Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003260.1 Hibiscus syriacus cultivar Beakdansim tig00006850_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: 203219
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
File 2 of 2
Found at i:162982 original size:29 final size:29
Alignment explanation
Indices: 162917--162983 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
162907 AACAACCTAT
* * * * *
162917 CAATTTTCCAGAATTTACGAATTTATCCT
1 CAATTTTTCAAAACTTACGAAATTATCCA
* *
162946 CAACTTTTCAAAACTTACGAAATTGTCCA
1 CAATTTTTCAAAACTTACGAAATTATCCA
162975 CAATTTTTC
1 CAATTTTTC
162984 TAAGGCTTGT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.39
Consensus pattern (29 bp):
CAATTTTTCAAAACTTACGAAATTATCCA
Found at i:163810 original size:30 final size:30
Alignment explanation
Indices: 163776--163839 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 30
163766 AAAATTACAT
*
163776 TTTGATC-CCTAAACTTT-CCAAAGTTTATAC
1 TTTGATCACC-AAACTTTACCAAA-TTTATAA
163806 TTTGATCACCAAACTTTACCAAATTTATAA
1 TTTGATCACCAAACTTTACCAAATTTATAA
163836 TTTG
1 TTTG
163840 GTCATTAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 24 0.77
31 7 0.23
ACGTcount: A:0.33, C:0.20, G:0.06, T:0.41
Consensus pattern (30 bp):
TTTGATCACCAAACTTTACCAAATTTATAA
Found at i:168246 original size:18 final size:18
Alignment explanation
Indices: 168212--168247 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
168202 CAACCCGATT
*
168212 CGACCGTTGACTATTGAC
1 CGACCGTTGACCATTGAC
*
168230 CGACCGTTGACCGTTGAC
1 CGACCGTTGACCATTGAC
168248 TTTGTCTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.31, G:0.25, T:0.25
Consensus pattern (18 bp):
CGACCGTTGACCATTGAC
Found at i:177410 original size:30 final size:28
Alignment explanation
Indices: 177354--177498 Score: 96
Period size: 30 Copynumber: 5.0 Consensus size: 28
177344 TTATGTGATG
* * *
177354 TTTTTACTTTCATTTTAATTTGTAAAAAGA
1 TTTTT-CTTTTATTGTAATTTATAAAAA-A
*
177384 TTTTTCTTTTTATTGTAAATTATAAAAAA
1 TTTTTC-TTTTATTGTAATTTATAAAAAA
* *
177413 TATTTATCCTTGATTGTAATTTATAAAATAA
1 T-TTT-TCTTTTATTGTAATTTATAAAA-AA
** *
177444 -TTTTCTCCTATTATAATTTATAAAAAGA
1 TTTTTCTTTTATTGTAATTTATAAAAA-A
* * * *
177472 TTTATCCTATATTATAATTTA-AAAAAA
1 TTTTTCTTTTATTGTAATTTATAAAAAA
177499 GATTTATCCT
Statistics
Matches: 93, Mismatches: 16, Indels: 15
0.75 0.13 0.12
Matches are distributed among these distances:
27 2 0.02
28 23 0.25
29 22 0.24
30 42 0.45
31 4 0.04
ACGTcount: A:0.39, C:0.07, G:0.04, T:0.50
Consensus pattern (28 bp):
TTTTTCTTTTATTGTAATTTATAAAAAA
Found at i:177446 original size:29 final size:30
Alignment explanation
Indices: 177394--177522 Score: 126
Period size: 29 Copynumber: 4.4 Consensus size: 30
177384 TTTTTCTTTT
* * *
177394 TATTGTAAATTATAAAAAATATTTATCCT-
1 TATTATAATTTATAAAAAAGATTTATCCTA
* * *
177423 TGATTGTAATTTATAAAATA-ATTT-T-CTCC
1 T-ATTATAATTTATAAAAAAGATTTATCCT-A
177452 TATTATAATTTAT-AAAAAGATTTATCCTA
1 TATTATAATTTATAAAAAAGATTTATCCTA
*
177481 TATTATAATTTA-AAAAAAGATTTATCCTC
1 TATTATAATTTATAAAAAAGATTTATCCTA
*
177510 TGTTATAATTTAT
1 TATTATAATTTAT
177523 TGTCCTATAA
Statistics
Matches: 85, Mismatches: 7, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
27 6 0.07
28 16 0.19
29 45 0.53
30 18 0.21
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.47
Consensus pattern (30 bp):
TATTATAATTTATAAAAAAGATTTATCCTA
Found at i:177490 original size:57 final size:59
Alignment explanation
Indices: 177394--177522 Score: 142
Period size: 57 Copynumber: 2.2 Consensus size: 59
177384 TTTTTCTTTT
* * * * *
177394 TATTGTAAATTATAAAAAATATTTATCCTTGATTGTAATTTATAAAATA-ATTT-T-CTCC
1 TATTATAATTTATAAAAAAGATTTATCCTTGATTATAATTTA-AAAAAAGATTTATCCT-C
177452 TATTATAATTTAT-AAAAAGATTTATCCTAT-ATTATAATTTAAAAAAAGATTTATCCTC
1 TATTATAATTTATAAAAAAGATTTATCCT-TGATTATAATTTAAAAAAAGATTTATCCTC
*
177510 TGTTATAATTTAT
1 TATTATAATTTAT
177523 TGTCCTATAA
