTAGAGATAGTAGTAGGTATATACTTGCATATGCTTG
1 ATCGTAGTAGAGATAGTAGTACGTATATACTTACATATGCTTG
* * *
84001 ATCGTAGTAGTGATAGTAGTTCGTATGTACTTACATATGCT
1 ATCGTAGTAGAGATAGTAGTACGTATATACTTACATATGCT
84042 CAATCGAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.29, C:0.11, G:0.24, T:0.37
Consensus pattern (43 bp):
ATCGTAGTAGAGATAGTAGTACGTATATACTTACATATGCTTG
Found at i:87309 original size:2 final size:2
Alignment explanation
Indices: 87302--87338 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
87292 ATTTTGTAAA
87302 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
87339 AATTTTATGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:87533 original size:34 final size:35
Alignment explanation
Indices: 87438--87522 Score: 145
Period size: 35 Copynumber: 2.5 Consensus size: 35
87428 TTATTCATTT
*
87438 AACCAAACACGAAAATCTTACATTACTGCTAAACC
1 AACCAAACACGAAAATCTTACATTCCTGCTAAACC
*
87473 AATCAAACACGAAAATCTTACATTCCTGCTAAACC
1 AACCAAACACGAAAATCTTACATTCCTGCTAAACC
87508 AACCAAACAC-AAAAT
1 AACCAAACACGAAAAT
87523 ACAACATTCC
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
34 5 0.11
35 42 0.89
ACGTcount: A:0.48, C:0.28, G:0.05, T:0.19
Consensus pattern (35 bp):
AACCAAACACGAAAATCTTACATTCCTGCTAAACC
Found at i:87575 original size:20 final size:20
Alignment explanation
Indices: 87550--87625 Score: 143
Period size: 20 Copynumber: 3.8 Consensus size: 20
87540 CTTATTCCCG
87550 GGTAATCTTACATTCCCACT
1 GGTAATCTTACATTCCCACT
87570 GGTAATCTTACATTCCCACT
1 GGTAATCTTACATTCCCACT
*
87590 GGTAATCTTACATTCCTACT
1 GGTAATCTTACATTCCCACT
87610 GGTAATCTTACATTCC
1 GGTAATCTTACATTCC
87626 GTAAACCAAA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.25, C:0.28, G:0.11, T:0.37
Consensus pattern (20 bp):
GGTAATCTTACATTCCCACT
Found at i:91604 original size:22 final size:18
Alignment explanation
Indices: 91562--91630 Score: 84
Period size: 18 Copynumber: 3.6 Consensus size: 18
91552 AGTTCAGTAT
*
91562 TCCCGTAGGACCACTATG
1 TCCCGAAGGACCACTATG
91580 TCCCGAAGGACCACTGTATATG
1 TCCCGAAGGACCAC----TATG
*
91602 TCCCGTAGGACCACTATG
1 TCCCGAAGGACCACTATG
91620 TCCCGAAGGAC
1 TCCCGAAGGAC
91631 TACTCCTTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
18 27 0.61
22 17 0.39
ACGTcount: A:0.25, C:0.32, G:0.23, T:0.20
Consensus pattern (18 bp):
TCCCGAAGGACCACTATG
Found at i:93222 original size:64 final size:62
Alignment explanation
Indices: 93117--93273 Score: 165
Period size: 64 Copynumber: 2.5 Consensus size: 62
93107 TAATGAAGGT
* * * *
93117 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATG-TTGTATTATTATAGAG
1 ATGCATCGATGCA-TACTAATGCATCGATGCATAAAATGCATTCGATGTTTCTATT-TTA-AAAG
* * *
93181 ATGCATCGATGTATGACTTATGCATCGATGCACT-AATTGCATTCGATGTTTCTATTTTAAAAG
1 ATGCATCGATGCAT-ACTAATGCATCGATGCA-TAAAATGCATTCGATGTTTCTATTTTAAAAG
*
93244 AGTGCATCGATGCATTACCAATGCATCGAT
1 A-TGCATCGATGCA-TACTAATGCATCGAT
93274 ACACCTTCAA
Statistics
Matches: 79, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
63 5 0.06
64 66 0.84
65 8 0.10
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (62 bp):
ATGCATCGATGCATACTAATGCATCGATGCATAAAATGCATTCGATGTTTCTATTTTAAAAG
Found at i:98108 original size:64 final size:62
Alignment explanation
