Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_645
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: 53623
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:566 original size:72 final size:72
Alignment explanation
Indices: 346--1587 Score: 1007
Period size: 72 Copynumber: 16.4 Consensus size: 72
336 AGTATGTGAT
* *
346 CTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAGACAGAAATTGAAAATACCT
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAA-ACAGAAATTGAAATTACCT
*
411 CAGCATGTGAAC
64 CAGC--GTG-TC
* *
423 C-GAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTGAAAACAGAAATTGAAAATACCT
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAACAGAAATTGAAATTACCT
*
487 CAACGTGTC
64 CAGCGTGTC
* ** * *
496 TTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAATAGAAATTGAAATTACCTCA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCTCA
561 GCGTGT-
66 GCGTGTC
567 CTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCTC
1 CT-GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCTC
632 AGCGTGTC
65 AGCGTGTC
* * * *
640 CCGAGGCTCAACTCACCTATCACAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCTCA
705 GCGTGTC
66 GCGTGTC
*
712 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCTCA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCTCA
777 GCGTGTC
66 GCGTGTC
* * *
784 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTGAAAAACAAAAATTGAAAAT
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-----TTTTTG-AAAACAGAAATTGAAATT
*
849 ACCTCAGCATGTC
60 ACCTCAGCGTGTC
* ** *
862 TTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCTCA
927 GCGTGTC
66 GCGTGTC
** * *
934 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGGTTTTTTTTAACAACAGAAATTGAAAATTAC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTT-G-ATTTTTGAA-AACAGAAATTG-AAATTAC
*
999 CTCAACGTGTC
62 CTCAGCGTGTC
* * * *
1010 ATGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTGAAAAATATAAATTGAAA--AG
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTG-A--TTTTTG-AAAACAGAAATTGAAATTAC
** ***
1073 CAGAAATTGAAATTAC
62 CTCAGCGTG----T-C
* * * * * * * * **** * **
1089 CTCAACGTGCCTTGAGGCTCAACTCAC-C--TCTCGCAATATGA--GTTGATTTTTGACAAACAG
1 CT-GA-G-G-C-TCA-ACTCACCTCTCGCAATAT-G-AGT-TGATTTTTGA--AAACAGAAATTG
*
1149 AAATTGAAATTACATCAGCGTGTC
55 AAAT------TACCTCAGCGTGTC
* ** * * * * **
1173 TTGAGGCTCAACTCATTTCTCGTAATATGAGTTGATTTTTTGAAAA-ATAGATTGAAA-CACAAA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAACAGAAATTGAAATTAC-CT
* * *
1236 AATTGACAAT-AC
64 CA--G-C-GTGTC
* * *
1248 CTCAGTGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTG
1 CT--GAG-G-CTC-A---AC---TCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTG
1313 AAATTACCTCAGCGTGTC
55 AAATTACCTCAGCGTGTC
* * *
1331 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTGAAAAACAAAAATTGAAAAT
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-----TTTTTG-AAAACAGAAATTGAAATT
*
1396 ACCTCAGCATGTC
60 ACCTCAGCGTGTC
* ** * *
1409 TTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACATAAATTGAAATTACCTCA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCTCA
1474 GCGTGTC
66 GCGTGTC
** *
1481 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTAACAACAGAAATTGAAAATTAC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAA-AACAGAAATTG-AAATTAC
*
1546 CTCAGTGTGTC
62 CTCAGCGTGTC
1557 CTGAGGCTCAACTCACC-CATCGCAATATGAG
1 CTGAGGCTCAACTCACCTC-TCGCAATATGAG
1588 CAGAAATTGA
Statistics
Matches: 952, Mismatches: 136, Indels: 155
0.77 0.11 0.12
Matches are distributed among these distances:
71 3 0.00
72 415 0.44
73 13 0.01
74 52 0.05
75 27 0.03
76 148 0.16
77 39 0.04
78 140 0.15
79 11 0.01
80 8 0.01
81 18 0.02
82 5 0.01
83 7 0.01
84 9 0.01
85 21 0.02
86 30 0.03
87 2 0.00
89 4 0.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (72 bp):
CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCTCA
GCGTGTC
Found at i:902 original size:150 final size:144
Alignment explanation
Indices: 346--1979 Score: 1627
Period size: 150 Copynumber: 10.9 Consensus size: 144
336 AGTATGTGAT
* *
346 CTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAGACAGAAATTGAAAATACCT
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAA-ACAGAAATTGAAATTACCT
** *
411 CAGCATGTGAACCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTGAAAACAGAAAT
64 CAGC--GTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAACAGAAAT
* *
476 TGAAAATACCTCAACGTGTC
125 TGAAATTACCTCAGCGTGTC
* ** * *
496 TTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAATAGAAATTGAAATTACCTCA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCTCA
*
561 GCGTGTCTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAAT
66 GCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAAT
626 TACCTCAGCGTGTC
131 TACCTCAGCGTGTC
* * * *
640 CCGAGGCTCAACTCACCTATCACAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCTCA
705 GCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAAT
66 GCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAAT
770 TACCTCAGCGTGTC
131 TACCTCAGCGTGTC
* * *
784 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTGAAAAACAAAAATTGAAAAT
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-----TTTTTG-AAAACAGAAATTGAAATT
* ** ** *
849 ACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAAT
60 ACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAAT
914 TGAAATTACCTCAGCGTGTC
125 TGAAATTACCTCAGCGTGTC
** * *
934 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGGTTTTTTTTAACAACAGAAATTGAAAATTAC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTT-G-ATTTTTGAA-AACAGAAATTG-AAATTAC
* **
999 CTCAACGTGTCATGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTGAAAAATATAA
62 CTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG-A------T------T-T--
*
1064 ATTGAAAAGCAGAAATTGAAATTACCTCAACGTG-C
111 -TTGAAAA-CAGAAATTGAAATTACCTCAGCGTGTC
*
1099 CTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATTGAAATTACAT
1 C-TGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA-AAACAGAAATTGAAATTACCT
** ** *
1164 CAGCGTGTCTTGAGGCTCAACTCATTTCTCGTAATATGAGTTGATTTTTTGAAAAATAGATTGAA
64 CAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA----TT------T---TTGAA
* * *
1229 ACACAAAAATTGACAA-TACCTCAGTGTGCC
116 A-ACAGAAATTGA-AATTACCTCAGCGTGTC
*
1259 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCTCA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCTCA
*
1324 GCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTGAAAAACAAAAAT
66 GCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-----TTTTTG-AAAACAGAAAT
* *
1389 TGAAAATACCTCAGCATGTC
125 TGAAATTACCTCAGCGTGTC
* ** * *
1409 TTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACATAAATTGAAATTACCTCA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCTCA
* ** *
1474 GCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTAACAACAGAAATTGA
66 GCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAA-AACAGAAATTG-
*
1539 AAATTACCTCAGTGTGTC
127 AAATTACCTCAGCGTGTC
*
1557 CTGAGGCTCAACTCACC-CATCGC-A-AT-A--TGA-----G----CAGAAATTGAAAATACCTC
1 CTGAGGCTCAACTCACCTC-TCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCTC
* ** * * *
1607 AACGTGTCTTGAGGCTTAACTCACCTCTTGCAATATGAGTTGATTTTTGAAAA-ATAAATTGAAA
65 AGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAA
* *
1671 ATACCTCAGCGTGCC
130 TTACCTCAGCGTGTC
* *
1686 CTGAGGCTTAACTCACCT-TCGCAATATGAGTTGATTTTTGACAAACATAAATTGAAATTACCTC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA-AAACAGAAATTGAAATTACCTC
* * *
1750 AGCGTGTGACCTGAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTTTTTCAAAGACAGAA
65 AGCGTGT--CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA----TTTTTGAAA-ACAGAA
* *
1815 ATTGAAAATACCTCAACGTGTC
123 ATTGAAATTACCTCAGCGTGTC
