Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007472.1 Hibiscus syriacus cultivar Beakdansim tig00020528_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: 61028
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:1737 original size:18 final size:18
Alignment explanation
Indices: 1716--1754 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1706 TTTTAATTAC
1716 AATTAT-TTATTATTTTAA
1 AATTATATTATTA-TTTAA
*
1734 AATTATATTTTTATTTAA
1 AATTATATTATTATTTAA
1752 AAT
1 AAT
1755 GACAATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
AATTATATTATTATTTAA
Found at i:3160 original size:21 final size:21
Alignment explanation
Indices: 3134--3174 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
3124 TACCAAGGAC
*
3134 GAGAAGACCATTCGTAAAGAT
1 GAGAAGACCATTCATAAAGAT
3155 GAGAAGACCATTCATAAAGA
1 GAGAAGACCATTCATAAAGA
3175 CATGAAGACC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.46, C:0.15, G:0.22, T:0.17
Consensus pattern (21 bp):
GAGAAGACCATTCATAAAGAT
Found at i:3181 original size:21 final size:21
Alignment explanation
Indices: 3135--3185 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
3125 ACCAAGGACG
* *
3135 AGAAGACCATTCGTAAAGATG
1 AGAAGACCATTCATAAAGATC
3156 AGAAGACCATTCATAAAGA-C
1 AGAAGACCATTCATAAAGATC
3176 ATGAAGACCA
1 A-GAAGACCA
3186 CTTTGCATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 1 0.04
21 26 0.96
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.16
Consensus pattern (21 bp):
AGAAGACCATTCATAAAGATC
Found at i:9466 original size:36 final size:36
Alignment explanation
Indices: 9419--9503 Score: 120
Period size: 36 Copynumber: 2.3 Consensus size: 36
9409 GGGCAAGTCA
9419 ATCTTAAGCCTTCACT-GAAGAGTAGTGAAGCAAAC-C
1 ATCTTAAGCCTTCACTAG-AG-GTAGTGAAGCAAACTC
*
9455 ATCTTAAGCCTTCACTAGAGGTAGTGAAGTAAACTC
1 ATCTTAAGCCTTCACTAGAGGTAGTGAAGCAAACTC
9491 ATCTATAAGCCTT
1 ATCT-TAAGCCTT
9504 TAGGTCAAGA
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
35 13 0.29
36 23 0.51
37 9 0.20
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (36 bp):
ATCTTAAGCCTTCACTAGAGGTAGTGAAGCAAACTC
Found at i:9866 original size:214 final size:213
Alignment explanation
Indices: 9489--9880 Score: 687
Period size: 214 Copynumber: 1.8 Consensus size: 213
9479 TGAAGTAAAC
*
9489 TCATCTATAAGCCTTTAGGTCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGG
1 TCATCTATAAGCCTTTAGGTAAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGG
* *
9554 ATGTTTTCACATGAATTGAAAATGAAAAATGATGTTTTATGAAGATGGAATTTTTGAAAACTAAG
66 ATGTTTTCACATGAATTGAAAATGAAAAATGACGTTTTATGAAGATGGAATTTTTGAAAAATAAG
*
9619 AATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATG
131 AATGCGATTTTCAAAATTTCACAATTAATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATG
9684 ATGCTTAAACCCTTCGGG
196 ATGCTTAAACCCTTCGGG
* *
9702 TCATCTGTAAGCCTTTAAGG-AAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAG
1 TCATCTATAAGCCTTT-AGGTAAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAG
*
9766 GATGTTTTCACATGAATTTGAGAATGAAAAATGACGTTTTATGAAGATGGAATTTTTGAAAAATA
65 GATGTTTTCACATGAA-TTGAAAATGAAAAATGACGTTTTATGAAGATGGAATTTTTGAAAAATA
*
9831 AGAATGCGATTTTCAAAATTTCACTATTAATAAGTCCTTCGGGCCATCAG
129 AGAATGCGATTTTCAAAATTTCACAATTAATAAGTCCTTCGGGCCATCAG
9881 GTCATCTGTA
Statistics
