Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold705
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: 40150
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Found at i:192 original size:72 final size:70
Alignment explanation
Indices: 107--263 Score: 182
Period size: 72 Copynumber: 2.2 Consensus size: 70
97 CGAGAAGAGT
*
107 TTGGCCTCAAAGACACGTTGAGGT-A-TCAATTCCTGTTTT-CAAAATTCA-ACTCATAT-TGCT
1 TTGGCCTCCAAGACACG-TGAGGTAATTCAATT-CTGTTTTCCAAAATTCACA-TCA-ATGTGC-
*
167 TGAGAAATGAG
61 -GAGAAATAAG
178 TTGAGCCTCCAAGACACGTGAGGTAATTTCAATTCTGTTTTCCAAAATTCACATCAATGTGCGAG
1 TTG-GCCTCCAAGACACGTGAGGTAA-TTCAATTCTGTTTTCCAAAATTCACATCAATGTGCGAG
243 AAATAAG
64 AAATAAG
250 TTGGCCT-CAAGACA
1 TTGGCCTCCAAGACA
264 TGCTAAGGGT
Statistics
Matches: 77, Mismatches: 2, Indels: 15
0.82 0.02 0.16
Matches are distributed among these distances:
70 7 0.09
71 13 0.17
72 26 0.34
73 9 0.12
74 21 0.27
75 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (70 bp):
TTGGCCTCCAAGACACGTGAGGTAATTCAATTCTGTTTTCCAAAATTCACATCAATGTGCGAGAA
ATAAG
Found at i:280 original size:72 final size:73
Alignment explanation
Indices: 132--298 Score: 175
Period size: 74 Copynumber: 2.3 Consensus size: 73
122 CGTTGAGGTA
*
132 TCAATTCCTGTTTT-CAAAATTCAACTCATATTGCTTGAGAAATGAGTTGAGCCTCCAAGACACG
1 TCAATT-CTGTTTTCCAAAATTCAACTCATATTGC-TGAGAAATAAGTTGAGCCTCCAAGACACG
*
196 TGAGGTAATT
64 TAAGGTAATT
*
206 TCAATTCTGTTTTCCAAAATTC-ACATCA-ATGTGC-GAGAAATAAGTTG-GCCT-CAAGACATG
1 TCAATTCTGTTTTCCAAAATTCAAC-TCATAT-TGCTGAGAAATAAGTTGAGCCTCCAAGACACG
*
266 CTAAGGGTATTT
64 -TAA-GGTAATT
*
278 TCAATTTCTTGTTTTCAAAAA
1 TCAA-TTC-TGTTTTCCAAAA
299 ATTAAAAAAC
Statistics
Matches: 81, Mismatches: 5, Indels: 14
0.81 0.05 0.14
Matches are distributed among these distances:
70 8 0.10
71 6 0.07
72 22 0.27
73 14 0.17
74 31 0.38
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (73 bp):
TCAATTCTGTTTTCCAAAATTCAACTCATATTGCTGAGAAATAAGTTGAGCCTCCAAGACACGTA
AGGTAATT
Found at i:886 original size:16 final size:18
Alignment explanation
Indices: 849--887 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
839 TGAGCCTTGG
849 TTCAATTGCTGATTTATT
1 TTCAATTGCTGATTTATT
*
867 TTCAATTTCTG-TTT-TT
1 TTCAATTGCTGATTTATT
883 TTCAA
1 TTCAA
888 AAAAATTCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
17 3 0.15
18 10 0.50
ACGTcount: A:0.21, C:0.13, G:0.08, T:0.59
Consensus pattern (18 bp):
TTCAATTGCTGATTTATT
Found at i:4759 original size:29 final size:28
Alignment explanation
Indices: 4717--4772 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
4707 GCAAAGCATA
4717 AATTAAAAGACTCAACTCAACTCTCGCAG
1 AATTAAAAGACTCAACTCAACT-TCGCAG
*
4746 AATTAAAA-AGCTCAACTCACCTTCGCA
1 AATTAAAAGA-CTCAACTCAACTTCGCA
4773 ATATGAGTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 6 0.24
29 19 0.76
ACGTcount: A:0.41, C:0.29, G:0.09, T:0.21
Consensus pattern (28 bp):
AATTAAAAGACTCAACTCAACTTCGCAG
Found at i:4842 original size:76 final size:75
Alignment explanation
Indices: 4755--5114 Score: 302
Period size: 72 Copynumber: 4.7 Consensus size: 75
4745 GAATTAAAAA
*
4755 GCTCAACTCACCTTCGCAATATGAGTTGAATTTTTTGAAAAAACAGAAATTGAAAATA-CTCAGC
1 GCTCAACTCACCTTCGCAATATGAGTTGATTTTTTTG-AAAAACAGAAATTGAAAATACCTCAG-
*
4819 ACTTGAGCCAAG
64 ACTTGAGCCGAG
* * *
4831 GCTCAACTCACCTTTCGCAATATGAGTTGA--TTTTGGAAAACAGAATTTGAAAAACAGATTTAA
