Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002541.1 Hibiscus syriacus cultivar Beakdansim tig00005160_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: 55650
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:6636 original size:104 final size:105
Alignment explanation
Indices: 6444--6653 Score: 386
Period size: 104 Copynumber: 2.0 Consensus size: 105
6434 ACGATGCAAC
*
6444 ACCTGTGGTAATGGACCCAGAAAATTAAAACCAGGAATCAGATTAAACTAGATCATCAGATGAAA
1 ACCTGTGGTAATGGACCCAGAAAATCAAAACCAGGAATCAGATTAAACTAGATCATCAGATGAAA
6509 GCAAGAAGAAAAATGGAGTAGTACCATGAAAGTCCTGGGG
66 GCAAGAAGAAAAATGGAGTAGTACCATGAAAGTCCTGGGG
*
6549 ACCTGTGGTAATGGACCCAGAAAATCGAAACCAGGAATCAGATT-AACTAGATCATCAGATGAAA
1 ACCTGTGGTAATGGACCCAGAAAATCAAAACCAGGAATCAGATTAAACTAGATCATCAGATGAAA
*
6613 GCAAGAAGAAAAATGGAGTAGTACCGTGAAAGTCCTGGGG
66 GCAAGAAGAAAAATGGAGTAGTACCATGAAAGTCCTGGGG
6653 A
1 A
6654 GCCATGCAAG
Statistics
Matches: 102, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
104 60 0.59
105 42 0.41
ACGTcount: A:0.42, C:0.16, G:0.25, T:0.18
Consensus pattern (105 bp):
ACCTGTGGTAATGGACCCAGAAAATCAAAACCAGGAATCAGATTAAACTAGATCATCAGATGAAA
GCAAGAAGAAAAATGGAGTAGTACCATGAAAGTCCTGGGG
Found at i:12601 original size:22 final size:22
Alignment explanation
Indices: 12554--12595 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
12544 AATGAACATA
*
12554 TAAACGAACATTAAACAAATAC
1 TAAACGAACACTAAACAAATAC
*
12576 TAAACGAACGCTAAACAAAT
1 TAAACGAACACTAAACAAAT
12596 GTTAAATGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.57, C:0.19, G:0.07, T:0.17
Consensus pattern (22 bp):
TAAACGAACACTAAACAAATAC
Found at i:12628 original size:23 final size:23
Alignment explanation
Indices: 12598--12660 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
12588 AAACAAATGT
* * *
12598 TAAATGAATATATTCGTTAGCGC
1 TAAATGAACATATTCGTGAACGC
* *
12621 TAAATGAACATGTTCGTGAATGC
1 TAAATGAACATATTCGTGAACGC
*
12644 TAAATGAACACATTCGT
1 TAAATGAACATATTCGT
12661 AAATATCAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (23 bp):
TAAATGAACATATTCGTGAACGC
Found at i:13242 original size:46 final size:47
Alignment explanation
Indices: 13156--13245 Score: 146
Period size: 47 Copynumber: 1.9 Consensus size: 47
13146 TTCAGTAGAG
**
13156 CGCTACCTAAAATGTTATTTTTTCCTACCGAAAATATTAATATCGGA
1 CGCTACCTAAAATGTTATTTTTTCCTACAAAAAATATTAATATCGGA
*
13203 CGCTACCTAAAATGTTATTTTTT-CTACAAAAAATGTTAATATC
1 CGCTACCTAAAATGTTATTTTTTCCTACAAAAAATATTAATATC
13246 AGAAATATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
46 17 0.43
47 23 0.57
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.38
Consensus pattern (47 bp):
CGCTACCTAAAATGTTATTTTTTCCTACAAAAAATATTAATATCGGA
Found at i:14098 original size:25 final size:25
Alignment explanation
Indices: 14064--14113 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
14054 ATTAATAATT
*
14064 TAATTCTACATCTTCTAAAATTTTA
1 TAATTCTACATCTTATAAAATTTTA
*
14089 TAATTTTACATCTTATAAAATTTTA
1 TAATTCTACATCTTATAAAATTTTA
14114 ATACAAATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (25 bp):