Matches: 169, Mismatches: 8, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
213 73 0.43
214 96 0.57
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.32
Consensus pattern (213 bp):
TCATCTATAAGCCTTTAGGTAAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGG
ATGTTTTCACATGAATTGAAAATGAAAAATGACGTTTTATGAAGATGGAATTTTTGAAAAATAAG
AATGCGATTTTCAAAATTTCACAATTAATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATG
ATGCTTAAACCCTTCGGG
Found at i:10295 original size:215 final size:215
Alignment explanation
Indices: 9880--10356 Score: 762
Period size: 215 Copynumber: 2.2 Consensus size: 215
9870 CGGGCCATCA
* * * *
9880 GGTCATCTGTAAGCCTTTTGAGCAAGATGACAAGTCTTGCGAGCCATCCATAAAACCTTCGGGTA
1 GGTCATCTGTAAGCCTTTTGAGCAAGATGATAAGTCTTTCGGGCCATCCATAAAACCTTCAGGTA
9945 GGATGTTTTCACATGAATTTGAAAATGAAAAAGTGATGTTTTAAGAAGATGGAATTTTTGAAAAT
66 GGATGTTTTCACATGAATTTGAAAATGAAAAAGTGATGTTTTAAGAAGATGGAATTTTTGAAAAT
* * * *
10010 GAAGAATACGATTTTCAAAATTTTACAATTTATAAGTCCTTCGGGCTATTAGTAAGTCTTTCGAG
131 GAAGAATACGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCACTAAGTCTTTCGAG
* *
10075 CATGATGCTTAAA-CTCTTCG
196 CATGATGATGAAATC-CTTCG
*
10095 GGTCATCTGTAAGCCTTTTGAGCAAGATGATAAATCTTTCGGGCCATCCATAAAACCTTCAGGTA
1 GGTCATCTGTAAGCCTTTTGAGCAAGATGATAAGTCTTTCGGGCCATCCATAAAACCTTCAGGTA
*
10160 GGATTTTTTCACATGAATTTGAAAATGAAAAAAGTGATGTTTTAAGAAGATGGAATTTTTGAAAA
66 GGATGTTTTCACATGAATTTGAAAATG-AAAAAGTGATGTTTTAAGAAGATGGAATTTTTGAAAA
10225 TGAAGAATGA-GATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCACTAAGTCTTT-G
130 TGAAGAAT-ACGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCACTAAGTCTTTCG
*
10288 TGCATGATGATGAAATCCTTCG
194 AGCATGATGATGAAATCCTTCG
* * *
10310 GGTCATCTGTAAGTCTTTAGAGCAAGATGATAAGTCCTTCGGGCCAT
1 GGTCATCTGTAAGCCTTTTGAGCAAGATGATAAGTCTTTCGGGCCAT
10357 TTTAAACCTC
Statistics
Matches: 242, Mismatches: 17, Indels: 6
0.91 0.06 0.02
Matches are distributed among these distances:
215 147 0.61
216 94 0.39
217 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Consensus pattern (215 bp):
GGTCATCTGTAAGCCTTTTGAGCAAGATGATAAGTCTTTCGGGCCATCCATAAAACCTTCAGGTA
GGATGTTTTCACATGAATTTGAAAATGAAAAAGTGATGTTTTAAGAAGATGGAATTTTTGAAAAT
GAAGAATACGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCACTAAGTCTTTCGAG
CATGATGATGAAATCCTTCG
Found at i:10323 original size:41 final size:41
Alignment explanation
Indices: 10257--10356 Score: 121
Period size: 41 Copynumber: 2.4 Consensus size: 41
10247 TTCACAATTT
* * *
10257 ATAAGTCCTTCGGGCCATCACTAAGTCTTT-GTGCATGATG
1 ATAAATCCTTCGGGCCATCACTAAGTCTTTAGAGCAAGATG
* **
10297 ATGAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCAAGATG
1 AT-AAATCCTTCGGGCCATCACTAAGTCTTTAGAGCAAGATG
*
10339 ATAAGTCCTTCGGGCCAT
1 ATAAATCCTTCGGGCCAT
10357 TTTAAACCTC
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
40 2 0.04
41 38 0.76
42 10 0.20
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (41 bp):
ATAAATCCTTCGGGCCATCACTAAGTCTTTAGAGCAAGATG
Found at i:10463 original size:56 final size:56
Alignment explanation
Indices: 10364--10507 Score: 191
Period size: 56 Copynumber: 2.6 Consensus size: 56
10354 CATTTTAAAC
* * * * * *
10364 CTCCTTGAAAGGAATAGGGACCGAACCCATTTTCAGAAGATTTCTTGAGTTCTATA
1 CTCCATGAAAGGAATAGGGAGCAAACCCGTTTTAAGAAAATTTCTTGAGTTCTATA
*