1 GCTCAACTCACC-TTCGCAATATGAGTTGATTTTTTTGAAAA-A-CA---G----A-A-ATTGAA
*
4894 AATACCT-TGACATTGA-CCGAG
54 AATACCTCAGAC-TTGAGCCGAG
* *
4915 GCTCAACTCACC-TCGCAATATGAGTTGATTTTTTTGAAAAATATAAATTGAAAAAATACCTCAG
1 GCTCAACTCACCTTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTG--AAAATACCTCAG
* *
4979 --TGTGATCTGA-
64 ACT-TGAGCCGAG
*
4989 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG-AAAACAGAAATTG-AAATAGCTCAGC
1 GCTCAACTCACCT-TCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAATACCTCAG-
* *
5052 GCGTGA---GAG
64 ACTTGAGCCGAG
5061 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG--AAACAGAAATTGAAAA
1 GCTCAACTCACCT-TCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAA
5115 ACGAAAATTG
Statistics
Matches: 241, Mismatches: 15, Indels: 60
0.76 0.05 0.19
Matches are distributed among these distances:
71 14 0.06
72 51 0.21
73 4 0.02
74 23 0.10
75 30 0.12
76 38 0.16
77 17 0.07
79 1 0.00
82 17 0.07
83 2 0.01
84 28 0.12
85 14 0.06
86 2 0.01
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (75 bp):
GCTCAACTCACCTTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAATACCTCAGAC
TTGAGCCGAG
Found at i:5069 original size:72 final size:71
Alignment explanation
Indices: 4912--5752 Score: 987
Period size: 72 Copynumber: 11.7 Consensus size: 71
4902 GACATTGACC
* *
4912 GAGGCTCAACTCA-C-CTCGCAATATGAGTTGATTTTTTTGAAAAATATAAATTGAAAAAATACC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTG-AAAACAGAAATTG---AAATACC
*
4975 TCAGTGTGATCT
61 TCAGCGTG-TCT
*
4987 GA-GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATTGAAATAGCTCAG
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAACAGAAATTGAAATACCTCAG
* **
5051 CGCGTGA
65 CGTGTCT
*
5058 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG-AAACAGAAATTGAAAAACGAAAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAACAGAAATTGAAATAC-----
* * * *
5122 TTGAAAATACCTCG-CGT
60 CT---CA-GCGT-GTC-T
* * * * *
5139 GTGCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGACAACAGAAATTGAAATTA
1 GAGGCTCA-ACTC-----ACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAA-TA
5204 CCTCAGCGTGTCCT
59 CCTCAGCGTGT-CT
*
5218 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAAAAACAGAAATTGAAAATA-CTC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTT-GAAAACAGAAATTG-AAATACCTC
*
5282 AGCATGTCCT
63 AGCGTGT-CT
5292 GAGGCTCAACTCACCTCTCGCAATATGAGTT--TTTTTTGAAAA-AGAAATTGAAAATACCTCAG
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTG-AAATACCTCAG
5354 CGTGTCT
65 CGTGTCT
*
5361 GAGGCTCAACTCA-TTCTCGCAATATGAGTTGA--TTTTGAAAAC--AAATTGAAATACCTCA-C
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAATACCTCAGC
5420 GTGT-T
66 GTGTCT
5425 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCA-
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTG-AAATACCTCAG
5489 CGTGTCTT
65 CGTGTC-T
5497 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCAG
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTG-AAATACCTCAG
*
5562 CGTG-CC
65 CGTGTCT
5568 GAGGCTCAACTCACCTCT--CAATATGAGTTGA-TTTTTGAAAACAGAAATTGAAATACCTCA-C
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAATACCTCAGC
5629 GTGTCT
66 GTGTCT
5635 GAGGCTCAACTCA--TCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAATACCTCAGC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAATACCTCAGC
*
5698 GTGTCC
66 GTGTCT