Indices: 98003--98159 Score: 165
Period size: 64 Copynumber: 2.5 Consensus size: 62
97993 TAATGAAGGT
* * * *
98003 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCAATG-TTGTATTATTATAGAG
1 ATGCATCGATGCA-TACTAATGCATCGATGCATAAAATGCATTCAATGTTTCTATT-TTA-AAAG
* * *
98067 ATGCATCGATGCATGACTTATGCATCGATGCACT-AATTGCATTCGATGTTTCTATTTTAAAAG
1 ATGCATCGATGCAT-ACTAATGCATCGATGCA-TAAAATGCATTCAATGTTTCTATTTTAAAAG
*
98130 AGTGCATCGATGCATTACCAATGCATCGAT
1 A-TGCATCGATGCA-TACTAATGCATCGAT
98160 ACACCTTCAA
Statistics
Matches: 80, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
63 5 0.06
64 67 0.84
65 8 0.10
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (62 bp):
ATGCATCGATGCATACTAATGCATCGATGCATAAAATGCATTCAATGTTTCTATTTTAAAAG
Found at i:103822 original size:15 final size:17
Alignment explanation
Indices: 103793--103825 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
103783 TAAGTATATT
103793 TTATCTTAATATAAAAA
1 TTATCTTAATATAAAAA
103810 TTAT-TTAAT-TAAAAA
1 TTATCTTAATATAAAAA
103825 T
1 T
103826 AGAGGGAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 5 0.31
17 4 0.25
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
TTATCTTAATATAAAAA
Found at i:104567 original size:8 final size:8
Alignment explanation
Indices: 104554--104588 Score: 70
Period size: 8 Copynumber: 4.4 Consensus size: 8
104544 TTTGAGTCGA
104554 TTTGAAAT
1 TTTGAAAT
104562 TTTGAAAT
1 TTTGAAAT
104570 TTTGAAAT
1 TTTGAAAT
104578 TTTGAAAT
1 TTTGAAAT
104586 TTT
1 TTT
104589 CAGTTATTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.54
Consensus pattern (8 bp):
TTTGAAAT
Found at i:105115 original size:20 final size:21
Alignment explanation
Indices: 105076--105177 Score: 69
Period size: 19 Copynumber: 5.2 Consensus size: 21
105066 TTCTTTAAAA
105076 TATAATATTATAAATATATTT
1 TATAATATTATAAATATATTT
*
105097 TATAAT-TTA-AAAT-TATAT
1 TATAATATTATAAATATATTT
*
105115 T-TAATA-TATTAAATA-ATAT
1 TATAATATTA-TAAATATATTT
* * *
105134 CATAATATAAATAAATATA-TA
1 TATAATAT-TATAAATATATTT
*
105155 TAT-ATA-TATAAATATATCT
1 TATAATATTATAAATATATTT
105174 TATA
1 TATA
105178 TAGTTAAAGA
Statistics
Matches: 62, Mismatches: 9, Indels: 21
0.67 0.10 0.23
Matches are distributed among these distances:
17 6 0.10
18 14 0.23
19 15 0.24
20 11 0.18
21 14 0.23
22 2 0.03
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
TATAATATTATAAATATATTT
Found at i:105150 original size:18 final size:18
Alignment explanation
Indices: 105118--105171 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
105108 ATTATATTTA
105118 ATATAT-TAAAT-AATAT
1 ATATATATAAATAAATAT
105134 CATA-ATATAAATAAATAT
1 -ATATATATAAATAAATAT
*
105152 ATATATATATATAAATAT
1 ATATATATAAATAAATAT
105170 AT
1 AT
105172 CTTATATAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
16 2 0.06
17 11 0.33
18 20 0.61
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (18 bp):
ATATATATAAATAAATAT
Found at i:105169 original size:10 final size:10
Alignment explanation
Indices: 105117--105171 Score: 55
Period size: 10 Copynumber: 5.7 Consensus size: 10
105107 AATTATATTT
105117 AATATAT-TA
1 AATATATATA
105126 AATA-ATATCA
1 AATATATAT-A
*
105136 TAATATAAATA
1 -AATATATATA
