Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000843.1 Hibiscus syriacus cultivar Beakdansim tig00001626_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: 47836
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1133 original size:29 final size:30
Alignment explanation
Indices: 1100--1159 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
1090 CATCCTCCAG
* *
1100 AAACGTGTCA-ATATGAAGTTTGATGGTAT
1 AAACGAGTCACATATAAAGTTTGATGGTAT
*
1129 AAACGAGTCATCATTTAAAGTTTGATGGTAT
1 AAACGAGTCA-CATATAAAGTTTGATGGTAT
1160 CGGTGTAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 9 0.35
31 17 0.65
ACGTcount: A:0.35, C:0.08, G:0.22, T:0.35
Consensus pattern (30 bp):
AAACGAGTCACATATAAAGTTTGATGGTAT
Found at i:6276 original size:31 final size:31
Alignment explanation
Indices: 6228--6352 Score: 180
Period size: 31 Copynumber: 4.0 Consensus size: 31
6218 CCCGAATGAC
* *
6228 CAGTCCATA-GATTCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
6259 CAATCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
6290 GAGTCCATATGTCCCGAATAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
6321 CAGTCCATATATCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
6352 C
1 C
6353 CCTCGACCCT
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
31 83 0.99
32 1 0.01
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:6570 original size:59 final size:59
Alignment explanation
Indices: 6460--6575 Score: 144
Period size: 59 Copynumber: 2.0 Consensus size: 59
6450 ATATCATTTC
* * * *
6460 TCTTATAAACACATATCTCTTATTTTCTGTCACGTATCACATGTACGTGTAATCATTGA
1 TCTTATAAACACATATCTCTTATTTTCTGTCACATACCACATGTACATGTAAACATTGA
* * * *
6519 TCTTATAATCACATATTTCTT-TTCTTCTGTCACATACCATATGTATATGTAAACATT
1 TCTTATAAACACATATCTCTTATT-TTCTGTCACATACCACATGTACATGTAAACATT
6576 TATTTCATAT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
58 2 0.04
59 46 0.96
ACGTcount: A:0.29, C:0.20, G:0.08, T:0.43
Consensus pattern (59 bp):
TCTTATAAACACATATCTCTTATTTTCTGTCACATACCACATGTACATGTAAACATTGA
Found at i:8941 original size:20 final size:20
Alignment explanation
Indices: 8916--8967 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
8906 GACCAATAAA
8916 TTCGCAACGCGATCTCCAAT
1 TTCGCAACGCGATCTCCAAT
* * *
8936 TTCGCAACCCAATTTCCAAT
1 TTCGCAACGCGATCTCCAAT
8956 TTCGCAACGCGA
1 TTCGCAACGCGA
8968 ATATGTAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.27, C:0.35, G:0.13, T:0.25
Consensus pattern (20 bp):
TTCGCAACGCGATCTCCAAT
Found at i:8979 original size:20 final size:20
Alignment explanation
Indices: 8956--9022 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
8946 AATTTCCAAT
8956 TTCGCAACGCGAATATGTAA
1 TTCGCAACGCGAATATGTAA
** * * **
8976 TTCGCATTGCGATTTTCCAAA
1 TTCGCAACGCGAATAT-GTAA
*
8997 TTCGCAACGCGAATCTGTAA
1 TTCGCAACGCGAATATGTAA
*
9017 ATCGCA
1 TTCGCA
9023 GCACAGAAGT
Statistics
Matches: 33, Mismatches: 13, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
20 19 0.58
21 14 0.42