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
56 5 0.08
57 28 0.46
58 26 0.43
59 2 0.03
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.47
Consensus pattern (59 bp):
TATTATAATTTATAAAAAAGATTTATCCTTGATTATAATTTAAAAAAAGATTTATCCTC
Found at i:183129 original size:31 final size:31
Alignment explanation
Indices: 183093--183151 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
183083 AACTTAAAAG
* *
183093 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
*
183124 AGTTTTACAATATTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
183152 CCATACAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:183202 original size:22 final size:22
Alignment explanation
Indices: 183176--183218 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
183166 TAATAAATTA
183176 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
183198 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
183219 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:183227 original size:22 final size:22
Alignment explanation
Indices: 183178--183226 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
183168 ATAAATTATT
**
183178 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
183200 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
183223 TAAA
1 TAAA
183227 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:183230 original size:54 final size:54
Alignment explanation
Indices: 183166--183776 Score: 554
Period size: 54 Copynumber: 11.4 Consensus size: 54
183156 ACAACTACAA
183166 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* ** *
183220 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTT
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATA--C
* * * * * *
183280 TAAAATAAATCAATTCATACAAATAAAT---TA-TTTAAAATAAATCAATCCATAC
1 T--AATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
183332 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* **
183386 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATA-
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATAC
** * ** ** ** *
183443 TTTTAAAATAAAT-AAATCCATACTAATAAAT-TATTTAAAATAAATCAATCCATATTT
1 TAATAAATTATTTAAAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATA--C
* * * * *
183500 TAAAATAAATCAATTCATACT-AATAAAT---TA-TTTAAAATAAATCAATCCATAC
1 T--AATAAAT-TATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
183552 -AACTACA--A--T--AATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* *
183600 TAATAAATTATTTAAAATAAACCAATCCATATTTTAAAATAAATCAATTCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
183654 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
183708 TAATAAATTATTTAAAAT--A--AAT---TATTTTAAAATAAATCAATCCAAAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
183755 TAATAAATTATTTAAAATAAAT
1 TAATAAATTATTTAAAATAAAT
183777 TATTTTAAAA
Statistics
Matches: 456, Mismatches: 58, Indels: 90
0.75 0.10 0.15
Matches are distributed among these distances:
43 2 0.00
44 6 0.01
47 45 0.10
48 25 0.05
49 5 0.01
50 26 0.06
52 3 0.01
53 2 0.00
54 241 0.53
55 7 0.02
56 7 0.02
57 18 0.04
58 39 0.09
59 5 0.01
60 4 0.01
61 2 0.00
62 19 0.04
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
Found at i:183271 original size:80 final size:80
Alignment explanation
Indices: 183181--183496 Score: 517
Period size: 80 Copynumber: 3.9 Consensus size: 80
183171 AATTATTTAA
183181 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
183246 CCATACAACTACAAT
66 CCATACAACTACAAT
* *
183261 AATAAATCAATCCATATTTTAAAATAAATCAATTCATACAAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
*
183326 CCATACTAA-TAAATTATTT
66 CCATAC-AACTACA--A--T
*
183345 AAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCA
1 --AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
183410 ATCCATACAACTACAAT
64 ATCCATACAACTACAAT
*