105147 AATATATAT-
1 AATATATATA
105156 -ATATATATA
1 AATATATATA
105165 AATATAT
1 AATATAT
105172 CTTATATAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
8 10 0.26
9 5 0.13
10 15 0.39
11 5 0.13
12 3 0.08
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (10 bp):
AATATATATA
Found at i:105280 original size:18 final size:19
Alignment explanation
Indices: 105244--105281 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
105234 CACGAAATGT
105244 AAGATTACCAGTAGGAATAA
1 AAGATTACCAG-AGGAATAA
105264 AAGATTACCAG-GGAATAA
1 AAGATTACCAGAGGAATAA
105282 GATTACTAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
20 11 0.61
ACGTcount: A:0.50, C:0.11, G:0.21, T:0.18
Consensus pattern (19 bp):
AAGATTACCAGAGGAATAA
Found at i:106038 original size:24 final size:24
Alignment explanation
Indices: 106000--106046 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
105990 ACTCATCAAC
*
106000 AAATTTCGCACCCCTAAAATTTTA
1 AAATTTCACACCCCTAAAATTTTA
* *
106024 AAATTTCACATCCCTACAATTTT
1 AAATTTCACACCCCTAAAATTTT
106047 TAGTATAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.36, C:0.26, G:0.02, T:0.36
Consensus pattern (24 bp):
AAATTTCACACCCCTAAAATTTTA
Found at i:107775 original size:3 final size:3
Alignment explanation
Indices: 107767--107806 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
107757 CTAAACAGAG
*
107767 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAT GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
107807 CAGATTGGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.62, C:0.00, G:0.35, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:108211 original size:16 final size:16
Alignment explanation
Indices: 108186--108216 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
108176 AACCGAATAA
108186 ATAAAAGAACAAAAAC
1 ATAAAAGAACAAAAAC
*
108202 ATAAACGAACAAAAA
1 ATAAAAGAACAAAAA
108217 AAAATTGTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.13, G:0.06, T:0.06
Consensus pattern (16 bp):
ATAAAAGAACAAAAAC
Found at i:109935 original size:30 final size:30
Alignment explanation
Indices: 109882--109957 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
109872 AGCAGTCCAA
* *
109882 ACACTTAAATGAATAATAGAATAAAACGTTAA-
1 ACAC-TAAATTAA-AATAAAAT-AAACGTTAAG
*
109914 ACCCTAAATTAAAATAAAATAAACGTTAAG
1 ACACTAAATTAAAATAAAATAAACGTTAAG
*
109944 ACATTAAATTAAAA
1 ACACTAAATTAAAA
109958 CGAATGATAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
29 9 0.24
30 19 0.50
31 7 0.18
32 3 0.08
ACGTcount: A:0.58, C:0.11, G:0.07, T:0.25
Consensus pattern (30 bp):
ACACTAAATTAAAATAAAATAAACGTTAAG
Found at i:111647 original size:22 final size:22
Alignment explanation
Indices: 111619--111666 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
111609 AATATAATCA
111619 TTCAGCGTTGAATGTTGAACCG
1 TTCAGCGTTGAATGTTGAACCG
*
111641 TTCAGCGTTGAATGTTGAATCG
1 TTCAGCGTTGAATGTTGAACCG
111663 TTCA
1 TTCA
111667 ACATTCAACG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (22 bp):
TTCAGCGTTGAATGTTGAACCG
Found at i:113810 original size:17 final size:17
Alignment explanation
Indices: 113756--113810 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 17
113746 AATTTAAACT
