Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008356.1 Hibiscus syriacus cultivar Beakdansim tig00111095_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: 12862612
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 56 of 56
Found at i:12784505 original size:229 final size:229
Alignment explanation
Indices: 12784104--12784642 Score: 936
Period size: 229 Copynumber: 2.4 Consensus size: 229
12784094 AAGTTCCATG
*
12784104 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
*
12784169 TGGTTTGGTATGAACCCCAAAAACCAATCATTAGATTTGAAAGATGAATGTGCTCATAGTAGAAA
66 TGGTTTGGTATGAACCCCAAAAACCAATCATTAGATTTGAAAGATAAATGTGCTCATAGTAGAAA
*
12784234 TAAGAAGACCCAATAGCATCTTTGGAAGTGTTCTTTGAGTTATCTGATCTAATTTAGTATGAACC
131 TAAGAAGACCCAATAGCATCTTTGGAAGTGTTCTTTGAGTTATCTGATATAATTTAGTATGAACC
* *
12784299 CCAAAAACCAATCATTGGATTTGAAAGATGAATT
196 CCAAAAACCAATCATTAGATTTAAAAGATGAATT
12784333 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
*
12784398 TGGTTTGGTATGAACCCCAAAAACCAATCATTAGATTTGAAAGATAAATTTGCTCATAGTAGAAA
66 TGGTTTGGTATGAACCCCAAAAACCAATCATTAGATTTGAAAGATAAATGTGCTCATAGTAGAAA
** *
12784463 TAAGAAGACCCAATAGCATCTTCTGGAA-TGTTCTTTGAGTTATCTGATATGGTTTGGTATGAAC
131 TAAGAAGACCCAATAGCATCTT-TGGAAGTGTTCTTTGAGTTATCTGATATAATTTAGTATGAAC
12784527 CCCAAAAACCAATCATTAGATTTAAAAGATGAATT
195 CCCAAAAACCAATCATTAGATTTAAAAGATGAATT
* * *
12784562 TGCTCATGGTAGAAATAAGGAGGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* *
12784627 TGGTTCGGTAGGAACC
66 TGGTTTGGTATGAACC
12784643 ACAGAACCAG
Statistics
Matches: 295, Mismatches: 14, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
229 290 0.98
230 5 0.02
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (229 bp):
TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TGGTTTGGTATGAACCCCAAAAACCAATCATTAGATTTGAAAGATAAATGTGCTCATAGTAGAAA
TAAGAAGACCCAATAGCATCTTTGGAAGTGTTCTTTGAGTTATCTGATATAATTTAGTATGAACC
CCAAAAACCAATCATTAGATTTAAAAGATGAATT
Found at i:12786674 original size:40 final size:40
Alignment explanation
Indices: 12786615--12786694 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
12786605 TGAGCAGAAG
12786615 CCACAGAAAAGGATAAATGTGTTGTCAAGTGTTTTACATC
1 CCACAGAAAAGGATAAATGTGTTGTCAAGTGTTTTACATC
*
12786655 CCACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTACATC
1 CCACAGAAAAGGATAAATGTGTTGTCAAGTGTTTTACATC
12786695 TGAGCTGAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (40 bp):
CCACAGAAAAGGATAAATGTGTTGTCAAGTGTTTTACATC
Found at i:12786777 original size:54 final size:52
Alignment explanation
Indices: 12786655--12786795 Score: 151
Period size: 54 Copynumber: 2.7 Consensus size: 52
12786645 GTTTTACATC
* * * *
12786655 CCACAGAAAAGGATGAATGTGTTGTCAAGTGTTTT--ACATCTGAGCTGAAA
1 CCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACACATCTGAGCAGAAA
* * * * *
12786705 CCACATGAGATTAAGAATGTGTTGTCAAATGTTTTACAAACATCTGAGCAGAAG
1 CCACAGGAAATGATGAATGTGTTGTCAAATGTTTTAC--ACATCTGAGCAGAAA
* *
12786759 CCACAGGAAATGATGAATGCGCTGTCAAATGTTTTAC
1 CCACAGGAAATGATGAATGTGTTGTCAAATGTTTTAC
12786796 GAACCTGCTA
Statistics
Matches: 72, Mismatches: 15, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
50 28 0.39
54 44 0.61
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.28
Consensus pattern (52 bp):
CCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACACATCTGAGCAGAAA
Found at i:12788284 original size:113 final size:113
Alignment explanation
Indices: 12787590--12788271 Score: 1042
Period size: 114 Copynumber: 6.0 Consensus size: 113
12787580 TAGCAAAGAT
12787590 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
*
12787655 AGAAGGAAGAAGAAATTCATAATGAGAAAAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
12787703 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
*
12787768 AGAATGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
12787816 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAG-AAAAAGTTCATAATGAGAAGAACTCATCTG
*
12787881 AAGAAGGAATAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
65 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
12787930 TCAAATCCATCATTTGATGGATCAGTTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAG-AAAAAGTTCATAATGAGAAGAACTCATCTG
* *
12787995 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAATCTTTTGT
65 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