10420 CTCTC-TGAAAGGAATATGGAGCAAACCCGTTTTAAGAAAATTTCTTGAGTTCTATA
1 CTC-CATGAAAGGAATAGGGAGCAAACCCGTTTTAAGAAAATTTCTTGAGTTCTATA
* *
10476 CTCCATGAAAGGAACAGGGAGCAAACACGTTT
1 CTCCATGAAAGGAATAGGGAGCAAACCCGTTT
10508 GCTGAAGATT
Statistics
Matches: 77, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
55 1 0.01
56 75 0.97
57 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (56 bp):
CTCCATGAAAGGAATAGGGAGCAAACCCGTTTTAAGAAAATTTCTTGAGTTCTATA
Found at i:12795 original size:17 final size:18
Alignment explanation
Indices: 12764--12806 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
12754 GTTGGTTTAA
12764 TTAAAATTAATTTTTATT
1 TTAAAATTAATTTTTATT
12782 TTAAAATTAATTTTTATT
1 TTAAAATTAATTTTTATT
*
12800 TAAAAAT
1 TTAAAAT
12807 GATAATGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTAAAATTAATTTTTATT
Found at i:16089 original size:17 final size:17
Alignment explanation
Indices: 16069--16128 Score: 111
Period size: 17 Copynumber: 3.5 Consensus size: 17
16059 TTGTTCACTA
16069 ATTAAACTAGTTCATTC
1 ATTAAACTAGTTCATTC
16086 ATTAAACTAGTTCATTC
1 ATTAAACTAGTTCATTC
*
16103 ATTAAACTAGTTCATTA
1 ATTAAACTAGTTCATTC
16120 ATTAAACTA
1 ATTAAACTA
16129 TATCATTTAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 42 1.00
ACGTcount: A:0.40, C:0.15, G:0.05, T:0.40
Consensus pattern (17 bp):
ATTAAACTAGTTCATTC
Found at i:16135 original size:17 final size:17
Alignment explanation
Indices: 16061--16128 Score: 109
Period size: 17 Copynumber: 4.0 Consensus size: 17
16051 CATAAAGCTT
*
16061 GTTCACTAATTAAACTA
1 GTTCATTAATTAAACTA
*
16078 GTTCATTCATTAAACTA
1 GTTCATTAATTAAACTA
*
16095 GTTCATTCATTAAACTA
1 GTTCATTAATTAAACTA
16112 GTTCATTAATTAAACTA
1 GTTCATTAATTAAACTA
16129 TATCATTTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 48 1.00
ACGTcount: A:0.38, C:0.16, G:0.06, T:0.40
Consensus pattern (17 bp):
GTTCATTAATTAAACTA
Found at i:22935 original size:45 final size:45
Alignment explanation
Indices: 22882--23290 Score: 471
Period size: 45 Copynumber: 9.0 Consensus size: 45
22872 TATACCATTT
* * * *
22882 TTTCATGCCAATAATGCACCAATATGTATTTCAATTATGGCATCT
1 TTTCATGCCGATAATGCACCCATATGTATTTCATTTATGGCATCC
* * * *
22927 TTTTATGCCGATAATGCACCCTTATGTATTTCCTTTATGGAATCC
1 TTTCATGCCGATAATGCACCCATATGTATTTCATTTATGGCATCC
*
22972 TTTCATGCCGATAATGCACCCATATGCATTTCATTTATGGCATCC
1 TTTCATGCCGATAATGCACCCATATGTATTTCATTTATGGCATCC
** *
23017 TTTCATGCCGATAATGCACCCATATCCATTTTC-TTTATGGCATCA
1 TTTCATGCCGATAATGCACCCATATGTA-TTTCATTTATGGCATCC
* * * *
23062 TTTCATGCAGATAATGCACCTATATGTATTTCATTAATGGAATCC
1 TTTCATGCCGATAATGCACCCATATGTATTTCATTTATGGCATCC
* * * * * *
23107 TTTCATGACAATAATGCACTCGTATGCATATTTCATTAATGGTATCC
1 TTTCATGCCGATAATGCACCCATATG--TATTTCATTTATGGCATCC
* *** * *
23154 TTTCATGACGATAATGCACTTGTATGCATTTCATTTATGGAATCC
1 TTTCATGCCGATAATGCACCCATATGTATTTCATTTATGGCATCC
23199 TTTCATGCCGATAATGCACCCATAT-TCATTTCATTTATGGCATCC
1 TTTCATGCCGATAATGCACCCATATGT-ATTTCATTTATGGCATCC
* * * * *
23244 TTTCATGCTGATAATACACCTATATGCATTTCATTTATGTCATCC
1 TTTCATGCCGATAATGCACCCATATGTATTTCATTTATGGCATCC
23289 TT
1 TT
23291 CTATGCCTTT
Statistics
Matches: 313, Mismatches: 45, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
44 4 0.01
45 263 0.84
46 4 0.01
47 42 0.13
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.39