* * *
1837 TTGAGGCTCAAC-CACCTCTCGTAATATGAGTTGATTTTTTGAAACATAAATTAAAACACAAAAA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTG------------AAA-ACAGAAA
** *
1901 TTGACAA-TACCTCAGCGTACCCCGAGGCTCAACTCACCTCTCGCAATATGAATTGATTTTTGAA
52 TTGA-AATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-A
*
1965 AAACATAAATTGAAA
115 AAACAGAAATTGAAA
1980 AATGGAAATC
Statistics
Matches: 1276, Mismatches: 123, Indels: 162
0.82 0.08 0.10
Matches are distributed among these distances:
128 4 0.00
129 32 0.03
130 9 0.01
131 3 0.00
132 7 0.01
133 3 0.00
134 54 0.04
138 2 0.00
143 26 0.02
144 204 0.16
145 33 0.03
146 42 0.03
147 34 0.03
148 100 0.08
149 24 0.02
150 285 0.22
151 52 0.04
152 6 0.00
153 1 0.00
154 1 0.00
158 76 0.06
159 78 0.06
160 10 0.01
161 1 0.00
162 35 0.03
163 48 0.04
164 39 0.03
165 13 0.01
166 54 0.04
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (144 bp):
CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCTCA
GCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAAT
TACCTCAGCGTGTC
Found at i:1158 original size:73 final size:73
Alignment explanation
Indices: 1065--1218 Score: 229
Period size: 73 Copynumber: 2.1 Consensus size: 73
1055 AAAATATAAA
*
1065 TTGAAAAGCAGAAATTGAAATTACCTCAACGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAGCAGAAATTGAAATTACATCAACGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGA
1130 GTTGATTT
66 GTTGATTT
* * ** *
1138 TTGACAAA-CAGAAATTGAAATTACATCAGCGTGTCTTGAGGCTCAACTCATTTCTCGTAATATG
1 TTGA-AAAGCAGAAATTGAAATTACATCAACGTGCCTTGAGGCTCAACTCACCTCTCGCAATATG
1202 AGTTGATTTT
65 AGTTGA-TTT
1212 TTGAAAA
1 TTGAAAA
1219 ATAGATTGAA
Statistics
Matches: 73, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
73 63 0.86
74 10 0.14
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (73 bp):
TTGAAAAGCAGAAATTGAAATTACATCAACGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTT
Found at i:1659 original size:59 final size:59
Alignment explanation
Indices: 1529--1645 Score: 166
Period size: 58 Copynumber: 2.0 Consensus size: 59
1519 TTTTTAACAA
**
1529 CAGAAATTGAAAATTACCTCAGTGTGTCCTGAGGCTCAACTCACCCATCGCAATATGAG
1 CAGAAATTGAAAATTACCTCAACGTGTCCTGAGGCTCAACTCACCCATCGCAATATGAG
* * *
1588 CAGAAATTGAAAA-TACCTCAACGTGTCTTGAGGCTTAACTCACCTC-TTGCAATATGAG
1 CAGAAATTGAAAATTACCTCAACGTGTCCTGAGGCTCAACTCACC-CATCGCAATATGAG
1646 TTGATTTTTG
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
58 38 0.73
59 14 0.27
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (59 bp):
CAGAAATTGAAAATTACCTCAACGTGTCCTGAGGCTCAACTCACCCATCGCAATATGAG
Found at i:2955 original size:18 final size:18
Alignment explanation
Indices: 2921--2954 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2911 CCCTCTCTCT
2921 TTTTCTTTTTCTTTTTTC
1 TTTTCTTTTTCTTTTTTC
2939 TTTTC-TTTTCTTTTTT
1 TTTTCTTTTTCTTTTTT
2955 TTAAGATGCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (18 bp):
TTTTCTTTTTCTTTTTTC
Found at i:12188 original size:18 final size:18
Alignment explanation
Indices: 12146--12239 Score: 70
Period size: 17 Copynumber: 5.1 Consensus size: 18
12136 GAAAAATAAG
*
12146 AATTTTT-AAAACACGGA
1 AATTTTTGAAAACACGAA
12163 AA-TTTTGAAAACACGAA
1 AATTTTTGAAAACACGAA
12180 AATTTTTG-AAAC-CTGAA
1 AATTTTTGAAAACAC-GAA
*
12197 TTTATTTTTTAGAAAAACACGAA
1 ---AATTTTT-G-AAAACACGAA
* *
12220 AAATTTTGGAAACACGAA
1 AATTTTTGAAAACACGAA
12238 AA
1 AA
12240 GTTTACAACA
Statistics
Matches: 62, Mismatches: 5, Indels: 19
0.72 0.06 0.22
Matches are distributed among these distances:
16 5 0.08
17 20 0.32
18 16 0.26
19 1 0.02
20 11 0.18
21 1 0.02
23 7 0.11
24 1 0.02
ACGTcount: A:0.48, C:0.11, G:0.12, T:0.30
Consensus pattern (18 bp):
AATTTTTGAAAACACGAA
Found at i:12810 original size:15 final size:17
Alignment explanation
Indices: 12790--12821 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
12780 TTAGGAATCG
12790 TACATAA-A-AAATATA
1 TACATAATATAAATATA