113756 TTTTATTAA-AATATAATA
1 TTTTATTAATAATA-AA-A
* *
113774 TCTTATT-ATAATCAATA
1 TTTTATTAATAAT-AAAA
113791 TTTTATTAATAATAAAA
1 TTTTATTAATAATAAAA
113808 TTT
1 TTT
113811 AAACTGTGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
17 14 0.47
18 15 0.50
19 1 0.03
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTTATTAATAATAAAA
Found at i:113919 original size:6 final size:6
Alignment explanation
Indices: 113908--113938 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
113898 TTATTTTCAA
113908 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT T
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT T
113939 GAGGTTAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTCT
Found at i:114582 original size:36 final size:37
Alignment explanation
Indices: 114542--114615 Score: 100
Period size: 37 Copynumber: 2.0 Consensus size: 37
114532 ATTAAACCTT
114542 TTTTAT-ATATTT-AATTTTGTAAA-AAAATTATATAAA
1 TTTTATGA-ATTTAAATTTTGTAAAGAAAA-TATATAAA
*
114578 TTTTATGAATTTAAATTTTTTAAAGAAAATATATAAA
1 TTTTATGAATTTAAATTTTGTAAAGAAAATATATAAA
114615 T
1 T
114616 ATTTTCCAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
36 10 0.29
37 20 0.59
38 4 0.12
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (37 bp):
TTTTATGAATTTAAATTTTGTAAAGAAAATATATAAA
Found at i:115994 original size:15 final size:15
Alignment explanation
Indices: 115976--116013 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
115966 TTCCGGAAAA
*
115976 TGAATTACTGGAATT
1 TGAATTACTAGAATT
*
115991 TGAACTACTAGAATT
1 TGAATTACTAGAATT
116006 TGAATTAC
1 TGAATTAC
116014 ATTTCTGGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (15 bp):
TGAATTACTAGAATT
Found at i:116046 original size:15 final size:14
Alignment explanation
Indices: 116022--116055 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
116012 ACATTTCTGG
*
116022 AAAACGTTTTTCGA
1 AAAATGTTTTTCGA
*
116036 AAAATGTTTTTCGT
1 AAAATGTTTTTCGA
116050 AAAATG
1 AAAATG
116056 AATTACATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (14 bp):
AAAATGTTTTTCGA
Found at i:116395 original size:23 final size:23
Alignment explanation
Indices: 116346--116408 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
116336 GTATTATATT
* **
116346 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAATATATTAATTAAA
* *
116369 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAATATATTAATTAAA
116392 ATATTATTTAAATATAT
1 ATA-T-TTTAAATATAT
116409 AAATAATATT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 21 0.66
24 1 0.03
25 10 0.31
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAATATATTAATTAAA
Found at i:116436 original size:19 final size:20
Alignment explanation
Indices: 116384--116436 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
116374 TTAAATATCT
116384 TTATTAAA-ATATTATTTAA
1 TTATTAAATATATTATTTAA
* *
116403 ATATATAAATAATATTA-TTCA
1 TTAT-TAAAT-ATATTATTTAA
116424 TTATTAAATATAT
1 TTATTAAATATAT
116437 AAAAATTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 7 0.25
20 9 0.32
21 6 0.21
22 6 0.21
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
TTATTAAATATATTATTTAA
Found at i:116472 original size:35 final size:33
Alignment explanation