183427 AATAAATCAATCCATATTTTAAAATAAATAAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
183492 CCATA
66 CCATA
183497 TTTTAAAATA
Statistics
Matches: 219, Mismatches: 9, Indels: 16
0.90 0.04 0.07
Matches are distributed among these distances:
80 140 0.64
81 2 0.01
82 2 0.01
84 2 0.01
85 2 0.01
86 71 0.32
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (80 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
CCATACAACTACAAT
Found at i:183303 original size:18 final size:18
Alignment explanation
Indices: 183282--183339 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
183272 CCATATTTTA
183282 AAATAAATCAATTCATAC
1 AAATAAATCAATTCATAC
*
183300 AAATAAAT-TATT--TA-
1 AAATAAATCAATTCATAC
*
183314 AAATAAATCAATCCATAC
1 AAATAAATCAATTCATAC
*
183332 TAATAAAT
1 AAATAAAT
183340 TATTTAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 8 0.25
15 4 0.12
17 5 0.16
18 15 0.47
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (18 bp):
AAATAAATCAATTCATAC
Found at i:183353 original size:166 final size:166
Alignment explanation
Indices: 183166--183729 Score: 705
Period size: 166 Copynumber: 3.5 Consensus size: 166
183156 ACAACTACAA
183166 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
*
183231 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATTC
66 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATAAATTC
183296 ATACAAATAAATTATTTAAAATAAATCAATCCATAC
131 ATACAAATAAATTATTTAAAATAAATCAATCCATAC
*
183332 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
*
183397 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATAAATCC
66 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATAAATTC
* *
183462 ATACTAATAAATTATTTAAAATAAATCAATCCATATTT
131 ATACAAATAAATTATTTAAAATAAATCAATCCATA--C
* * * * * *
183500 TAAAATAAATCAATTCATACT-AATAAAT---TA-TTTAAAATAAATCAATCCATAC-AACTACA
1 T--AATAAAT-TATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAA-TAAA
* ** ** * **
183559 --A--T--AATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATACTAATAAATTATTTA
62 TTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATA-TTTTAAAATAAATA
* * * ** *
183614 AAAT-AAACCAATCCA-TATTTTAAAATAAATCAATTCATAC
126 AATTCATACAAATAAATTA-TTTAAAATAAATCAATCCATAC
183654 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
183719 TTAAAATAAAT
66 TTAAAATAAAT
183730 TATTTTAAAA
Statistics
Matches: 344, Mismatches: 34, Indels: 44
0.82 0.08 0.10
Matches are distributed among these distances:
151 6 0.02
152 13 0.04
154 1 0.00
155 4 0.01
156 68 0.20
157 17 0.05
158 1 0.00
160 16 0.05
162 8 0.02
164 1 0.00
165 2 0.01
166 185 0.54
167 2 0.01
168 1 0.00
170 13 0.04
171 6 0.02
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (166 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATAAATTC
ATACAAATAAATTATTTAAAATAAATCAATCCATAC
Found at i:183368 original size:134 final size:131
Alignment explanation
Indices: 183230--183684 Score: 562
Period size: 134 Copynumber: 3.4 Consensus size: 131
183220 TAATAAATTA
*
183230 TTTAAAATAAATCAATCCATAC-AACTACA-A-T-AATAAATCAATCCATATTTTAAAATA-AAT
1 TTTAAAATAAATCAATCCATACTAA-TAAATATTAAATAAATCAATCCATA----AAAATACAAT
**
183290 CAATTCATACAAATAAAT-TATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
61 -AATAAAT-C-AATAAATAT-TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
183354 CAATCCATAT
122 CAATCCATAT
* * *
183364 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA-TT-AAATAAATCAATCCATAAAAATACAATAA
** *
183429 TAAATCAATCCATATTTTAAAATAAATAAATCCATACTAATAAATTATTTAAAATAAATCAATCC
63 TAAATCAATAAATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCC
183494 ATAT
128 ATAT
* * *
183498 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA-TT-AAATAAATCAATCCATAAAAATACAATAA
** *
183563 TAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAACCAATCC
63 TAAATCAATAAATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCC
183628 ATAT
128 ATAT
*