5704 GAGGCTCAACTCACCT-T-GCAATATGAGTTGATTTTTTGAAAACAGAAAT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAAT
5753 AAAACATCAA
Statistics
Matches: 679, Mismatches: 40, Indels: 100
0.83 0.05 0.12
Matches are distributed among these distances:
64 14 0.02
65 26 0.04
66 14 0.02
67 53 0.08
68 73 0.11
69 99 0.15
70 29 0.04
71 44 0.06
72 116 0.17
73 25 0.04
74 59 0.09
75 28 0.04
76 29 0.04
78 4 0.01
79 9 0.01
80 3 0.00
81 6 0.01
82 3 0.00
83 1 0.00
86 7 0.01
87 35 0.05
88 2 0.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (71 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAATACCTCAGC
GTGTCT
Found at i:5126 original size:85 final size:86
Alignment explanation
Indices: 5034--5200 Score: 259
Period size: 87 Copynumber: 1.9 Consensus size: 86
5024 TTGAAAACAG
*
5034 AAATTG-AAATAGCTCAGCGCGTG-AGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
1 AAATTGAAAATACCTC-GCGCGTGCAGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTT
5097 TGA-AACAGAAATTGAAAAACGA
64 TGACAACAGAAATTGAAAAACGA
* *
5119 AAATTGAAAATACCTCGCGTGTGCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
1 AAATTGAAAATACCTCGCGCGTG-CAGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
5184 GACAACAGAAATTGAAA
65 GACAACAGAAATTGAAA
5201 TTACCTCAGC
Statistics
Matches: 75, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
85 12 0.16
86 16 0.21
87 47 0.63
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (86 bp):
AAATTGAAAATACCTCGCGCGTGCAGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTG
ACAACAGAAATTGAAAAACGA
Found at i:5338 original size:69 final size:72
Alignment explanation
Indices: 5119--5752 Score: 926
Period size: 69 Copynumber: 9.1 Consensus size: 72
5109 TGAAAAACGA
5119 AAATTGAAAATACCTC-GCGTGTGCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1 AAATTGAAAATACCTCAGCGTGT-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG-TTTTT
*
5183 TGACAACAG
64 TGAAAACAG
*
5192 AAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
1 AAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG--TTTTT
*
5257 TAAAAAACAG
64 T-GAAAACAG
*
5267 AAATTGAAAATA-CTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT-TTTTTTG
1 AAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGTTTTTTG
5330 AAAA-AG
66 AAAACAG
* *
5336 AAATTGAAAATACCTCAGCGTGT-CTGAGGCTCAACTCA-TTCTCGCAATATGAGTTG-ATTTTG
1 AAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGTTTTTTG
5398 AAAAC--
66 AAAACAG
5403 AAATTG-AAATACCTCA-CGTGT--TGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
1 AAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG-TTTTTT
5464 GAAAACAG
65 GAAAACAG
*
5472 AAATTGAAAATACCTCA-CGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
1 AAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG-TTTTTT
5536 GAAAACAG
65 GAAAACAG
*
5544 AAATTGAAAATACCTCAGCGTG-CC-GAGGCTCAACTCACCTCT--CAATATGAGTTGATTTTTG
1 AAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGTTTTTTG
5605 AAAACAG
66 AAAACAG
5612 AAATTG-AAATACCTCA-CGTGT-CTGAGGCTCAACTCA--TCTCGCAATATGAGTTGATTTTTT
1 AAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG-TTTTTT
5672 GAAAACAG
65 GAAAACAG
5680 AAATTG-AAATACCTCAGCGTGTCC-GAGGCTCAACTCACCT-T-GCAATATGAGTTGATTTTTT
1 AAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG-TTTTTT
5741 GAAAACAG
65 GAAAACAG
5749 AAAT
1 AAAT
5753 AAAACATCAA