Indices: 116400--116487 Score: 92
Period size: 31 Copynumber: 2.7 Consensus size: 33
116390 AAATATTATT
* *
116400 TAAATATATAAA-TAATATTATTCATTATTAAA
1 TAAATATAAAAATTTATATTATTCATTATTAAA
*
116432 T--ATATAAAAATTTATATTATTTATTATTAAA
1 TAAATATAAAAATTTATATTATTCATTATTAAA
* *
116463 TAAAAATATAATATCTTATATTATT
1 TAAATATA-AAAAT-TTATATTATT
116488 ATAATATAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
30 8 0.17
31 19 0.41
32 1 0.02
33 4 0.09
34 4 0.09
35 10 0.22
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (33 bp):
TAAATATAAAAATTTATATTATTCATTATTAAA
Found at i:116476 original size:28 final size:28
Alignment explanation
Indices: 116393--116546 Score: 85
Period size: 31 Copynumber: 5.4 Consensus size: 28
116383 TTTATTAAAA
*
116393 TATTATTTAAATATATAA-ATAATATTATT
1 TATTA-TTAAATA-AAAATATAATATTATT
* * *
116422 CATTATTAAATATATAAAAATTTATATTATT
1 TATTATTAAATA-A-AAATA-TAATATTATT
*
116453 TATTATTAAATAAAAATATAATATCT-TA
1 TATTATTAAATAAAAATATAATAT-TATT
116481 TATTATT--AT---AATATAATTGATTA-T
1 TATTATTAAATAAAAATATAA-T-ATTATT
116505 T-TTATATAATATTAAAAATATAATATTATAT
1 TATTAT-TAA-A-TAAAAATATAATATTAT-T
116536 TATTA-TAAATA
1 TATTATTAAATA
116547 TTAATAAATA
Statistics
Matches: 99, Mismatches: 8, Indels: 37
0.69 0.06 0.26
Matches are distributed among these distances:
23 11 0.11
24 4 0.04
25 2 0.02
26 2 0.02
27 1 0.01
28 25 0.25
29 16 0.16
30 6 0.06
31 29 0.29
32 3 0.03
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (28 bp):
TATTATTAAATAAAAATATAATATTATT
Found at i:116534 original size:22 final size:23
Alignment explanation
Indices: 116509--116552 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
116499 GATTATTTTA
116509 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
* *
116531 TATATTATTATAAATATTAATA
1 TATAATATTAAAAATATTAATA
116553 AATAAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:118285 original size:21 final size:21
Alignment explanation
Indices: 118261--118306 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 21
118251 ATAGATGTTG
118261 AAATATC-CTTTTAA-CTAAATA
1 AAATATCAC-TTTAACCT-AATA
118282 AAAT-TCACTTTAACCTAATA
1 AAATATCACTTTAACCTAATA
118302 AAATA
1 AAATA
118307 AAATTGTGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (21 bp):
AAATATCACTTTAACCTAATA
Found at i:123767 original size:45 final size:45
Alignment explanation
Indices: 123682--123768 Score: 104
Period size: 45 Copynumber: 1.9 Consensus size: 45
123672 ATCAGTATCA
* * *
123682 GGTTCAGCAGGACTGCTACTCGCATATGTTGCTTCATCAATATTG
1 GGTTCAGCAGGACTGCTACACACATATGTTGCTGCATCAATATTG
* * *
123727 GGTTCAGCAGGGCTGCTGCACACATCTGTTGCTGGC-TCAATA
1 GGTTCAGCAGGACTGCTACACACATATGTTGCT-GCATCAATA
123769 CTTCCAGATT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
45 34 0.97
46 1 0.03
ACGTcount: A:0.21, C:0.24, G:0.25, T:0.30
Consensus pattern (45 bp):
GGTTCAGCAGGACTGCTACACACATATGTTGCTGCATCAATATTG
Found at i:129772 original size:36 final size:36
Alignment explanation
Indices: 129726--129801 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
129716 TTTGAGTTTT
* * *
129726 AGTCTAGCTTAAAAATTTTAGCCTCTC-AAGTTTTCG
1 AGTCCAGCTTAAAAATTTCAGCCTCACGAA-TTTTCG
*
129762 AGTCCAGCTTAAAAATTTCAGGCTCACGAATTTTCG
