Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_2440
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: 23391
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:2365 original size:14 final size:14
Alignment explanation
Indices: 2346--2379 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2336 TTGCTTTACT
2346 GAAAATGACTTCCG
1 GAAAATGACTTCCG
* *
2360 GAAAATGATTTCTG
1 GAAAATGACTTCCG
2374 GAAAAT
1 GAAAAT
2380 AATTTACTTT
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:0.41, C:0.12, G:0.21, T:0.26
Consensus pattern (14 bp):
GAAAATGACTTCCG
Found at i:4511 original size:19 final size:19
Alignment explanation
Indices: 4487--4555 Score: 61
Period size: 19 Copynumber: 3.6 Consensus size: 19
4477 TAATAATAAT
4487 ATAAAATAATAGTATGTAC
1 ATAAAATAATAGTATGTAC
* *
4506 ATAAAAATATATA-TATATGC
1 AT-AAAATA-ATAGTATGTAC
* *
4526 ATATAATAAAAGTATGTA-
1 ATAAAATAATAGTATGTAC
4544 ATAATAATAATA
1 ATAA-AATAATA
4556 TCTACAATAA
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
18 5 0.13
19 17 0.45
20 13 0.34
21 3 0.08
ACGTcount: A:0.57, C:0.03, G:0.07, T:0.33
Consensus pattern (19 bp):
ATAAAATAATAGTATGTAC
Found at i:5752 original size:17 final size:17
Alignment explanation
Indices: 5730--5763 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
5720 TCTACAACTT
5730 CAATCTACTCTTCTATC
1 CAATCTACTCTTCTATC
5747 CAATCTACTCTTCTATC
1 CAATCTACTCTTCTATC
5764 GCTTCAGTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.35, G:0.00, T:0.41
Consensus pattern (17 bp):
CAATCTACTCTTCTATC
Found at i:6073 original size:88 final size:85
Alignment explanation
Indices: 5978--6389 Score: 267
Period size: 88 Copynumber: 4.8 Consensus size: 85
5968 AAAAATAGAA
*
5978 ATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
1 ATTGAAAATACCTC-GCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
6043 GAAACTTAACTTGAAAAGCAGAT
65 GAAACTTAA-TT-AAAAGCAGAT
* * * * *
6066 TTTGAAAATACCTCGATATGTGA-CTGAAGGTTCAACTCACCTCTCGCAATATGAGTTGA-TTTT
1 ATTGAAAATACCTCG-CACGTGAGC-CAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
* * **
6129 TGAAAAATAGAAATTAAAAGACTCA-
64 TG-AAACT--TAATTAAAAG-CAGAT
* * * ** *** *
6154 ACT-CAACT--CTCGCA-GAAATTAAAAAGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTT
1 ATTGAAAATACCTCGCACGTGA-GCCAAGGCTCAACTCACCTCTCGCAATATGAGTTG-A-TTTT
*
6215 TTGAAA---AA--AAAA-CAGAA
63 TTGAAACTTAATTAAAAGCAGAT
* * * * *
6232 ATTGAAAATAGCTTAGCACGTAAGCCAAGGCTCAACTCACTTCTTGCAATATGAGTTGA-TTTTT
1 ATTGAAAATA-CCTCGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
* *
6296 GAAAACATAATCTGAAAAACAGAT
65 G-AAACTTAAT-T-AAAAGCAGAT
* * * * * *
6320 TTTGAAAATACCTCGACATGTGACCCGAGGCTCAACTCACATCTCGCAATGTGAGTTGATTTTTT
1 ATTGAAAATACCTCG-CACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTT
6385 TGAAA
64 TGAAA
6390 AATATAAATT
Statistics
Matches: 249, Mismatches: 46, Indels: 57
0.71 0.13 0.16
Matches are distributed among these distances:
77 2 0.01
78 2 0.01
79 13 0.05
80 3 0.01
81 3 0.01
82 33 0.13
83 7 0.03
84 31 0.12
85 5 0.02
86 3 0.01
87 24 0.10
88 108 0.43
89 7 0.03
90 8 0.03
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (85 bp):
ATTGAAAATACCTCGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTG
AAACTTAATTAAAAGCAGAT
Found at i:6173 original size:30 final size:30