Consensus pattern (45 bp):
TTTCATGCCGATAATGCACCCATATGTATTTCATTTATGGCATCC
Found at i:22986 original size:90 final size:90
Alignment explanation
Indices: 22882--23384 Score: 498
Period size: 90 Copynumber: 5.6 Consensus size: 90
22872 TATACCATTT
* * * * * *
22882 TTTCATGCCAATAATGCACCAATATGTATTTCAATTATGGCATCTTTTTATGCCGATAATGCACC
1 TTTCATGCCGATAATGCACCTATATGCATTTCATTTATGGCATCCTTTCATGCCGATAATGCACC
* * *
22947 CTTATGTATTTCCTTTATGGAATCC
66 CATATGTATTTCATTTATGGCATCC
*
22972 TTTCATGCCGATAATGCACCCATATGCATTTCATTTATGGCATCCTTTCATGCCGATAATGCACC
1 TTTCATGCCGATAATGCACCTATATGCATTTCATTTATGGCATCCTTTCATGCCGATAATGCACC
** *
23037 CATATCCATTTTC-TTTATGGCATCA
66 CATATGTA-TTTCATTTATGGCATCC
* * * * * * *
23062 TTTCATGCAGATAATGCACCTATATGTATTTCATTAATGGAATCCTTTCATGACAATAATGCACT
1 TTTCATGCCGATAATGCACCTATATGCATTTCATTTATGGCATCCTTTCATGCCGATAATGCACC
* * *
23127 CGTATGCATATTTCATTAATGGTATCC
66 CATATG--TATTTCATTTATGGCATCC
* * * *
23154 TTTCATGACGATAATGCACTTGTATGCATTTCATTTATGGAATCCTTTCATGCCGATAATGCACC
1 TTTCATGCCGATAATGCACCTATATGCATTTCATTTATGGCATCCTTTCATGCCGATAATGCACC
23219 CATAT-TCATTTCATTTATGGCATCC
66 CATATGT-ATTTCATTTATGGCATCC
* * * ** *
23244 TTTCATGCTGATAATACACCTATATGCATTTCATTTATGTCATCC-TTCTATGCC--TTTTACAC
1 TTTCATGCCGATAATGCACCTATATGCATTTCATTTATGGCATCCTTTC-ATGCCGATAATGCAC
* **
23306 ACTACTATACATTTCATTTATGGCATCC
65 -CCA-TATGTATTTCATTTATGGCATCC
** * * * *
23334 TTT-ATTGCCTTTTATACA-CTATTATACATTTCATTTATGGCATTCTTTCAT
1 TTTCA-TGCCGATAATGCACCTA-TATGCATTTCATTTATGGCATCCTTTCAT
23385 CTAACTGAAA
Statistics
Matches: 345, Mismatches: 56, Indels: 24
0.81 0.13 0.06
Matches are distributed among these distances:
88 5 0.01
89 10 0.03
90 249 0.72
91 11 0.03
92 70 0.20
ACGTcount: A:0.26, C:0.22, G:0.11, T:0.41
Consensus pattern (90 bp):
TTTCATGCCGATAATGCACCTATATGCATTTCATTTATGGCATCCTTTCATGCCGATAATGCACC
CATATGTATTTCATTTATGGCATCC
Found at i:23192 original size:182 final size:179
Alignment explanation
Indices: 22882--23278 Score: 537
Period size: 182 Copynumber: 2.2 Consensus size: 179
22872 TATACCATTT
* * * * * *
22882 TTTCATGCCA-ATAATGCACCAATATGTATTTCAATTATGGCATCTTTTTATGCCGATAATGCAC
1 TTTCATG-CAGATAATGCACCTATATGTATTTC-ATTATGGAATCCTTTCATGACAATAATGCAC
* * * *
22946 CCTTATGTATTTCCTTTATGGAATCCTTTCATGCCGATAATGCACCCATATGCATTTCATTTATG
64 CCGTATGTATTTCATTAATGGAATCCTTTCATGACGATAATGCACCCATATGCATTTCATTTATG
*
23011 GCATCCTTTCATGCCGATAATGCACCCATATCCATTTTC-TTTATGGCATCA
129 GAATCCTTTCATGCCGATAATGCACCCATATCCA-TTTCATTTATGGCATCA
*
23062 TTTCATGCAGATAATGCACCTATATGTATTTCATTAATGGAATCCTTTCATGACAATAATGCACT
1 TTTCATGCAGATAATGCACCTATATGTATTTCATT-ATGGAATCCTTTCATGACAATAATGCACC
* ***
23127 CGTATGCATATTTCATTAATGGTATCCTTTCATGACGATAATGCACTTGTATGCATTTCATTTAT
65 CGTATG--TATTTCATTAATGGAATCCTTTCATGACGATAATGCACCCATATGCATTTCATTTAT
* *
23192 GGAATCCTTTCATGCCGATAATGCACCCATATTCATTTCATTTATGGCATCC
128 GGAATCCTTTCATGCCGATAATGCACCCATATCCATTTCATTTATGGCATCA
* * *
23244 TTTCATGCTGATAATACACCTATATGCATTTCATT
1 TTTCATGCAGATAATGCACCTATATGTATTTCATT
23279 TATGTCATCC
Statistics
Matches: 191, Mismatches: 21, Indels: 8
0.87 0.10 0.04
Matches are distributed among these distances:
179 5 0.03
180 56 0.29
181 4 0.02
182 126 0.66
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.39
Consensus pattern (179 bp):