12805 TACATAATATAAATATA
1 TACATAATATAAATATA
12822 ATATATACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 1 0.07
17 7 0.47
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (17 bp):
TACATAATATAAATATA
Found at i:13363 original size:11 final size:11
Alignment explanation
Indices: 13329--13370 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
13319 AAATCATTTT
13329 GAAGAGAGAAA
1 GAAGAGAGAAA
* *
13340 GAA-AAAAAAA
1 GAAGAGAGAAA
*
13350 GAAGGGAGAAA
1 GAAGAGAGAAA
13361 GAAGAGAGAA
1 GAAGAGAGAA
13371 GGGAGGGGGG
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
10 8 0.33
11 16 0.67
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (11 bp):
GAAGAGAGAAA
Found at i:20604 original size:22 final size:21
Alignment explanation
Indices: 20571--20618 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
20561 TTTTTTCTAT
*
20571 TTTTTGAATTTTTGAATTATTA
1 TTTTTGAATTTTAGAATTA-TA
*
20593 TTTTT-AATTTTTAGATTTATA
1 TTTTTGAA-TTTTAGAATTATA
20614 TTTTT
1 TTTTT
20619 TAAAAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (21 bp):
TTTTTGAATTTTAGAATTATA
Found at i:20618 original size:21 final size:22
Alignment explanation
Indices: 20571--20618 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
20561 TTTTTTCTAT
20571 TTTTTGAATTTTTGAATTATTA
1 TTTTTGAATTTTTGAATTATTA
*
20593 TTTTT-AATTTTTAGATTTA-TA
1 TTTTTGAATTTTT-GAATTATTA
20614 TTTTT
1 TTTTT
20619 TAAAAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (22 bp):
TTTTTGAATTTTTGAATTATTA
Found at i:20770 original size:29 final size:30
Alignment explanation
Indices: 20736--20796 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 30
20726 TTTCCAATTT
*
20736 TTATATTTAT-TATTTTGAAATTTTA-AAAA
1 TTATATTTATATATTTAG-AATTTTATAAAA
20765 TTATATTTATATATTTAGAATTTTATAAAA
1 TTATATTTATATATTTAGAATTTTATAAAA
20795 TT
1 TT
20797 TTTAAAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 17 0.59
30 12 0.41
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (30 bp):
TTATATTTATATATTTAGAATTTTATAAAA
Found at i:22000 original size:33 final size:33
Alignment explanation
Indices: 21963--22030 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
21953 AGATTACTTT
*
21963 ATATTTTACATATCATTATATTAAATTATTTAA
1 ATATTTAACATATCATTATATTAAATTATTTAA
**
21996 ATATTTAATTTATCATTATATTAAATTATTTAA
1 ATATTTAACATATCATTATATTAAATTATTTAA
22029 AT
1 AT
22031 CTTATTTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (33 bp):
ATATTTAACATATCATTATATTAAATTATTTAA
Found at i:22003 original size:17 final size:16
Alignment explanation
Indices: 21980--22030 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
21970 ACATATCATT
21980 ATATTAAATTATTTAA
1 ATATTAAATTATTTAA
*
21996 ATATTTAATTTATCATT--
1 ATA-TTAAATTAT--TTAA
22013 ATATTAAATTATTTAA
1 ATATTAAATTATTTAA
22029 AT
1 AT
22031 CTTATTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 10
0.70 0.05 0.25
Matches are distributed among these distances:
14 2 0.07
16 13 0.46
17 11 0.39
19 2 0.07
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (16 bp):
ATATTAAATTATTTAA
Found at i:22017 original size:25 final size:29
Alignment explanation
Indices: 21989--22046 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 29
21979 TATATTAAAT
21989 TATTTAAA-TATTT-AAT-TTA-TCATTA
1 TATTTAAATTATTTAAATCTTATTCATTA
*
22014 TA-TTAAATTATTTAAATCTTATTTATTA
1 TATTTAAATTATTTAAATCTTATTCATTA
22042 TATTT
1 TATTT
22047 GATTTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
24 5 0.19
25 7 0.26
26 3 0.11
27 3 0.11
28 7 0.26
29 2 0.07
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (29 bp):
TATTTAAATTATTTAAATCTTATTCATTA
Found at i:22019 original size:16 final size:16
Alignment explanation
Indices: 21973--22024 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
21963 ATATTTTACA
21973 TATCATTATATTAAAT
1 TATCATTATATTAAAT
*
21989 TAT--TTAAATATTTAATT
1 TATCATT--ATA-TTAAAT