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (20 bp):
TTCGCAACGCGAATATGTAA
Found at i:9041 original size:20 final size:20
Alignment explanation
Indices: 9018--9084 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
9008 AATCTGTAAA
*
9018 TCGCAGCACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
9038 TCGCAACGC-GATAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
* *
9058 TCGTAACACAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
9078 TCGCAAC
1 TCGCAAC
9085 GCGAATCTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
19 2 0.05
20 36 0.92
21 1 0.03
ACGTcount: A:0.40, C:0.25, G:0.16, T:0.18
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:9048 original size:40 final size:40
Alignment explanation
Indices: 8993--9104 Score: 147
Period size: 40 Copynumber: 2.8 Consensus size: 40
8983 TGCGATTTTC
* *
8993 CAAATTCGCAACGCGAATCTGTAAATCGCAGCACAGAAGT
1 CAAATTCGCAACGCGAATCTGTAAATCGCAACACAAAAGT
* *
9033 CAAATTCGCAACGCG-AT-AGTCAAATTCGTAACACAAAAGT
1 CAAATTCGCAACGCGAATCTGT-AAA-TCGCAACACAAAAGT
*
9073 CAAATTCGCAACGCGAATCTATAAATCGCAAC
1 CAAATTCGCAACGCGAATCTGTAAATCGCAAC
9105 GCGAATTTGT
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
38 2 0.03
39 5 0.08
40 48 0.79
41 5 0.08
42 1 0.02
ACGTcount: A:0.40, C:0.25, G:0.16, T:0.19
Consensus pattern (40 bp):
CAAATTCGCAACGCGAATCTGTAAATCGCAACACAAAAGT
Found at i:9162 original size:60 final size:59
Alignment explanation
Indices: 9028--9164 Score: 163
Period size: 60 Copynumber: 2.3 Consensus size: 59
9018 TCGCAGCACA
9028 GAAGTCAAATTCGCAACGCGATAGTCAAATTCGTAACACAAAAGTCAAATTCGCAACGC
1 GAAGTCAAATTCGCAACGCGATAGTCAAATTCGTAACACAAAAGTCAAATTCGCAACGC
* * * * *
9087 GAA-TCTATAAATCGCAACGCGAATTTGT-AAA-TCGTAACACATAAGTTAAATTTGCAACGC
1 GAAGTC-A-AATTCGCAACGCG-A-TAGTCAAATTCGTAACACAAAAGTCAAATTCGCAACGC
9147 GATAGTCAAATTCGCAAC
1 GA-AGTCAAATTCGCAAC
9165 TGAATTTCAA
Statistics
Matches: 66, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
58 2 0.03
59 4 0.06
60 49 0.74
61 6 0.09
62 5 0.08
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.23
Consensus pattern (59 bp):
GAAGTCAAATTCGCAACGCGATAGTCAAATTCGTAACACAAAAGTCAAATTCGCAACGC
Found at i:9163 original size:20 final size:20
Alignment explanation
Indices: 9030--9164 Score: 100
Period size: 20 Copynumber: 6.8 Consensus size: 20
9020 GCAGCACAGA
9030 AGTCAAATTCGCAACGCGAT
1 AGTCAAATTCGCAACGCGAT
* * * *
9050 AGTCAAATTCGTAACACAAA
1 AGTCAAATTCGCAACGCGAT
9070 AGTCAAATTCGCAACGCGA-
1 AGTCAAATTCGCAACGCGAT
*
9089 A-TCTATAAATCGCAACGCGAATT
1 AGTC-A-AATTCGCAACGCG-A-T
* * *
9112 TGT-AAA-TCGTAACAC-AT
1 AGTCAAATTCGCAACGCGAT
* *
9129 AAGTTAAATTTGCAACGCGAT
1 -AGTCAAATTCGCAACGCGAT
9150 AGTCAAATTCGCAAC
1 AGTCAAATTCGCAAC
9165 TGAATTTCAA
Statistics
Matches: 88, Mismatches: 17, Indels: 20
0.70 0.14 0.16
Matches are distributed among these distances:
17 1 0.01
18 5 0.06
19 5 0.06
20 70 0.80
21 5 0.06
22 1 0.01
24 1 0.01
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.23