Statistics
Matches: 522, Mismatches: 15, Indels: 52
0.89 0.03 0.09
Matches are distributed among these distances:
64 14 0.03
65 25 0.05
66 15 0.03
67 51 0.10
68 73 0.14
69 97 0.19
70 30 0.06
71 25 0.05
72 66 0.13
73 54 0.10
74 55 0.11
75 17 0.03
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (72 bp):
AAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGTTTTTTG
AAAACAG
Found at i:5486 original size:136 final size:141
Alignment explanation
Indices: 5112--5752 Score: 928
Period size: 136 Copynumber: 4.6 Consensus size: 141
5102 CAGAAATTGA
5112 AAAACGAAAATTGAAAATACCTC-GCGTGTGCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
1 AAAAC-AAAATTGAAAATACCTCAGCGTGT--CTGAGGCTCAACTCACCTCTCGCAATATGAGTT
* *
5176 GATTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAA
63 GATTTTTTGAAAACAGAAATTGAAAATACCTCA-CGTGT-CTGAGGCTCAACTCACCTCTCGCAA
*
5241 TATGAGTTGATTTTTTTAA
126 TATGAGTTGA--TTTTT-G
*
5260 AAAACAGAAATTGAAAATA-CTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT-
1 AAAACA-AAATTGAAAATACCTCAGCGTGT-CTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
*
5323 -TTTTTTGAAAA-AGAAATTGAAAATACCTCAGCGTGTCTGAGGCTCAACTCA-TTCTCGCAATA
64 ATTTTTTGAAAACAGAAATTGAAAATACCTCA-CGTGTCTGAGGCTCAACTCACCTCTCGCAATA
5385 TGAGTTGA-TTTTG
128 TGAGTTGATTTTTG
5398 AAAAC-AAATTG-AAATACCTCA-CGTGT-TGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
1 AAAACAAAATTGAAAATACCTCAGCGTGTCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
5459 TTTTTGAAAACAGAAATTGAAAATACCTCACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATG
66 TTTTTGAAAACAGAAATTGAAAATACCTCACGTGTC-TGAGGCTCAACTCACCTCTCGCAATATG
5524 AGTTGATTTTTTG
130 AGTTGA-TTTTTG
*
5537 AAAACAGAAATTGAAAATACCTCAGCGTG-CCGAGGCTCAACTCACCTCT--CAATATGAGTTGA
1 AAAACA-AAATTGAAAATACCTCAGCGTGTCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
5599 -TTTTTGAAAACAGAAATTG-AAATACCTCACGTGTCTGAGGCTCAACTCA--TCTCGCAATATG
65 TTTTTTGAAAACAGAAATTGAAAATACCTCACGTGTCTGAGGCTCAACTCACCTCTCGCAATATG
5660 AGTTGATTTTTTG
130 AGTTGA-TTTTTG
*
5673 AAAACAGAAATTG-AAATACCTCAGCGTGTCCGAGGCTCAACTCACCT-T-GCAATATGAGTTGA
1 AAAACA-AAATTGAAAATACCTCAGCGTGTCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
5735 TTTTTTGAAAACAGAAAT
65 TTTTTTGAAAACAGAAAT
5753 AAAACATCAA
Statistics
Matches: 467, Mismatches: 8, Indels: 47
0.89 0.02 0.09
Matches are distributed among these distances:
133 32 0.07
135 42 0.09
136 112 0.24
137 35 0.07
138 19 0.04
139 30 0.06
140 19 0.04
141 19 0.04
142 28 0.06
143 37 0.08
144 24 0.05
145 10 0.02
147 38 0.08
148 22 0.05
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (141 bp):
AAAACAAAATTGAAAATACCTCAGCGTGTCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
TTTTTGAAAACAGAAATTGAAAATACCTCACGTGTCTGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTTTTG
Found at i:17581 original size:16 final size:15
Alignment explanation
Indices: 17555--17589 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
17545 TGATGTGAAT
17555 AATATAAAATATTAA
1 AATATAAAATATTAA
*
17570 AATATCAAAATATTAG
1 AATAT-AAAATATTAA
17586 AATA
1 AATA
17590 ATAATAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (15 bp):
AATATAAAATATTAA
Found at i:17759 original size:20 final size:20
Alignment explanation
Indices: 17702--17761 Score: 59
Period size: 23 Copynumber: 2.9 Consensus size: 20
17692 AATACTACAT