183632 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA-TT-AAATAAATCAATCCATA
183685 TTTTAAAATA
Statistics
Matches: 299, Mismatches: 13, Indels: 18
0.91 0.04 0.05
Matches are distributed among these distances:
134 265 0.89
135 4 0.01
136 10 0.03
137 3 0.01
138 1 0.00
140 16 0.05
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (131 bp):
TTTAAAATAAATCAATCCATACTAATAAATATTAAATAAATCAATCCATAAAAATACAATAATAA
ATCAATAAATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA
T
Found at i:183393 original size:22 final size:22
Alignment explanation
Indices: 183344--183392 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
183334 ATAAATTATT
**
183344 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
183366 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCCATA-TAA
183389 TAAA
1 TAAA
183393 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:183502 original size:22 final size:22
Alignment explanation
Indices: 183476--183518 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
183466 TAATAAATTA
183476 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
183498 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
183519 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:183504 original size:188 final size:191
Alignment explanation
Indices: 183310--183776 Score: 639
Period size: 188 Copynumber: 2.5 Consensus size: 191
183300 AAATAAATTA
183310 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
* * *
183375 TCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATAC-AACTACA-A-T-AATAAATCA
66 TCAATCAATACTAATAAATTATTTAAAATAAATCAATCCATACTAA-TAAATATTAAATAAACCA
183436 ATCCATATTTTAAAATAAATAAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
130 ATCCATATTTTAAAATAAATAAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
* *** *
183498 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAAT-A
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAA
* *
183562 ATAAATCAAT-C-CAT--A-T-TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAA
65 ATCAATCAATACTAATAAATTATTTAAAATAAATCAATCCATACTAATAAA-TA-TT-AAATAAA
* *
183621 CCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATAT
127 CCAATCCATATTTTAAAATAAATAAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
183686 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAAT--A--AAT---TATTTTAAAATAAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
183744 TCAATCCAA-ACTAATAAATTATTTAAAATAAAT
66 TCAAT-CAATACTAATAAATTATTTAAAATAAAT
183777 TATTTTAAAA
Statistics
Matches: 244, Mismatches: 19, Indels: 33
0.82 0.06 0.11
Matches are distributed among these distances:
180 5 0.02
181 8 0.03
182 29 0.12
183 5 0.02
184 5 0.02
185 1 0.00
186 5 0.02
187 13 0.05
188 168 0.69
189 5 0.02
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (191 bp):
TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
TCAATCAATACTAATAAATTATTTAAAATAAATCAATCCATACTAATAAATATTAAATAAACCAA
TCCATATTTTAAAATAAATAAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
Found at i:183527 original size:22 final size:22
Alignment explanation
Indices: 183478--183526 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
183468 ATAAATTATT
**
183478 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
183500 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
183523 TAAA
1 TAAA
183527 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:183565 original size:80 final size:80
Alignment explanation
Indices: 183481--183630 Score: 282
Period size: 80 Copynumber: 1.9 Consensus size: 80
183471 AATTATTTAA
* *
183481 AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAACCAAT
183546 CCATACAACTACAAT
66 CCATACAACTACAAT
183561 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAACCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAACCAAT
183626 CCATA
66 CCATA