** * * ** * *
12788044 TTGAATTCATCATTTGATGGATCAGCATCCCCAGTGAAAGAGTTCATAATGAGAAGAACTCATAT
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCA--GAAAAAGTTCATAATGAGAAGAACTCATCT
* *
12788109 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTCGC
64 GAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTT-GC
* * * * * * *
12788159 TCGAATTCATCACTCGATGGATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
** * * ** *
12788224 AGAAATAAGAAGAAGTTTATAATGAGAAGAGCTTGTTCGACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
12788272 ATGAATCTAT
Statistics
Matches: 530, Mismatches: 34, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
113 212 0.40
114 223 0.42
115 94 0.18
116 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (113 bp):
TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:12788337 original size:17 final size:17
Alignment explanation
Indices: 12788315--12788373 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
12788305 CAGCATTTTC
12788315 AGAAGAAGTTCACAATG
1 AGAAGAAGTTCACAATG
*
12788332 AGAAGAA-CTCATCTGAA-G
1 AGAAGAAGTTCA-C--AATG
12788350 AAGAAGAAGTTCACAATG
1 -AGAAGAAGTTCACAATG
12788368 AGAAGA
1 AGAAGA
12788374 GCTTGTTCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
16 3 0.09
17 16 0.47
18 2 0.06
19 10 0.29
20 3 0.09
ACGTcount: A:0.49, C:0.12, G:0.24, T:0.15
Consensus pattern (17 bp):
AGAAGAAGTTCACAATG
Found at i:12788617 original size:3 final size:3
Alignment explanation
Indices: 12788611--12788691 Score: 146
Period size: 3 Copynumber: 27.0 Consensus size: 3
12788601 TTTACCCATT
12788611 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
12788659 TTA -TA TTA TTA TTA TATA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
12788692 AAAAATAATT
Statistics
Matches: 76, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.03
3 71 0.93
4 3 0.04
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:12790316 original size:20 final size:20
Alignment explanation
Indices: 12790291--12790333 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
12790281 TTATTTTATA
12790291 AATTATATATTAATTGTTTT
1 AATTATATATTAATTGTTTT
* * *
12790311 AATTATTTATTTATTTTTTT
1 AATTATATATTAATTGTTTT
12790331 AAT
1 AAT
12790334 ATCCAAGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (20 bp):
AATTATATATTAATTGTTTT
Found at i:12790928 original size:13 final size:13
Alignment explanation
Indices: 12790900--12790938 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
12790890 TGGGCAATGT
*
12790900 TTTGAAAA-ACTA
1 TTTGAAAATAATA
12790912 TTTGAAAATAATA
1 TTTGAAAATAATA
12790925 TTTGAAAATAATA
1 TTTGAAAATAATA
12790938 T
1 T
12790939 GTATAGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
12 8 0.32
13 17 0.68
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.38
Consensus pattern (13 bp):
TTTGAAAATAATA
Found at i:12795763 original size:20 final size:20
Alignment explanation
Indices: 12795738--12795777 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
12795728 TTTCATCGTC
12795738 ATCATCATCGTCATTCGAAT
1 ATCATCATCGTCATTCGAAT
12795758 ATCATCATCGTCATTCGAAT
1 ATCATCATCGTCATTCGAAT
12795778 CACTCTCATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.25, G:0.10, T:0.35
Consensus pattern (20 bp):
ATCATCATCGTCATTCGAAT
Found at i:12797427 original size:64 final size:65
Alignment explanation
Indices: 12797312--12797471 Score: 166
Period size: 64 Copynumber: 2.5 Consensus size: 65
12797302 GTGCACTCTT
* * * *
12797312 AGTGCATCGATGCATCAAGTGAAATCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGCT
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGG-T
12797376 -
65 A
* * * *
12797376 GGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCA-TGCATCGGTGCATGGT
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCACAGTGCATCGATGCATGGT
12797439 A
65 A
* * * *
12797440 AGTGCATCGATTCATGAAATACATTTGATGTT
1 AGTGCATCGATGCATCAAATGCATTCGATGTT
12797472 CAATTTAATT
Statistics
Matches: 80, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
63 1 0.01
64 67 0.84
65 9 0.11
66 3 0.04
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (65 bp):
AGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGTA
Found at i:12804942 original size:24 final size:22
Alignment explanation
Indices: 12804915--12804987 Score: 69
Period size: 24 Copynumber: 3.1 Consensus size: 22
12804905 TAAACTTAAT