TTTCATGCAGATAATGCACCTATATGTATTTCATTATGGAATCCTTTCATGACAATAATGCACCC
GTATGTATTTCATTAATGGAATCCTTTCATGACGATAATGCACCCATATGCATTTCATTTATGGA
ATCCTTTCATGCCGATAATGCACCCATATCCATTTCATTTATGGCATCA
Found at i:23319 original size:45 final size:44
Alignment explanation
Indices: 23220--23381 Score: 179
Period size: 45 Copynumber: 3.6 Consensus size: 44
23210 TAATGCACCC
* *
23220 ATATTCATTTCATTTATGGCATCCTTTCA-TG-CTGATAATACAC-CT
1 ATATACATTTCATTTATGGCATCCTTT-ATTGCCT--T-TTACACACT
* *
23265 ATATGCATTTCATTTATGTCATCCTTCTA-TGCCTTTTACACACT
1 ATATACATTTCATTTATGGCATCCTT-TATTGCCTTTTACACACT
*
23309 ACTATACATTTCATTTATGGCATCCTTTATTGCCTTTTATACACT
1 A-TATACATTTCATTTATGGCATCCTTTATTGCCTTTTACACACT
*
23354 ATTATACATTTCATTTATGGCATTCTTT
1 A-TATACATTTCATTTATGGCATCCTTT
23382 CATCTAACTG
Statistics
Matches: 104, Mismatches: 8, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
43 5 0.05
44 6 0.06
45 90 0.87
46 3 0.03
ACGTcount: A:0.25, C:0.22, G:0.07, T:0.46
Consensus pattern (44 bp):
ATATACATTTCATTTATGGCATCCTTTATTGCCTTTTACACACT
Found at i:23322 original size:227 final size:224
Alignment explanation
Indices: 22882--23336 Score: 562
Period size: 227 Copynumber: 2.0 Consensus size: 224
22872 TATACCATTT
* * * *
22882 TTTCATGCCAATAATGCACCAATATGTATTTCAATTATGGCATCTTTTTATGCCGATAATGCACC
1 TTTCATGACAATAATGCACCAATATGTATTTCAATTATGGCATCCTTTCATGACGATAATGCACC
* *
22947 CTTATGTATTTCCTTTATGGAATCCTTTCATGCCGATAATGCACCCATATGCATTTCATTTATGG
66 CTTATGCATTTCATTTATGGAATCCTTTCATGCCGATAATGCACCCATATGCATTTCATTTATGG
*
23012 CATCCTTTCATGCCGATAATGCACCCATATCCATTTTCTTTATGGCATCATTTCATGCAGATAAT
131 CATCCTTTCATGCCGATAATACACCCATATCCATTTTCTTTATGGCATCATTTCATGCA-ATAAT
* **
23077 GCACCTATATGTATTTCATTAATGGAATCC
195 ACACCTATATACATTTCATTAATGGAATCC
* *
23107 TTTCATGACAATAATGCACTC-GTATGCATATTTC-ATTAATGGTATCCTTTCATGACGATAATG
1 TTTCATGACAATAATGCAC-CAATATG--TATTTCAATT-ATGGCATCCTTTCATGACGATAATG
* *
23170 CA-CTTGTATGCATTTCATTTATGGAATCCTTTCATGCCGATAATGCACCCATATTCATTTCATT
62 CACCCT-TATGCATTTCATTTATGGAATCCTTTCATGCCGATAATGCACCCATATGCATTTCATT
* * * * *
23234 TATGGCATCCTTTCATGCTGATAATACACCTATATGCA-TTTCATTTATGTCATC-CTTCTATGC
126 TATGGCATCCTTTCATGCCGATAATACACCCATATCCATTTTC-TTTATGGCATCATTTC-ATGC
* ** * *
23297 -CTTTTACACACTACTATACATTTCATTTATGGCATCC
189 AATAATACAC-CTA-TATACATTTCATTAATGGAATCC
23334 TTT
1 TTT
23337 ATTGCCTTTT
Statistics
Matches: 197, Mismatches: 24, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
225 27 0.14
226 16 0.08
227 154 0.78
ACGTcount: A:0.26, C:0.22, G:0.12, T:0.40
Consensus pattern (224 bp):
TTTCATGACAATAATGCACCAATATGTATTTCAATTATGGCATCCTTTCATGACGATAATGCACC
CTTATGCATTTCATTTATGGAATCCTTTCATGCCGATAATGCACCCATATGCATTTCATTTATGG
CATCCTTTCATGCCGATAATACACCCATATCCATTTTCTTTATGGCATCATTTCATGCAATAATA
CACCTATATACATTTCATTAATGGAATCC
Found at i:23486 original size:68 final size:68
Alignment explanation
Indices: 23378--23703 Score: 334
Period size: 68 Copynumber: 4.8 Consensus size: 68
23368 TTATGGCATT
** ** * * *
23378 CTTTCATCTAACTGAAACGATTGATACCTTTC-ATTCAAATGCATAGCTAGGCCACAAAGGCACA
1 CTTTCATCTAACTGGCATAATTGACACCTTTCTA-TCAAATGCACAGCTAGGCCACAAAGGCACT
*
23442 TAGT
65 TAGC
* * * * * *
23446 CTTTCATCTAACTGGCATTATTGACACCTTTCTGTCAAATGCACAGCTAGGACTCAAAGGAACCT
1 CTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCACAGCTAGGCCACAAAGGCACTT
*
