Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002301.1 Hibiscus syriacus cultivar Beakdansim tig00004685_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: 48598
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:2084 original size:25 final size:24
Alignment explanation
Indices: 2044--2103 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 24
2034 TAAAATAAAG
*
2044 AAAATAAATGAA--TAAAAA-AAT
1 AAAATAAATAAAGGTAAAAAGAAT
2065 ACAAATAAAGTAAAGGTAAAAATGAAT
1 A-AAATAAA-TAAAGGTAAAAA-GAAT
2092 AAAATAAATAAA
1 AAAATAAATAAA
2104 ATGAAGAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
21 1 0.03
22 7 0.22
23 3 0.09
25 10 0.31
26 7 0.22
27 4 0.12
ACGTcount: A:0.72, C:0.02, G:0.08, T:0.18
Consensus pattern (24 bp):
AAAATAAATAAAGGTAAAAAGAAT
Found at i:2093 original size:35 final size:34
Alignment explanation
Indices: 2017--2132 Score: 116
Period size: 35 Copynumber: 3.4 Consensus size: 34
2007 CAAACAAATG
* *
2017 AAATGAAGAAAGTAATATAAAATAAAGAAA-AT--
1 AAATGAATAAAATAA-ATAAAATAAAGAAAGATAA
*
2049 AAATGAATAAAA-AAATACAAATAAAGTAAAGGTAA
1 AAATGAATAAAATAAATA-AAATAAAG-AAAGATAA
*
2084 AAATGAATAAAATAAATAAAATGAAGAAAGATAA
1 AAATGAATAAAATAAATAAAATAAAGAAAGATAA
*
2118 TAAT-AATAATAATAA
1 AAATGAATAA-AATAA
2133 TATATACATA
Statistics
Matches: 71, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
30 3 0.04
31 10 0.14
32 13 0.18
33 6 0.08
34 15 0.21
35 19 0.27
36 5 0.07
ACGTcount: A:0.69, C:0.01, G:0.10, T:0.20
Consensus pattern (34 bp):
AAATGAATAAAATAAATAAAATAAAGAAAGATAA
Found at i:2101 original size:9 final size:9
Alignment explanation
Indices: 2033--2148 Score: 53
Period size: 9 Copynumber: 12.6 Consensus size: 9
2023 AGAAAGTAAT
2033 ATAAAATAA
1 ATAAAATAA
*
2042 AGAAAATAA
1 ATAAAATAA
*
2051 AT-GAATAA
1 ATAAAATAA
2059 A-AAAATACAA
1 ATAAAAT--AA
*
2069 ATAAAGTAA
1 ATAAAATAA
*
2078 AGGTAAAAATGA
1 A--T-AAAATAA
2090 ATAAAATAA
1 ATAAAATAA
*
2099 ATAAAATGA
1 ATAAAATAA
*
2108 AGAAAGAT-A
1 ATAAA-ATAA
2117 ATAATAAT-A
1 ATAA-AATAA
*
2126 ATAATAATAT
1 ATAA-AATAA
*
2136 AT-ACATAA
1 ATAAAATAA
2144 ATAAA
1 ATAAA
2149 TATTAGTAAA
Statistics
Matches: 81, Mismatches: 15, Indels: 22
0.69 0.13 0.19
Matches are distributed among these distances:
8 14 0.17
9 47 0.58
10 9 0.11
11 5 0.06
12 6 0.07
ACGTcount: A:0.69, C:0.02, G:0.08, T:0.22
Consensus pattern (9 bp):
ATAAAATAA
Found at i:2324 original size:22 final size:22
Alignment explanation
Indices: 2299--2342 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2289 CATAGAAGGT
*
2299 AATAAAATAAGAATATAAAATA
1 AATAAAAGAAGAATATAAAATA
*
2321 AATAAAAGAAGAATATATAATA
1 AATAAAAGAAGAATATAAAATA
2343 TGATATTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (22 bp):
AATAAAAGAAGAATATAAAATA
Found at i:3966 original size:2 final size:2
Alignment explanation
Indices: 3959--3989 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3949 TATAACTGTA
3959 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3990 CACTAATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4310 original size:22 final size:23
Alignment explanation
Indices: 4278--4320 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
4268 TGACCGATTA
**
4278 ATTTAGACCGGTTATATTATATT
1 ATTTAGACCGGAAATATTATATT
4301 ATTTA-ACCGGAAATATTATA
1 ATTTAGACCGGAAATATTATA
4321 AAGTACAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.42
Consensus pattern (23 bp):
ATTTAGACCGGAAATATTATATT
Found at i:4896 original size:23 final size:23
Alignment explanation
Indices: 4837--4908 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
4827 GATACTTTAC
*
4837 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
4860 AT-TAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
4882 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
4905 ATAT
1 ATAT
4909 TTTTACCTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
22 20 0.45
23 24 0.55
ACGTcount: A:0.38, C:0.22, G:0.06, T:0.35
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:5333 original size:23 final size:23
Alignment explanation
Indices: 5307--5379 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