TAATTCTACATCTTATAAAATTTTA
Found at i:18698 original size:2 final size:2
Alignment explanation
Indices: 18691--18764 Score: 148
Period size: 2 Copynumber: 37.0 Consensus size: 2
18681 TTATAAAATA
18691 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18733 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18765 GAGATTATAT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21096 original size:42 final size:42
Alignment explanation
Indices: 21037--21123 Score: 165
Period size: 42 Copynumber: 2.1 Consensus size: 42
21027 TATTCATTGA
*
21037 CCCAATCAGCACGTGTCTCAACCGGCTTTCACCCATTCCCTC
1 CCCAATCAGCACGTGTCTCAACCGGCTTTCACCCATGCCCTC
21079 CCCAATCAGCACGTGTCTCAACCGGCTTTCACCCATGCCCTC
1 CCCAATCAGCACGTGTCTCAACCGGCTTTCACCCATGCCCTC
21121 CCC
1 CCC
21124 TTAACCACCG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.18, C:0.47, G:0.13, T:0.22
Consensus pattern (42 bp):
CCCAATCAGCACGTGTCTCAACCGGCTTTCACCCATGCCCTC
Found at i:26737 original size:10 final size:10
Alignment explanation
Indices: 26719--26754 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
26709 TTTGTTTGCT
26719 AACTCAATTC
1 AACTCAATTC
*
26729 AATTCAATTC
1 AACTCAATTC
*
26739 AACTCAACTC
1 AACTCAATTC
26749 AACTCA
1 AACTCA
26755 TTCTTGTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.42, C:0.31, G:0.00, T:0.28
Consensus pattern (10 bp):
AACTCAATTC
Found at i:28269 original size:64 final size:64
Alignment explanation
Indices: 28201--28357 Score: 176
Period size: 64 Copynumber: 2.5 Consensus size: 64
28191 TTGAAGGTGT
* ***
28201 ATCGATGCATTAGTAATGCATCGATGCA-CTCTTTTAA-AATAGAAACATCGAATGCA-ATTAGT
1 ATCGATGCATAAGTAATGCATCGATGCATC-CCAGTAATAATA-AAACATCGAATGCATATTA-T
28263 GC
63 GC
* * *
28265 ATCGATGCATAAGTCATGCATCGATGCATCCCAGTAATAATACAACATCGAATGCATTTTATGC
1 ATCGATGCATAAGTAATGCATCGATGCATCCCAGTAATAATAAAACATCGAATGCATATTATGC
* * *
28329 ACCGATGCATCAGTAGTGCATCGATGCAT
1 ATCGATGCATAAGTAATGCATCGATGCAT
28358 ACCCTCATTA
Statistics
Matches: 79, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
64 71 0.90
65 8 0.10
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (64 bp):
ATCGATGCATAAGTAATGCATCGATGCATCCCAGTAATAATAAAACATCGAATGCATATTATGC
Found at i:29001 original size:149 final size:150
Alignment explanation
Indices: 28812--29127 Score: 573
Period size: 150 Copynumber: 2.1 Consensus size: 150
28802 GGGTAGAGGG
* *
28812 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTT-GAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
*
28876 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
28941 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
*
28961 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
29026 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
29091 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
29111 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
29128 TGCATTTATA
Statistics
Matches: 161, Mismatches: 4, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
149 52 0.32
150 109 0.68