Consensus pattern (20 bp):
AGTCAAATTCGCAACGCGAT
Found at i:9197 original size:20 final size:19
Alignment explanation
Indices: 9152--9203 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 19
9142 AACGCGATAG
*
9152 TCAAATTCGCAACTGAATT
1 TCAAATTCACAACTGAATT
*
9171 TCAAATTCACAACTAGATTT
1 TCAAATTCACAACT-GAATT
* *
9191 TCGAATTTACAAC
1 TCAAATTCACAAC
9204 ACGAATTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.33
Consensus pattern (19 bp):
TCAAATTCACAACTGAATT
Found at i:10193 original size:24 final size:24
Alignment explanation
Indices: 10166--10219 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
10156 GTATTCGAAA
10166 TTTGATCTTGGTCAATACCTGGAC
1 TTTGATCTTGGTCAATACCTGGAC
* * *
10190 TTTGATCTTGGTCAATTCTTGGAT
1 TTTGATCTTGGTCAATACCTGGAC
10214 TTTGAT
1 TTTGAT
10220 GATGTGATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.19, C:0.15, G:0.20, T:0.46
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCTGGAC
Found at i:12502 original size:18 final size:18
Alignment explanation
Indices: 12479--12514 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
12469 AAGCAAAAGG
*
12479 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
12497 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
12515 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:14599 original size:4 final size:4
Alignment explanation
Indices: 14578--14615 Score: 58
Period size: 4 Copynumber: 9.5 Consensus size: 4
14568 GGGCCACTGA
* *
14578 AAAT AAAT TAAT ACAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
14616 TACCGAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:16636 original size:19 final size:19
Alignment explanation
Indices: 16585--16638 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
16575 AGTAGTTTCT
* *
16585 GAAACTTAAATTCGCAATGC
1 GAAAC-TAAAATCGCAACGC
*
16605 GAAAATGAAAATCGCAACGC
1 GAAACT-AAAATCGCAACGC
16625 GAAACTAAAATCGC
1 GAAACTAAAATCGC
16639 GTTGCGATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 9 0.31
20 20 0.69
ACGTcount: A:0.46, C:0.20, G:0.17, T:0.17
Consensus pattern (19 bp):
GAAACTAAAATCGCAACGC
Found at i:17178 original size:41 final size:41
Alignment explanation
Indices: 17133--17213 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 41
17123 ATATTGTGTT
*
17133 TCGCGTTGTGAATTTGAAA-TTATGTGTTGCAAATTTGACTA
1 TCGCGTTGCGAATTT-AAACTTATGTGTTGCAAATTTGACTA
* * *
17174 TCGCGTTGCGAGTTTAAACTTTTGTGTTGCGAATTTGACT
1 TCGCGTTGCGAATTTAAACTTATGTGTTGCAAATTTGACT
17214 TTTGTGTTGC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 3 0.09
41 32 0.91
ACGTcount: A:0.22, C:0.12, G:0.23, T:0.42
Consensus pattern (41 bp):
TCGCGTTGCGAATTTAAACTTATGTGTTGCAAATTTGACTA
Found at i:17216 original size:20 final size:20
Alignment explanation
Indices: 17155--17265 Score: 114
Period size: 20 Copynumber: 5.5 Consensus size: 20
17145 TTTGAAATTA
* *
17155 TGTGTTGCAAATTTGACTAT
1 TGTGTTGCGAATTTGACTTT
* * * *
17175 CGCGTTGCGAGTTTAAACTTT