1 AGTCCAGCTTAAAAATTTCAGCCTCACGAATTTTCG
129798 AGTC
1 AGTC
129802 GAGTCGAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 33 0.94
37 2 0.06
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (36 bp):
AGTCCAGCTTAAAAATTTCAGCCTCACGAATTTTCG
Found at i:133111 original size:25 final size:26
Alignment explanation
Indices: 133066--133121 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
133056 AGAGAGGTCC
* * * *
133066 AATTA-TAAAATATATATATATATAG
1 AATTATTAAAAAATATAAATATAGAA
133091 AATTATTAAAAAATA-AAATATAGAA
1 AATTATTAAAAAATATAAATATAGAA
133116 AATTAT
1 AATTAT
133122 GAATATTGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 18 0.69
26 8 0.31
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.36
Consensus pattern (26 bp):
AATTATTAAAAAATATAAATATAGAA
Found at i:133232 original size:7 final size:7
Alignment explanation
Indices: 133220--133244 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
133210 TATTTTTTAT
133220 ATTTAGA
1 ATTTAGA
133227 ATTTAGA
1 ATTTAGA
133234 ATTTAGA
1 ATTTAGA
133241 ATTT
1 ATTT
133245 TTTTTGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (7 bp):
ATTTAGA
Found at i:137887 original size:42 final size:41
Alignment explanation
Indices: 137824--137907 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 41
137814 CGACTGTAAT
137824 GTATTTGAGTTTTATTGTTAAACGATAAAATATTTGAAATA
1 GTATTTGAGTTTTATTGTTAAACGATAAAATATTTGAAATA
*
137865 GTATTTGAGTTTTTATTGTTAAACGATAAAGTATTTGAAATA
1 GTATTTGAG-TTTTATTGTTAAACGATAAAATATTTGAAATA
137907 G
1 G
137908 ATACTACCTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
41 9 0.22
42 32 0.78
ACGTcount: A:0.37, C:0.02, G:0.17, T:0.44
Consensus pattern (41 bp):
GTATTTGAGTTTTATTGTTAAACGATAAAATATTTGAAATA
Found at i:140341 original size:3 final size:3
Alignment explanation
Indices: 140286--140328 Score: 63
Period size: 3 Copynumber: 14.7 Consensus size: 3
140276 TTCATTTAAA
140286 TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT TAT T-T TAT TAT TA
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
140329 ATAAATATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 3 0.08
3 33 0.89
4 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:142554 original size:19 final size:19
Alignment explanation
Indices: 142530--142572 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
142520 TAATTCTTTC
* *
142530 TTTTCAAATTTTTTATATA
1 TTTTCAAAGTATTTATATA
*
142549 TTTTCATAGTATTTATATA
1 TTTTCAAAGTATTTATATA
142568 TTTTC
1 TTTTC
142573 TTATTAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTTCAAAGTATTTATATA
Found at i:145870 original size:15 final size:15
Alignment explanation
Indices: 145850--145881 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
145840 ATCAATACCT
145850 TTTTGCATACATACA
1 TTTTGCATACATACA
*
145865 TTTTGCATACATTCA
1 TTTTGCATACATACA
145880 TT
1 TT
145882 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATACA
Found at i:153180 original size:11 final size:10
Alignment explanation
Indices: 153159--153244 Score: 86
Period size: 10 Copynumber: 8.1 Consensus size: 10
153149 GCTTGAAGAG
*
153159 AAAAGAACAA
1 AAAAGAAAAA
153169 AAAAGAAACAA
1 AAAAGAAA-AA
153180 AAAAGAAAAA
1 AAAAGAAAAA