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.34
Consensus pattern (150 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
ATATGGCACTACGGTGCAAT
Found at i:29139 original size:23 final size:23
Alignment explanation
Indices: 29095--29139 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
29085 ATCATTATAT
*
29095 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
29118 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
29140 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:30491 original size:42 final size:42
Alignment explanation
Indices: 30432--30530 Score: 182
Period size: 42 Copynumber: 2.4 Consensus size: 42
30422 ATACTAGAAG
30432 AACAATATCGATACCATAAGGTAAAAATGTATGAATCCTTTA
1 AACAATATCGATACCATAAGGTAAAAATGTATGAATCCTTTA
30474 AACAATATCGATACCATAAGGTAAAAATGTATGAATCCTTTA
1 AACAATATCGATACCATAAGGTAAAAATGTATGAATCCTTTA
30516 AACAGA-ATCGATACC
1 AACA-ATATCGATACC
30531 GAAGGAGTAG
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
42 55 0.98
43 1 0.02
ACGTcount: A:0.45, C:0.16, G:0.12, T:0.26
Consensus pattern (42 bp):
AACAATATCGATACCATAAGGTAAAAATGTATGAATCCTTTA
Found at i:31162 original size:14 final size:15
Alignment explanation
Indices: 31143--31193 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
31133 TTACATGAAA
31143 ATGTGA-TATAAGCT
1 ATGTGACTATAAGCT
* *
31157 ATGTGACCATAACCT
1 ATGTGACTATAAGCT
* *
31172 ATGTGATTATATGTCT
1 ATGTGACTATAAG-CT
31188 ATGTGA
1 ATGTGA
31194 TACAAGATAT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
14 6 0.21
15 15 0.52
16 8 0.28
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.37
Consensus pattern (15 bp):
ATGTGACTATAAGCT
Found at i:31192 original size:45 final size:45
Alignment explanation
Indices: 31087--31205 Score: 123
Period size: 45 Copynumber: 2.6 Consensus size: 45
31077 ATCTTACGTG
* * **
31087 TTACATGATCTATGTGATATAAACTATGTGACATTGATTTATGTGA
1 TTACATG-TCTATGTGATATAAGCTATGTGACATTAACCTATGTGA
***
31133 TTACATGAAAATGTGATATAAGCTATGTGACCA-TAACCTATGTGA
1 TTACATGTCTATGTGATATAAGCTATGTGA-CATTAACCTATGTGA
* * *
31178 TTATATGTCTATGTGATACAAGATATGT
1 TTACATGTCTATGTGATATAAGCTATGT
31206 AAATTGTGTA
Statistics
Matches: 59, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
45 50 0.85
46 9 0.15
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (45 bp):
TTACATGTCTATGTGATATAAGCTATGTGACATTAACCTATGTGA
Found at i:31309 original size:23 final size:23
Alignment explanation
Indices: 31283--31379 Score: 88
Period size: 23 Copynumber: 4.2 Consensus size: 23
31273 GAGTCGAGAG
31283 TTCTATGCGGTCCTTCGGGACAA
1 TTCTATGCGGTCCTTCGGGACAA
* * * *
31306 TTCTACGTGGTCTTTTGGGA-AA
1 TTCTATGCGGTCCTTCGGGACAA
* **
31328 TTTCTGTGCGGTCCTTTAGGACAA
1 -TTCTATGCGGTCCTTCGGGACAA
* * *
31352 TACTATGTGGTCCTTCGGGACAT
1 TTCTATGCGGTCCTTCGGGACAA
31375 TTCTA
1 TTCTA
31380 CGTGGCACTT
Statistics
Matches: 56, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
22 2 0.04
23 52 0.93
24 2 0.04
ACGTcount: A:0.18, C:0.21, G:0.25, T:0.37
Consensus pattern (23 bp):
TTCTATGCGGTCCTTCGGGACAA