22006 TATCATTATATTAAAT
1 TATCATTATATTAAAT
22022 TAT
1 TAT
22025 TTAAATCTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
14 2 0.07
16 14 0.48
17 11 0.38
19 2 0.07
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (16 bp):
TATCATTATATTAAAT
Found at i:24966 original size:28 final size:28
Alignment explanation
Indices: 24926--25079 Score: 265
Period size: 28 Copynumber: 5.5 Consensus size: 28
24916 TAAATTGTAC
24926 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
24954 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
24982 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
25010 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
* *
25038 AGCACTAAGTGTGCAAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
25065 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
25080 GACTTAATAT
Statistics
Matches: 122, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
27 23 0.19
28 99 0.81
ACGTcount: A:0.27, C:0.12, G:0.28, T:0.34
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATGT
Found at i:24992 original size:56 final size:56
Alignment explanation
Indices: 24901--25079 Score: 270
Period size: 56 Copynumber: 3.2 Consensus size: 56
24891 GAGATTGGCG
* * * *
24901 CTAAGTGTGCGGGTTTAAATTGTACAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
*
24958 CTAAGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
* *
25014 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCAAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
*
25069 CTGAGTGTGCG
1 CTAAGTGTGCG
25080 GACTTAATAT
Statistics
Matches: 113, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
55 23 0.20
56 75 0.66
57 15 0.13
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34
Consensus pattern (56 bp):
CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
Found at i:33061 original size:28 final size:28
Alignment explanation
Indices: 33021--33173 Score: 256
Period size: 28 Copynumber: 5.5 Consensus size: 28
33011 TAAATTGTAC
33021 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
33049 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
33077 AGCACT-AGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
33104 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
* *
33132 AGCACTAAGTGTGCAAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
33159 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
33174 GACTTAATAT
Statistics
Matches: 120, Mismatches: 4, Indels: 3
0.94 0.03 0.02
Matches are distributed among these distances:
27 50 0.42
28 70 0.58
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATGT
Found at i:33093 original size:55 final size:56
Alignment explanation
Indices: 32996--33173 Score: 261
Period size: 55 Copynumber: 3.2 Consensus size: 56
32986 GAGATTGGCG
* * * *
32996 CTAAGTGTGCGGGTTTAAATTGTACAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
*
33053 CTAAGTGTGCGAGTTTGATTATGTAGCACT-AGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
* *
33108 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCAAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
*
33163 CTGAGTGTGCG
1 CTAAGTGTGCG
33174 GACTTAATAT
Statistics
Matches: 111, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
55 77 0.69
56 19 0.17
57 15 0.14
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34
Consensus pattern (56 bp):
CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
Found at i:33170 original size:83 final size:83
Alignment explanation
Indices: 33021--33173 Score: 263
Period size: 83 Copynumber: 1.8 Consensus size: 83
33011 TAAATTGTAC
* * *
33021 AGCACTAAGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAGTTTGATTATGTAGCACTAGT
1 AGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCAAGTTTGATTATATAGCACTAGT
33086 GTGCGAGTTTGATTATGT
66 GTGCGAGTTTGATTATGT
33104 AGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCAAG-TTGATTATATAGCACTGAG
