Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1622
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: 28274
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Found at i:10515 original size:14 final size:13
Alignment explanation
Indices: 10496--10531 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 13
10486 CCTTGAGGTA
10496 TTTTCAAACTTCTG
1 TTTTCAAA-TTCTG
10510 TTTTCAGAATTCTG
1 TTTTCA-AATTCTG
10524 TTTTCAAA
1 TTTTCAAA
10532 AAATCAACTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.10
14 17 0.81
15 2 0.10
ACGTcount: A:0.25, C:0.17, G:0.08, T:0.50
Consensus pattern (13 bp):
TTTTCAAATTCTG
Found at i:11151 original size:94 final size:88
Alignment explanation
Indices: 10994--11400 Score: 370
Period size: 85 Copynumber: 4.6 Consensus size: 88
10984 CGGTTGTGAC
*
10994 GAGGCTCAACTCACCTCTCGTAATATGAGTTGA-TTTTTGCAAAGCATAAATT-AAAAAATAAAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTG-AAA-CA-AAATTGAAAAAA-AAAA
11057 ATCAATTGGAAAATACCTC-GCGTGTTGATCT
62 A--AATT-GAAAATACCTCAGCGTG-TG-TCT
11088 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAAACAAAATTGAAAAAAAAAAG
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTG--AAACAAAATTGAAAAAAAAAA-
* *
11153 AAATTG-AAATATCTCAGCGTGTCT-T
62 AAATTGAAAATACCTCAGCGTGTGTCT
* *
11178 GAGGCT-AACTCACCTCTCGCAATATGAGTTGATTTTTTGAAACAAAAATTTG---AAAAACAGA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAC-AAAA-TTGAAAAAAAAAAAA
*
11239 ATTGAAAATACCTCAGCGTGAGTC-
64 ATTGAAAATACCTCAGCGTGTGTCT
* * * *
11263 AAGGCTCAACTCACCACTCGCAATATGAGCTGATTTTTTTGAAACACAAAATTG-----AAAACA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTG-AA-ACAAAATTGAAAAAAAAAAA
*
11323 AA-TGAAAATCACCTCA--G-GTCT-T
63 AATTGAAAAT-ACCTCAGCGTGTGTCT
*
11345 GAGG-TCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAACAGAATTGAAAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTGAAACAAAATTGAAAA
11401 TACCTCAGTG
Statistics
Matches: 272, Mismatches: 20, Indels: 52
0.79 0.06 0.15
Matches are distributed among these distances:
80 8 0.03
81 28 0.10
82 13 0.05
83 1 0.00
84 12 0.04
85 37 0.14
86 28 0.10
87 14 0.05
88 16 0.06
89 28 0.10
90 7 0.03
91 1 0.00
92 9 0.03
93 6 0.02
94 36 0.13
95 9 0.03
96 15 0.06
97 4 0.01
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.29
Consensus pattern (88 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAACAAAATTGAAAAAAAAAAAAAT
TGAAAATACCTCAGCGTGTGTCT
Found at i:11205 original size:89 final size:88
Alignment explanation
Indices: 10994--11400 Score: 393
Period size: 94 Copynumber: 4.6 Consensus size: 88
10984 CGGTTGTGAC
* *
10994 GAGGCTCAACTCACCTCTCGTAATATGAGTTGA--TTTTTGCAAAGCATAAATTAAAAAATAAAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG-AAA-CA-AAATTGAAAAA-AAAA
* *
11057 ATCAATTGGAAAATACCTC-GCGTGTTGATCT
62 A-GAATT-GAAAATACCTCAGCGTG-T-CT-T
11088 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAAACAAAATTGAAAAAAAAAAG
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG--AAACAAAATTGAAAAAAAAAAG
*
11153 AAATTG-AAATATCTCAGCGTGTCTT
64 -AATTGAAAATACCTCAGCGTGTCTT
*
11178 GAGGCT-AACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAACAAAAATTTG---AAAAACAG
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAC-AAAA-TTGAAAAAAAAAAG
** *
11238 AATTGAAAATACCTCAGCGTGAGTC
64 AATTGAAAATACCTCAGCGTGTCTT
* * * *
11263 AAGGCTCAACTCACCACTCGCAATATGAGCTGATTTTTTTGAAACACAAAATTG----AAAACA-
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG-AA-ACAAAATTGAAAAAAAAAAG
11323 AA-TGAAAATCACCTCA--G-GTCTT
64 AATTGAAAAT-ACCTCAGCGTGTCTT
*