17702 AAATATGTACAT-ATATAAA
1 AAATATGTACATAATATAAA
** *
17721 AAATAAATACGTGATAATATTAA
1 AAATATGTAC---ATAATATAAA
17744 AAATATGTACATAATATA
1 AAATATGTACATAATATA
17762 GTGTAAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
19 8 0.26
20 7 0.23
22 2 0.06
23 14 0.45
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.32
Consensus pattern (20 bp):
AAATATGTACATAATATAAA
Found at i:17852 original size:25 final size:25
Alignment explanation
Indices: 17738--17955 Score: 107
Period size: 25 Copynumber: 8.9 Consensus size: 25
17728 TACGTGATAA
* *
17738 TATTAAAAATATGTACATAATATAG
1 TATTAAAGATATATACATAATATAG
* * * *
17763 TGTAAAAAATACATACATAATATA-
1 TATTAAAGATATATACATAATATAG
*
17787 -ATTAAA-ATATATACATAAGATAACATG
1 TATTAAAGATATATACAT-A-AT-ATA-G
** * *
17814 TAAAAAAAAAATATATAAATAATATAG
1 T--ATTAAAGATATATACATAATATAG
*
17841 TATTAAAGATATATACATAAAATAG
1 TATTAAAGATATATACATAATATAG
* *
17866 TA-TAATATATATATACGTAATATAG
1 TATTAA-AGATATATACATAATATAG
* * *
17891 AATT-TAGA-ATATACCTAATATA-
1 TATTAAAGATATATACATAATATAG
* * *
17913 T-TAAAAGA-ATATATATAATATAA
1 TATTAAAGATATATACATAATATAG
*
17936 TATT-AAGAAATATA-ATAATA
1 TATTAAAGATATATACATAATA
17956 ACAAAAAAAA
Statistics
Matches: 148, Mismatches: 30, Indels: 32
0.70 0.14 0.15
Matches are distributed among these distances:
21 1 0.01
22 24 0.16
23 29 0.20
24 13 0.09
25 60 0.41
26 1 0.01
27 2 0.01
28 2 0.01
29 2 0.01
30 5 0.03
31 9 0.06
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.33
Consensus pattern (25 bp):
TATTAAAGATATATACATAATATAG
Found at i:18591 original size:30 final size:30
Alignment explanation
Indices: 18439--18583 Score: 254
Period size: 30 Copynumber: 4.8 Consensus size: 30
18429 ACAAGTGGTG
18439 GTGGAGCAAGTGTGGCTAGTGGAGTAGGTA
1 GTGGAGCAAGTGTGGCTAGTGGAGTAGGTA
18469 GTGGAGCAAGTGTGGCTAGTGGAGTAGGTA
1 GTGGAGCAAGTGTGGCTAGTGGAGTAGGTA
18499 GTGGAGCAAGTGTGGCTAGTGGAGTAGGTA
1 GTGGAGCAAGTGTGGCTAGTGGAGTAGGTA
* * * *
18529 GTGGAGTAAGTGTAGCTAGTGGAGTTGGTG
1 GTGGAGCAAGTGTGGCTAGTGGAGTAGGTA
18559 GTGGAGCAAGTGTGGCTAGTGGAGT
1 GTGGAGCAAGTGTGGCTAGTGGAGT
18584 TGGTGGTGAC
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 109 1.00
ACGTcount: A:0.22, C:0.06, G:0.47, T:0.25
Consensus pattern (30 bp):
GTGGAGCAAGTGTGGCTAGTGGAGTAGGTA
Found at i:19506 original size:123 final size:123
Alignment explanation
Indices: 19363--19614 Score: 470
Period size: 123 Copynumber: 2.0 Consensus size: 123
19353 GTTAGTCCAC
* *
19363 TAGTTCTCAGTTTGATTAGTTTGTTTGGTTCGATCAAATAAATTATAAAAACCCATAAAATTTTA
1 TAGTTCTCAGTTTGAGTAGTTTGTTTGGTTCGATCAAATAAATTATAAAAACCCATAAAA-TTAA
19428 A-AAAAATAGAGAAATTTGGTTCAACTGCTTTCTTTAGCTTGATTCAACCAGTCTATAT
65 ACAAAAATAGAGAAATTTGGTTCAACTGCTTTCTTTAGCTTGATTCAACCAGTCTATAT
19486 TAGTTCTCAGTTTGAGTAGTTTGTTTGGTTCGATCAAATAAATTATAAAAACCCATAAAATTAAA
1 TAGTTCTCAGTTTGAGTAGTTTGTTTGGTTCGATCAAATAAATTATAAAAACCCATAAAATTAAA
19551 CAAAAATAGAGAAATTTGGTTCAACTGCTTTCTTTAGCTTGATTCAACCAGTCTATAT
66 CAAAAATAGAGAAATTTGGTTCAACTGCTTTCTTTAGCTTGATTCAACCAGTCTATAT
19609 TAGTTC
1 TAGTTC
19615 ATGGATCAAT
Statistics
Matches: 126, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
122 4 0.03
123 122 0.97
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.38
Consensus pattern (123 bp):
TAGTTCTCAGTTTGAGTAGTTTGTTTGGTTCGATCAAATAAATTATAAAAACCCATAAAATTAAA
CAAAAATAGAGAAATTTGGTTCAACTGCTTTCTTTAGCTTGATTCAACCAGTCTATAT
Done.