153190 GAAAAGAAAAA
1 -AAAAGAAAAA
153201 AAAGAGAAGAACA
1 AAA-AGAA-AA-A
153214 AAAA-AAAAGA
1 AAAAGAAAA-A
153224 AAAA-AAAAGA
1 AAAAGAAAA-A
153234 AAAAGAAAAA
1 AAAAGAAAAA
153244 A
1 A
153245 GGGGGTCAAG
Statistics
Matches: 68, Mismatches: 2, Indels: 12
0.83 0.02 0.15
Matches are distributed among these distances:
10 31 0.46
11 30 0.44
12 3 0.04
13 4 0.06
ACGTcount: A:0.84, C:0.03, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAAGAAAAA
Found at i:153243 original size:16 final size:15
Alignment explanation
Indices: 153157--153244 Score: 95
Period size: 16 Copynumber: 5.5 Consensus size: 15
153147 ATGCTTGAAG
* *
153157 AGAAAAGAACAAAAA
1 AGAAAAAAAAAAAAA
153172 AGAAACAAAAAAGAAAA
1 AGAAA-AAAAAA-AAAA
*
153189 AGAAAAGAAAAAAAAG
1 AGAAAA-AAAAAAAAA
*
153205 AGAAGAACAAAAAAAA
1 AGAA-AAAAAAAAAAA
153221 AGAAAAAAAAAGAAAA
1 AGAAAAAAAAA-AAAA
153237 AGAAAAAA
1 AGAAAAAA
153245 GGGGGTCAAG
Statistics
Matches: 62, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
15 11 0.18
16 35 0.56
17 16 0.26
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (15 bp):
AGAAAAAAAAAAAAA
Found at i:154381 original size:93 final size:93
Alignment explanation
Indices: 154140--154910 Score: 1291
Period size: 91 Copynumber: 8.4 Consensus size: 93
154130 GTCTCTATAC
154140 AAACCCCATCATTGGACTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGT
1 AAACCCCATCATTGGACTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGT
***
154205 TATCTGATCTGGTTTGGTAT-AA-AAAA
66 TATCTGATCTGGTTTGGTATGAACCCCA
*
154231 AAACCCCATCATTGGACTTGAAAGATGAATGTACTCATAGCATCTTCTGGAAGTGTTCTTTGAGT
1 AAACCCCATCATTGGACTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGT
*
154296 TATCTGATCTGGTTTGGTATAAACCCCA
66 TATCTGATCTGGTTTGGTATGAACCCCA
* *
154324 AAACCCCATCATTAGACTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAATGTTCTTTGAGT
1 AAACCCCATCATTGGACTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGT
154389 TATCTGATCTGGTTT-GTATGAA-CCCA
66 TATCTGATCTGGTTTGGTATGAACCCCA
154415 AAACCCCATCATTGGACTTGAAAGATGAA--TG-TCATAGCATCTTCTGGAAGTGTTCTTTGAGT
1 AAACCCCATCATTGGACTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGT
154477 TATCTGATCTGGTTTGGTATGAACCCCA
66 TATCTGATCTGGTTTGGTATGAACCCCA
* *
154505 AAACCCCATCATTAGACTTGAAAGATGAGTGTGCTCATAGCATCTTCT-GAAGTG-TCTTTGAGT
1 AAACCCCATCATTGGACTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGT
*
154568 TATTTGATCTGGTTTGGTATGAACCCCA
66 TATCTGATCTGGTTTGGTATGAACCCCA
*
154596 AAACCCCATCATTGGACTTGAAAGATGAGTGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGT
1 AAACCCCATCATTGGACTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGT
154661 TATCTGATCTGGTTTGGTA-GAACCCCA
66 TATCTGATCTGGTTTGGTATGAACCCCA
154688 AAA-CCCATCATTGGACTTGAAAGATGAA--TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGT
1 AAACCCCATCATTGGACTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGT
154750 TATCTGATCTGGTTTGGTATGAACCCCA
66 TATCTGATCTGGTTTGGTATGAACCCCA
154778 AAACCCCATCATTGGACTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGT
1 AAACCCCATCATTGGACTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGT
**
154843 TATCTGATCTGGTTTGGTATGAAACTACA
66 TATCTGATCTGGTTTGGTATG-AACCCCA
* * *