12804915 TAAAATAATTAAAATAACAAATAA
1 TAAAA-AATTAAAATAACAAA-AA
12804939 TAAAAAATAGTAAAA-AACATAAAA
1 TAAAAAAT--TAAAATAACA-AAAA
12804963 TAAAAAA-TAAACATAAACAAAAA
1 TAAAAAATTAAA-AT-AACAAAAA
12804986 TA
1 TA
12804988 CAAGGAGCTA
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
21 4 0.09
22 1 0.02
23 9 0.21
24 22 0.51
25 7 0.16
ACGTcount: A:0.74, C:0.05, G:0.01, T:0.19
Consensus pattern (22 bp):
TAAAAAATTAAAATAACAAAAA
Found at i:12804962 original size:17 final size:18
Alignment explanation
Indices: 12804924--12804979 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 18
12804914 TTAAAATAAT
*
12804924 TAAAATAACAAATAATA-A
1 TAAAATAAAAAATAA-ACA
**
12804942 -AAAATAGTAAA-AAACA
1 TAAAATAAAAAATAAACA
12804958 TAAAATAAAAAATAAACA
1 TAAAATAAAAAATAAACA
12804976 TAAA
1 TAAA
12804980 CAAAAATACA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
15 1 0.03
16 3 0.10
17 18 0.58
18 9 0.29
ACGTcount: A:0.75, C:0.05, G:0.02, T:0.18
Consensus pattern (18 bp):
TAAAATAAAAAATAAACA
Found at i:12805062 original size:22 final size:20
Alignment explanation
Indices: 12805019--12805064 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
12805009 ATTAAATTAC
12805019 TAAACTAAAAGGGCATAAAT
1 TAAACTAAAAGGGCATAAAT
12805039 TAAACATAAAATGGG-ACTAAAT
1 TAAAC-TAAAA-GGGCA-TAAAT
12805061 TAAA
1 TAAA
12805065 AAAATTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 5 0.22
21 6 0.26
22 12 0.52
ACGTcount: A:0.57, C:0.09, G:0.13, T:0.22
Consensus pattern (20 bp):
TAAACTAAAAGGGCATAAAT
Found at i:12811829 original size:2 final size:2
Alignment explanation
Indices: 12811822--12811858 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
12811812 AGACTATGTC
12811822 AT AT AT 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 AT AT AT A
12811859 CTTCTTAACC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12811915 original size:18 final size:19
Alignment explanation
Indices: 12811885--12811925 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
12811875 GTTTATATAC
12811885 TATTCTTCTTTATAT-TTT
1 TATTCTTCTTTATATATTT
*
12811903 TATTCTATC-TTATTTATTT
1 TATTCT-TCTTTATATATTT
12811922 TATT
1 TATT
12811926 TTGATTTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.71
Consensus pattern (19 bp):
TATTCTTCTTTATATATTT
Found at i:12813191 original size:53 final size:54
Alignment explanation
Indices: 12813080--12813192 Score: 135
Period size: 53 Copynumber: 2.1 Consensus size: 54
12813070 TGCCTATCCT
* *
12813080 GAAATTTGAATTTCTTTATGTTAGTTATTTATTTTACTGATGTTACTCACTCTA
1 GAAATTTGAATTTCTTTATGTTAGTTATTCATTTTACTGATGTGACTCACTCTA
* * *
12813134 -AAATTTGAATTTTTTTCATGTT-GATTCTTCATTTTAGTGATGTGAC-CAC-CTA
1 GAAATTTGAATTTCTTT-ATGTTAG-TTATTCATTTTACTGATGTGACTCACTCTA
12813186 GAAATTT
1 GAAATTT
12813193 TATTTGTCCT
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
52 3 0.06
53 25 0.49
54 23 0.45
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.50
Consensus pattern (54 bp):
GAAATTTGAATTTCTTTATGTTAGTTATTCATTTTACTGATGTGACTCACTCTA
Found at i:12813512 original size:32 final size:32
Alignment explanation
Indices: 12813476--12813548 Score: 137
Period size: 33 Copynumber: 2.2 Consensus size: 32
12813466 ATAAAGTTTA
12813476 CGATAATTCAAATACTTAAAAACTTCCAAGTT
1 CGATAATTCAAATACTTAAAAACTTCCAAGTT
12813508 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
1 CGAT-AATTCAAATACTTAAAAACTTCCAAGTT
12813541 CGATAATT
1 CGATAATT
12813549 GAAACAAAGT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
32 8 0.20
33 32 0.80
ACGTcount: A:0.44, C:0.18, G:0.07, T:0.32
Consensus pattern (32 bp):
CGATAATTCAAATACTTAAAAACTTCCAAGTT
Found at i:12813566 original size:21 final size:21
Alignment explanation
Indices: 12813541--12813582 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
12813531 CTTCCAAGTT
12813541 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
12813562 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
12813583 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:12818023 original size:14 final size:15
Alignment explanation
Indices: 12817984--12818016 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
12817974 GAAATGAAGA
12817984 ATACAATATAC-AAAT
1 ATAC-ATATACGAAAT
12817999 ATACATATACGAAAT
1 ATACATATACGAAAT
12818014 ATA
1 ATA
12818017 TTATACGTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.58, C:0.12, G:0.03, T:0.27
