Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006772.1 Hibiscus syriacus cultivar Beakdansim tig00017120_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: 73981
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:9 original size:3 final size:3
Alignment explanation
Indices: 2--338 Score: 526
Period size: 3 Copynumber: 112.7 Consensus size: 3
1 G
2 AGA AGA AGA AGA AG- AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
*
49 AGA AGA AG- AGAA AGA AGA AGA GGA AGA AG- AGA AGA A-A AGA AGA
1 AGA AGA AGA AG-A AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
92 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* *
140 AGA AGGA AGA AGA AGA AGA AGA AGA GGA AGA AGA AGA AGG AGA AGA
1 AGA A-GA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
*
186 AGA AGA A-A AGA AGA AG- AGAA AGAA AGA AGA AGAA AGA AAA AGA AGA
1 AGA AGA AGA AGA AGA AGA AG-A AG-A AGA AGA AG-A AGA AGA AGA AGA
232 AGA AGA AGA GAGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA -AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
278 AGA AGA AGA AGA AGA AGA AGA AGA AGA A-A AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
*
325 AGA AGA AGG AGA AG
1 AGA AGA AGA AGA AG
339 GAGATGGAGA
Statistics
Matches: 312, Mismatches: 10, Indels: 24
0.90 0.03 0.07
Matches are distributed among these distances:
2 14 0.04
3 281 0.90
4 17 0.05
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:3432 original size:9 final size:9
Alignment explanation
Indices: 3418--3443 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
3408 TAGATCAAGT
3418 AAATGAAGA
1 AAATGAAGA
3427 AAATGAAGA
1 AAATGAAGA
3436 AAATGAAG
1 AAATGAAG
3444 TTTATTTGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.23, T:0.12
Consensus pattern (9 bp):
AAATGAAGA
Found at i:7922 original size:14 final size:14
Alignment explanation
Indices: 7905--7956 Score: 60
Period size: 14 Copynumber: 4.0 Consensus size: 14
7895 TGAAAAAAGT
7905 GAAAAAAAATAGAA
1 GAAAAAAAATAGAA
7919 G---AAAAATAGAA
1 GAAAAAAAATAGAA
7930 GAAAAAAAATTAG-A
1 GAAAAAAAA-TAGAA
7944 GAAAAAAAA-AGAA
1 GAAAAAAAATAGAA
7957 AAAGAAGAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
11 11 0.33
12 2 0.06
13 1 0.03
14 16 0.48
15 3 0.09
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (14 bp):
GAAAAAAAATAGAA
Found at i:7923 original size:11 final size:11
Alignment explanation
Indices: 7909--7935 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
7899 AAAAGTGAAA
7909 AAAAATAGAAG
1 AAAAATAGAAG
7920 AAAAATAGAAG
1 AAAAATAGAAG
7931 AAAAA
1 AAAAA
7936 AAATTAGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (11 bp):
AAAAATAGAAG
Found at i:7933 original size:25 final size:24
Alignment explanation
Indices: 7905--7959 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 24
7895 TGAAAAAAGT
*
7905 GAAAAAAAA-TAGAAGAAAAATAGAA
1 GAAAAAAAATTAG-AGAAAAA-AAAA
7930 GAAAAAAAATTAGAGAAAAAAAAA
1 GAAAAAAAATTAGAGAAAAAAAAA
7954 GAAAAA
1 GAAAAA
7960 GAAGAATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 9 0.32
25 16 0.57
26 3 0.11
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (24 bp):
GAAAAAAAATTAGAGAAAAAAAAA
Found at i:7959 original size:11 final size:11
Alignment explanation
Indices: 7875--7959 Score: 53
Period size: 11 Copynumber: 7.3 Consensus size: 11
7865 ATTCATATTC
7875 AAAAAAAAGAA
1 AAAAAAAAGAA
* * **
7886 AAAGAGAAGTG
1 AAAAAAAAGAA
**
7897 AAAAAAGTGAA
1 AAAAAAAAGAA
*
7908 AAAAAATAGAA
1 AAAAAAAAGAA
7919 GAAAAATAGAAGAA
1 -AAAAA-A-AAGAA
*
7933 AAAAAATTAGAGA
1 AAAAAA-AAGA-A
7946 AAAAAAAAGAA
1 AAAAAAAAGAA
7957 AAA
1 AAA
7960 GAAGAATAAA
Statistics
Matches: 54, Mismatches: 16, Indels: 8
0.69 0.21 0.10
Matches are distributed among these distances:
11 25 0.46
12 12 0.22
13 13 0.24
14 4 0.07
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.07
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:7975 original size:36 final size:33
Alignment explanation
Indices: 7875--7975 Score: 94
Period size: 36 Copynumber: 2.8 Consensus size: 33
7865 ATTCATATTC
* *
7875 AAAAAAAAGAAAAAGAGAAGTGAAAAAAGTGAAA
1 AAAAAAAAGAAAAAGAGAA-TAAAAAAATTGAAA
* * *
7909 AAAAATAGAAGAAAAATAGAAGAAAAAAAATTAGAGA
1 AAAAA-A-AAGAAAAAGAGAA-TAAAAAAATT-GAAA
7946 AAAAAAAAGAAAAAGAAGAATAAATAAAAT
1 AAAAAAAAGAAAAAG-AGAATAAA-AAAAT
7976 AGGTCAAGTA
Statistics