Alignment explanation
Indices: 6137--6197 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
6127 TTTGAAAAAT
6137 AGAAATT-AAAAGACTCAACTCAACTCTCGC
1 AGAAATTAAAAAG-CTCAACTCAACTCTCGC
*
6167 AGAAATTAAAAAGCTCAACTCACCTCTCGC
1 AGAAATTAAAAAGCTCAACTCAACTCTCGC
6197 A
1 A
6198 ATATGAGTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 24 0.83
31 5 0.17
ACGTcount: A:0.43, C:0.28, G:0.10, T:0.20
Consensus pattern (30 bp):
AGAAATTAAAAAGCTCAACTCAACTCTCGC
Found at i:6515 original size:77 final size:78
Alignment explanation
Indices: 6347--6884 Score: 388
Period size: 76 Copynumber: 6.9 Consensus size: 78
6337 ATGTGACCCG
* * * * *
6347 AGGCTCAACTCACATCTCGCAATGTGAGTTGATTTTTTTGAAAAATATAAATTGAAAAAATACCT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTG--AAAATACCT
* * * *
6412 CAGTGTGTGATCTGA
64 CAGCGCGTGAGCTCA
*
6427 A-GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATAGCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATACCTCA
6491 GCGCGTGAGC-CA
66 GCGCGTGAGCTCA
*
6503 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAGGCAGAAATTGGAAAACGGAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTGAAAGACAGAAATT-G---A---AA
** ** * *
6568 ATTGAAAATACCTCGGCGTGTGAC-CTG
58 A-T--ACCT-CAGC-GCGTGAG-CTC-A
* ** * * *
6595 AGGCTCAACTCGCCTCTTACAATACGAGTTGATTTTTTTGACA-ACAGAAATTGAAATTACCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATACCTCA
** *
6659 --GCGTGTCCT-G
66 GCGCGTGAGCTCA
* * *
6669 AGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTTTGAAAAATAGAAATTGAAAATACCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATACCTCA
* * **
6734 --GCATG-TCTTG
66 GCGCGTGAGCTCA
** * * *
6744 AGGCTCAACTCATTTCTCACAATATGAGTTGATTTTTTTTGAAAAACAGAAATTAAAAATACCTC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTGAAAGACAGAAATTGAAAATACCTC
* * *
6809 A--GCATG-TCTTA
65 AGCGCGTGAGCTCA
* ** * *
6820 AGGCTCAACTAATTTCTCGCAATATGAGTTGA--ATTTTGAAA-ACAGAAATTGAAATTACCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATACCTCA
6882 GCG
66 GCG
6885 TGTCTTGAGG
Statistics
Matches: 386, Mismatches: 50, Indels: 50
0.79 0.10 0.10
Matches are distributed among these distances:
72 19 0.05
73 8 0.02
74 41 0.11
75 53 0.14
76 78 0.20
77 47 0.12
78 20 0.05
79 49 0.13
80 3 0.01
82 2 0.01
83 2 0.01
85 3 0.01
86 2 0.01
88 2 0.01
89 3 0.01
90 14 0.04
91 12 0.03
92 28 0.07
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Consensus pattern (78 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATACCTCA
GCGCGTGAGCTCA
Found at i:6605 original size:169 final size:165
Alignment explanation
Indices: 6403--6856 Score: 474
Period size: 151 Copynumber: 2.8 Consensus size: 165
6393 ATAAATTGAA
* * * *
6403 AAAATACCTCAGTGTGTGATCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAA
1 AAAATACCTCAGCGTGTGACCTGAAGCTCAACTCACCTCTCACAATACGAGTTGATTTTTTTGAA
*
6468 AGACAGAAATTGAAAATAGCTCAGCGCGTGAGCC-AAGGCTCAACTCACCTCTCGCAATATGAGT
66 A-ACAGAAATTGAAAATACCTCA--GCGTG-GCCTAAGGCTCAACTCACCTCTCGCAATATGAGT
6532 TGATTTTTTTTGAAAGGCAGAAATTGGAAAACGGAAATTG
127 TGA-TTTTTTTGAAAGGCAGAAATTGGAAAACGGAAATTG
* * * * *
6572 AAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCTCTTACAATACGAGTTGATTTTTTTGAC
1 AAAATACCTCAGCGTGTGACCTGAAGCTCAACTCACCTCTCACAATACGAGTTGATTTTTTTGAA
* * * *