1 TGTGTTGCGAATTT-GACTTT
17196 TGTGTTGCGAATTTGACTTT
1 TGTGTTGCGAATTTGACTTT
* *
17216 TGTGTTGCGGATTTGACTAT
1 TGTGTTGCGAATTTGACTTT
* * *
17236 CGCGTTGCGAATTTGACTTA
1 TGTGTTGCGAATTTGACTTT
17256 TGTGTTGCGA
1 TGTGTTGCGA
17266 TTTACAGATT
Statistics
Matches: 71, Mismatches: 19, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
20 56 0.79
21 15 0.21
ACGTcount: A:0.18, C:0.14, G:0.26, T:0.42
Consensus pattern (20 bp):
TGTGTTGCGAATTTGACTTT
Found at i:17223 original size:61 final size:61
Alignment explanation
Indices: 17137--17265 Score: 170
Period size: 61 Copynumber: 2.1 Consensus size: 61
17127 TGTGTTTCGC
* * *
17137 GTTGTGAATTTGAAATTATGTGTTGCAAATTTGACTATCGCGTTGCGAGTTTAAACTTTTGT
1 GTTGCGAATTTGAAATTATGTGTTGCAAATTTGACTATCGCGTTGCGAATTT-AACTTATGT
* * ** *
17199 GTTGCGAATTTG-ACTTTTGTGTTGCGGATTTGACTATCGCGTTGCGAATTTGACTTATGT
1 GTTGCGAATTTGAAATTATGTGTTGCAAATTTGACTATCGCGTTGCGAATTTAACTTATGT
17259 GTTGCGA
1 GTTGCGA
17266 TTTACAGATT
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
60 14 0.24
61 34 0.58
62 11 0.19
ACGTcount: A:0.20, C:0.12, G:0.26, T:0.43
Consensus pattern (61 bp):
GTTGCGAATTTGAAATTATGTGTTGCAAATTTGACTATCGCGTTGCGAATTTAACTTATGT
Found at i:17253 original size:40 final size:40
Alignment explanation
Indices: 17199--17285 Score: 124
Period size: 40 Copynumber: 2.2 Consensus size: 40
17189 AAACTTTTGT
* *
17199 GTTGCGAATTTGACTTTTGTGTTGCGGATTTGAC-TA-TCGC
1 GTTGCGAATTTGACTTATGTGTTGC-GATTT-ACAGATTCGC
17239 GTTGCGAATTTGACTTATGTGTTGCGATTTACAGATTCGC
1 GTTGCGAATTTGACTTATGTGTTGCGATTTACAGATTCGC
17279 GTTGCGA
1 GTTGCGA
17286 TTTACAGATT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
38 2 0.05
39 6 0.14
40 35 0.81
ACGTcount: A:0.17, C:0.15, G:0.28, T:0.40
Consensus pattern (40 bp):
GTTGCGAATTTGACTTATGTGTTGCGATTTACAGATTCGC
Found at i:17282 original size:20 final size:20
Alignment explanation
Indices: 17259--17305 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
17249 TGACTTATGT
17259 GTTGCGATTTACAGATTCGC
1 GTTGCGATTTACAGATTCGC
17279 GTTGCGATTTACAGATTCGC
1 GTTGCGATTTACAGATTCGC
17299 GTTGCGA
1 GTTGCGA
17306 AATTGGAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (20 bp):
GTTGCGATTTACAGATTCGC
Found at i:26310 original size:12 final size:12
Alignment explanation
Indices: 26293--26317 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
26283 TATCAAGGCG
26293 GCAAATATTGTA
1 GCAAATATTGTA
26305 GCAAATATTGTA
1 GCAAATATTGTA
26317 G
1 G
26318 TTGCCTAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (12 bp):
GCAAATATTGTA
Found at i:27413 original size:92 final size:93
Alignment explanation
Indices: 27253--27510 Score: 279
Period size: 93 Copynumber: 2.8 Consensus size: 93
27243 GTCATCATGC
* * * * *
27253 ATCCAAGTTATTACATTAATGGATGGAAATTTAAAAAGCGTTGAAATGTTTAAATTAAACACTCT
1 ATCCAAGTTATTACATTAATGAATGAAAATTTAAATAGCGTTGAAATGTTTAAACTAAACACTTT
*
27318 GATGTTTACGA-ACT-AAGATGTTAACTT
66 GATGTTTAC-ATACTAAAGAAGTTAACTT
* * * * *