11345 GAGG-TCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAACAGAATTGAAAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTGAAACAAAATTGAAAA
11401 TACCTCAGTG
Statistics
Matches: 275, Mismatches: 20, Indels: 46
0.81 0.06 0.13
Matches are distributed among these distances:
80 8 0.03
81 28 0.10
82 13 0.05
83 1 0.00
84 12 0.04
85 35 0.13
86 34 0.12
87 14 0.05
88 16 0.06
89 28 0.10
90 7 0.03
91 1 0.00
92 9 0.03
93 6 0.02
94 41 0.15
95 10 0.04
96 8 0.03
97 4 0.01
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.29
Consensus pattern (88 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAACAAAATTGAAAAAAAAAAGAA
TTGAAAATACCTCAGCGTGTCTT
Found at i:11299 original size:175 final size:176
Alignment explanation
Indices: 10994--11382 Score: 455
Period size: 175 Copynumber: 2.2 Consensus size: 176
10984 CGGTTGTGAC
* *
10994 GAGGCTCAACTCACCTCTCGTAATATGAGTTGA-TTTTTGCAAAGCATAAATTAAAAAATAAAAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGCAAAGCAAAAATT-AAAAATAAAAA
* * * *
11058 TCAATTGGAAAATACCTCGCGTGTTGATCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
65 TCAATTGGAAAATACCTCGCGTGTAGATCTAAGGCTCAACTCACCACTCGCAATATGAGCTGATT
*
11123 TTTTTGACAA-ACAAAATTGAAAAAAAAAAGAAATTGAAAT-ATCTCAGCGTGTCTT
130 TTTTTGA-AACACAAAATTG-AAAAAAAAAG--A---AAATCACCTCA--G-GTCTT
** *
11178 GAGGCT-AACTCACCTCTCGCAATATGAGTTGATTTTTTG-AAA-CAAAAATT-TGAA-AAACA-
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGCAAAGCAAAAATTAAAAATAAAAAT
*
11237 GAATT-GAAAATACCTCAGCGTG-AG-TC-AAGGCTCAACTCACCACTCGCAATATGAGCTGATT
66 CAATTGGAAAATACCTC-GCGTGTAGATCTAAGGCTCAACTCACCACTCGCAATATGAGCTGATT
* *
11298 TTTTTGAAACACAAAATTGAAAACAAATGAAAATCACCTCAGGTCTT
130 TTTTTGAAACACAAAATTGAAAAAAAAAGAAAATCACCTCAGGTCTT
11345 GAGG-TCAACTCACCTCTCGCAATATGAGTTGATTTTTT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
11383 TTGAAACAGA
Statistics
Matches: 187, Mismatches: 13, Indels: 27
0.82 0.06 0.12
Matches are distributed among these distances:
166 1 0.01
167 41 0.22
168 1 0.01
169 4 0.02
170 5 0.03
172 1 0.01
174 10 0.05
175 48 0.26
176 2 0.01
177 12 0.06
178 9 0.05
179 4 0.02
180 2 0.01
182 7 0.04
183 28 0.15
184 12 0.06
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.29
Consensus pattern (176 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGCAAAGCAAAAATTAAAAATAAAAAT
CAATTGGAAAATACCTCGCGTGTAGATCTAAGGCTCAACTCACCACTCGCAATATGAGCTGATTT
TTTTGAAACACAAAATTGAAAAAAAAAGAAAATCACCTCAGGTCTT
Found at i:11579 original size:71 final size:73
Alignment explanation
Indices: 11314--12265 Score: 1263
Period size: 73 Copynumber: 13.3 Consensus size: 73
11304 AAACACAAAA
11314 TTGAAAAC--AAA-TGAAAATCACCTCA-G-GTCTTGAGG-TCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAAAT-ACCTCACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAG
11373 TTGATTTTTT
65 TTGA-TTTTT
*
11383 TTG-AAACAG-AATTGAAAATACCTCA-GTGTC-TGAGGCTCAACTCACCTCTCGTAATATGAGT
1 TTGAAAACAGAAATTGAAAATACCTCACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGT
11444 TGA-TTTT
66 TGATTTTT
* *
11451 TTGAAAACAAAAATTGAAAATACCTCA-GCGTCTTGAGGCTTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAAATACCTCACGTGTCTTGAGGC-TCAACTCACCTCTCGCAATATGAG
11515 TTGATTTTT
65 TTGATTTTT
*
11524 TTGAAAA-AGAAATTGAAAATA-CTCACGTGTCTTGAGGTTCAACTCACCTCTCGCAATATGAGT
1 TTGAAAACAGAAATTGAAAATACCTCACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGT
11587 TGA-TTTT
66 TGATTTTT
11594 TT-AAAACA-AAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAAATACCTCA-CGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAG
11657 -TGA-TTTT