Matches: 55, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
34 5 0.09
35 12 0.22
36 30 0.55
37 8 0.15
ACGTcount: A:0.75, C:0.00, G:0.16, T:0.09
Consensus pattern (33 bp):
AAAAAAAAGAAAAAGAGAATAAAAAAATTGAAA
Found at i:10222 original size:42 final size:41
Alignment explanation
Indices: 10151--10241 Score: 119
Period size: 42 Copynumber: 2.2 Consensus size: 41
10141 AAGCGCTACA
* * *
10151 GGCCATCAGTTAGTCTTTCGAGCATGATGATTAAATCATTCG
1 GGCCATCTGTCAGTCTTTCGAGCAAGATGA-TAAATCATTCG
* * *
10193 GGTCATCTGTCAGTCTTTCGAGTAAGATGATAAGTCATTCG
1 GGCCATCTGTCAGTCTTTCGAGCAAGATGATAAATCATTCG
10234 GGCCATCT
1 GGCCATCT
10242 ATAAGACCTT
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 17 0.40
42 25 0.60
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (41 bp):
GGCCATCTGTCAGTCTTTCGAGCAAGATGATAAATCATTCG
Found at i:10343 original size:17 final size:16
Alignment explanation
Indices: 10313--10347 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
10303 AGTTTCTCAT
10313 TAAAATTTTCAAAAAA
1 TAAAATTTTCAAAAAA
**
10329 TAAAATTTTTGAAAAA
1 TAAAATTTTCAAAAAA
10345 TAA
1 TAA
10348 GAAATCAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (16 bp):
TAAAATTTTCAAAAAA
Found at i:10591 original size:16 final size:15
Alignment explanation
Indices: 10570--10600 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
10560 AATTTCTCAT
10570 TAAAATTTTCAGAAAA
1 TAAAATTTTC-GAAAA
10586 TAAAATTTTCGAAAA
1 TAAAATTTTCGAAAA
10601 GTAAGAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.32
Consensus pattern (15 bp):
TAAAATTTTCGAAAA
Found at i:10806 original size:258 final size:260
Alignment explanation
Indices: 9998--10963 Score: 1374
Period size: 257 Copynumber: 3.8 Consensus size: 260
9988 CCAGAACATT
* * * * **
9998 AAGATGATTTCATATGACAATTTGAAAAATGAGAAAGCGGTTTTCAAAGTTTCTCATTTAGTATT
1 AAGATGCTTTCATATGATAATTTGAAAAATAAGAAAGCGATTTTCAAAGTTTCTCATTTAAAATT
* * *
10063 TTCAGAAAATGAAATTTTTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACCTAGTAAACTAT
66 TTCAAAAAATAAAATTTTTGAAAAGTAAGAAATCGATTTCCAAAGTTTCTTACCTAGTAAACTAT
* * * *
10128 TTCCAAAATTGGTAAG-CGCTACAGGCCATCAGTTAGTCTTTCGAGCATGATGATTAAATCATTC
131 TTCCAAAATTGGTAAGTCACTTCAGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTC
*
10192 GGGTCATCTGTCAGTCTTTCGAGTAAGATGATAAGTCATTCGGGCCATCTATAAGACCTTCGGGC
196 GGGTCATCTGTCAGTCTTTCGAGAAAGATGATAAGTCATTCGGGCCATCTATAAGACCTTCGGGC
* ** *
10257 AAGATTCTTGAATATGATAATTTGAAAAATGAGAAA-CGATTTTCAAAGTTTCTCA-TTAAAATT
1 AAGATGCTTTCATATGATAATTTGAAAAATAAGAAAGCGATTTTCAAAGTTTCTCATTTAAAATT
* *
10320 TTCAAAAAATAAAATTTTTGAAAAATAAGAAATCAATTTCCAAAGTTTCTTACCTAGTAAACTAT
66 TTCAAAAAATAAAATTTTTGAAAAGTAAGAAATCGATTTCCAAAGTTTCTTACCTAGTAAACTAT
* *
10385 TTCCAAAATAGGTAAGTCA--TCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTC
131 TTCCAAAATTGGTAAGTCACTTCAGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTC
* * * * * *
10448 GGGCCATCTGTCAGTCTTTCGAGAAAGGTTATAAGTCCTTCGAGCCATCTATAAGACCTTCGGAC
196 GGGTCATCTGTCAGTCTTTCGAGAAAGATGATAAGTCATTCGGGCCATCTATAAGACCTTCGGGC
* * *
10513 AAGATGCTTTCATATGATAATCTGAAAACTAAGAAAGCGATTTTCAAAATTTCTCA-TTAAAATT
1 AAGATGCTTTCATATGATAATTTGAAAAATAAGAAAGCGATTTTCAAAGTTTCTCATTTAAAATT
* *
10577 TTCAGAAAATAAAATTTTCGAAAAGTAAGAAATCGATTTCCAAAGTTTCTTACCTAGTAAACTAT
66 TTCAAAAAATAAAATTTTTGAAAAGTAAGAAATCGATTTCCAAAGTTTCTTACCTAGTAAACTAT
* ** * * * * *
10642 TTCCAAAATTGGTAAG-CACTTTAGATCATCAGTAAATCTTTTGAGCTTCATAATTAAATCCTTC
131 TTCCAAAATTGGTAAGTCACTTCAGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTC
* *
10706 GGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCATTCGGGCCATCTATAAGACCTTCGGGT
196 GGGTCATCTGTCAGTCTTTCGAGAAAGATGATAAGTCATTCGGGCCATCTATAAGACCTTCGGGC
* **
10771 AAGATGCTTTCATATTATAATTTGAAAAATAAGAAATTGATTTTCAAAGTTTCTCATTTAAAATT
1 AAGATGCTTTCATATGATAATTTGAAAAATAAGAAAGCGATTTTCAAAGTTTCTCATTTAAAATT
* * * ***
10836 TTCAAAAAATGAAATTTGTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTGGGCTAGTAAACTAT
66 TTCAAAAAATAAAATTTTTGAAAAGTAAGAAATCGATTTCCAAAGTTTCTTACCTAGTAAACTAT
* * *
10901 TTTCAAAATTGGTAAGTC-CTTTAGGCCATCAGTAAGTCTTTCGAGCAAGATGA-TAAATCCTTC
131 TTCCAAAATTGGTAAGTCACTTCAGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTC
10964 AGAGTTGTTT
Statistics
Matches: 623, Mismatches: 78, Indels: 13
0.87 0.11 0.02
Matches are distributed among these distances:
256 130 0.21
257 183 0.29
258 171 0.27
259 138 0.22
260 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (260 bp):
AAGATGCTTTCATATGATAATTTGAAAAATAAGAAAGCGATTTTCAAAGTTTCTCATTTAAAATT
TTCAAAAAATAAAATTTTTGAAAAGTAAGAAATCGATTTCCAAAGTTTCTTACCTAGTAAACTAT
TTCCAAAATTGGTAAGTCACTTCAGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTC
GGGTCATCTGTCAGTCTTTCGAGAAAGATGATAAGTCATTCGGGCCATCTATAAGACCTTCGGGC
Found at i:11086 original size:3 final size:3
Alignment explanation
Indices: 11078--11117 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
11068 CCCAGATCTT
* *
11078 TTA TTA TTA TTA TTA TTA CTA TTA TTA CTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
11118 AGGCCCATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:12354 original size:11 final size:11
Alignment explanation
Indices: 12323--12359 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
12313 TTTATAACCC
12323 TTTAATTTCAT
1 TTTAATTTCAT
*
12334 TTCCAATTTCAT
1 TT-TAATTTCAT
12346 TTTAATTTCAT
1 TTTAATTTCAT
12357 TTT
1 TTT
12360 TTATTTAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.24, C:0.14, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTAATTTCAT
Found at i:12360 original size:12 final size:12
Alignment explanation
Indices: 12323--12365 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
12313 TTTATAACCC
12323 TTTAATTTCATT
1 TTTAATTTCATT
**
12335 TCCAATTTCA-T
1 TTTAATTTCATT
12346 TTTAATTTCATT
1 TTTAATTTCATT
*
12358 TTTTATTT
1 TTTAATTT
12366 AATAATTTGA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
11 9 0.36
12 16 0.64
ACGTcount: A:0.23, C:0.12, G:0.00, T:0.65
Consensus pattern (12 bp):
TTTAATTTCATT
Found at i:18831 original size:76 final size:76
Alignment explanation
Indices: 18700--18913 Score: 214
Period size: 76 Copynumber: 2.8 Consensus size: 76
18690 AATAATCTTT
* * * * * * * * *
18700 AGAAACACTAAATTGAACTTTCTATGATACAAATCTTAAGAAA-GCTAAGATTGAGGTTTTTAAG
1 AGAAACATTAAACTAAACTTTCTAAGAGACAAGTCCTAAGAAATTC-AAGATTGAGGTTTCTAAG
*
18764 GAAACAATCTTA
65 GAAACAAACTTA
* ** * * * *
18776 AGGAACATTAAACTAAGTTTTCTAGGAGACAAGTCCTAAGAAATTCAAGAATGAGGTTCCTCAGG
1 AGAAACATTAAACTAAACTTTCTAAGAGACAAGTCCTAAGAAATTCAAGATTGAGGTTTCTAAGG
* *
18841 GAACAAACTTT
66 AAACAAACTTA
* * *
18852 AGAAACATTAAACTAAACTTTCTAAGATATAAGTCCTAAGACATTCAAGATTGAGGTTTCTA
1 AGAAACATTAAACTAAACTTTCTAAGAGACAAGTCCTAAGAAATTCAAGATTGAGGTTTCTA
18914 TGAAAATAGT
Statistics
Matches: 109, Mismatches: 28, Indels: 2
0.78 0.20 0.01
Matches are distributed among these distances:
76 108 0.99
77 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.29
Consensus pattern (76 bp):
AGAAACATTAAACTAAACTTTCTAAGAGACAAGTCCTAAGAAATTCAAGATTGAGGTTTCTAAGG
AAACAAACTTA
Found at i:18932 original size:76 final size:75
Alignment explanation
Indices: 18672--18932 Score: 211
Period size: 76 Copynumber: 3.4 Consensus size: 75
18662 GAAAAACTAA
* * * * * * * * *
18672 ATTGAGTTTTCTTTGGAAAATAATCTTTAGAAACACTAAATTGAACTTTCTATGATACAAATCTT
1 ATTGAGGTTTCTAT-GAAAATAATCTTAAGAAACATTAAACTAAACTTTCTAAGATACAAGTCCT
**
18737 AAGAAAGCTAAG
65 AAGAATTC-AAG
* * * * * ** * *
18749 ATTGAGGTTTTTAAGGAAACAATCTTAAGGAACATTAAACTAAGTTTTCTAGGAGACAAGTCCTA
1 ATTGAGGTTTCTATGAAAATAATCTTAAGAAACATTAAACTAAACTTTCTAAGATACAAGTCCTA
18814 AGAAATTCAAG
66 AG-AATTCAAG
* * * * * *
18825 AATGAGGTTCCTCAGGGAACA-AA-CTTTAGAAACATTAAACTAAACTTTCTAAGATATAAGTCC
1 ATTGAGGTTTCT-A-TGAAAATAATCTTAAGAAACATTAAACTAAACTTTCTAAGATACAAGTCC
18888 TAAGACATTCAAG
64 TAAGA-ATTCAAG
*
18901 ATTGAGGTTTCTATGAAAATAGTCTTAAGAAA
1 ATTGAGGTTTCTATGAAAATAATCTTAAGAAA
18933 AAAATTGATT
Statistics
Matches: 140, Mismatches: 38, Indels: 13
0.73 0.20 0.07
Matches are distributed among these distances:
74 4 0.03
75 3 0.02
76 114 0.81
77 16 0.11
78 3 0.02
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.31
Consensus pattern (75 bp):
ATTGAGGTTTCTATGAAAATAATCTTAAGAAACATTAAACTAAACTTTCTAAGATACAAGTCCTA
AGAATTCAAG
Found at i:24093 original size:9 final size:9
Alignment explanation
Indices: 24057--24149 Score: 51
Period size: 9 Copynumber: 9.2 Consensus size: 9
24047 TTTCACTTTG
24057 TTCATTTCA
1 TTCATTTCA
*
24066 TAGCATCTTCCA
1 T-TCAT-TT-CA
24078 TTCATTTCA
1 TTCATTTCA
*
24087 TTTATTTCA
1 TTCATTTCA
*
24096 TAGCATGTATCA
1 T-TCAT-T-TCA
*
24108 TTCATTTAA
1 TTCATTTCA
24117 TTCATTTCA
1 TTCATTTCA
*
24126 TAGCATGTATCA