6637 AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGTAATATGAGTTGAT
66 AACAGAAATTGAAAATACCTCAGCGTGGCCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
6702 TTTTTTG--A---A-AAA-T-----A--GAAATTG
131 TTTTTTGAAAGGCAGAAATTGGAAAACGGAAATTG
* * * ** *
6723 AAAATACCTCAGCATGT--CTTGAGGCTCAACTCATTTCTCACAATATGAGTTGATTTTTTTTGA
1 AAAATACCTCAGCGTGTGACCTGAAGCTCAACTCACCTCTCACAATACGAGTTGA-TTTTTTTG-
* * * * * **
6786 AAAACAGAAATTAAAAATACCTCAGCATGTCTTAAGGCTCAACTAATTTCTCGCAATATGAGTTG
64 AAAACAGAAATTGAAAATACCTCAGCGTGGCCTAAGGCTCAACTCACCTCTCGCAATATGAGTTG
*
6851 AATTTT
129 ATTTTT
6857 GAAAACAGAA
Statistics
Matches: 249, Mismatches: 33, Indels: 24
0.81 0.11 0.08
Matches are distributed among these distances:
149 30 0.12
150 8 0.03
151 82 0.33
153 1 0.00
158 1 0.00
159 3 0.01
160 1 0.00
163 1 0.00
165 10 0.04
166 36 0.14
168 19 0.08
169 57 0.23
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (165 bp):
AAAATACCTCAGCGTGTGACCTGAAGCTCAACTCACCTCTCACAATACGAGTTGATTTTTTTGAA
AACAGAAATTGAAAATACCTCAGCGTGGCCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
TTTTTTGAAAGGCAGAAATTGGAAAACGGAAATTG
Found at i:6707 original size:76 final size:75
Alignment explanation
Indices: 6559--6903 Score: 419
Period size: 76 Copynumber: 4.6 Consensus size: 75
6549 CAGAAATTGG
* * * * * *
6559 AAAACGGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCTCTTACAATACGAGT
1 AAAACAGAAATTGAAAATACCTCAGCGTGT--CTTGAGGCTCAACTCACCTCTCACAATATGAGT
6624 TGATTTTTTTG-
64 TGATTTTTTTGA
* * * **
6635 ACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGTAATATGAGTTG
1 AAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCACAATATGAGTTG
6700 ATTTTTTTGA
66 ATTTTTTTGA
* * **
6710 AAAATAGAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCACAATATGAGTTG
1 AAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCACAATATGAGTTG
6775 ATTTTTTTTGA
66 A-TTTTTTTGA
* * * * ** *
6786 AAAACAGAAATTAAAAATACCTCAGCATGTCTTAAGGCTCAACTAATTTCTCGCAATATGAGTTG
1 AAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCACAATATGAGTTG
*
6851 A--ATTTTG-
66 ATTTTTTTGA
*
6858 AAAACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCA
1 AAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCA
6904 TTTTGAACAG
Statistics
Matches: 238, Mismatches: 29, Indels: 8
0.87 0.11 0.03
Matches are distributed among these distances:
72 41 0.17
73 5 0.02
74 39 0.16
75 57 0.24
76 96 0.40
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (75 bp):
AAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCACAATATGAGTTG
ATTTTTTTGA
Found at i:6844 original size:151 final size:146
Alignment explanation
Indices: 6558--6906 Score: 437
Period size: 151 Copynumber: 2.3 Consensus size: 146
6548 GCAGAAATTG
* * * *** *
6558 GAAAACGGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCTCTTACAATACGAG
1 GAAAACAGAAATTGAAAATACCTCAGCGTGT--CTTGAGGCTCAACTCATTTCTCACAATACGAG
* * * * * *
6623 TTGATTTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCG
64 TTGATTTTTTTGAAAACAGAAATTAAAAATACCTCAGCATGTCCTAAGGCTCAACTAACCTCTCG
* *
6688 TAATATGAGTTGATTTTTTT
129 CAATATGAGTTGA--ATTTT
* * *
6708 GAAAAATAGAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCACAATATGAGT
1 G-AAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCACAATACGAGT
* **