Consensus pattern (15 bp):
ATACATATACGAAAT
Found at i:12820058 original size:10 final size:10
Alignment explanation
Indices: 12820043--12820089 Score: 76
Period size: 10 Copynumber: 4.6 Consensus size: 10
12820033 TGGAAGACTA
12820043 AATTTATTTT
1 AATTTATTTT
12820053 AATTTATTTT
1 AATTTATTTT
*
12820063 AAATTATTTT
1 AATTTATTTT
12820073 AATTTATTTTT
1 AATTTA-TTTT
12820084 AATTTA
1 AATTTA
12820090 ATATATTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
10 24 0.71
11 10 0.29
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
AATTTATTTT
Found at i:12820382 original size:28 final size:30
Alignment explanation
Indices: 12820341--12820398 Score: 84
Period size: 28 Copynumber: 2.0 Consensus size: 30
12820331 TATCTCTTTA
*
12820341 TTTATTTAACTTATTGAATAT-TTTTATTT
1 TTTATTTAACTTATTAAATATATTTTATTT
*
12820370 TTTA-TTAATTTATTAAATATATTTTATTT
1 TTTATTTAACTTATTAAATATATTTTATTT
12820399 ATCTTAATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 14 0.54
29 12 0.46
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (30 bp):
TTTATTTAACTTATTAAATATATTTTATTT
Found at i:12820405 original size:28 final size:27
Alignment explanation
Indices: 12820337--12820425 Score: 81
Period size: 28 Copynumber: 3.2 Consensus size: 27
12820327 AAATTATCTC
* *
12820337 TTTATTTATTTAACTTATTGAATAT-T
1 TTTATTTATTTAATTTATTAAATATAT
*
12820363 TTTATTTTTTATTAATTTATTAAATATAT
1 TTTA-TTTAT-TTAATTTATTAAATATAT
* **
12820392 TTTATTTATCTTAATGTAAAAATATATAT
1 TTTATTTAT-TTAATTTATTAA-ATATAT
12820421 TTTAT
1 TTTAT
12820426 CTTTATCATC
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
26 4 0.08
27 4 0.08
28 27 0.53
29 16 0.31
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (27 bp):
TTTATTTATTTAATTTATTAAATATAT
Found at i:12820517 original size:31 final size:33
Alignment explanation
Indices: 12820481--12820553 Score: 96
Period size: 31 Copynumber: 2.3 Consensus size: 33
12820471 AATATATTTA
12820481 AATATTTTACTATTAATTTAATATAAAA-ATAT
1 AATATTTTACTATTAATTTAATATAAAATATAT
* * * *
12820513 -ATATTTTACTCTTATTTTTATTTAAAATATAT
1 AATATTTTACTATTAATTTAATATAAAATATAT
12820545 AATATTTTA
1 AATATTTTA
12820554 ATATATTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
31 23 0.66
32 4 0.11
33 8 0.23
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (33 bp):
AATATTTTACTATTAATTTAATATAAAATATAT
Found at i:12820801 original size:29 final size:29
Alignment explanation
Indices: 12820729--12820804 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 29
12820719 ATATTTTTGT
* *
12820729 ATTAAAATAAAAACAAAATATATTTAATA
1 ATTAAAACAAAAATAAAATATATTTAATA
*
12820758 AATAAATACAAAAATAAAA-ATATTTAATA
1 ATTAAA-ACAAAAATAAAATATATTTAATA
12820787 AGTTAAAACAAAAATAAA
1 A-TTAAAACAAAAATAAA
12820805 TAGATAATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
29 27 0.66
30 14 0.34
ACGTcount: A:0.68, C:0.04, G:0.01, T:0.26
Consensus pattern (29 bp):
ATTAAAACAAAAATAAAATATATTTAATA
Found at i:12821719 original size:42 final size:41
Alignment explanation
Indices: 12821673--12822097 Score: 541
Period size: 42 Copynumber: 10.1 Consensus size: 41
12821663 CATATTCGCA
* *
12821673 TTGCGATAGTCCAAGTTCGCGTTGCGA-TAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTATTCCAAGTT--CG
* *
12821715 TTGCGATTTATTCCAAATT--CGTTGCGATTTATTCCAAGTTCG
1 TTGCGA--TAGTCCAAGTTCGCGTTGCGA-TTATTCCAAGTTCG
* * *
12821757 TTGCGATAGTCGAAGTTCGCGTTGCGTTTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCG-ATTATTCCAAGTTCG
12821799 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGA-TTATTCCAAGTTCG
** *
12821841 TTGCGATAGTCGTAGTTCGTGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGA-TTATTCCAAGTTCG
* * * *
12821883 TAGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTTG
1 TTGCGATAGTCCAAGTTCGCGTTGCGA-TTATTCCAAGTTCG
*
12821925 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGA-TTATTCCAAGTTCG
12821967 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGA-TTATTCCAAGTTCG
*
12822009 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGA-TTATTCCAAGTTCG
* * *
12822051 TTGCGATAGTCGAAGTTCGCGTTGCAATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGA-TTATTCCAAGTTCG
12822093 TTGCG
1 TTGCG
12822098 CGTTGCGATT
Statistics
Matches: 348, Mismatches: 27, Indels: 16
0.89 0.07 0.04
Matches are distributed among these distances:
40 8 0.02
42 322 0.93