1 T-TCAT-T-TCA
24138 TTCACTTTCA
1 TTCA-TTTCA
24148 TT
1 TT
24150 TCATATCATA
Statistics
Matches: 64, Mismatches: 10, Indels: 19
0.69 0.11 0.20
Matches are distributed among these distances:
9 23 0.36
10 16 0.25
11 13 0.20
12 12 0.19
ACGTcount: A:0.26, C:0.20, G:0.05, T:0.48
Consensus pattern (9 bp):
TTCATTTCA
Found at i:24096 original size:30 final size:30
Alignment explanation
Indices: 24060--24159 Score: 130
Period size: 30 Copynumber: 3.3 Consensus size: 30
24050 CACTTTGTTC
*
24060 ATTTCATAGCATCT-TCCATTCATTTCATTT
1 ATTTCATAGCATGTAT-CATTCATTTCATTT
* *
24090 ATTTCATAGCATGTATCATTCATTTAATTC
1 ATTTCATAGCATGTATCATTCATTTCATTT
24120 ATTTCATAGCATGTATCATTCACTTTCATTT
1 ATTTCATAGCATGTATCATTCA-TTTCATTT
*
24151 CATATCATA
1 -ATTTCATA
24160 TACTATTCAC
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
30 47 0.77
31 7 0.11
32 7 0.11
ACGTcount: A:0.28, C:0.20, G:0.05, T:0.47
Consensus pattern (30 bp):
ATTTCATAGCATGTATCATTCATTTCATTT
Found at i:24115 original size:25 final size:27
Alignment explanation
Indices: 24057--24185 Score: 100
Period size: 30 Copynumber: 4.5 Consensus size: 27
24047 TTTCACTTTG
*
24057 TTCATTTCATAGCATCT-TCCATTCATTT
1 TTCATTTCATAGCATGTAT-CATTCA-TT
*
24085 CATTTATTTCATAGCATGTATCATTCATTT
1 --TTCATTTCATAGCATGTATCATTCA-TT
*
24115 AATTCATTTCATAGCATGTATCATTCACT
1 --TTCATTTCATAGCATGTATCATTCATT
* *
24144 TTCATTTCATATCATATA-CTATTCACTTT
1 TTCATTTCATAGCATGTATC-ATTCA--TT
*
24173 TTCATTTCGTAGC
1 TTCATTTCATAGC
24186 CCAATGTAAA
Statistics
Matches: 85, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
26 1 0.01
27 21 0.25
29 13 0.15
30 49 0.58
31 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.05, T:0.48
Consensus pattern (27 bp):
TTCATTTCATAGCATGTATCATTCATT
Found at i:24167 original size:27 final size:27
Alignment explanation
Indices: 24083--24172 Score: 87
Period size: 27 Copynumber: 3.3 Consensus size: 27
24073 TTCCATTCAT
*
24083 TTCA-TTT-ATTTCATAGCATGTATCA
1 TTCACTTTCATTTCATAGCATATATCA
* *
24108 TTCATTTAATTCATTTCATAGCATGTATCA
1 TTCA-CT--TTCATTTCATAGCATATATCA
*
24138 TTCACTTTCATTTCATATCATATA-CTA
1 TTCACTTTCATTTCATAGCATATATC-A
24165 TTCACTTT
1 TTCACTTT
24173 TTCATTTCGT
Statistics
Matches: 56, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
25 4 0.07
26 1 0.02
27 26 0.46
29 3 0.05
30 22 0.39
ACGTcount: A:0.28, C:0.19, G:0.04, T:0.49
Consensus pattern (27 bp):
TTCACTTTCATTTCATAGCATATATCA
Found at i:24577 original size:55 final size:54
Alignment explanation
Indices: 24455--24614 Score: 158
Period size: 57 Copynumber: 2.8 Consensus size: 54
24445 AGTATCATAC
* ** *
24455 AGTAGCACCACTGTCACACAGATGTCAGACACGTGCTATAAGTATAATGCAGCTACT
1 AGTAGCACCACT-TCACACAGACGTCAGACACGTGC--TAAGTATAACACAACTACT
**
24512 AGTAGCACCACTATCACACAGACGTCAGACACGTGCTAAGTATAACACAACTGTT
1 AGTAGCACCACT-TCACACAGACGTCAGACACGTGCTAAGTATAACACAACTACT
* * * *
24567 AGTAACACCACCTTCACATAAGTGACATCAGACACGTGCTAAATATAA
1 AGTAGCACCA-CTTCACA-CA--GACGTCAGACACGTGCTAAGTATAA
24615 TGCTCCAACT
Statistics
Matches: 88, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
55 28 0.32
56 3 0.03
57 34 0.39
58 23 0.26
ACGTcount: A:0.37, C:0.26, G:0.16, T:0.21
Consensus pattern (54 bp):
AGTAGCACCACTTCACACAGACGTCAGACACGTGCTAAGTATAACACAACTACT
Found at i:28112 original size:2 final size:2
Alignment explanation
Indices: 28107--28132 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28097 ACACACACAC
28107 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
28133 GTTAATACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30380 original size:21 final size:21
Alignment explanation
Indices: 30354--30510 Score: 235
Period size: 21 Copynumber: 7.5 Consensus size: 21
30344 ATTTTGATCA
30354 CTATCGCAATGGTGAACAGTG
1 CTATCGCAATGGTGAACAGTG
30375 CTATCGCAATGGTGAACAGTG
1 CTATCGCAATGGTGAACAGTG
* *
30396 CTATCGTAATGGTGAACAGTA
1 CTATCGCAATGGTGAACAGTG
*
30417 CTATCGCAATGGTGAACAGTA
1 CTATCGCAATGGTGAACAGTG
*
30438 CTATCGC-ATCGTGAACAGTG
1 CTATCGCAATGGTGAACAGTG
* *
30458 CTATCGTAACGGTGAACAGTG
1 CTATCGCAATGGTGAACAGTG
* *
30479 ATATCGCAACGGTGAACAGTG
1 CTATCGCAATGGTGAACAGTG
30500 CTATCGCAATG
1 CTATCGCAATG
30511 CGATTTTGGA
Statistics
Matches: 123, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
20 17 0.14
21 106 0.86
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (21 bp):