27345 ATTCAAGTTGTTACATTAATGAATGAAAATTTTAATAGTGTTGAAATGTTTTAACTAAACACTTT
1 ATCCAAGTTATTACATTAATGAATGAAAATTTAAATAGCGTTGAAATGTTTAAACTAAACACTTT
* *
27410 GATGTTTGCATATTAAAGAAGTTAACTT
66 GATGTTTACATACTAAAGAAGTTAACTT
* * * * * * * *
27438 ATCCAAATTATTTCATTGAT-AGATGAAAGTTTAAATAGCGTTGAAAAGTATGAACTAAACAATT
1 ATCCAAGTTATTACATTAATGA-ATGAAAATTTAAATAGCGTTGAAATGTTTAAACTAAACACTT
*
27502 TAATGTTTA
65 TGATGTTTA
27511 TGTATTAAGA
Statistics
Matches: 136, Mismatches: 27, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
91 1 0.01
92 66 0.49
93 69 0.51
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (93 bp):
ATCCAAGTTATTACATTAATGAATGAAAATTTAAATAGCGTTGAAATGTTTAAACTAAACACTTT
GATGTTTACATACTAAAGAAGTTAACTT
Found at i:27483 original size:93 final size:90
Alignment explanation
Indices: 27253--27510 Score: 266
Period size: 92 Copynumber: 2.8 Consensus size: 90
27243 GTCATCATGC
* * *
27253 ATCCAAGTTATTACATTAATGGATGGAAATTTAAAAAGCGTTGAAATGTTTAAATTAAACACTCT
1 ATCCAAGTTATTACATTAAT-GAT-GAAATTTAAATAGCGTTGAAATGTTTAAACTAAACACTTT
*
27318 GATGTTTACGAACTAAGATGTTAACTT
64 GATGTTTACGAACTAAGAAGTTAACTT
* * * * *
27345 ATTCAAGTTGTTACATTAATGAATGAAAATTTTAATAGTGTTGAAATGTTTTAACTAAACACTTT
1 ATCCAAGTTATTACATTAATG-ATG-AAATTTAAATAGCGTTGAAATGTTTAAACTAAACACTTT
* *
27410 GATGTTTGC-ATATTAAAGAAGTTAACTT
64 GATGTTTACGA-ACT-AAGAAGTTAACTT
* * * * * * *
27438 ATCCAAATTATTTCATTGATAGATGAAAGTTTAAATAGCGTTGAAAAGTATGAACTAAACAATTT
1 ATCCAAGTTATTACATTAAT-GATGAAA-TTTAAATAGCGTTGAAATGTTTAAACTAAACACTTT
*
27503 AATGTTTA
64 GATGTTTA
27511 TGTATTAAGA
Statistics
Matches: 136, Mismatches: 24, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
91 3 0.02
92 66 0.49
93 66 0.49
94 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (90 bp):
ATCCAAGTTATTACATTAATGATGAAATTTAAATAGCGTTGAAATGTTTAAACTAAACACTTTGA
TGTTTACGAACTAAGAAGTTAACTT
Found at i:28819 original size:15 final size:16
Alignment explanation
Indices: 28793--28825 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
28783 GAAATTTTAT
28793 TTGATGTATTTTACTA
1 TTGATGTATTTTACTA
*
28809 TTGAT-TATTTTATTA
1 TTGATGTATTTTACTA
28824 TT
1 TT
28826 TATTTTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.24, C:0.03, G:0.09, T:0.64
Consensus pattern (16 bp):
TTGATGTATTTTACTA
Found at i:31839 original size:14 final size:13
Alignment explanation
Indices: 31812--31878 Score: 55
Period size: 14 Copynumber: 4.9 Consensus size: 13
31802 TTATAAAATT
*
31812 ATAAA-TAAAGAA
1 ATAAATTAAATAA
31824 ATAAATATAAATAA
1 ATAAAT-TAAATAA
* *
31838 ATAACTTAATTTAA
1 ATAAATTAA-ATAA
31852 ATAAATTAAATTAA
1 ATAAATTAAA-TAA
*
31866 ATTTAATTAAATA
1 A-TAAATTAAATA
31879 GTATTATTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
12 5 0.11
13 3 0.07
14 28 0.64
15 8 0.18
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (13 bp):
ATAAATTAAATAA
Found at i:33279 original size:37 final size:37
Alignment explanation
Indices: 33228--33308 Score: 135
Period size: 37 Copynumber: 2.2 Consensus size: 37