44 18 0.05
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (41 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTATTCCAAGTTCG
Found at i:12821814 original size:126 final size:123
Alignment explanation
Indices: 12821673--12822097 Score: 609
Period size: 126 Copynumber: 3.4 Consensus size: 123
12821663 CATATTCGCA
* * *
12821673 TTGCGATAGTCCAAGTTCGCGTTGCGA-TAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGT
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTATTCCAAGTT--CGTTGCGA--TAGTCCAAATTCGT
*
12821737 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGTTTTATTCCAAATTCG
62 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
** *
12821799 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGTAGTTCGTGTT
1 TTGCGATAGTCCAAGTTCGCGTTGCGA-TTATTCCAAGTTCGTTGCGATAGTCCAAATTC--GTT
* *
12821864 GCGATTTATTCCAAGTTCGTAGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTTG
63 GCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
* *
12821925 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTT
1 TTGCGATAGTCCAAGTTCGCGTTGCGA-TTATTCCAAGTTCGTTGCGATAGTCCAAATT--CGTT
*
12821990 GCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
63 GCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
* * *
12822051 TTGCGATAGTCGAAGTTCGCGTTGCAATTTATTCCAAATTCGTTGCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGA-TTATTCCAAGTTCGTTGCG
12822098 CGTTGCGATT
Statistics
Matches: 276, Mismatches: 17, Indels: 12
0.90 0.06 0.04
Matches are distributed among these distances:
124 8 0.03
126 258 0.93
128 10 0.04
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (123 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTATTCCAAGTTCGTTGCGATAGTCCAAATTCGTTGCG
ATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:12822108 original size:28 final size:28
Alignment explanation
Indices: 12822068--12822125 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
12822058 AGTCGAAGTT
12822068 CGCGTTGCAATTTATTCCAAATTCGTTG
1 CGCGTTGCAATTTATTCCAAATTCGTTG
*
12822096 CGCGTTGCGATTTATTCCAAATTCGTTG
1 CGCGTTGCAATTTATTCCAAATTCGTTG
12822124 CG
1 CG
12822126 ATAGTCCAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.19, C:0.22, G:0.21, T:0.38
Consensus pattern (28 bp):
CGCGTTGCAATTTATTCCAAATTCGTTG
Found at i:12822109 original size:70 final size:70
Alignment explanation
Indices: 12822026--12822167 Score: 248
Period size: 70 Copynumber: 2.0 Consensus size: 70
12822016 AGTCGAAGTT
* *
12822026 CGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCAATTTATTCCAAATT
1 CGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCAATTTATTCCAAATT
12822091 CGTTG
66 CGTTG
* *
12822096 CGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTT
1 CGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCAATTTATTCCAAATT
12822161 CGTTG
66 CGTTG
12822166 CG
1 CG
12822168 ATAGTCCAAA
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 68 1.00
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.37
Consensus pattern (70 bp):
CGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCAATTTATTCCAAATT
CGTTG
Found at i:12822139 original size:19 final size:19
Alignment explanation
Indices: 12822111--12822176 Score: 78
Period size: 21 Copynumber: 3.3 Consensus size: 19
12822101 TGCGATTTAT
*
12822111 TCCAAATTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
*
12822130 TCCAAGTTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGA--TAG
12822153 TCCAAGTTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
12822172 TCCAA
1 TCCAA
12822177 AATCACAACG
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
19 14 0.35
21 16 0.40
23 10 0.25
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (19 bp):
TCCAAGTTCGTTGCGATAG
Found at i:12822155 original size:42 final size:42
Alignment explanation
Indices: 12822096--12822176 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
12822086 AAATTCGTTG
12822096 CGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTT
1 CGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTT
*
12822138 CGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCCAA
1 CGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAA
12822177 AATCACAACG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.35
Consensus pattern (42 bp):
CGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTT
Found at i:12822953 original size:6 final size:6
Alignment explanation
Indices: 12822936--12822967 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
12822926 TCTCGTCTCG
12822936 GGTCGT -GTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
12822968 AATACGTGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.00, C:0.16, G:0.50, T:0.34
Consensus pattern (6 bp):
GGTCGT
Found at i:12823089 original size:21 final size:20
Alignment explanation
Indices: 12823064--12823134 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 20
12823054 ATTTTGGACT
12823064 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAAT-A
* *
12823085 ATCGCAACGCGAACTTCGACT-
1 ATCGCAA--CGAACTTGGAATA
*
12823106 ATCGCAACGAACATGGAATTA
1 ATCGCAACGAACTTGGAA-TA
12823127 ATCGCAAC
1 ATCGCAAC
12823135 TATTGCAACG
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
19 8 0.20
20 1 0.02
21 22 0.54
23 10 0.24
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.18
Consensus pattern (20 bp):
ATCGCAACGAACTTGGAATA
Found at i:12823153 original size:30 final size:28
Alignment explanation
Indices: 12823103--12823160 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 28
12823093 GCGAACTTCG
12823103 ACTATCGCAACGAACATGGAATTAATCGCA
1 ACTATCGCAACGAACATGGAA--AATCGCA
* **
12823133 ACTATTGCAACGAATTTGGAAAATCGCA
1 ACTATCGCAACGAACATGGAAAATCGCA
12823161 TTGCGATAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 7 0.28
30 18 0.72
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.22
Consensus pattern (28 bp):
ACTATCGCAACGAACATGGAAAATCGCA
Found at i:12823185 original size:21 final size:21
Alignment explanation
Indices: 12823156--12823208 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
12823146 ATTTGGAAAA
*
12823156 TCGCATTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCGAAGT
*
12823177 TCGCGTTGCGATAGTCGATGT
1 TCGCGTTGCGATAGTCGAAGT
12823198 TCGCGTTGCGA
1 TCGCGTTGCGA
12823209 ATCTGGAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.17, C:0.21, G:0.32, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCGAAGT
Found at i:12826959 original size:41 final size:41
Alignment explanation
Indices: 12826891--12826989 Score: 101
Period size: 41 Copynumber: 2.4 Consensus size: 41
12826881 AGGTTTTTAA
*
12826891 CGGC-TTTTTTTAAAAACGCCGCAAAAGGTAATGAAATGTAG
1 CGGCGTTTTTTT-CAAACGCCGCAAAAGGTAATGAAATGTAG
* * * * *
12826932 CGGCGTTTTTTTCAAACGTCGCTAAAGGTTATGATATTTAG
1 CGGCGTTTTTTTCAAACGCCGCAAAAGGTAATGAAATGTAG
* * *
12826973 TGGTGTTTTCTTCAAAC
1 CGGCGTTTTTTTCAAAC
12826990 ACCGTTATTT
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
41 41 0.85
42 7 0.15
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.35
Consensus pattern (41 bp):
CGGCGTTTTTTTCAAACGCCGCAAAAGGTAATGAAATGTAG
Found at i:12827332 original size:21 final size:21
Alignment explanation
Indices: 12827308--12827366 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
12827298 ATTATCCAAT
*
12827308 AAACTTGACATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
*
12827329 AAACTTGAAATCCATAACAAG
1 AAACTTGAAATCCATAACAAC
*
12827350 AAACTTGAAATCTATAA
1 AAACTTGAAATCCATAA
12827367 TAATAAATCA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.51, C:0.20, G:0.07, T:0.22
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Found at i:12830028 original size:41 final size:41
Alignment explanation
Indices: 12829983--12830079 Score: 149
Period size: 41 Copynumber: 2.4 Consensus size: 41
12829973 TAAATTGTGA
*
12829983 CGTTTGTATAAAAACACCACTAAAATAATAGTCTTTAGCGG
1 CGTTTGTATAAAAACACCACTAAAATAAGAGTCTTTAGCGG
* * * *
12830024 CGTTTGTATAAAAATACCACTAAATTACGAGTCTTTGGCGG
1 CGTTTGTATAAAAACACCACTAAAATAAGAGTCTTTAGCGG
12830065 CGTTTGTATAAAAAC
1 CGTTTGTATAAAAAC
12830080 TGTAACACCC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31
Consensus pattern (41 bp):
CGTTTGTATAAAAACACCACTAAAATAAGAGTCTTTAGCGG
Found at i:12830664 original size:17 final size:17
Alignment explanation
Indices: 12830642--12830674 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12830632 TAACCATTTG
12830642 TTTAATTTGCCCAGACT
1 TTTAATTTGCCCAGACT
*
12830659 TTTAATTTGTCCAGAC
1 TTTAATTTGCCCAGAC
12830675 GTATAATACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.21, G:0.12, T:0.42
Consensus pattern (17 bp):
TTTAATTTGCCCAGACT
Found at i:12830808 original size:23 final size:22