183631 TTTTAAAATA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
80 68 1.00
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (80 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAACCAAT
CCATACAACTACAAT
Found at i:183607 original size:22 final size:23
Alignment explanation
Indices: 183532--183606 Score: 82
Period size: 22 Copynumber: 3.2 Consensus size: 23
183522 ATAAATTATT
183532 TAAAATAAATCAATCCATAC-AA
1 TAAAATAAATCAATCCATACTAA
**
183554 CTACAATAATAAATCAATCCATA-TTT
1 -T--AA-AATAAATCAATCCATACTAA
183580 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATACTAA
183603 TAAA
1 TAAA
183607 TTATTTAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 16 0.37
23 8 0.19
25 3 0.07
26 16 0.37
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (23 bp):
TAAAATAAATCAATCCATACTAA
Found at i:183636 original size:22 final size:22
Alignment explanation
Indices: 183610--183652 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
183600 TAATAAATTA
183610 TTTAAAATAAACCAATCCATAT
1 TTTAAAATAAACCAATCCATAT
* *
183632 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAACCAATCCATA
183653 CTAATAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAACCAATCCATAT
Found at i:183690 original size:22 final size:22
Alignment explanation
Indices: 183664--183706 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
183654 TAATAAATTA
183664 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
183686 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
183707 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:183715 original size:22 final size:22
Alignment explanation
Indices: 183666--183714 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
183656 ATAAATTATT
**
183666 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
183688 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
183711 TAAA
1 TAAA
183715 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:183738 original size:15 final size:15
Alignment explanation
Indices: 183709--183920 Score: 215
Period size: 15 Copynumber: 14.5 Consensus size: 15
183699 AATCCATACT
183709 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
183723 AATAAATTATTTTAA
1 AATAAATTATTTTAA
* ***
183738 AATAAATCAATCCAAA
1 AATAAAT-TATTTTAA
183754 CTAATAAATTA-TTTAA
1 --AATAAATTATTTTAA
183770 AATAAATTATTTTAA
1 AATAAATTATTTTAA
* * *
183785 AATAAATCA--AT-C
1 AATAAATTATTTTAA
* *
183797 CAT--ATT-TTTTAT
1 AATAAATTATTTTAA
*
183809 AATAATTTATTTTAA
1 AATAAATTATTTTAA
* *
183824 AATAATTTATTTTAT
1 AATAAATTATTTTAA
*
183839 AATAAATTATTTTAT
1 AATAAATTATTTTAA
183854 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
183869 AATAAATTATTTTAT
1 AATAAATTATTTTAA
183884 AATAAATTATTTTAA
1 AATAAATTATTTTAA
183899 AATAAATTATTTTAA
1 AATAAATTATTTTAA
183914 AATAAAT
1 AATAAAT
183921 AACCTTATTA
Statistics
Matches: 164, Mismatches: 23, Indels: 21
0.79 0.11 0.10
Matches are distributed among these distances:
10 2 0.01
11 1 0.01
12 4 0.02
13 1 0.01
14 20 0.12
15 122 0.74
16 6 0.04
17 1 0.01
18 7 0.04
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:183767 original size:134 final size:138
Alignment explanation
Indices: 183361--183776 Score: 418
Period size: 134 Copynumber: 3.1 Consensus size: 138
183351 AATCAATCCA
183361 TATTTTAAAATAAATCAA-TCTATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACA
1 TATTTTAAAATAAATCAATTC-ATACTAATAAATTATTTAAAATAAATCAATCCAT--AACTACA
* *
183425 ATAATAAATCAATCCATATTTTAAAATAAATAAATCCATACTAATAAATTA-TTTAAAATAAATC
63 ATAATAAATCAATCCATA-TCT-AAATAAATAAAT-CATACAAATAAATTATTTTAAAATAAATC
183489 AATC--C-----A-
125 AATCAACTAATAAT
183495 TATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAA
1 TATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCAT--AACTACAA
* * * *
183560 TAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTA-TTTAAAATAAACCA
64 TAATAAATCAATCCATA-TCT-AAATAAATAAAT-CATACAAATAAATTATTTTAAAATAAATCA