CTATCGCAATGGTGAACAGTG
Found at i:30477 original size:62 final size:63
Alignment explanation
Indices: 30353--30507 Score: 251
Period size: 62 Copynumber: 2.5 Consensus size: 63
30343 TATTTTGATC
* *
30353 ACTATCGCAATGGTGAACAGTGCTATCGCAATGGTGAACAGTGCTATCGTAATGGTGAACAGT-
1 ACTATCGCAATGGTGAACAGTGCTATCGC-ATCGTGAACAGTGCTATCGTAACGGTGAACAGTG
*
30416 ACTATCGCAATGGTGAACAGTACTATCGCATCGTGAACAGTGCTATCGTAACGGTGAACAGTG
1 ACTATCGCAATGGTGAACAGTGCTATCGCATCGTGAACAGTGCTATCGTAACGGTGAACAGTG
*
30479 A-TATCGCAACGGTGAACAGTGCTATCGCA
1 ACTATCGCAATGGTGAACAGTGCTATCGCA
30508 ATGCGATTTT
Statistics
Matches: 86, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
62 57 0.66
63 29 0.34
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (63 bp):
ACTATCGCAATGGTGAACAGTGCTATCGCATCGTGAACAGTGCTATCGTAACGGTGAACAGTG
Found at i:30504 original size:83 final size:84
Alignment explanation
Indices: 30353--30510 Score: 246
Period size: 83 Copynumber: 1.9 Consensus size: 84
30343 TATTTTGATC
* * * * *
30353 ACTATCGCAATGGTGAACAGTGCTATCGCAATGGTGAACAGTGCTATCGTAATGGTGAACAGTAC
1 ACTATCGCAATCGTGAACAGTGCTATCGCAACGGTGAACAGTGATATCGCAACGGTGAACAGTAC
30418 TATCGCAATGGTGAACAGT
66 TATCGCAATGGTGAACAGT
* *
30437 ACTATCGC-ATCGTGAACAGTGCTATCGTAACGGTGAACAGTGATATCGCAACGGTGAACAGTGC
1 ACTATCGCAATCGTGAACAGTGCTATCGCAACGGTGAACAGTGATATCGCAACGGTGAACAGTAC
30501 TATCGCAATG
66 TATCGCAATG
30511 CGATTTTGGA
Statistics
Matches: 67, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
83 59 0.88
84 8 0.12
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (84 bp):
ACTATCGCAATCGTGAACAGTGCTATCGCAACGGTGAACAGTGATATCGCAACGGTGAACAGTAC
TATCGCAATGGTGAACAGT
Found at i:31142 original size:34 final size:34
Alignment explanation
Indices: 31098--31167 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 34
31088 GTCATTGACA
*
31098 ACACACATACCTTGTAGACACAGCCGATCCCTCG
1 ACACACATACCTTGTAGACACAGCCAATCCCTCG
* * *
31132 ACACATATACCTTGTAGACACATCTAATCCCTCG
1 ACACACATACCTTGTAGACACAGCCAATCCCTCG
31166 AC
1 AC
31168 TATAAGATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.31, C:0.36, G:0.11, T:0.21
Consensus pattern (34 bp):
ACACACATACCTTGTAGACACAGCCAATCCCTCG
Found at i:37869 original size:21 final size:21
Alignment explanation
Indices: 37827--37869 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
37817 TTTCTGGGCT
* *
37827 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
37848 AGGGGAATCGATCCCCCCTCA
1 AGGGGAATCGATACCCACTCA
37869 A
1 A
37870 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:37922 original size:20 final size:20
Alignment explanation
Indices: 37897--37934 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
37887 GAATGCTAGA
*
37897 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
37917 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
37935 TAATGAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:39215 original size:31 final size:31
Alignment explanation
Indices: 39131--39236 Score: 97
Period size: 31 Copynumber: 3.4 Consensus size: 31
39121 GAGTCGAGGG
* * * *
39131 TACCTATGTTCTACGGAACATATAGACGGAA
1 TACCTATGTTCTAAGGAACATATGGACAGTA
***
39162 TTACCTATG-TCTTTCGAGACATATGGACAGTA
1 -TACCTATGTTCTAAGGA-ACATATGGACAGTA
* *
39194 TACCTATGTTCTAAGGAACATATGGATAGTT
1 TACCTATGTTCTAAGGAACATATGGACAGTA
*
39225 TACCTAGGTTCT
1 TACCTATGTTCT
39237 TCGGGACCTA
Statistics
Matches: 60, Mismatches: 12, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
31 36 0.60
32 24 0.40
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (31 bp):
TACCTATGTTCTAAGGAACATATGGACAGTA
Found at i:39275 original size:30 final size:30
Alignment explanation
Indices: 39241--39463 Score: 410
Period size: 30 Copynumber: 7.4 Consensus size: 30
39231 GGTTCTTCGG
*
39241 GACCTATGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
39271 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
39301 GACCTCTGGATAGTTACTGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
39331 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
39361 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
39391 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
39421 GACCTCTGGATAGTTACTGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
39451 GACCTTTGGATAG
1 GACCTCTGGATAG
39464 GTCCTTCGGA
Statistics