Alignment explanation
Indices: 12830751--12830840 Score: 89
Period size: 21 Copynumber: 4.1 Consensus size: 22
12830741 TCGTAATTTG
12830751 CACCGAAGTGCCACATAATTGT
1 CACCGAAGTGCCACATAATTGT
* *
12830773 C-CCGAAG-GACCACATAGGTTTT
1 CACCGAAGTG-CCACATA-ATTGT
*
12830795 CACCGAAGTGCCACATATTTGT
1 CACCGAAGTGCCACATAATTGT
*
12830817 C-CCGAAG-GACCGCATAATTGT
1 CACCGAAGTG-CCACATAATTGT
12830838 CAC
1 CAC
12830841 TGAGAACCAC
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
20 2 0.04
21 30 0.54
22 10 0.18
23 13 0.23
24 1 0.02
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (22 bp):
CACCGAAGTGCCACATAATTGT
Found at i:12841919 original size:20 final size:20
Alignment explanation
Indices: 12841894--12841972 Score: 61
Period size: 20 Copynumber: 3.9 Consensus size: 20
12841884 TTTTGGTGCA
*
12841894 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCCAT
* **
12841914 GAGGGAACCGATTCCCCTTT
1 GAGGGAACCGATACCCCCAT
*
12841934 GAAGGGGAACCGAT-CCCCCAC
1 G-A-GGGAACCGATACCCCCAT
* * *
12841955 AATGGAATCGATACCCCC
1 GAGGGAACCGATACCCCC
12841973 CCTGGGGTTC
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
19 8 0.17
20 23 0.50
21 5 0.11
22 10 0.22
ACGTcount: A:0.28, C:0.33, G:0.24, T:0.15
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCAT
Found at i:12847306 original size:21 final size:21
Alignment explanation
Indices: 12847280--12847321 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
12847270 ATTTGAATAT
*
12847280 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
12847301 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
12847322 CCCATTATGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:12849496 original size:43 final size:44
Alignment explanation
Indices: 12849448--12849574 Score: 138
Period size: 42 Copynumber: 3.0 Consensus size: 44
12849438 CAGCTCGTAA
12849448 TTTGCACCGAAGTGCCACATAATTGT-CCGAAGGACCACATAGG
1 TTTGCACCGAAGTGCCACATAATTGTCCCGAAGGACCACATAGG
* * * *
12849491 TTTGCACCGAAGTGTCACATATTTGTCCCGAAGTACCACATA-A
1 TTTGCACCGAAGTGCCACATAATTGTCCCGAAGGACCACATAGG
* * *
12849534 TTAT-C-CCGGAG-GACCACATAATTATCCCGGAGGACCACATA
1 TT-TGCACCGAAGTG-CCACATAATTGTCCCGAAGGACCACATA
12849575 AAACCCTCGA
Statistics
Matches: 71, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
41 1 0.01
42 28 0.39
43 27 0.38
44 15 0.21
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.23
Consensus pattern (44 bp):
TTTGCACCGAAGTGCCACATAATTGTCCCGAAGGACCACATAGG
Found at i:12849521 original size:21 final size:21
Alignment explanation
Indices: 12849454--12849541 Score: 74
Period size: 21 Copynumber: 4.1 Consensus size: 21
12849444 GTAATTTGCA
*
12849454 CCGAAGTGCCACATAATTGT-
1 CCGAAGTGCCACATATTTGTC
12849474 CCGAAG-GACCACATAGGTTTG-C
1 CCGAAGTG-CCACATA--TTTGTC
*
12849496 ACCGAAGTGTCACATATTTGTC
1 -CCGAAGTGCCACATATTTGTC
* * *
12849518 CCGAAGTACCACATAATTATC
1 CCGAAGTGCCACATATTTGTC
12849539 CCG
1 CCG
12849542 GAGGACCACA
Statistics
Matches: 55, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
19 1 0.02
20 13 0.24
21 24 0.44
22 4 0.07
23 12 0.22
24 1 0.02
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (21 bp):
CCGAAGTGCCACATATTTGTC
Found at i:12849549 original size:21 final size:21
Alignment explanation
Indices: 12849506--12849575 Score: 104
Period size: 21 Copynumber: 3.3 Consensus size: 21
12849496 ACCGAAGTGT
* * * *
12849506 CACATATTTGTCCCGAAGTAC
1 CACATAATTATCCCGGAGGAC
12849527 CACATAATTATCCCGGAGGAC
1 CACATAATTATCCCGGAGGAC
12849548 CACATAATTATCCCGGAGGAC
1 CACATAATTATCCCGGAGGAC
12849569 CACATAA
1 CACATAA
12849576 AACCCTCGAC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.34, C:0.29, G:0.16, T:0.21
Consensus pattern (21 bp):
CACATAATTATCCCGGAGGAC
Found at i:12849807 original size:13 final size:13
Alignment explanation
Indices: 12849789--12849813 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12849779 TATTCATATA
12849789 ATCTTTCACATAC
1 ATCTTTCACATAC
12849802 ATCTTTCACATA
1 ATCTTTCACATA
12849814 GCGTTATCAA
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:0.32, C:0.28, G:0.00, T:0.40
Consensus pattern (13 bp):
ATCTTTCACATAC
Found at i:12850446 original size:20 final size:20
Alignment explanation
Indices: 12850402--12850479 Score: 72
Period size: 19 Copynumber: 3.9 Consensus size: 20
12850392 TGTTTGCGTG
* * *
12850402 GTATCGATACCATCCTT-CG
1 GTATCGATACTACCCTTACA