183624 ATC--C-----A-
126 ATCAACTAATAAT
* **
183629 TATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCAT-ATTTTAA-A
1 TATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATAACTACAATA
* *
183692 ATAAATCAATCCATA-CT-AATAAAT-TAT-TTA-AAATAAATTATTTTAAAATAAATCAATCCA
66 ATAAATCAATCCATATCTAAATAAATAAATCATACAAATAAATTATTTTAAAATAAATCAAT-C-
183752 AACTAATAAAT
129 AACTAAT-AAT
183763 TA-TTTAAAATAAAT
1 TATTTTAAAATAAAT
183777 TATTTTAAAA
Statistics
Matches: 259, Mismatches: 10, Indels: 27
0.88 0.03 0.09
Matches are distributed among these distances:
122 9 0.03
123 17 0.07
124 1 0.00
125 2 0.01
126 7 0.03
127 1 0.00
128 1 0.00
130 16 0.06
131 4 0.02
133 13 0.05
134 186 0.72
135 2 0.01
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (138 bp):
TATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATAACTACAATA
ATAAATCAATCCATATCTAAATAAATAAATCATACAAATAAATTATTTTAAAATAAATCAATCAA
CTAATAAT
Found at i:183823 original size:101 final size:93
Alignment explanation
Indices: 183629--183920 Score: 279
Period size: 101 Copynumber: 3.0 Consensus size: 93
183619 AACCAATCCA
183629 TATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAAT
1 TATTTTAAAATAAATCAA-TCATACTAATAAATTATTTAAAAT--A--AAT---TATTTTAAAAT
*
183694 AAATCAATCCATACTAATAAATTATTTAAAATAAAT
58 AAATCAATCCATAATAATAAATTATTTAAAATAAAT
*
183730 TATTTTAAAATAAATCAATCCAAACTAATAAATTATTTAAAATAAATTATTTTAAAATAAATCAA
1 TATTTTAAAATAAATCAAT-CATACTAATAAATTATTTAAAATAAATTATTTTAAAATAAATCAA
* *
183795 TCCATATTTTTTATAATAATTTATTTTAAAATAATT
65 TCCATA------ATAATAAATTA-TTTAAAATAAAT
* * ** * *
183831 TATTTTATAATAAAT-TATTTTA-TAATAAATTATTTTAAAATAAATTATTTTATAATAAAT-TA
1 TATTTTAAAATAAATCAATCATACTAATAAATTA-TTTAAAATAAATTATTTTAAAATAAATCAA
**
183893 T-TTTAA-AATAAATTATTTTAAAATAAAT
65 TCCATAATAATAAATTA-TTTAAAATAAAT
183921 AACCTTATTA
Statistics
Matches: 167, Mismatches: 15, Indels: 29
0.79 0.07 0.14
Matches are distributed among these distances:
90 20 0.12
91 1 0.01
94 24 0.14
97 5 0.03
98 12 0.07
99 28 0.17
100 12 0.07
101 65 0.39
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (93 bp):
TATTTTAAAATAAATCAATCATACTAATAAATTATTTAAAATAAATTATTTTAAAATAAATCAAT
CCATAATAATAAATTATTTAAAATAAAT
Found at i:191432 original size:25 final size:28
Alignment explanation
Indices: 191401--191466 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 28
191391 AATTATAGAG
191401 TATTATTAGTTATA-TT-TATAT-GTTA
1 TATTATTAGTTATAGTTATATATAGTTA
191426 TATTATTA-TTATTAGTTATATATAAGTTA
1 TATTATTAGTTA-TAGTTATATAT-AGTTA
191455 -ATTATTAGTTAT
1 TATTATTAGTTAT
191467 TATCGGTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
24 3 0.09
25 10 0.29
26 2 0.06
27 5 0.14
28 8 0.23
29 7 0.20
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.58
Consensus pattern (28 bp):
TATTATTAGTTATAGTTATATATAGTTA
Found at i:191439 original size:31 final size:28
Alignment explanation
Indices: 191401--191468 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 28
191391 AATTATAGAG
*
191401 TATTATTAGTTATATTTATATGTTATATTAT
1 TATTATTAGTTATA--TATAAGTTA-ATTAT
191432 TATTATTAGTTATATATAAGTTAATTAT
1 TATTATTAGTTATATATAAGTTAATTAT
191460 TAGTTATTA
1 TA-TTATTA
191469 TCGGTAATGT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
28 7 0.20
29 14 0.40
31 14 0.40
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (28 bp):
TATTATTAGTTATATATAAGTTAATTAT
Found at i:191449 original size:22 final size:22
Alignment explanation
Indices: 191369--191466 Score: 62
Period size: 22 Copynumber: 4.4 Consensus size: 22
191359 TATATGTGGG
191369 TTAGTTAT-TA-ATTATTATTA
1 TTAGTTATATATATTATTATTA
* * *
191389 CTAATTATAGAGTATTATTAGTTA
1 TTAGTTATATA-TATTATTA-TTA
*
191413 -TATTTATATGTTATATTATTATTA
1 TTAGTTATA---TATATTATTATTA
191437 TTAGTTATATATA--AGTTAATTA
1 TTAGTTATATATATTA-TT-ATTA
191459 TTAGTTAT
1 TTAGTTAT
191467 TATCGGTAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