6773 TGATTTTTTTTGAAAAACAGAAATTAAAAATACCTCAGCATGTCTTAAGGCTCAACTAATTTCTC
65 TGA-TTTTTTTG-AAAACAGAAATTAAAAATACCTCAGCATGTCCTAAGGCTCAACTAACCTCTC
6838 GCAATATGAGTTGAATTTT
128 GCAATATGAGTTGAATTTT
*
6857 GAAAACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCATTT
1 GAAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTT
6907 TGAACAGAAA
Statistics
Matches: 172, Mismatches: 24, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
148 46 0.27
149 35 0.20
150 9 0.05
151 82 0.48
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (146 bp):
GAAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCACAATACGAGTT
GATTTTTTTGAAAACAGAAATTAAAAATACCTCAGCATGTCCTAAGGCTCAACTAACCTCTCGCA
ATATGAGTTGAATTTT
Found at i:6926 original size:49 final size:49
Alignment explanation
Indices: 6860--6955 Score: 183
Period size: 49 Copynumber: 2.0 Consensus size: 49
6850 GAATTTTGAA
*
6860 AACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCATTTTG
1 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTTG
6909 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTT
1 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTT
6956 CTCGCAATAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (49 bp):
AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTTG
Found at i:6945 original size:121 final size:121
Alignment explanation
Indices: 6788--7027 Score: 417
Period size: 121 Copynumber: 2.0 Consensus size: 121
6778 TTTTTTGAAA
*
6788 AACAGAAATTAAAAATACCTCAGCATGTCTTAAGGCTCAACTAATTTCTCGCAATATGAGTTGAA
1 AACAGAAATTAAAAATACCTCAACATGTCTTAAGGCTCAACTAATTTCTCGCAATATGAGTTGAA
*
6853 TTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCATTTTG
66 TTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTTG
* * * * *
6909 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
1 AACAGAAATTAAAAATACCTCAACATGTCTTAAGGCTCAACTAATTTCTCGCAATATGAGTTGAA
6974 TTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTT
66 TTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTT
7028 CTCGCAATAT
Statistics
Matches: 112, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
121 112 1.00
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.31
Consensus pattern (121 bp):
AACAGAAATTAAAAATACCTCAACATGTCTTAAGGCTCAACTAATTTCTCGCAATATGAGTTGAA
TTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTTG
Found at i:6989 original size:72 final size:72
Alignment explanation
Indices: 6909--7133 Score: 292
Period size: 72 Copynumber: 3.0 Consensus size: 72
6899 ACTCATTTTG
6909 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
1 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
6974 TTTTGAA
66 TTTTGAA
6981 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
1 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
7046 TTTTTTTTTGAA
66 -----TTTTGAA
* * * * ** *
7058 AGACAGAAATTGAAAATACCTCAGCATGTGAAC-CGAGGCTCAACTCACCTCTCGCAATATGAGC
1 A-ACAGAAATTGAAATTACCTCA--ACGTG-TCTTGAGGCTCAACTCATTTCTCGCAATATGAGT
7122 TG-ATTTTGAA
62 TGAATTTTGAA
7132 AA
1 AA
7134 AGTAGAAATT
Statistics
Matches: 137, Mismatches: 7, Indels: 17
0.85 0.04 0.11
Matches are distributed among these distances:
72 65 0.47
73 1 0.01
74 8 0.06
77 8 0.06
78 20 0.15
79 1 0.01
80 33 0.24
81 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (72 bp):
AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
TTTTGAA
Found at i:7197 original size:54 final size:55
Alignment explanation
Indices: 7097--7202 Score: 144
Period size: 54 Copynumber: 1.9 Consensus size: 55
7087 GAACCGAGGC
* *
7097 TCAACTCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAGAAATT-AAAAGGT
1 TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGCAGAAATTGAAAAGGT
* * *
7151 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGAACAA-CATAAATTGAAAA
1 TCAACCCACCTCTCGCAATATGAGCTGATT-TTGAAAAAGCAGAAATTGAAAA
7203 CAGAAATTGA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
54 34 0.76
55 11 0.24
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (55 bp):
TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGCAGAAATTGAAAAGGT
Found at i:7209 original size:13 final size:13
Alignment explanation
Indices: 7182--7215 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
7172 GAGTTGATTC
*
7182 TTGAACAACATAAA
1 TTGAA-AACAGAAA
7196 TTGAAAACAGAAA
1 TTGAAAACAGAAA
7209 TTGAAAA
1 TTGAAAA
7216 TACCTCAGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.59, C:0.09, G:0.12, T:0.21
Consensus pattern (13 bp):
TTGAAAACAGAAA
Found at i:7263 original size:140 final size:140
Alignment explanation
Indices: 7053--7675 Score: 1144
Period size: 140 Copynumber: 4.4 Consensus size: 140
7043 GAATTTTTTT
7053 TTGAAAGACAGAAATTGAAAATACCTCAGCATGTGAACC-GAGGCTCAACTCACCTCTCGCAATA
1 TTGAAA-ACAGAAATTGAAAATACCTCAGC--GTG-ACCTGAGGCTCAACTCACCTCTCGCAATA
7117 TGAGCTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTC
62 TGAGCTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTC
*
7182 TTGAACAACATAAA
127 TTGAACAACGTAAA
7196 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
* *
7261 CTGGTTTTGAAAAAGTAGAAATT-AAAGGTTCAACCCACTTCTCGCAATATGAGTTGATTCTTGA
66 CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGA
7325 ACAACGTAAA
131 ACAACGTAAA
* *
7335 TT-AAAACAGAAATTGAAAATACCTTAGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
7399 CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGA
66 CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGA
7464 ACAACGTAAA
131 ACAACGTAAA
7474 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
7539 CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGA
66 CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGA
7604 ACAACGTAAA
131 ACAACGTAAA
7614 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATAT
7676 TAGTTGAAAT
Statistics
Matches: 468, Mismatches: 9, Indels: 9
0.96 0.02 0.02
Matches are distributed among these distances:
138 82 0.18
139 106 0.23
140 251 0.54
142 23 0.05
143 6 0.01
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.25
Consensus pattern (140 bp):
TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGA
ACAACGTAAA
Found at i:7336 original size:53 final size:52
Alignment explanation
Indices: 7237--7339 Score: 127
Period size: 53 Copynumber: 1.9 Consensus size: 52
7227 GACCTGAGGC
* *
7237 TCAACTCACCTCTCGCAATATGAGCTGGTTTTGAAAAAGTAGAAATTAAAGGT
1 TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTA-AAATTAAAGGT
* * *
7290 TCAACCCACTTCTCGCAATATGAGTTGATTCTTGAACAACGT-AAATTAAA
1 TCAACCCACCTCTCGCAATATGAGCTGATT-TTGAA-AAAGTAAAATTAAA
7340 ACAGAAATTG