65 TTGATTTTT
* *
11664 TTGAAAAAAAAAATTG-AAATACCTCAGCGTGTC-TGAGG--CAACTCACCTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAAATACCTCA-CGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAG
*
11725 CTGATTTTT
65 TTGATTTTT
11734 TTG---ACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAAATACCTC-ACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAG
11796 TTGA--TTT
65 TTGATTTTT
* * * * *
11803 TTGACAAACAAAAATTGAAATTACCTCA-GCGTCTTGAGGTTCAACTCACCTATCGCAATATGAG
1 TTGA-AAACAGAAATTGAAAATACCTCACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAG
11867 TTGATTTTT
65 TTGATTTTT
*
11876 TTGAAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGTTCAACTCACCTCTCGCAATATGA
1 TTG-AAAACAGAAATTGAAAATACCTC-ACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
*
11941 GCTGATTTTT
64 GTTGATTTTT
11951 TT-AAAGACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAA-ACAGAAATTGAAAATACCTC-ACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
12015 GTTGA--TTT
64 GTTGATTTTT
* * * *
12023 TTGACAAACAAAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTATCGCAATATGA
1 TTGA-AAACAGAAATTGAAAATACCTCA-CGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
12088 GTTGATTTTT
64 GTTGATTTTT
*
12098 TTGAAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTTGCAATATGA
1 TTG-AAAACAGAAATTGAAAATACCTC-ACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
*
12163 GTTGA--GTT
64 GTTGATTTTT
* * * *
12171 TTGACAAACAAAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACTTCTCGCAATATGA
1 TTGA-AAACAGAAATTGAAAATACCTCA-CGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
12236 GTTGATTTTT
64 GTTGATTTTT
* *
12246 TT-AGAAACATAAATTAAAAA
1 TTGA-AAACAGAAATTGAAAA
12266 AACGAAAATT
Statistics
Matches: 795, Mismatches: 44, Indels: 83
0.86 0.05 0.09
Matches are distributed among these distances:
67 8 0.01
68 49 0.06
69 53 0.07
70 89 0.11
71 159 0.20
72 65 0.08
73 179 0.23
74 79 0.10
75 112 0.14
76 2 0.00
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (73 bp):
TTGAAAACAGAAATTGAAAATACCTCACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGT
TGATTTTT
Found at i:12158 original size:148 final size:147
Alignment explanation
Indices: 11314--12332 Score: 1303
Period size: 148 Copynumber: 7.0 Consensus size: 147
11304 AAACACAAAA
11314 TTGAAAAC--AAA-TGAAAATCACCTCA--G-GTCTTGAGG-TCAACTCACCTCTCGCAATATGA
1 TTGAAAACAAAAATTGAAAAT-ACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
11372 GTTGATTTTTTTTG--AAACAG-AATTGAAAATACCTC-A-GTGTC-TGAGGCTCAACTCACCTC
65 GTTGA-TTTTTTTGAAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTC
*
11431 TCGTAATATGAGTTGATTTT
129 TCGCAATATGAGTTGA-TTT
11451 TTGAAAACAAAAATTGAAAATACCTCAGC--GTCTTGAGGCTTCAACTCACCTCTCGCAATATGA
1 TTGAAAACAAAAATTGAAAATACCTCAGCGTGTCTTGAGGC-TCAACTCACCTCTCGCAATATGA
*
11514 GTTGATTTTTTTG-AAAA-AGAAATTGAAAATA-CTC-ACGTGTCTTGAGGTTCAACTCACCTCT
65 GTTGATTTTTTTGAAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCT
11575 CGCAATATGAGTTGATTT
130 CGCAATATGAGTTGATTT
*
11593 TTTAAAAC-AAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAAAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAG
* *
11657 -TGA-TTTTTTGAAAAA-AAAAATTG-AAATACCTCAGCGTGTC-TGAGG--CAACTCACCTCTC
66 TTGATTTTTTTGAAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTC
*
11715 GCAATATGAGCTGATTT
131 GCAATATGAGTTGATTT
*** * *
11732 TT-TTGACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAAAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAG
* * * * * *
11796 TTGA--TTTTTGACAAACAAAAATTGAAATTACCTC-A-GCGTCTTGAGGTTCAACTCACCTATC
66 TTGATTTTTTTGAAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTC
11857 GCAATATGAGTTGATTTTT
131 GCAATATGAGTTGA--TTT
* * *
11876 TTGAAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGTTCAACTCACCTCTCGCAATATGA
1 TTG-AAAACAAAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
* *
11941 GCTGATTTTTTT-AAAGACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCT
65 GTTGATTTTTTTGAAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCT
12005 CGCAATATGAGTTGATTT
130 CGCAATATGAGTTGATTT
* * *
12023 TTGACAAACAAAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTATCGCAATATGA
1 TTGA-AAACAAAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
12088 GTTGATTTTTTTGAAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCT
65 GTTGATTTTTTTGAAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCT
* *
12153 TGCAATATGAGTTGAGTT
130 CGCAATATGAGTTGATTT
* * *
12171 TTGACAAACAAAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACTTCTCGCAATATGA
1 TTGA-AAACAAAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
* * *
12236 GTTGATTTTTTTAGAAACATAAATTAAAAAAACGAAAATTGAAAATACCTCAGCGTGTCCTGAGG
65 GTTGATTTTTTT-G-----------AAAAACA-G-AAATTGAAAATACCTCAACGTGTCTTGAGG
12301 CTCAACTCACCTCTCGCAATATGAGTTGATTT
116 CTCAACTCACCTCTCGCAATATGAGTTGATTT
12333 GAAAAGCAGA
Statistics
Matches: 789, Mismatches: 46, Indels: 69
0.87 0.05 0.08
Matches are distributed among these distances:
137 8 0.01
138 2 0.00
139 108 0.14
140 44 0.06
141 64 0.08
142 112 0.14
143 42 0.05
144 5 0.01
146 62 0.08
147 91 0.12
148 148 0.19
149 38 0.05
160 6 0.01
161 1 0.00
162 58 0.07
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (147 bp):
TTGAAAACAAAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAG
TTGATTTTTTTGAAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTC
GCAATATGAGTTGATTT
Found at i:12470 original size:14 final size:13
Alignment explanation
Indices: 12435--12479 Score: 72
Period size: 13 Copynumber: 3.4 Consensus size: 13
12425 TTGATTTTTG
12435 AAAAACAGAAATT
1 AAAAACAGAAATT
*
12448 AAAAGCAGAAATT
1 AAAAACAGAAATT
12461 GAAAAACAGAAATT
1 -AAAAACAGAAATT
12475 AAAAA
1 AAAAA
12480 TACCTCGGCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 17 0.59
14 12 0.41
ACGTcount: A:0.69, C:0.07, G:0.11, T:0.13
Consensus pattern (13 bp):
AAAAACAGAAATT
Found at i:12500 original size:100 final size:101
Alignment explanation
Indices: 12263--12622 Score: 450
Period size: 100 Copynumber: 3.7 Consensus size: 101
12253 CATAAATTAA
*
12263 AAAAAC-GAAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
1 AAAAACAG-AAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
* * * *
12327 TGA--TTTGAAAAGCAGAATTTGTAAGGCAAAAATTG
65 TGATTTTTGAAAAGCAGAAATTGAAAAGCAGAAATTG
12362 AAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
1 AAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
*
12427 GATTTTTGAAAAACAGAAATT-AAAAGCAGAAATTG
66 GATTTTTGAAAAGCAGAAATTGAAAAGCAGAAATTG
* * * *
12462 AAAAACAGAAATTAAAAATACCTCGGCGTGCCCCGAGGCTCAGCTCACCTCTCGCAATATGAGTT
1 AAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
*
12527 GATTTTTGAAAAGCATAAATT--------G--A---
66 GATTTTTGAAAAGCAGAAATTGAAAAGCAGAAATTG
* *
12550 AAAAAC-GAAATTGAAAATACCTCAGCGTGTGACCTGAGGCCCAACTCACCTCTCGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGC--GTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAG
12614 TTGATTTTT
64 TTGATTTTT
12623 TTGAAAGATA
Statistics
Matches: 238, Mismatches: 18, Indels: 20
0.86 0.07 0.07
Matches are distributed among these distances:
87 18 0.08
88 6 0.03
89 41 0.17
91 1 0.00
93 1 0.00
99 64 0.27
100 92 0.39
101 15 0.06
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (101 bp):
AAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
GATTTTTGAAAAGCAGAAATTGAAAAGCAGAAATTG
Found at i:12642 original size:89 final size:88
Alignment explanation
Indices: 12448--12622 Score: 237
Period size: 89 Copynumber: 2.0 Consensus size: 88
12438 AACAGAAATT
* * * * *
12448 AAAAGCAGAAATTG-AAAAACAGAAATTAAAAATACCTCGGCGTGCCCCGAGGCTCAGCTCACCT
1 AAAAGCATAAAATGAAAAAACAGAAATTAAAAATACCTCGGCGTGACCCGAGGCCCAACTCACCT
12512 CTCGCAATATGAGTTGATTTTTG
66 CTCGCAATATGAGTTGATTTTTG
* * * *
12535 AAAAGCATAAATTGAAAAAAC-GAAATTGAAAATACCTCAGCGTGTGACCTGAGGCCCAACTCAC
1 AAAAGCATAAAATGAAAAAACAGAAATTAAAAATACCTC-G-GCGTGACCCGAGGCCCAACTCAC
12599 CTCTCGCAATATGAGTTGATTTTT
64 CTCTCGCAATATGAGTTGATTTTT
12623 TTGAAAGATA
Statistics
Matches: 78, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
87 29 0.37
88 7 0.09
89 42 0.54
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.24
Consensus pattern (88 bp):
AAAAGCATAAAATGAAAAAACAGAAATTAAAAATACCTCGGCGTGACCCGAGGCCCAACTCACCT
CTCGCAATATGAGTTGATTTTTG
Found at i:24689 original size:25 final size:23
Alignment explanation
Indices: 24637--24691 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
24627 TATAAATAGT
24637 AATAGTGTTAGAAATATACTATA
1 AATAGTGTTAGAAATATACTATA
* *
24660 TATAGTGTTTGAAGTATATAC-ATAA
1 AATAGTGTTAGAA--ATATACTAT-A
24685 AATAGTG
1 AATAGTG
24692 AAAATATAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 11 0.42
24 2 0.08
25 13 0.50
ACGTcount: A:0.44, C:0.04, G:0.16, T:0.36
Consensus pattern (23 bp):
AATAGTGTTAGAAATATACTATA
Found at i:24806 original size:21 final size:21
Alignment explanation
Indices: 24782--24821 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
24772 ATAGTGTAAA
*
24782 AAATACATACATAATATAATT
1 AAATACATACATAAGATAATT
*
24803 AAATATATACATAAGATAA
1 AAATACATACATAAGATAA
24822 CATGTAGAAA
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:0.60, C:0.07, G:0.03, T:0.30
Consensus pattern (21 bp):
AAATACATACATAAGATAATT
Found at i:24812 original size:25 final size:25
Alignment explanation
Indices: 24754--24815 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
24744 ATAGATATAA
** *
24754 AAAAAATATGTACATAATATAGTGT
1 AAAAAATACATACATAATATAATGT
24779 AAAAAATACATACATAATATAAT-T
1 AAAAAATACATACATAATATAATGT
*
24803 AAATATATACATA
1 AAA-AAATACATA
24816 AGATAACATG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 4 0.12
25 28 0.88
ACGTcount: A:0.58, C:0.06, G:0.05, T:0.31
Consensus pattern (25 bp):
AAAAAATACATACATAATATAATGT
Found at i:24863 original size:23 final size:23
Alignment explanation
Indices: 24837--24964 Score: 59
Period size: 23 Copynumber: 5.5 Consensus size: 23
24827 AGAAAAAAAA
24837 ATATAAATAATATAGTATTAAAG
1 ATATAAATAATATAGTATTAAAG
* *
24860 ATATATACATAAAATAGTA-TAATAT
1 ATATA-A-ATAATATAGTATTAA-AG
** * *
24885 ATATACGTAATATAGAATT-TAG
1 ATATAAATAATATAGTATTAAAG
** *
24907 AATATACCTAATATA-T-TAAAAG
1 -ATATAAATAATATAGTATTAAAG
* * *
24929 AATATATATATATATAATATTAAAA
1 -ATATAAATA-ATATAGTATTAAAG
24954 ATAT-AATAATA
1 ATATAAATAATA
24965 ACAAAAAAAA
Statistics
Matches: 79, Mismatches: 17, Indels: 19
0.69 0.15 0.17
Matches are distributed among these distances:
21 1 0.01
22 14 0.18
23 34 0.43
24 10 0.13
25 20 0.25
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.36
Consensus pattern (23 bp):
ATATAAATAATATAGTATTAAAG
Found at i:25277 original size:16 final size:16
Alignment explanation