33218 TATTATAACG
* * *
33228 AATTCAATTTAAAAATAATCTACTATGTAACTAATTT
1 AATTTAATCTAAAAATAATCTACTAAGTAACTAATTT
33265 AATTTAATCTAAAAATAATCTACTAAGTAACTAATTT
1 AATTTAATCTAAAAATAATCTACTAAGTAACTAATTT
33302 AATTTAA
1 AATTTAA
33309 ACAAGTAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.48, C:0.10, G:0.02, T:0.40
Consensus pattern (37 bp):
AATTTAATCTAAAAATAATCTACTAAGTAACTAATTT
Found at i:33644 original size:20 final size:20
Alignment explanation
Indices: 33610--33672 Score: 85
Period size: 20 Copynumber: 3.2 Consensus size: 20
33600 TTTAACTTTA
*
33610 TTCTCTTCT-TCTTCTTTCT
1 TTCTCTTTTCTCTTCTTTCT
*
33629 TTCTTTTTTCTCTTCTTTCT
1 TTCTCTTTTCTCTTCTTTCT
*
33649 TCCTCTTTTCTCTTCTTT-T
1 TTCTCTTTTCTCTTCTTTCT
33668 TTCTC
1 TTCTC
33673 CCCTTATTTC
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
19 12 0.32
20 26 0.68
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (20 bp):
TTCTCTTTTCTCTTCTTTCT
Found at i:33655 original size:26 final size:26
Alignment explanation
Indices: 33605--33656 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
33595 TCGACTTTAA
*
33605 CTTTATTCTCTTCTTCTTCTTTCTTT
1 CTTTATTCTCTTCTTCTTCTCTCTTT
*
33631 CTTTTTTCTCTTCTTTCTTC-CTCTTT
1 CTTTATTCTCTTC-TTCTTCTCTCTTT
33657 TCTCTTCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 17 0.74
27 6 0.26
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (26 bp):
CTTTATTCTCTTCTTCTTCTCTCTTT
Found at i:33725 original size:2 final size:2
Alignment explanation
Indices: 33718--33744 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
33708 CCCTACACCC
33718 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
33745 TTAAAACCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:34199 original size:100 final size:99
Alignment explanation
Indices: 33867--34199 Score: 369
Period size: 99 Copynumber: 3.4 Consensus size: 99
33857 ATGCATGACT
* * * **
33867 TGCAGGGGGAGTAACATGGATTTCCATGCGTCTTCCAGGGATTTTGTTTTCAACATGGCAACATC
1 TGCAGGGGGAGTCACATGGATTTCCATGCGTCTTCCAGGGTTTTTGTTTTCAACGTGGCAACAAA
* ** *
33932 GAATGAGGTGGCAACAACAACAGTGCATGGGGCA
66 GAATGGGGTGGCAGTAACAGCAGTGCATGGGGCA
* * *
33966 TGCAGGGGGAGTCACATGGATTTCCATGAGTCTTCCAGGGTTTTTATTTTCAACGTGGTAACAAA
1 TGCAGGGGGAGTCACATGGATTTCCATGCGTCTTCCAGGGTTTTTGTTTTCAACGTGGCAACAAA
* * * *
34031 GAATGGGGAGGCAGTAACAGTAGTGCATAGGGAA
66 GAATGGGGTGGCAGTAACAGCAGTGCATGGGGCA
* * * * * * * *
34065 TGTAGGGTGAGTCGCATGTATTTTCATGCATCTTCCAAGGGTTTTTGTTTTCAACGTGGCAGCAG
1 TGCAGGGGGAGTCACATGGATTTCCATGCGTCTTCC-AGGGTTTTTGTTTTCAACGTGGCAACAA
* * * *
34130 GGAATGGGGTGGCAGTAGCAGCAGCGAATGGGGCA
65 AGAATGGGGTGGCAGTAACAGCAGTGCATGGGGCA
* * * *
34165 TGCAGGGGGAATCGCATGAATTTCCATTCGTCTTC
1 TGCAGGGGGAGTCACATGGATTTCCATGCGTCTTC
34200 GTGGGGAGAC
Statistics
Matches: 191, Mismatches: 42, Indels: 1
0.82 0.18 0.00
Matches are distributed among these distances:
99 112 0.59
100 79 0.41
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (99 bp):
TGCAGGGGGAGTCACATGGATTTCCATGCGTCTTCCAGGGTTTTTGTTTTCAACGTGGCAACAAA