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
53 34 0.79
54 5 0.12
55 4 0.09
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (52 bp):
TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAAAATTAAAGGT
Found at i:7393 original size:278 final size:280
Alignment explanation
Indices: 7053--7675 Score: 1144
Period size: 278 Copynumber: 2.2 Consensus size: 280
7043 GAATTTTTTT
7053 TTGAAAGACAGAAATTGAAAATACCTCAGCATGTGAACC-GAGGCTCAACTCACCTCTCGCAATA
1 TTGAAA-ACAGAAATTGAAAATACCTCAG--TGTG-ACCTGAGGCTCAACTCACCTCTCGCAATA
7117 TGAGCTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTC
62 TGAGCTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTC
7182 TTGAACAACATAAATTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACC
127 TTGAACAACATAAATTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACC
* *
7247 TCTCGCAATATGAGCTGGTTTTGAAAAAGTAGAAATT-AAAGGTTCAACCCACTTCTCGCAATAT
192 TCTCGCAATATGAGCTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATAT
7311 GAGTTGATTCTTGAACAACGTAAA
257 GAGTTGATTCTTGAACAACGTAAA
*
7335 TT-AAAACAGAAATTGAAAATACCTTAGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAAATACCTCAGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
7399 CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGA
66 CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGA
*
7464 ACAACGTAAATTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTC
131 ACAACATAAATTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTC
7529 GCAATATGAGCTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGT
196 GCAATATGAGCTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGT
7594 TGATTCTTGAACAACGTAAA
261 TGATTCTTGAACAACGTAAA
*
7614 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAACAGAAATTGAAAATACCTCAGTGTGACCTGAGGCTCAACTCACCTCTCGCAATAT
7676 TAGTTGAAAT
Statistics
Matches: 332, Mismatches: 6, Indels: 8
0.96 0.02 0.02
Matches are distributed among these distances:
277 3 0.01
278 194 0.58
279 52 0.16
280 78 0.23
281 3 0.01
282 2 0.01
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.25
Consensus pattern (280 bp):
TTGAAAACAGAAATTGAAAATACCTCAGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGA
ACAACATAAATTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTC
GCAATATGAGCTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGT
TGATTCTTGAACAACGTAAA
Found at i:7475 original size:54 final size:54
Alignment explanation
Indices: 7375--7480 Score: 144
Period size: 54 Copynumber: 1.9 Consensus size: 54
7365 GACCTGAGGC
*
7375 TCAACTCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAGAAATT-AAAAGGT
1 TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTA-AAATTGAAAAGGT
* *
7429 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGAACAACGT-AAATTGAAAA
1 TCAACCCACCTCTCGCAATATGAGCTGATT-TTGAA-AAAGTAAAATTGAAAA
7481 CAGAAATTGA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
54 33 0.72
55 9 0.20
56 4 0.09
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (54 bp):
TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAAAATTGAAAAGGT
Found at i:7615 original size:54 final size:54
Alignment explanation
Indices: 7515--7620 Score: 144
Period size: 54 Copynumber: 1.9 Consensus size: 54
7505 GACCTGAGGC
*
7515 TCAACTCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAGAAATT-AAAAGGT