1 AGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCAAGTTTGATTATATAGCACT-AG
33168 TGTGCG
65 TGTGCG
33174 GACTTAATAT
Statistics
Matches: 66, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
82 15 0.23
83 51 0.77
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34
Consensus pattern (83 bp):
AGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCAAGTTTGATTATATAGCACTAGT
GTGCGAGTTTGATTATGT
Found at i:41054 original size:16 final size:17
Alignment explanation
Indices: 41008--41055 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
40998 TTAACCAATT
**
41008 ATTATAATTAATTAATTA
1 ATTA-AATTAATTTTTTA
41026 ATTAAATTAATTTTTTA
1 ATTAAATTAATTTTTTA
41043 ATTAAA-TAATTTT
1 ATTAAATTAATTTT
41056 CTCAATCCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.25
17 17 0.61
18 4 0.14
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTAAATTAATTTTTTA
Found at i:46079 original size:4 final size:4
Alignment explanation
Indices: 46070--46107 Score: 58
Period size: 4 Copynumber: 9.0 Consensus size: 4
46060 AAGTTTTATT
46070 TTTA TTTA TTTA TTTA TTTA TTTA TTTTA TTTA GTTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA -TTTA
46108 AATTTTTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
4 24 0.75
5 8 0.25
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:46087 original size:12 final size:13
Alignment explanation
Indices: 46064--46107 Score: 63
Period size: 12 Copynumber: 3.3 Consensus size: 13
46054 GTTGTAAAGT
46064 TTTATTTTTATTTA
1 TTTA-TTTTATTTA
46078 TTTA-TTTATTTA
1 TTTATTTTATTTA
46090 TTTATTTTATTTA
1 TTTATTTTATTTA
46103 GTTTA
1 -TTTA
46108 AATTTTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
12 12 0.43
13 8 0.29
14 8 0.29
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:46115 original size:26 final size:26
Alignment explanation
Indices: 46064--46116 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
46054 GTTGTAAAGT
*
46064 TTTATTTTTATTTATTTATTTATTTA
1 TTTATTTTTATTTATTTAATTATTTA
46090 TTTA-TTTTATTTAGTTTAAATT-TTTA
1 TTTATTTTTATTTA-TTT-AATTATTTA
46116 T
1 T
46117 ATTCAGTCCA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 9 0.38
26 12 0.50
27 3 0.12
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.74
Consensus pattern (26 bp):
TTTATTTTTATTTATTTAATTATTTA
Found at i:47012 original size:20 final size:20
Alignment explanation
Indices: 46987--47024 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
46977 ATTGAGCCAG
46987 AAATATTTTTATAAATATGT
1 AAATATTTTTATAAATATGT
47007 AAATATTTTTATAAATAT
1 AAATATTTTTATAAATAT
47025 TTACAGAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
AAATATTTTTATAAATATGT
Found at i:49145 original size:79 final size:82
Alignment explanation
Indices: 49034--49218 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
49024 GCTACTCGTT
* * *
49034 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
49097 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
49114 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
49177 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
49194 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
49219 CATCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:49218 original size:40 final size:40
Alignment explanation
Indices: 49015--49218 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
49005 CGGAATTTAA
** *
49015 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
49055 CCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
49095 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
49134 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
49174 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
49214 CCGGA
1 CCGGA
49219 CATCATTCAA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.24
40 92 0.66
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Done.