23511 AAC
66 AGC
* * * * *
23514 CTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAACTGCACA-CCATGG-CATCAGAGGTAC
1 CTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCACAGCTA-GGCCA-CAAAGGCAC
23577 TTAGC
64 TTAGC
* * * * *
23582 CTTTCATCTAACTGACATAATTGACACATTTCTATAAAATGCATAGCTAGGCCTCAAAGGCACTT
1 CTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCACAGCTAGGCCACAAAGGCACTT
*
23647 GGC
66 AGC
* * * *
23650 CTTTTATCTAACTGGCATAGTTGACACCTTTCTATCAAATGCACAACGAGGCCA
1 CTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCACAGCTAGGCCA
23704 TTAATCTGTT
Statistics
Matches: 212, Mismatches: 41, Indels: 10
0.81 0.16 0.04
Matches are distributed among these distances:
67 3 0.01
68 206 0.97
69 3 0.01
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (68 bp):
CTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCACAGCTAGGCCACAAAGGCACTT
AGC
Found at i:23951 original size:57 final size:57
Alignment explanation
Indices: 23908--24183 Score: 419
Period size: 57 Copynumber: 4.8 Consensus size: 57
23898 TAAAGTTATT
* * * *
23908 ATACAAAAATTCATAAACAAATTATTAATTTCTTAACTTTTTGCACCCGAAGTGCCC
1 ATACGAAAATTCATAAACAAATTATAAATTTCTTAACTTTTTGCACACAAAGTGCCC
*
23965 ATACTG-AAATTCATAAACAAATTATAAATTTCTTAACTTTTTGCACACAAAGTTCCC
1 ATAC-GAAAATTCATAAACAAATTATAAATTTCTTAACTTTTTGCACACAAAGTGCCC
* *
24022 ATACGGAAATTCATAAACAAATTATAAATTTCTTAACTTTTTACACACAAAGTGCCC
1 ATACGAAAATTCATAAACAAATTATAAATTTCTTAACTTTTTGCACACAAAGTGCCC
* * *
24079 ATTCGAAAATTCATAAACAAATTATAAATTTATTAACTTTTTGTACACAAAGTGCCC
1 ATACGAAAATTCATAAACAAATTATAAATTTCTTAACTTTTTGCACACAAAGTGCCC
* * *
24136 ATACGAAAATTCATAAACAAATTATGAATTTCCTAACTTTTTGTACAC
1 ATACGAAAATTCATAAACAAATTATAAATTTCTTAACTTTTTGCACAC
24184 TTAGTACCAT
Statistics
Matches: 201, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
56 1 0.00
57 200 1.00
ACGTcount: A:0.41, C:0.18, G:0.07, T:0.34
Consensus pattern (57 bp):
ATACGAAAATTCATAAACAAATTATAAATTTCTTAACTTTTTGCACACAAAGTGCCC
Found at i:28269 original size:45 final size:45
Alignment explanation
Indices: 28184--28857 Score: 854
Period size: 45 Copynumber: 15.0 Consensus size: 45
28174 CTTCATACTT
* * ** * *
28184 ATAATGCA-CCATTCTGCATTTTCATTTATGCCATTTTTTCATCCCA
1 ATAATGCACCCA-TATGCA-TTTCATTTATGGCATCCTTTCATGCCG
* *
28230 ATAATGCACCCATATGCATTTCAATTATGGCATCCTTTCATACCG
1 ATAATGCACCCATATGCATTTCATTTATGGCATCCTTTCATGCCG
* * * * *
28275 ATAATGCACGCATATTCATGTC-TTATATGGCA-ACTTTCATACCG
1 ATAATGCACCCATATGCATTTCATT-TATGGCATCCTTTCATGCCG
* * *
28319 ATAATGTTA-TCATATGCATTTCATTTATGGCATCATTTCATGCCG
1 ATAATG-CACCCATATGCATTTCATTTATGGCATCCTTTCATGCCG
* *
28364 ATAATGCATCCATATGTATTTCATTTATGGCATCCTTTCATGCCG
1 ATAATGCACCCATATGCATTTCATTTATGGCATCCTTTCATGCCG
* *
28409 ATTATGCACCCATATGCATTTCATTTATGGTATCCTTTCATGCCG
1 ATAATGCACCCATATGCATTTCATTTATGGCATCCTTTCATGCCG
28454 ATAATGCACCCATATGCATTTCATTTATGGCATCCTTTCATGCCG
1 ATAATGCACCCATATGCATTTCATTTATGGCATCCTTTCATGCCG
* * * *
28499 ATAATGCACCCATACGCATTTCATTTATCGAATCCTTTCATGCAG
1 ATAATGCACCCATATGCATTTCATTTATGGCATCCTTTCATGCCG
* * * *
28544 ATAATGCACCCATTTGCATTTCATTTATGGTATCCTTTCACGCTG
1 ATAATGCACCCATATGCATTTCATTTATGGCATCCTTTCATGCCG
*
28589 ATAATGCACCCATATTCATTTCATTTATGGCATCCTTTCATGCCG
1 ATAATGCACCCATATGCATTTCATTTATGGCATCCTTTCATGCCG
* * *
28634 ATAATGCACCCATATTCATTTCATTTATGGCATCATTTCATGTCG