1 TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTA-AAATTGAAAAGGT
* *
7569 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGAACAACGT-AAATTGAAAA
1 TCAACCCACCTCTCGCAATATGAGCTGATT-TTGAA-AAAGTAAAATTGAAAA
7621 CAGAAATTGA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
54 33 0.72
55 9 0.20
56 4 0.09
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (54 bp):
TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAAAATTGAAAAGGT
Found at i:7693 original size:71 final size:71
Alignment explanation
Indices: 7611--7775 Score: 242
Period size: 71 Copynumber: 2.3 Consensus size: 71
7601 TGAACAACGT
* * * *
7611 AAATTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATAT
1 AAATTAAAAACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATAT
*
7676 TAGTTG
66 GAGTTG
*
7682 AAATTAAAAACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATAT
1 AAATTAAAAACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATAT
7747 GAGTTG
66 GAGTTG
**
7753 ATTTTGAAAAACAAAAATT-AAAA
1 AAATT-AAAAACAAAAATTGAAAA
7776 GGCTTAACTC
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
71 72 0.85
72 13 0.15
ACGTcount: A:0.42, C:0.21, G:0.15, T:0.23
Consensus pattern (71 bp):
AAATTAAAAACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATAT
GAGTTG
Found at i:7868 original size:121 final size:122
Alignment explanation
Indices: 7651--7894 Score: 377
Period size: 121 Copynumber: 2.0 Consensus size: 122
7641 GCGTGACCTG
* *
7651 AGGCTCAACTCACCTCTCGCAATATTAGTTGAAATTAAAAACAAAAATTGAAAATACCTCAGCGT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAAACAAAAACTGAAAATACCTCAGCGT
7716 GCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAA
66 GCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTG-AAAA-AAAAATTAAA
* * * *
7775 AGGCTTAACTCACCTCTCGCAATATGAG-T-CAATTTAAAACATAAACT-AAAATACCTCAGCGT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAAACAAAAACTGAAAATACCTCAGCGT
* *
7837 GCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAAAAAATTAAA
66 GCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAAAAAATTAAA
7894 A
1 A
7895 ATACCTCAAC
Statistics
Matches: 112, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
119 11 0.10
120 4 0.04
121 56 0.50
122 14 0.12
123 1 0.01
124 26 0.23
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.25
Consensus pattern (122 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAAACAAAAACTGAAAATACCTCAGCGT
GCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAAAAAATTAAA
Found at i:7922 original size:70 final size:69
Alignment explanation
Indices: 7775--7947 Score: 208
Period size: 70 Copynumber: 2.5 Consensus size: 69
7765 AAAAATTAAA
* * * * * *
7775 AGGCTTAACTCACCTCTCGCAATATGAG-TCAATTTAAAACATAAACTAAAATACCTCAGCGTGC
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAACAAAAACTAAAATACCTCAACGTGC
7839 CCCG
66 CCCG
*
7843 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAA-AAAAATTAAAAATACCTCAACGT
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTT-AAAACAAAAACT-AAAATACCTCAACGT
* **
7907 GTCTTG
64 GCCCCG
7913 AGGCTCAACTCA-TCTCTCGCAATATGAGTTGATTT
1 AGGCTCAACTCACT-TCTCGCAATATGAGTTGATTT
7948 CCCTTGAAAA
Statistics
Matches: 91, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