Matches: 188, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 188 1.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:42836 original size:21 final size:21
Alignment explanation
Indices: 42794--42836 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
42784 TTTCTGGGCT
* *
42794 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
42815 AGGGGAATCGATCCCCCCTCA
1 AGGGGAATCGATACCCACTCA
42836 A
1 A
42837 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:42889 original size:20 final size:20
Alignment explanation
Indices: 42864--42901 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
42854 GAATGCTAGA
*
42864 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
42884 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
42902 TAATGAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:44184 original size:31 final size:31
Alignment explanation
Indices: 44100--44205 Score: 97
Period size: 31 Copynumber: 3.4 Consensus size: 31
44090 GAGTCGAGGG
* * * *
44100 TACCTATGTTCTACGGAACATATGGACGGAA
1 TACCTAGGTTCTAAGGAACATATGGACAGTA
* ***
44131 TTACCTATG-TCTTTCGAGACATATGGACAGTA
1 -TACCTAGGTTCTAAGGA-ACATATGGACAGTA
* *
44163 TACCTAGGTTCTAAGGAACATATGGATAGTT
1 TACCTAGGTTCTAAGGAACATATGGACAGTA
44194 TACCTAGGTTCT
1 TACCTAGGTTCT
44206 TCGGGACCTA
Statistics
Matches: 61, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
31 36 0.59
32 25 0.41
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (31 bp):
TACCTAGGTTCTAAGGAACATATGGACAGTA
Found at i:44218 original size:31 final size:31
Alignment explanation
Indices: 44143--44224 Score: 101
Period size: 31 Copynumber: 2.6 Consensus size: 31
44133 ACCTATGTCT
* * *
44143 TTCGAGACATATGGACAGTATACCTAGGTTC
1 TTCGGGACATATGGATAGTTTACCTAGGTTC
** *
44174 TAAGGAACATATGGATAGTTTACCTAGGTTC
1 TTCGGGACATATGGATAGTTTACCTAGGTTC
*
44205 TTCGGGACCTATGGATAGTT
1 TTCGGGACATATGGATAGTT
44225 ACCGAGGATC
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (31 bp):
TTCGGGACATATGGATAGTTTACCTAGGTTC
Found at i:44244 original size:30 final size:30
Alignment explanation
Indices: 44210--44432 Score: 419
Period size: 30 Copynumber: 7.4 Consensus size: 30
44200 GGTTCTTCGG
*
44210 GACCTATGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
44240 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
44270 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
44300 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
44330 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
44360 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
44390 GACCTCTGGATAGTTACTGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
44420 GACCTTTGGATAG
1 GACCTCTGGATAG
44433 GTCCTTCGGA
Statistics
Matches: 190, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 190 1.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.34
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:45170 original size:2 final size:2
Alignment explanation
Indices: 45163--45191 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
45153 ATAATTAGGT
45163 TA 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 TA T
45192 TTGATACATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:45235 original size:16 final size:16
Alignment explanation
Indices: 45210--45242 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
45200 TCTGGGTAAA
*
45210 TACAATAAAATATATG
1 TACAAGAAAATATATG
45226 TACAAGAAAATATATG
1 TACAAGAAAATATATG
45242 T
1 T
45243 TCAAAGACTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.06, G:0.09, T:0.30
Consensus pattern (16 bp):
TACAAGAAAATATATG
Found at i:47228 original size:27 final size:27
Alignment explanation
Indices: 47190--47243 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
47180 GTTAATATGC
47190 TTACTAGGATATGATTAAAATTTTAAT
1 TTACTAGGATATGATTAAAATTTTAAT
*
47217 TTACTAGGATATGATTAAATTTTTAAT
1 TTACTAGGATATGATTAAAATTTTAAT
47244 CTCATAACCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.39, C:0.04, G:0.11, T:0.46
Consensus pattern (27 bp):
TTACTAGGATATGATTAAAATTTTAAT
Found at i:50783 original size:16 final size:17
Alignment explanation
Indices: 50737--50777 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
50727 GACTTTGACC
50737 AAAAGTCAAATTTTTTG
1 AAAAGTCAAATTTTTTG
50754 AAAAGTCAAATTTTTTG
1 AAAAGTCAAATTTTTTG
50771 AAAAGTC
1 AAAAGTC