5297 AGATACTTTA
*
5307 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
5330 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
5353 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
5376 ATAT
1 ATAT
5380 TTTTACCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:5339 original size:471 final size:474
Alignment explanation
Indices: 4449--5693 Score: 2098
Period size: 471 Copynumber: 2.6 Consensus size: 474
4439 TTATAATATG
4449 TTGAAAGTGTCTATACTTTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCTATAC-TTTTTAT-AAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
4514 TTCAA-TTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAA--TAAT-ATTTCATTTGCA
64 TTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
4575 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAAT-A-ATTTAGAATTTAAATTTAACAATAT
129 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTT-A-AATAT
4638 TAACCAAAG--AATAATAAATATGTAATATATG-TTATTG-TTTTAATTTAATAATAATATATAT
192 TAACCAAAGATAATAATAAATATGTAATATATGTTTATTGTTTTTAA-TT--TAATAATA-ATAT
4699 CGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCA
253 CGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCA
*
4764 AAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTGGGCACTTTTATAAAAAGGATAGA
318 AAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTGGACACTTTTATAAAAAGGATAGA
4829 TACTTTACATATAAGCACTACCTATTACATTATTAAACGCTACCTATTACATTATATAAGCGCTA
383 TACTTTACATATAAGCACTACCTATTACATTATTAAACGCTACCTATTACATTATATAAGCGCTA
4894 CCTATTACATCATATTTTTACCTATTA
448 CCTATTACATCATATTTTTACCTATTA
*
4921 TTGAAAGTGTCTATACTTTTTATAAAAAGGATCGATAATTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCTATACTTTTTATAAAAA-GATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
*
4986 TCAATTTTTTTAGTAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
65 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
5051 -AAAAA-TATTTGATTG-TTTGATATTTTATAAAATAATATTTAGAATTTAAATTT-AATATTAA
130 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAAATATTAA
*
5112 CCAAAGATAATAATAAATATGTAATATATGTTTATTGTTTTTAATTTAATAATAATATCGTAATG
195 CCAAAGATAATAATAAATATGTAATATATGTTTATTGTTTTTAATTTAATAATAATATCGTAACG
* *
5177 T-AAAAA-AAATAATTAGACGCCTATAATTACTAAATTAATATCTTAAACCTCACTCAAAAGATA
260 TAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATA
*
5240 ACCTTAAATTAATGTTTTTCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGATACTT
325 ACCTTAAATTAATGTTTTCCACAGTGAAAAAAG--TGGACACTTTTATAAAAAGGATAGATACTT
5305 TA-ATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGCGCTACCTA
388 TACATATAAGCACTACCTATTACATTAT-TAAACGCTACCTATTACATTATATAAGCGCTACCTA
5369 TTACATCATATTTTTACCTATTA
452 TTACATCATATTTTTACCTATTA
*
5392 TTGAAAGTGTCTATAC--TTTATAAAAA-ATCAATACTTTTTTTAAAGTTATGTAATTTATGTTT
1 TTGAAAGTGTCTATACTTTTTATAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTT
5454 CAATTTTTTTTAATAGTGTTTCATGTTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
66 CAA-TTTTTTTAATAGTGTTTCATG-TTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
5519 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
129 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTT-A-AATAT
*
5584 TAACCAAAGATAATAATAAATATGTATATATATTTTTATTGTTTTTAATTTAATAATAATATACC
192 TAACCAAAGATAATAATAAATATGTA-ATATATGTTTATTGTTTTTAATTTAATAATAATAT--C
5649 GTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTA
254 GTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTA
5694 TACGGGATTT
Statistics
Matches: 733, Mismatches: 13, Indels: 46
0.93 0.02 0.06
Matches are distributed among these distances:
467 37 0.05
468 20 0.03
469 137 0.19
470 40 0.05
471 187 0.26
472 119 0.16
473 33 0.05
474 34 0.05
475 50 0.07
476 34 0.05
478 7 0.01
479 5 0.01
480 30 0.04
ACGTcount: A:0.40, C:0.11, G:0.08, T:0.42
Consensus pattern (474 bp):
TTGAAAGTGTCTATACTTTTTATAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTT
CAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACA
AAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAAATATTAAC
CAAAGATAATAATAAATATGTAATATATGTTTATTGTTTTTAATTTAATAATAATATCGTAACGT
AAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAA
CCTTAAATTAATGTTTTCCACAGTGAAAAAAGTGGACACTTTTATAAAAAGGATAGATACTTTAC
ATATAAGCACTACCTATTACATTATTAAACGCTACCTATTACATTATATAAGCGCTACCTATTAC
ATCATATTTTTACCTATTA
Found at i:6991 original size:179 final size:182
Alignment explanation
Indices: 6487--8117 Score: 2563
Period size: 179 Copynumber: 9.1 Consensus size: 182
6477 CTTAAAATTA
*
6487 CCGACACAATATTAAAAAGTATCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA-T
1 CCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATT
6551 TATA-CGGTTATATTACAAAATTATC-ATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCG
66 TATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCG-TGTGTAAATGTCG
*
6614 ACAC-TTTTGACAATGTATCG--ACATTTTTCTTCCAATCTGGACATAAAGTA
130 ACACTTTTTGACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTT
*
6664 CCGACATAATATTAAAAAGTGTCGATATAGGTTGT--ACCTATTCGCTCATAAAACCGGTATATT
1 CCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATT
*
6727 T-TCACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGTTTCCGATGTGTAAATGTC
66 TAT-ACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCG-TGTGTAAATGTC
*
6791 GACACTTTTTGACAATGTATCGATACATTTTTCTTCCAATCTGGACATAAAGTT
129 GACACTTTTTGACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTT
6845 CCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACC-G-ATATT
1 CCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATT
6908 TATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCG-GTGTAAATGTCGA
66 TATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGTGTGTAAATGTCGA
6972 CACTTTTTGACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTT
131 CACTTTTTGACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTT
7024 CCGACA-AA-A-TAAAAAGTGTCGATAT---TTGTAGACCTATTCGCTCATAAAACCGGTATATT
1 CCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATT
7083 TATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCG
66 TATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCG-TGTGTAAATGTCG
* * *
7148 ACACTTTTTAACAATGTATCGACACATTTTTCTTCCAATCTGGACATAGAGTA
130 ACACTTTTTGACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTT
*
7201 CCGACACAATATTAAAAAGGGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACC-GTATATT
1 CCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATT
* * *
7265 TACACCGGTTATATTATAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGTCG
66 TATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCG-TGTGTAAATGTCG
*
7330 ACAC-TTTTGACAATGTCTCGACACATTTTTCTTCCAATCTGGACATAAAGTT
130 ACACTTTTTGACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTT
*
7382 CC-A-ACAATATTAAAAAGTGTCGATATAGGTTGT--ACCTATTCGCTCATAAAACAGGTATA-T
1 CCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATT
7442 TATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGT-AATGTCG
66 TATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCG-TGTGTAAATGTCG
7506 ACACTTTTTGACAATGTATCGACACATTTTTCTTCCAATC-GGACATAAAGTT
130 ACACTTTTTGACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTT
*
7558 CCGACAAAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCAT-AAACCGGTATATT
1 CCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATT
7622 TATACCGGTTATATTAC-AAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCG
66 TATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCG-TGTGTAAATGTCG
7686 ACACTTTTTGACAATGTATCGACACATTTTT-TTCCAATCTGGACATAAAGTT
130 ACACTTTTTGACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTT
**
7738 CATACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCAT-AAACCGGTATATT
1 CCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATT
* *
7802 TATACCGGTTATATTACAAAATTATCTATTACATTATTA-T-GGGGTTCCGATGTGTAAATGTCG
66 TATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCG-TGTGTAAATGTCG
*
7865 ATACTTTTTGACAATGTATCGACACA-TTTTCTTCCAATCTGGACATAAAGTT
130 ACACTTTTTGACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTT
*
7917 CCTACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATT--CTCATAAAACCGGTATATT