68 26 0.29
69 11 0.12
70 54 0.59
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.28
Consensus pattern (69 bp):
AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAACAAAAACTAAAATACCTCAACGTGC
CCCG
Found at i:17772 original size:19 final size:20
Alignment explanation
Indices: 17748--17798 Score: 84
Period size: 21 Copynumber: 2.5 Consensus size: 20
17738 ATATATAAAG
17748 AAAGAAAAAACAACACAAAA
1 AAAGAAAAAACAACACAAAA
*
17768 AAGAAAAAAAACAACACAAAA
1 AA-AGAAAAAACAACACAAAA
17789 AAAGAAAAAA
1 AAAGAAAAAA
17799 AGATTCGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 9 0.32
21 19 0.68
ACGTcount: A:0.82, C:0.12, G:0.06, T:0.00
Consensus pattern (20 bp):
AAAGAAAAAACAACACAAAA
Found at i:17778 original size:21 final size:22
Alignment explanation
Indices: 17752--17799 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
17742 ATAAAGAAAG
17752 AAAAAACAACAC-AAAAAAGAA
1 AAAAAACAACACAAAAAAAGAA
17773 AAAAAACAACACAAAAAAAGAA
1 AAAAAACAACACAAAAAAAGAA
17795 AAAAA
1 AAAAA
17800 GATTCGAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 12 0.46
22 14 0.54
ACGTcount: A:0.83, C:0.12, G:0.04, T:0.00
Consensus pattern (22 bp):
AAAAAACAACACAAAAAAAGAA
Found at i:18124 original size:12 final size:13
Alignment explanation
Indices: 18102--18128 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
18092 GGGGGTTAGG
18102 TTTTTCTTTTTTT
1 TTTTTCTTTTTTT
18115 TTTTTCTTTTTTT
1 TTTTTCTTTTTTT
18128 T
1 T
18129 AGGTTAGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (13 bp):
TTTTTCTTTTTTT
Found at i:18140 original size:16 final size:15
Alignment explanation
Indices: 18121--18172 Score: 79
Period size: 16 Copynumber: 3.4 Consensus size: 15
18111 TTTTTTTTTC
18121 TTTTTTTTAGGTTAGG
1 TTTTTTTT-GGTTAGG
18137 TTTTTTTTGGGTTAGG
1 TTTTTTTT-GGTTAGG
18153 TTTTTTTTGGTTA-G
1 TTTTTTTTGGTTAGG
18167 TTTTTT
1 TTTTTT
18173 GAGGGGGCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
14 7 0.20
15 5 0.14
16 23 0.66
ACGTcount: A:0.08, C:0.00, G:0.23, T:0.69
Consensus pattern (15 bp):
TTTTTTTTGGTTAGG
Found at i:21544 original size:131 final size:133
Alignment explanation
Indices: 21379--21639 Score: 381
Period size: 131 Copynumber: 2.0 Consensus size: 133
21369 TTTTTAAAAT
21379 TTAAATCAAATAAGTGCATAATAAATAACAAAGAGAAATGTTAATAT-AAACCTAAAAAC-ATTT
1 TTAAATCAAATAAGTGCATAATAAATAACAAAGAGAAA--TTAATATAAAACCTAAAAACAATTT
* * *
21442 AATGCCAATTTTTAAGGA-AATACATATGGTTCTAAAATTC-AAACAAGTACTCCTA-AAAGCAT
64 AATGCCAATTTTTAAAGAGAATACATATGATTCTAAAATTCAAAACAAGGACTCC-ACAAAGCAT
21504 CCAAAC
128 CCAAAC
* *
21510 TTAAATCAAATAATTGCATAATAACATAAC-AAGAGAAATTATTATAAAACCTAAAAACAATTTA
1 TTAAATCAAATAAGTGCATAATAA-ATAACAAAGAGAAATTAATATAAAACCTAAAAACAATTTA
* *
21574 ATGCCAATTTTTAAAGAGATTACATATGATTCTAAAATTCAAAACAGGGACTCCACAAAGCATCC
65 ATGCCAATTTTTAAAGAGAATACATATGATTCTAAAATTCAAAACAAGGACTCCACAAAGCATCC
21639 A
130 A
21640 TACATATTAA
Statistics
Matches: 117, Mismatches: 7, Indels: 10
0.87 0.05 0.07
Matches are distributed among these distances:
129 6 0.05
130 12 0.10
131 52 0.44
132 26 0.22
133 21 0.18
ACGTcount: A:0.49, C:0.15, G:0.09, T:0.27
Consensus pattern (133 bp):
TTAAATCAAATAAGTGCATAATAAATAACAAAGAGAAATTAATATAAAACCTAAAAACAATTTAA
TGCCAATTTTTAAAGAGAATACATATGATTCTAAAATTCAAAACAAGGACTCCACAAAGCATCCA
AAC
Done.