1 ATAATGCACCCATATGCATTTCATTTATGGCATCCTTTCATGCCG
* ** *
28679 ATAATGCACCAATATGGTTTTCATTTATGGCATCCTTTCATGCCT
1 ATAATGCACCCATATGCATTTCATTTATGGCATCCTTTCATGCCG
* *
28724 ATAATGCACCCACATTCATTTCATTTATGGCATCCTTTCATGCCG
1 ATAATGCACCCATATGCATTTCATTTATGGCATCCTTTCATGCCG
* *
28769 ATAATGCACCCATATGCATTACATTTATGGCATCCTTTCATGCCT
1 ATAATGCACCCATATGCATTTCATTTATGGCATCCTTTCATGCCG
* * * * * *
28814 TTAATACA-CTACTATACATTTCATTTATAGCACCCTTTCATGCC
1 ATAATGCACCCA-TATGCATTTCATTTATGGCATCCTTTCATGCC
28858 TTTTACACAC
Statistics
Matches: 551, Mismatches: 70, Indels: 15
0.87 0.11 0.02
Matches are distributed among these distances:
44 38 0.07
45 497 0.90
46 13 0.02
47 3 0.01
ACGTcount: A:0.26, C:0.25, G:0.11, T:0.38
Consensus pattern (45 bp):
ATAATGCACCCATATGCATTTCATTTATGGCATCCTTTCATGCCG
Found at i:28879 original size:40 final size:44
Alignment explanation
Indices: 28785--28886 Score: 132
Period size: 45 Copynumber: 2.3 Consensus size: 44
28775 CACCCATATG
* *
28785 CATTACATTTATGGCATCCTTTCATGCCTTTAATACACTACTATA
1 CATTACATTTATAGCACCCTTTCATGCCTTT-ATACACTACTATA
* * *
28830 CATTTCATTTATAGCACCCTTTCATGCCTTTTACACACTATTATA
1 CATTACATTTATAGCACCCTTTCATGCC-TTTATACACTACTATA
*
28875 CATTTCATTTAT
1 CATTACATTTAT
28887 GGAATCCTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
45 48 0.94
46 3 0.06
ACGTcount: A:0.27, C:0.25, G:0.05, T:0.43
Consensus pattern (44 bp):
CATTACATTTATAGCACCCTTTCATGCCTTTATACACTACTATA
Found at i:28983 original size:68 final size:67
Alignment explanation
Indices: 28900--29216 Score: 384
Period size: 68 Copynumber: 4.7 Consensus size: 67
28890 ATCCTTTAAA
* * * *
28900 CTAATTGGCATAATTGACACCTCTTTGTCAAATACACAGCTAGGCCTCAAAGGCAGTTTGTCTTT
1 CTAACTGGCATAATTGACACCT-TTTGTCAAATGCACAGCTAGGCCTCAAAGGCAGTTAGCCTTT
*
28965 AAT
65 CAT
* * * * * *
28968 ATATCTGGCATAATTGACACCTTTTTGTTAAATGCATAACTAGGCCTCGAAGGCACG-TAGCCTT
1 CTAACTGGCATAATTGACACC-TTTTGTCAAATGCACAGCTAGGCCTCAAAGGCA-GTTAGCCTT
29032 TCAT
64 TCAT
* * *
29036 CTAACAGGTATAATTGACACCTTTTGTCAAATGCACAGCTAGGCCTCAAAGGCAATTAGCCTTTC
1 CTAACTGGCATAATTGACACCTTTTGTCAAATGCACAGCTAGGCCTCAAAGGCAGTTAGCCTTTC
29101 AT
66 AT
* * * **
29103 CTAACTGGCATAATTGTCACCTTTCTGTCAAATGCATAGCTAGGCCTCAAAGGAACCTAGCCTTT
1 CTAACTGGCATAATTGACACCTTT-TGTCAAATGCACAGCTAGGCCTCAAAGGCAGTTAGCCTTT
29168 CAT
65 CAT
* * *
29171 CTAACTGGCATAATTGACACATTTCTTTCAAATGCACAACTAGGCC
1 CTAACTGGCATAATTGACACCTTT-TGTCAAATGCACAGCTAGGCC
29217 ATTAATCTTT
Statistics
Matches: 213, Mismatches: 32, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
67 61 0.29
68 150 0.70
69 2 0.01
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (67 bp):
CTAACTGGCATAATTGACACCTTTTGTCAAATGCACAGCTAGGCCTCAAAGGCAGTTAGCCTTTC
AT
Found at i:29165 original size:135 final size:135
Alignment explanation
Indices: 28906--29216 Score: 433
Period size: 135 Copynumber: 2.3 Consensus size: 135
28896 TAAACTAATT
* * * *
28906 GGCATAATTGACACCTCTTTGTCAAATACACAGCTAGGCCTCAAAGGCAGTTTGTCTTTAATATA
1 GGCATAATTGACACCT-TTTGTCAAATGCACAGCTAGGCCTCAAAGGCAATTAGCCTTTAATATA
* * * * * *
28971 TCTGGCATAATTGACACCTTTTTGTTAAATGCATAACTAGGCCTCGAAGGCACGTAGCCTTTCAT
65 ACTGGCATAATTGACACCTTTCTGTCAAATGCATAACTAGGCCTCAAAGGAACCTAGCCTTTCAT
29036 CTAACA
130 CTAACA
* * *
29042 GGTATAATTGACACCTTTTGTCAAATGCACAGCTAGGCCTCAAAGGCAATTAGCCTTTCATCTAA