50778 TATTTTATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (17 bp):
AAAAGTCAAATTTTTTG
Found at i:53019 original size:17 final size:18
Alignment explanation
Indices: 52992--53025 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
52982 CTTATATTTT
*
52992 ATTTATAAATGTTTTACG
1 ATTTATAAATGGTTTACG
53010 ATTT-TAAATGGTTTAC
1 ATTTATAAATGGTTTAC
53026 CAAAAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.32, C:0.06, G:0.12, T:0.50
Consensus pattern (18 bp):
ATTTATAAATGGTTTACG
Found at i:55293 original size:28 final size:25
Alignment explanation
Indices: 55270--55373 Score: 86
Period size: 28 Copynumber: 3.9 Consensus size: 25
55260 AAATTTTTGA
*
55270 AATATTTTTGAATATTTTATATTTTT
1 AATAATTTT-AATATTTTATATTTTT
55296 AATAAATTTTCAATTATTTTATAATTTTT
1 AAT-AATTTT-AA-TATTTTAT-ATTTTT
* *
55325 AATAATTATAAAAATATTTATATTTTTT
1 AATAATT-TTAATAT-TTTATA-TTTTT
*
55353 AAT-TTTTTAATATTTTA-ATTT
1 AATAATTTTAATATTTTATATTT
55374 ATTTAAAATT
Statistics
Matches: 65, Mismatches: 7, Indels: 15
0.75 0.08 0.17
Matches are distributed among these distances:
23 3 0.05
24 1 0.02
25 4 0.06
26 8 0.12
27 12 0.18
28 27 0.42
29 10 0.15
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.61
Consensus pattern (25 bp):
AATAATTTTAATATTTTATATTTTT
Found at i:55304 original size:18 final size:19
Alignment explanation
Indices: 55270--55368 Score: 54
Period size: 18 Copynumber: 5.4 Consensus size: 19
55260 AAATTTTTGA
55270 AATATTTTTGAAT--ATTTT
1 AATATTTTT-AATAAATTTT
55288 -ATATTTTTAATAAATTTT
1 AATATTTTTAATAAATTTT
*
55306 CAAT-TATTTT-ATAATTTTT
1 -AATAT-TTTTAATAAATTTT
* *
55325 AATAATTATAA-AAATATTT
1 AATATTTTTAATAAAT-TTT
*
55344 -ATATTTTT--TAATTTTTT
1 AATATTTTTAATAA-ATTTT
55361 AATATTTT
1 AATATTTT
55369 AATTTATTTA
Statistics
Matches: 63, Mismatches: 7, Indels: 22
0.68 0.08 0.24
Matches are distributed among these distances:
16 3 0.05
17 13 0.21
18 28 0.44
19 13 0.21
20 6 0.10
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (19 bp):
AATATTTTTAATAAATTTT
Found at i:55359 original size:8 final size:8
Alignment explanation
Indices: 55341--55379 Score: 51
Period size: 8 Copynumber: 4.6 Consensus size: 8
55331 TATAAAAATA
55341 TTTATATTT
1 TTTA-ATTT
55350 TTTAATTT
1 TTTAATTT
*
55358 TTTAATAT
1 TTTAATTT
55366 TTTAATTT
1 TTTAATTT
55374 ATTTAA
1 -TTTAA
55380 AATTATCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
8 18 0.67
9 9 0.33
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (8 bp):
TTTAATTT
Found at i:55368 original size:17 final size:17
Alignment explanation
Indices: 55348--55404 Score: 53
Period size: 19 Copynumber: 3.2 Consensus size: 17
55338 ATATTTATAT
55348 TTTTTAATTTTTTAATA
1 TTTTTAATTTTTTAATA
*
55365 -TTTTAATTTATTTAAAA
1 TTTTTAATTT-TTTAATA
* *
55382 TTATCATATATTTTTAATA
1 TTTTTA-AT-TTTTTAATA
55401 TTTT
1 TTTT
55405 CTAAGAGTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
16 9 0.29
17 6 0.19
18 3 0.10
19 11 0.35
20 2 0.06
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTTAATTTTTTAATA
Found at i:63286 original size:23 final size:22
Alignment explanation
Indices: 63260--63323 Score: 71
Period size: 20 Copynumber: 3.0 Consensus size: 22
63250 GATGGTAAAG
63260 GAAGAAGAAAAAAGAAGAAAGAT
1 GAAGAAGAAAAAAGAA-AAAGAT
* * *
63283 GAAGAA-AATAAGGAAATAGA-
1 GAAGAAGAAAAAAGAAAAAGAT
63303 GAAGAAG-AAAAAGAAAAAGAT
1 GAAGAAGAAAAAAGAAAAAGAT
63324 TGGTGTTGCT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
20 16 0.48
21 4 0.12
22 7 0.21
23 6 0.18
ACGTcount: A:0.69, C:0.00, G:0.25, T:0.06
Consensus pattern (22 bp):
GAAGAAGAAAAAAGAAAAAGAT
Found at i:63382 original size:12 final size:12
Alignment explanation
Indices: 63365--63401 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
63355 GACTCAAATA
63365 ATGAAGATAAAG
1 ATGAAGATAAAG
63377 ATGAAGATAAAG
1 ATGAAGATAAAG
63389 ATGAAGATAAAG
1 ATGAAGATAAAG
63401 A
1 A
63402 AATGTCAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.59, C:0.00, G:0.24, T:0.16
Consensus pattern (12 bp):
ATGAAGATAAAG
Found at i:63383 original size:6 final size:6
Alignment explanation
Indices: 63368--63401 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
63358 TCAAATAATG
* *
63368 AAGATA AAGATG AAGATA AAGATG AAGATA AAGA
1 AAGATA AAGATA AAGATA AAGATA AAGATA AAGA
63402 AATGTCAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.15