GAATGGGGTGGCAGTAACAGCAGTGCATGGGGCA
Found at i:36787 original size:38 final size:38
Alignment explanation
Indices: 36736--36825 Score: 117
Period size: 38 Copynumber: 2.4 Consensus size: 38
36726 AATTTATATA
* * *
36736 TATCTTGATTTAATTTTAAACAAATTTACTGCCAATCT
1 TATCTCGATTTAATTTCAAACAAATTTACTGACAATCT
* * * *
36774 TATCTCGATTTAATTTCAAATAAATTTATTTATAATCT
1 TATCTCGATTTAATTTCAAACAAATTTACTGACAATCT
36812 TATCTCGATTTAAT
1 TATCTCGATTTAAT
36826 ATAAAATATT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 45 1.00
ACGTcount: A:0.34, C:0.13, G:0.04, T:0.48
Consensus pattern (38 bp):
TATCTCGATTTAATTTCAAACAAATTTACTGACAATCT
Found at i:37813 original size:13 final size:13
Alignment explanation
Indices: 37763--37806 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
37753 TCTATATAAA
37763 CAGTTAATCAAAT
1 CAGTTAATCAAAT
**
37776 CAGTTTCTCAAAT
1 CAGTTAATCAAAT
*
37789 CAGCTAATCAAAT
1 CAGTTAATCAAAT
37802 CAGTT
1 CAGTT
37807 GGTCAAACCA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (13 bp):
CAGTTAATCAAAT
Found at i:37829 original size:26 final size:26
Alignment explanation
Indices: 37767--37820 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
37757 TATAAACAGT
* *
37767 TAATCAAATCAGTTTCTCAAATCAGC
1 TAATCAAATCAGTTGCTCAAACCAGC
*
37793 TAATCAAATCAGTTGGTCAAACCAGC
1 TAATCAAATCAGTTGCTCAAACCAGC
37819 TA
1 TA
37821 CTAGAATCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.39, C:0.22, G:0.11, T:0.28
Consensus pattern (26 bp):
TAATCAAATCAGTTGCTCAAACCAGC
Found at i:40219 original size:30 final size:30
Alignment explanation
Indices: 40183--40247 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
40173 TTTCTAACAT
* *
40183 TTGTTATTAAAGGTCTAATTTTTTCAATAC
1 TTGTTATGAAAGGTCCAATTTTTTCAATAC
* *
40213 TTGTTATGAATGGTCCAATTTTTTCAATAT
1 TTGTTATGAAAGGTCCAATTTTTTCAATAC
40243 TTGTT
1 TTGTT
40248 CTTAGGGTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.26, C:0.09, G:0.12, T:0.52
Consensus pattern (30 bp):
TTGTTATGAAAGGTCCAATTTTTTCAATAC
Found at i:41067 original size:16 final size:17
Alignment explanation
Indices: 41038--41084 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 17
41028 AAAATATTTT
41038 ATATATAATTAATATAAA
1 ATATATAA-TAATATAAA
* *
41056 ATATATAA-AATATTAT
1 ATATATAATAATATAAA
41072 ATATATATATAAT
1 ATATATA-ATAAT
41085 CGGGGCGGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 13 0.52
17 1 0.04
18 11 0.44
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATATATAATAATATAAA
Found at i:43010 original size:23 final size:22
Alignment explanation
Indices: 42950--43001 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
42940 TTTATTGAAT
42950 GTGCCCACTCTGAATTTTTGTC
1 GTGCCCACTCTGAATTTTTGTC
42972 GTGCCCACTCTGAATTTTTGTC
1 GTGCCCACTCTGAATTTTTGTC
*
42994 GTGTCCAC
1 GTGCCCAC
43002 CTTGAAATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.13, C:0.29, G:0.19, T:0.38
Consensus pattern (22 bp):
GTGCCCACTCTGAATTTTTGTC
Done.