Indices: 25239--25277 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
25229 TCTCCAAAAA
*
25239 AAAAACTAGCCTCTCC
1 AAAAACTAGCCTCTAC
*
25255 AAAAACTAGCCTTTAC
1 AAAAACTAGCCTCTAC
*
25271 AATAACT
1 AAAAACT
25278 CTCTCCTTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.44, C:0.28, G:0.05, T:0.23
Consensus pattern (16 bp):
AAAAACTAGCCTCTAC
Found at i:25458 original size:18 final size:18
Alignment explanation
Indices: 25435--25488 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
25425 TACAAGTGTG
25435 GTGGAGCAAGTGTGGCTA
1 GTGGAGCAAGTGTGGCTA
*
25453 GTGGAG-TAG-GT-G---
1 GTGGAGCAAGTGTGGCTA
25465 GTGGAGCAAGTGTGGCTA
1 GTGGAGCAAGTGTGGCTA
25483 GTGGAG
1 GTGGAG
25489 TTGGTGTGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 12
0.67 0.05 0.29
Matches are distributed among these distances:
12 6 0.21
13 2 0.07
14 2 0.07
15 2 0.07
16 2 0.07
17 2 0.07
18 12 0.43
ACGTcount: A:0.20, C:0.07, G:0.50, T:0.22
Consensus pattern (18 bp):
GTGGAGCAAGTGTGGCTA
Found at i:25467 original size:30 final size:30
Alignment explanation
Indices: 25432--25512 Score: 132
Period size: 30 Copynumber: 2.8 Consensus size: 30
25422 AGGTACAAGT
25432 GTGGTGGAGCAAGTGTGGCTAGTGGAGTAG
1 GTGGTGGAGCAAGTGTGGCTAGTGGAGTAG
*
25462 GTGGTGGAGCAAGTGTGGCTAGTGGAGTTG
1 GTGGTGGAGCAAGTGTGGCTAGTGGAGTAG
25492 GT-GT-GAGC-AGTGTGGCTAGTG
1 GTGGTGGAGCAAGTGTGGCTAGTG
25513 TGGCAAAGGC
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
27 13 0.26
28 4 0.08
29 2 0.04
30 31 0.62
ACGTcount: A:0.17, C:0.07, G:0.49, T:0.26
Consensus pattern (30 bp):
GTGGTGGAGCAAGTGTGGCTAGTGGAGTAG
Found at i:26964 original size:50 final size:50
Alignment explanation
Indices: 26840--27088 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
26830 GATAATAACA
* * ** * *
26840 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
26891 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
26941 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
26991 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
27046 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
27089 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:27018 original size:100 final size:104
Alignment explanation
Indices: 26839--27088 Score: 357
Period size: 100 Copynumber: 2.4 Consensus size: 104
26829 TGATAATAAC
**
26839 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
26904 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
26941 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
27004 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
27046 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
27089 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:27205 original size:12 final size:12
Alignment explanation
Indices: 27183--27213 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
27173 GCTTGGATCA
27183 TCATCAAATAAAT
1 TCAT-AAATAAAT
27196 TCATAAATAAAT
1 TCATAAATAAAT
27208 TCATAA
1 TCATAA
27214 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 14 0.78
13 4 0.22
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (12 bp):
TCATAAATAAAT
Found at i:27458 original size:30 final size:29
Alignment explanation
Indices: 27423--27479 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
27413 CCTCGACTCT
*
27423 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTAC-ATTTTGCCCCTA
*
27453 AACTTTTACATAATTACATTTTGCCCC
1 AACTTTTACAAAATTACATTTTGCCCC
27480 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.40
Consensus pattern (29 bp):
AACTTTTACAAAATTACATTTTGCCCCTA
Done.