Found at i:31362 original size:46 final size:46
Alignment explanation
Indices: 31283--31379 Score: 122
Period size: 46 Copynumber: 2.1 Consensus size: 46
31273 GAGTCGAGAG
* * * *
31283 TTCTATGCGGTCCTTCGGGACAATTCTACGTGGTCTTTTGGGAAAT
1 TTCTATGCGGTCCTTCAGGACAATACTACGTGGTCCTTCGGGAAAT
* * * *
31329 TTCTGTGCGGTCCTTTAGGACAATACTATGTGGTCCTTCGGGACAT
1 TTCTATGCGGTCCTTCAGGACAATACTACGTGGTCCTTCGGGAAAT
31375 TTCTA
1 TTCTA
31380 CGTGGCACTT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.18, C:0.21, G:0.25, T:0.37
Consensus pattern (46 bp):
TTCTATGCGGTCCTTCAGGACAATACTACGTGGTCCTTCGGGAAAT
Found at i:31384 original size:23 final size:23
Alignment explanation
Indices: 31291--31392 Score: 82
Period size: 23 Copynumber: 4.4 Consensus size: 23
31281 AGTTCTATGC
31291 GGTCCTTCGGGACAATTCTACGT
1 GGTCCTTCGGGACAATTCTACGT
* * ** *
31314 GGTCTTTTGGGA-AATTTCTGTGC
1 GGTCCTTCGGGACAA-TTCTACGT
** * *
31337 GGTCCTTTAGGACAATACTATGT
1 GGTCCTTCGGGACAATTCTACGT
*
31360 GGTCCTTCGGGACATTTCTACGT
1 GGTCCTTCGGGACAATTCTACGT
31383 GG-CACTTCGG
1 GGTC-CTTCGG
31393 TGCATATTTT
Statistics
Matches: 61, Mismatches: 15, Indels: 6
0.74 0.18 0.07
Matches are distributed among these distances:
22 3 0.05
23 56 0.92
24 2 0.03
ACGTcount: A:0.17, C:0.22, G:0.27, T:0.34
Consensus pattern (23 bp):
GGTCCTTCGGGACAATTCTACGT
Found at i:31410 original size:24 final size:24
Alignment explanation
Indices: 31373--31429 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
31363 CCTTCGGGAC
* *
31373 ATTTCTACGTGGCACTTCGGTGCA
1 ATTTATACGCGGCACTTCGGTGCA
31397 TATTT-TACGCGGCACTTCGGTGCA
1 -ATTTATACGCGGCACTTCGGTGCA
31421 ATTTATACG
1 ATTTATACG
31430 AGTTGTGGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 4 0.13
24 22 0.73
25 4 0.13
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.35
Consensus pattern (24 bp):
ATTTATACGCGGCACTTCGGTGCA
Found at i:38270 original size:35 final size:35
Alignment explanation
Indices: 38212--38307 Score: 138
Period size: 35 Copynumber: 2.7 Consensus size: 35
38202 AATGAATTAT
* *
38212 GAATTTGGGGTTGAGCATATAATTGAAATATTTTG
1 GAATTTGGGGTTTAGAATATAATTGAAATATTTTG
* * *
38247 GAATTTGAGGTTTAGAATGTAATTGAAGTATTTTG
1 GAATTTGGGGTTTAGAATATAATTGAAATATTTTG
*
38282 GACTTTGGGGTTTAGAATATAATTGA
1 GAATTTGGGGTTTAGAATATAATTGA
38308 TGAATGTGTT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 53 1.00
ACGTcount: A:0.31, C:0.02, G:0.26, T:0.41
Consensus pattern (35 bp):
GAATTTGGGGTTTAGAATATAATTGAAATATTTTG
Found at i:45055 original size:25 final size:24
Alignment explanation
Indices: 45011--45057 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
45001 TAATGAATAT
*
45011 AATTTAATTTTCTTTAATTTTTAC
1 AATTTAATTTTATTTAATTTTTAC
45035 AATTATAATTTTA-TTATATTTTT
1 AATT-TAATTTTATTTA-ATTTTT
45058 CTTTATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (24 bp):
AATTTAATTTTATTTAATTTTTAC
Found at i:45563 original size:13 final size:13
Alignment explanation
Indices: 45547--45571 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
45537 TTTATACTAT
45547 ACTTTCATTTTTC
1 ACTTTCATTTTTC