154872 GAA-CCAATCATTGGATTTGAAAGATGAATGTGCTCATAG
1 AAACCCCATCATTGGACTTGAAAGATGAATGTGCTCATAG
154911 TACAAATAAA
Statistics
Matches: 645, Mismatches: 21, Indels: 26
0.93 0.03 0.04
Matches are distributed among these distances:
88 45 0.07
89 62 0.10
90 42 0.07
91 248 0.38
92 33 0.05
93 208 0.32
94 7 0.01
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (93 bp):
AAACCCCATCATTGGACTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGT
TATCTGATCTGGTTTGGTATGAACCCCA
Found at i:154631 original size:272 final size:276
Alignment explanation
Indices: 154140--154910 Score: 1299
Period size: 272 Copynumber: 2.8 Consensus size: 276
154130 GTCTCTATAC
154140 AAACCCCATCATTGGACTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGT
1 AAACCCCATCATTGGACTTGAAAGATGAA--TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGT
*** *
154205 TATCTGATCTGGTTTGGTAT-AA-AAAAAAACCCCATCATTGGACTTGAAAGATGAATGTACTCA
64 TATCTGATCTGGTTTGGTATGAACCCCAAAACCCCATCATTGGACTTGAAAGATGAATGTGCTCA
*
154268 TAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATAAACCCCAAAACCCCAT
129 TAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAACCCCAT
*
154333 CATTAGACTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATC
194 CATTGGACTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATC
154398 TGGTTT-GTATGAA-CCCA
259 TGGTTTGGTA-GAACCCCA
154415 AAACCCCATCATTGGACTTGAAAGATGAATG-TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
1 AAACCCCATCATTGGACTTGAAAGATGAATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
* *
154479 TCTGATCTGGTTTGGTATGAACCCCAAAACCCCATCATTAGACTTGAAAGATGAGTGTGCTCATA
66 TCTGATCTGGTTTGGTATGAACCCCAAAACCCCATCATTGGACTTGAAAGATGAATGTGCTCATA
*
154544 GCATCTTCT-GAAGTG-TCTTTGAGTTATTTGATCTGGTTTGGTATGAACCCCAAAACCCCATCA
131 GCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAACCCCATCA
* *
154607 TTGGACTTGAAAGATGAGTGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
196 TTGGACTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTG
154672 GTTTGGTAGAACCCCA
261 GTTTGGTAGAACCCCA
154688 AAA-CCCATCATTGGACTTGAAAGATGAATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
1 AAACCCCATCATTGGACTTGAAAGATGAATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
154752 TCTGATCTGGTTTGGTATGAACCCCAAAACCCCATCATTGGACTTGAAAGATGAATGTGCTCATA
66 TCTGATCTGGTTTGGTATGAACCCCAAAACCCCATCATTGGACTTGAAAGATGAATGTGCTCATA
** * *
154817 GCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACTACAGAA-CCAATC
131 GCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATG-AACCCCAAAACCCCATC
*
154881 ATTGGATTTGAAAGATGAATGTGCTCATAG
195 ATTGGACTTGAAAGATGAATGTGCTCATAG
154911 TACAAATAAA
Statistics
Matches: 468, Mismatches: 20, Indels: 16
0.93 0.04 0.03
Matches are distributed among these distances:
272 193 0.41
273 125 0.27
274 52 0.11
275 91 0.19
276 7 0.01
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (276 bp):
AAACCCCATCATTGGACTTGAAAGATGAATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
TCTGATCTGGTTTGGTATGAACCCCAAAACCCCATCATTGGACTTGAAAGATGAATGTGCTCATA
GCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAACCCCATCA
TTGGACTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTG
GTTTGGTAGAACCCCA
Done.