1 CCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATT
** * * * * *
7980 TATAATGG-TATCA--CCAAAATTATCTATAACATTATAATTCTGGGTTCCATGTTTTTTCAA--
66 TATACCGGTTAT-ATTACAAAATTATCTATTACATTATAATTCTGGGTTCC--G-TGTGTAAATG
* * *
8040 TCGACACTTTTTTA-AATGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTA
127 TCGACACTTTTTGACAAT-GTATCGACACATTTTTCTTCCAATCTGGACATAAAGTT
*
8096 CAGACACAATATTAAAAAGTGT
1 CCGACACAATATTAAAAAGTGT
8118 GAAAGCTTTG
Statistics
Matches: 1366, Mismatches: 49, Indels: 76
0.92 0.03 0.05
Matches are distributed among these distances:
173 26 0.02
174 1 0.00
175 83 0.06
176 65 0.05
177 244 0.18
178 133 0.10
179 328 0.24
180 183 0.13
181 182 0.13
182 75 0.05
183 46 0.03
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (182 bp):
CCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATT
TATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGTGTGTAAATGTCGA
CACTTTTTGACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTT
Found at i:9309 original size:3 final size:3
Alignment explanation
Indices: 9301--9388 Score: 77
Period size: 3 Copynumber: 29.0 Consensus size: 3
9291 ACTTGTTTGG
* * * *
9301 ATC ATC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTTC ATC GTC AGC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC -ATC ATC ATC ATC
* * * * * *
9347 TTC ATC GTC ATC ATC ATC GTC ATC TTC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
9389 GTCAGCTTCA
Statistics
Matches: 64, Mismatches: 20, Indels: 2
0.74 0.23 0.02
Matches are distributed among these distances:
3 62 0.97
4 2 0.03
ACGTcount: A:0.23, C:0.33, G:0.07, T:0.38
Consensus pattern (3 bp):
ATC
Found at i:9318 original size:12 final size:12
Alignment explanation
Indices: 9302--9405 Score: 113
Period size: 12 Copynumber: 8.8 Consensus size: 12
9292 CTTGTTTGGA
* *
9302 TCATCATCATCA
1 TCATCGTCATCT
* *
9314 TCATCATCATCG
1 TCATCGTCATCT
*
9326 TCATCATC-T-T
1 TCATCGTCATCT
*
9336 TCATCGTCAGCT
1 TCATCGTCATCT
*
9348 TCATCGTCATCA
1 TCATCGTCATCT
9360 TCATCGTCATCT
1 TCATCGTCATCT
9372 TCATCGTCATCT
1 TCATCGTCATCT
*
9384 TCATCGTCAGCT
1 TCATCGTCATCT
*
9396 TCATCTTCAT
1 TCATCGTCAT
9406 TGACCGCTGG
Statistics
Matches: 80, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
10 7 0.09
11 1 0.01
12 72 0.90
ACGTcount: A:0.21, C:0.33, G:0.08, T:0.38
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:11721 original size:199 final size:200
Alignment explanation
Indices: 10885--11813 Score: 1627
Period size: 200 Copynumber: 4.7 Consensus size: 200
10875 TTATATACCA
*
10885 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTGTACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
* *
10950 TTGGGTTTTC-ATGTTTATGGGATCGACAC-TTTTATATATGGAT---CACTTTATGGTTGCAGC
66 TT-GGTTTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACC
11010 CTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTT
130 CTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTT
*
11075 AGACCT
195 AGACAT
* * *
11081 ATTATCTCATAAAATCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
* * *
11146 TTGGTTTTCGATGTTTTTGGGATCGATACTTTTTATATATGGATTGACACTTTACGGTTGCACCC
66 TTGGTTTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
* * *
11211 TGTTTGCCATTAATTCTGGACTAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTA
131 TGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTA
11276 GACAT
196 GACAT
11281 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
*
11346 TTGGTTTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGTACCC
66 TTGGTTTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
**
11411 TGTTGACCATTCATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTA
131 TGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTA
11476 GACAT
196 GACAT
11481 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
11546 TTGGTTTTCGATGTTTTTGGGATCGACACTTTTT-TATATGGATCGACACTTTATGGTTGCACCC
66 TTGGTTTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
*
11610 TGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGACAAATTATTTA
131 TGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTA
11675 GACAT
196 GACAT
*
11680 ATTCTCTCATAAAACCAGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
* *
11745 TTGGTTTTCGATGTTTTTGGGATCGACACTTTTTATATATGGTTCGACACTTTATGGTTGCACCA
66 TTGGTTTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
11810 TGTT
131 TGTT
11814 GGCCATATTG
Statistics
Matches: 697, Mismatches: 30, Indels: 8
0.95 0.04 0.01
Matches are distributed among these distances:
195 7 0.01
196 80 0.11
197 14 0.02
199 194 0.28
200 402 0.58
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (200 bp):
ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
TTGGTTTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
TGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTA
GACAT
Found at i:11758 original size:399 final size:400
Alignment explanation
Indices: 10885--11819 Score: 1630
Period size: 399 Copynumber: 2.4 Consensus size: 400
10875 TTATATACCA
*
10885 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTGTACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
* *
10950 TTGGGTTTTC-ATGTTTATGGGATCGACAC-TTTTATATATGGAT---CACTTTATGGTTGCAGC
66 TT-GGTTTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACC
**
11010 CTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTT
130 CTGTTGACCATTCATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTT
* *
11075 AGACCTATTATCTCATAAAATCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATT
195 AGACATATTATCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATT
* *
11140 ATACTTTTGGTTTTCGATGTTTTTGGGATCGATACTTTTTATATATGGATTGACACTTTACGGTT
260 ATACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTACGGTT
* *
11205 GCACCCTGTTTGCCATTAATTCTGGACTAAAAATATCGACACAAACTAAAAAAGTGTCGACACAT
325 GCACCCTGTTTGCCATTAATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGACAAAT
11270 TATTTAGACAT
390 TATTTAGACAT
11281 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
*
11346 TTGGTTTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGTACCC
66 TTGGTTTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
11411 TGTTGACCATTCATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTA
131 TGTTGACCATTCATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTA
* *
11476 GACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTA
196 GACATATTATCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTA
*
11541 TACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTTT-TATATGGATCGACACTTTATGGTTG
261 TACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTACGGTTG
* *
11605 CACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGACAAATT
326 CACCCTGTTTGCCATTAATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGACAAATT
11670 ATTTAGACAT
391 ATTTAGACAT
*
11680 ATTCTCTCATAAAACCAGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
* *
11745 TTGGTTTTCGATGTTTTTGGGATCGACACTTTTTATATATGGTTCGACACTTTATGGTTGCACCA
66 TTGGTTTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
*
11810 TGTTGGCCAT
131 TGTTGACCAT
11820 ATTGTAAATT
Statistics
Matches: 512, Mismatches: 22, Indels: 7
0.95 0.04 0.01
Matches are distributed among these distances:
395 7 0.01
396 84 0.16
397 14 0.03
399 229 0.45
400 178 0.35
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (400 bp):
ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
TTGGTTTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
TGTTGACCATTCATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTA
GACATATTATCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTA
TACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTACGGTTG
CACCCTGTTTGCCATTAATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGACAAATT
ATTTAGACAT
Found at i:11943 original size:18 final size:18
Alignment explanation
Indices: 11920--11980 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
11910 TCTCATTCAT
*
11920 AATTATATTCACATACAA
1 AATTATAATCACATACAA
**
11938 AATTATAAATCGTATACAA
1 AATTAT-AATCACATACAA
**
11957 AATTATAAATCTTATACAA
1 AATTAT-AATCACATACAA
11976 AATTA
1 AATTA
11981 ACCCTACATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