20 7 0.11
21 3 0.05
22 16 0.26
23 14 0.23
24 6 0.10
25 15 0.24
26 1 0.02
ACGTcount: A:0.36, C:0.01, G:0.08, T:0.55
Consensus pattern (22 bp):
TTAGTTATATATATTATTATTA
Found at i:191464 original size:11 final size:10
Alignment explanation
Indices: 191368--191469 Score: 66
Period size: 10 Copynumber: 9.8 Consensus size: 10
191358 ATATATGTGG
191368 GTTAGTTATTA
1 GTTA-TTATTA
*
191379 ATTATTATTA
1 GTTATTATTA
* *
191389 CTAATTA-TA
1 GTTATTATTA
*
191398 GAGTATTATTA
1 G-TTATTATTA
*
191409 GTTATATTTATA
1 GTTAT-TAT-TA
191421 TGTTA-TATTA
1 -GTTATTATTA
191431 -TTATTATTA
1 GTTATTATTA
*
191440 GTTATATATAA
1 GTTAT-TATTA
191451 GTTAATTATTA
1 GTT-ATTATTA
191462 GTTATTAT
1 GTTATTAT
191470 CGGTAATGTG
Statistics
Matches: 71, Mismatches: 11, Indels: 19
0.70 0.11 0.19
Matches are distributed among these distances:
8 3 0.04
9 7 0.10
10 29 0.41
11 24 0.34
12 4 0.06
13 4 0.06
ACGTcount: A:0.35, C:0.01, G:0.09, T:0.55
Consensus pattern (10 bp):
GTTATTATTA
Found at i:197141 original size:23 final size:23
Alignment explanation
Indices: 197110--197168 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
197100 CACCACAGCT
*
197110 CGTATAATTGCACCAAAGTGCCA
1 CGTAGAATTGCACCAAAGTGCCA
** *
197133 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCAAAGTGCCA
197156 CGTAGAATTGCAC
1 CGTAGAATTGCAC
197169 GTAGTTCCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCAAAGTGCCA
Found at i:197254 original size:13 final size:13
Alignment explanation
Indices: 197236--197262 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
197226 CATATACTAG
197236 GGATCAAGTATGT
1 GGATCAAGTATGT
197249 GGATCAAGTATGT
1 GGATCAAGTATGT
197262 G
1 G
197263 TCTCACCAGA
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:0.30, C:0.07, G:0.33, T:0.30
Consensus pattern (13 bp):
GGATCAAGTATGT
Found at i:202137 original size:21 final size:20
Alignment explanation
Indices: 202100--202152 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 20
202090 TAACCCTATC
*
202100 ACACATATAT--CATATCAT
1 ACACATATATCACAAATCAT
*
202118 GCACATCATATCACAAATCAT
1 ACACAT-ATATCACAAATCAT
*
202139 ATACATATATCACA
1 ACACATATATCACA
202153 TACATTGTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 5 0.18
19 4 0.14
20 8 0.29
21 11 0.39
ACGTcount: A:0.45, C:0.25, G:0.02, T:0.28
Consensus pattern (20 bp):
ACACATATATCACAAATCAT
Found at i:202342 original size:23 final size:23
Alignment explanation
Indices: 202316--202384 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
202306 CACCACAGCT
*
202316 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
202339 CGTAGAATTGCACC-AGAGTACCG
1 CGTAGAATTGCACCGA-AGTGCCA
*
202362 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
202385 TATAATAATA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
22 1 0.03
23 37 0.97
ACGTcount: A:0.29, C:0.26, G:0.25, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:202560 original size:100 final size:98
Alignment explanation
Indices: 202411--202606 Score: 322
Period size: 100 Copynumber: 2.0 Consensus size: 98
202401 AGGACTACAT
* *
202411 ATCATTCCTTAAGAATATATACATATACTAGGGATCAAGTGTGTCTCACCAGACTTCACACATGT
1 ATCATTCCTTAAGAATATATACATATACCAAGGATCAAGTGTGTCTCACCAGACTTCACACATGT
202476 TCCAAAGAATACATATATGT-CCGAAGGACCAC
66 TCCAAAGAATACATATATGTCCCGAAGGACCAC
* *
202508 ATCATTCCTTAAGAATCATATACATATGCCAAGGATTAAGTATGTGTCTCACCAGACTTCACACA
1 ATCATTCCTTAAGAAT-ATATACATATACCAAGGATCAAG--TGTGTCTCACCAGACTTCACACA
202573 TGTTCCAAAGAATACATATATGTCCCGAAGGACC
63 TGTTCCAAAGAATACATATATGTCCCGAAGGACC
202607 GCGTAGACCC
Statistics
Matches: 91, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
97 16 0.18
98 19 0.21
100 46 0.51
101 10 0.11
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (98 bp):
ATCATTCCTTAAGAATATATACATATACCAAGGATCAAGTGTGTCTCACCAGACTTCACACATGT
TCCAAAGAATACATATATGTCCCGAAGGACCAC
Done.