1 GGCATAATTGACACCTTTTGTCAAATGCACAGCTAGGCCTCAAAGGCAATTAGCCTTTAATATAA
* *
29107 CTGGCATAATTGTCACCTTTCTGTCAAATGCATAGCTAGGCCTCAAAGGAACCTAGCCTTTCATC
66 CTGGCATAATTGACACCTTTCTGTCAAATGCATAACTAGGCCTCAAAGGAACCTAGCCTTTCATC
*
29172 TAACT
131 TAACA
* * *
29177 GGCATAATTGACACATTTCTTTCAAATGCACAACTAGGCC
1 GGCATAATTGACACCTTT-TGTCAAATGCACAGCTAGGCC
29217 ATTAATCTTT
Statistics
Matches: 154, Mismatches: 20, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
135 120 0.78
136 34 0.22
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (135 bp):
GGCATAATTGACACCTTTTGTCAAATGCACAGCTAGGCCTCAAAGGCAATTAGCCTTTAATATAA
CTGGCATAATTGACACCTTTCTGTCAAATGCATAACTAGGCCTCAAAGGAACCTAGCCTTTCATC
TAACA
Found at i:29466 original size:57 final size:57
Alignment explanation
Indices: 29382--29696 Score: 427
Period size: 57 Copynumber: 5.5 Consensus size: 57
29372 CCAATAAAGT
* * * **
29382 AATTCATATAATTTCTT-AGTTTTTGCACATAAAGTTCTTATACGGAAATTCATAAACA
1 AATT-ATA-AATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACA
* * *
29440 AATTATGAATTTCTTAACTTTTTGCACCCAAAGTGCCCATACAGAAATTCATAAACA
1 AATTATAAATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACA
29497 AATTATAAATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACA
1 AATTATAAATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACA
*** *
29554 AATTATAAATTTCTTAACTTTTTGCACACAAAGTGCATTTACGGAAATTCATAAAAA
1 AATTATAAATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACA
* *
29611 AATTATAAATTTCTTAACTTTTTGCACACAATA-TGCCCATATGGAAATTTATAAACA
1 AATTATAAATTTCTTAACTTTTTGCACACAA-AGTGCCCATACGGAAATTCATAAACA
** * *
29668 AATTATGGATTTCCTAACTTTTTGTACAC
1 AATTATAAATTTCTTAACTTTTTGCACAC
29697 TCAATACCGT
Statistics
Matches: 230, Mismatches: 25, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
56 8 0.03
57 217 0.94
58 5 0.02
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.36
Consensus pattern (57 bp):
AATTATAAATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACA
Found at i:33114 original size:22 final size:22
Alignment explanation
Indices: 33071--33125 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
33061 GTGGAACCAA
*
33071 GAAGGTAACTG-ACACTAGCTG
1 GAAGGTAGCTGAACACTAGCTG
*
33092 GAAGGTAGCTGAACAGTAGCTG
1 GAAGGTAGCTGAACACTAGCTG
*
33114 GATGGTAGCTGA
1 GAAGGTAGCTGA
33126 GGACTCAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 10 0.33
22 20 0.67
ACGTcount: A:0.31, C:0.15, G:0.35, T:0.20
Consensus pattern (22 bp):
GAAGGTAGCTGAACACTAGCTG
Found at i:54153 original size:11 final size:12
Alignment explanation
Indices: 54132--54157 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
54122 AGATAAAGAT
54132 AAAGAAAAAAAA
1 AAAGAAAAAAAA
54144 AAAGAAAAAAAA
1 AAAGAAAAAAAA
54156 AA
1 AA
54158 TTATTATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAGAAAAAAAA
Found at i:59274 original size:12 final size:12
Alignment explanation
Indices: 59253--59287 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
59243 AATAAGCCTG
59253 AAAATAATAAAGT
1 AAAAT-ATAAAGT
59266 AAAATATAAAGT
1 AAAATATAAAGT
*
59278 AAACTATAAA
1 AAAATATAAA
59288 AAATAAAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 16 0.76
13 5 0.24
ACGTcount: A:0.69, C:0.03, G:0.06, T:0.23
Consensus pattern (12 bp):
AAAATATAAAGT
Done.