18 6 0.16
19 32 0.84
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.34
Consensus pattern (18 bp):
AATTATAATCACATACAA
Found at i:11956 original size:19 final size:19
Alignment explanation
Indices: 11932--11980 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
11922 TTATATTCAC
11932 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
11951 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
11970 ATACAAAATTA
1 ATACAAAATTA
11981 ACCCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:13805 original size:33 final size:33
Alignment explanation
Indices: 13768--13833 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
13758 CATCTTAATA
*
13768 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
13801 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
13834 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:13892 original size:21 final size:21
Alignment explanation
Indices: 13867--13931 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
13857 CCCCTTATGC
* *
13867 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
13888 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
13909 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
13930 CT
1 CT
13932 TGATTGTCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.17, C:0.31, G:0.11, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:16200 original size:20 final size:20
Alignment explanation
Indices: 16158--16205 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
16148 CATTTTACCG
*
16158 GTTTTATCATTTTGATACCT
1 GTTTTATCATTTTGATACAT
*
16178 GTTTTATCATATTT-TTACAT
1 GTTTTATCAT-TTTGATACAT
*
16198 GTTATATC
1 GTTTTATC
16206 GTTGTGGATC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 21 0.88
21 3 0.12
ACGTcount: A:0.23, C:0.12, G:0.08, T:0.56
Consensus pattern (20 bp):
GTTTTATCATTTTGATACAT
Found at i:16358 original size:20 final size:20
Alignment explanation
Indices: 16331--16377 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
16321 TTCGGTAACG
16331 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
16350 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
16371 TTTTACC
1 TTTTACC
16378 TGGTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:16430 original size:181 final size:180
Alignment explanation
Indices: 16117--16588 Score: 658
Period size: 181 Copynumber: 2.6 Consensus size: 180
16107 CGTACTTACG
* * * * *
16117 AAAGTAGCGACACTTTCAATATATCCTGTATCATTTTACCGGTTTTATCATTTTGATACCTGTTT
1 AAAGTACCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
16182 TATCATATTTTTACATGTTATATCGTTGTGGATCGATATATTTTTTTAAAATATCGACACATTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACA-TTTTTTAAAATATCGACACATTAT
*
16247 AGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
130 AGG-ACTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * *
16298 AAAGTATCGACACTTTCAATATATTCGGTAACGTTTTACCGGTTTTATCATTTTGTTACCGGTTT
1 AAAGTACCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
16363 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAA-TATCGACACATTAT
* **
16428 AGGATTAAAACTGCTTCTCTTTTAAATTCATGAAGTGTCGATCCTTATATT
130 AGGACTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * * * ** **
16479 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTTACCGGTTTTATCATTTCAATATTGGTTT
1 AAAGTACCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
16544 TGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
16589 AATTTGGATC
Statistics
Matches: 258, Mismatches: 31, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
180 52 0.20
181 206 0.80
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (180 bp):
AAAGTACCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAATATCGACACATTATA
GGACTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
Found at i:17109 original size:30 final size:30
Alignment explanation
Indices: 17069--17135 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
17059 TAAGTGCTTT
*
17069 AAGT-TTTTTTT-AGTTAAAATAGGTACCTA
1 AAGTATTTTTTTGA-TTAAAATAGATACCTA
17098 AAGTATTTTTTTGATTAAAATAGATACCTA