45560 ACTTTCATTTTT
1 ACTTTCATTTTT
45572 ATTTAAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.20, G:0.00, T:0.64
Consensus pattern (13 bp):
ACTTTCATTTTTC
Found at i:46335 original size:16 final size:15
Alignment explanation
Indices: 46314--46347 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
46304 ATTATTTTAA
*
46314 TTTTAATTTTTATAAT
1 TTTTAA-TTGTATAAT
46330 TTTTAATTGTATAAT
1 TTTTAATTGTATAAT
46345 TTT
1 TTT
46348 ATTATATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (15 bp):
TTTTAATTGTATAAT
Found at i:46689 original size:14 final size:15
Alignment explanation
Indices: 46660--46691 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
46650 AAATAATTAA
46660 AATAATATATTTTAT
1 AATAATATATTTTAT
46675 AATAATATA-TTTAT
1 AATAATATATTTTAT
46689 AAT
1 AAT
46692 TATTTATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AATAATATATTTTAT
Found at i:47311 original size:14 final size:15
Alignment explanation
Indices: 47283--47311 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
47273 GATGATTCGA
47283 GTTTAAATATCAAAT
1 GTTTAAATATCAAAT
47298 GTTTAAAT-TCAAAT
1 GTTTAAATATCAAAT
47312 TCAATTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (15 bp):
GTTTAAATATCAAAT
Found at i:47339 original size:15 final size:16
Alignment explanation
Indices: 47318--47355 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
47308 AAATTCAATT
47318 ATATTTTAAT-TAAAC
1 ATATTTTAATCTAAAC
*
47333 TTATTTTAATCTAAAC
1 ATATTTTAATCTAAAC
47349 ATATTTT
1 ATATTTT
47356 CGAAAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (16 bp):
ATATTTTAATCTAAAC
Found at i:52026 original size:29 final size:29
Alignment explanation
Indices: 51954--52036 Score: 114
Period size: 29 Copynumber: 2.8 Consensus size: 29
51944 ATCGTTAATC
*
51954 TATTAAACTTTCAATTACTCTAATTATATT
1 TATTAAACTTT-AATTGCTCTAATTATATT
*
51984 TATTAAAATTTTAATTGCTCTAATTATA-T
1 TATT-AAACTTTAATTGCTCTAATTATATT
52013 TATTAAACTATTAATTGCTCTAAT
1 TATTAAACT-TTAATTGCTCTAAT
52037 ATAATACTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
28 4 0.08
29 19 0.40
30 19 0.40
31 6 0.12
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.49
Consensus pattern (29 bp):
TATTAAACTTTAATTGCTCTAATTATATT
Found at i:52244 original size:84 final size:84
Alignment explanation
Indices: 52103--52270 Score: 336
Period size: 84 Copynumber: 2.0 Consensus size: 84
52093 CGGCATGATG
52103 CTATGGACAAACCTTTTTGTCAATATGATAACATGGATAAAACGATATCGTTTTAGGTAGTTACC
1 CTATGGACAAACCTTTTTGTCAATATGATAACATGGATAAAACGATATCGTTTTAGGTAGTTACC
52168 TTTAATAGTGTATCAATTT
66 TTTAATAGTGTATCAATTT
52187 CTATGGACAAACCTTTTTGTCAATATGATAACATGGATAAAACGATATCGTTTTAGGTAGTTACC
1 CTATGGACAAACCTTTTTGTCAATATGATAACATGGATAAAACGATATCGTTTTAGGTAGTTACC
52252 TTTAATAGTGTATCAATTT
66 TTTAATAGTGTATCAATTT
52271 TGCCATTAGA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 84 1.00
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.38
Consensus pattern (84 bp):
CTATGGACAAACCTTTTTGTCAATATGATAACATGGATAAAACGATATCGTTTTAGGTAGTTACC
TTTAATAGTGTATCAATTT
Done.