Consensus pattern (6 bp):
AAGATA
Found at i:64669 original size:66 final size:63
Alignment explanation
Indices: 64563--64704 Score: 160
Period size: 66 Copynumber: 2.2 Consensus size: 63
64553 TTGTTGAAGG
* * * **
64563 TGCATCGATGCATAAGGAGTGCATCGATGCACTCATTTAAATTAAATTAACATCGAATTCCATTT
1 TGCATCGATGCATAAAGAGTGCATCGATGAACTCA-TTAAAATAAA--AACATCGAATAACATTT
64628 A
63 A
* *
64629 TGCATCGATGCATAAAGAGTGCATCGATGAACCTGC-TTAAAATACAAACATCGAATAAGATTTA
1 TGCATCGATGCATAAAGAGTGCATCGATGAA-CT-CATTAAAATAAAAACATCGAATAACATTTA
*
64693 TGCACCGATGCA
1 TGCATCGATGCA
64705 AGTGCATCGA
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
64 26 0.39
66 37 0.56
67 2 0.03
68 1 0.02
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (63 bp):
TGCATCGATGCATAAAGAGTGCATCGATGAACTCATTAAAATAAAAACATCGAATAACATTTA
Found at i:65338 original size:2 final size:2
Alignment explanation
Indices: 65331--65389 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
65321 ACACAGTTAG
65331 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
65373 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
65390 GATTGTATAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:66105 original size:22 final size:22
Alignment explanation
Indices: 66080--66135 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
66070 GGGTATATTA
*
66080 GTCCTTCAGGATGTATCCAGTG
1 GTCCTTCAGGACGTATCCAGTG
* *
66102 GTCCTTCGGGACGTATCTAGTG
1 GTCCTTCAGGACGTATCCAGTG
* *
66124 ATCCTTCGGGAC
1 GTCCTTCAGGAC
66136 ATAGTGGTCC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.16, C:0.25, G:0.29, T:0.30
Consensus pattern (22 bp):
GTCCTTCAGGACGTATCCAGTG
Found at i:66146 original size:18 final size:20
Alignment explanation
Indices: 66098--66155 Score: 66
Period size: 18 Copynumber: 2.9 Consensus size: 20
66088 GGATGTATCC
66098 AGTGGTCCTTCGGGACGTATCT
1 AGTGGTCCTTCGGGACG-A-CT
*
66120 AGTGATCCTTCGGGAC-A-T
1 AGTGGTCCTTCGGGACGACT
*
66138 AGTGGTCCTTTGGGACGA
1 AGTGGTCCTTCGGGACGA
66156 ATATTGAACA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
18 15 0.47
19 1 0.03
20 1 0.03
22 15 0.47
ACGTcount: A:0.17, C:0.21, G:0.33, T:0.29
Consensus pattern (20 bp):
AGTGGTCCTTCGGGACGACT
Found at i:70487 original size:19 final size:20
Alignment explanation
Indices: 70442--70487 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
70432 ATGTGTTTTG
*
70442 GAGTTTCAATACTTTTCCAA
1 GAGTTTCAATACTTTGCCAA
*
70462 GAGTTTCCATACTTTGCCAA
1 GAGTTTCAATACTTTGCCAA
70482 -AGTTTC
1 GAGTTTC
70488 GAAACTCCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.39
Consensus pattern (20 bp):
GAGTTTCAATACTTTGCCAA
Found at i:70505 original size:20 final size:20
Alignment explanation
Indices: 70480--70519 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
70470 ATACTTTGCC
70480 AAAGTTTCGAAACTCCTTGT
1 AAAGTTTCGAAACTCCTTGT
* *
70500 AAAGTTTTGAAACTCGTTGT
1 AAAGTTTCGAAACTCCTTGT
70520 GCAGCAACCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (20 bp):
AAAGTTTCGAAACTCCTTGT
Found at i:70839 original size:15 final size:15
Alignment explanation
Indices: 70819--70849 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
70809 TAAAATGTAT
70819 CGAAACTTTATTTCA
1 CGAAACTTTATTTCA
70834 CGAAACTTTATTTCA
1 CGAAACTTTATTTCA
70849 C
1 C
70850 TCTTTATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.39
Consensus pattern (15 bp):
CGAAACTTTATTTCA
Found at i:72493 original size:19 final size:17
Alignment explanation
Indices: 72469--72510 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
72459 TGAATGATAT
72469 ATAATTTGATAAATTAATG
1 ATAATTT-ATAAATT-ATG
*
72488 ATAATTTTTAAATTATG
1 ATAATTTATAAATTATG
72505 A-AATTT
1 ATAATTT
72511 TTACAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 5 0.23
17 4 0.18
18 6 0.27
19 7 0.32
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (17 bp):
ATAATTTATAAATTATG
Found at i:72512 original size:17 final size:18
Alignment explanation
Indices: 72478--72513 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
72468 TATAATTTGA
72478 TAAATTAATGATAATTTT
1 TAAATTAATGATAATTTT
72496 TAAATT-ATGA-AATTTT
1 TAAATTAATGATAATTTT
72512 TA
1 TA
72514 CAAAAAAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
17 4 0.22
18 6 0.33
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (18 bp):
TAAATTAATGATAATTTT
Done.