1 AAGTATTTTTTTGATTAAAATAGATACCTA
*
17128 AAGCATTT
1 AAGTATTT
17136 AATATTTTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 4 0.12
30 29 0.85
31 1 0.03
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.43
Consensus pattern (30 bp):
AAGTATTTTTTTGATTAAAATAGATACCTA
Found at i:22276 original size:21 final size:20
Alignment explanation
Indices: 22252--22317 Score: 60
Period size: 21 Copynumber: 3.2 Consensus size: 20
22242 GCAAATTCGC
22252 GTTGCATTTCGCGTTGCGAT
1 GTTGCATTTCGCGTTGCGAT
* ** *
22272 AGTTGAAAATCGCGTTGCTAT
1 -GTTGCATTTCGCGTTGCGAT
* *
22293 TTTCCATTTCGCGTTGCGATT
1 GTTGCATTTCGCGTTGCGA-T
22314 GTTG
1 GTTG
22318 AAAATCACGT
Statistics
Matches: 32, Mismatches: 12, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
20 13 0.41
21 19 0.59
ACGTcount: A:0.15, C:0.18, G:0.26, T:0.41
Consensus pattern (20 bp):
GTTGCATTTCGCGTTGCGAT
Found at i:22439 original size:5 final size:5
Alignment explanation
Indices: 22412--22451 Score: 53
Period size: 5 Copynumber: 7.4 Consensus size: 5
22402 AGACACGTAT
22412 GACCAC GACCAC GACCAC GACCC GACCC GACCC GACCC GA
1 GACC-C GACC-C GACC-C GACCC GACCC GACCC GACCC GA
22452 GACGGATGGC
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 18 0.53
6 16 0.47
ACGTcount: A:0.28, C:0.53, G:0.20, T:0.00
Consensus pattern (5 bp):
GACCC
Found at i:22945 original size:6 final size:6
Alignment explanation
Indices: 22936--22962 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
22926 GTCCGTCTCG
22936 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
22963 AATACGTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:23104 original size:19 final size:21
Alignment explanation
Indices: 23060--23108 Score: 75
Period size: 19 Copynumber: 2.4 Consensus size: 21
23050 CAACGAATTT
23060 TCGCAACGAATTTTAAAAATA
1 TCGCAACGAATTTTAAAAATA
*
23081 TCGCAACGAA-TTTGAAAA-A
1 TCGCAACGAATTTTAAAAATA
23100 TCGCAACGA
1 TCGCAACGA
23109 CAACTGTAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 10 0.37
20 7 0.26
21 10 0.37
ACGTcount: A:0.45, C:0.18, G:0.14, T:0.22
Consensus pattern (21 bp):
TCGCAACGAATTTTAAAAATA
Found at i:28928 original size:23 final size:23
Alignment explanation
Indices: 28897--28942 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
28887 GAAAAATGTA
28897 TCACAAAGACAG-AGATAAACGTG
1 TCACAAAGACAGCA-ATAAACGTG
*
28920 TCACGAAGACAGCAATAAACGTG
1 TCACAAAGACAGCAATAAACGTG
28943 CAACACAGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 20 0.95
24 1 0.05
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.13
Consensus pattern (23 bp):
TCACAAAGACAGCAATAAACGTG
Found at i:38128 original size:15 final size:16
Alignment explanation
Indices: 38088--38131 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
38078 TTAATGCAAT
*
38088 TTAAATTTATTATGAA
1 TTAAATTTTTTATGAA
**
38104 TTCTATTTTTTATG-A
1 TTAAATTTTTTATGAA
38119 TTAAATTTTTTAT
1 TTAAATTTTTTAT
38132 ATATTAAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (16 bp):
TTAAATTTTTTATGAA
Found at i:39025 original size:35 final size:35
Alignment explanation
Indices: 38940--39044 Score: 149
Period size: 35 Copynumber: 3.0 Consensus size: 35
38930 TCCCATTATC
* * *
38940 ATTTTC-AACAAACATCTACCAAACTTTGAAAAATT
1 ATTTTCAAAAAAACATTTACCAAACTTTG-AAAACT
38975 ATTTTTCAAAAAAACATTTACCAAACTTTGAAAACT
1 A-TTTTCAAAAAAACATTTACCAAACTTTGAAAACT
*
39011 ATTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 ATTTTCAAAAAAACATTTACCAAACTTTGAAAAC
39045 CAATTTTTCA
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
35 33 0.52
36 11 0.17
37 20 0.31
ACGTcount: A:0.47, C:0.18, G:0.04, T:0.31
Consensus pattern (35 bp):
ATTTTCAAAAAAACATTTACCAAACTTTGAAAACT
Found at i:42350 original size:15 final size:15
Alignment explanation
Indices: 42330--42361 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
42320 AGAATCTTTC
*
42330 TTTCCCGTTCTTGAT
1 TTTCCCGTTCTGGAT
42345 TTTCCCGTTCTGGAT
1 TTTCCCGTTCTGGAT
42360 TT
1 TT
42362 GGATCTGCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.25, G:0.16, T:0.53
Consensus pattern (15 bp):
TTTCCCGTTCTGGAT
Done.