12850421 GTATCGATACTACCCTTACA
1 GTATCGATACTACCCTTACA
*
12850441 GTATCGATAC--CTCTTCAACAA
1 GTATCGATACTACCCTT--AC-A
12850462 GTATCGATACTACCCTTA
1 GTATCGATACTACCCTTA
12850480 ATAATTTCAC
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
18 4 0.08
19 15 0.31
20 13 0.27
21 12 0.25
23 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.12, T:0.31
Consensus pattern (20 bp):
GTATCGATACTACCCTTACA
Found at i:12851295 original size:41 final size:40
Alignment explanation
Indices: 12851235--12851375 Score: 140
Period size: 40 Copynumber: 3.5 Consensus size: 40
12851225 ATTGGGATGT
* * * *
12851235 TACAAAAACGTCACGAAAGTACGAGTATTTAACGACGTTTG
1 TACAAAAATGCCACTAAAGTA-GAGTATTTAACGGCGTTTG
* ** *
12851276 TACAAAAATGCCACTAAAGTATAGTATTTAACGGTATTTA
1 TACAAAAATGCCACTAAAGTAGAGTATTTAACGGCGTTTG
* *
12851316 TATAAAAATGCCACTAAAGTATGAGTATTTACCGGCGTTTG
1 TACAAAAATGCCACTAAAGTA-GAGTATTTAACGGCGTTTG
*
12851357 TTTA-AAAAATGCCGCTAAA
1 --TACAAAAATGCCACTAAA
12851376 AATCCCTCTA
Statistics
Matches: 82, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
40 34 0.41
41 32 0.39
42 14 0.17
43 2 0.02
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.29
Consensus pattern (40 bp):
TACAAAAATGCCACTAAAGTAGAGTATTTAACGGCGTTTG
Found at i:12851823 original size:31 final size:31
Alignment explanation
Indices: 12851787--12851864 Score: 111
Period size: 31 Copynumber: 2.5 Consensus size: 31
12851777 GTTTCAAAAG
* *
12851787 TAATAAATTGGTCACTAATGTTATCGATTTA
1 TAATAAAATGGTCACTAACGTTATCGATTTA
* * *
12851818 TAATAAAATAGTTACTAACGTTATTGATTTA
1 TAATAAAATGGTCACTAACGTTATCGATTTA
12851849 TAATAAAATGGTCACT
1 TAATAAAATGGTCACT
12851865 CTCCCATTAT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.40
Consensus pattern (31 bp):
TAATAAAATGGTCACTAACGTTATCGATTTA
Found at i:12852485 original size:15 final size:15
Alignment explanation
Indices: 12852467--12852522 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
12852457 TAACCGGTTT
12852467 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
12852482 CGGTTTTTTTAAAAAAC
1 CGG--TTTTAAAAAAAC
*
12852499 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
12852514 CGATTTTAA
1 CGGTTTTAA
12852523 TATTCCAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 20 0.59
17 14 0.41
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:12852495 original size:17 final size:17
Alignment explanation
Indices: 12852470--12852520 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
12852460 CCGGTTTCGG
12852470 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
*
12852487 TTTTTAAAAAACCGG--
1 TTTTAAAAAAACCGGTT
* *
12852502 TTATAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
12852519 TT
1 TT
12852521 AATATTCCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 12 0.43
17 16 0.57
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:12852929 original size:13 final size:13
Alignment explanation
Indices: 12852913--12852942 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
12852903 AAGTTCAATA
12852913 AATTCAAATACTT
1 AATTCAAATACTT
*
12852926 AATTGAAATACTT
1 AATTCAAATACTT
12852939 AATT
1 AATT
12852943 AACTCAACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.40
Consensus pattern (13 bp):
AATTCAAATACTT
Found at i:12853049 original size:32 final size:33
Alignment explanation
Indices: 12852953--12853051 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
12852943 AACTCAACAT
* * *
12852953 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
12852986 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
12853019 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
12853051 A
1 A
12853052 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:12853070 original size:21 final size:21
Alignment explanation
Indices: 12853046--12853085 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
12853036 ACTTCAAGTT
12853046 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
12853067 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
12853086 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:12858793 original size:31 final size:31
Alignment explanation
Indices: 12858727--12858793 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
12858717 GTAACGATAG
* * *
12858727 AGTGATCATTTTGTTAGAAATCGATAACGTC
1 AGTGATCATTTTGTTACAAATAGATAAAGTC
* *
12858758 AGTGATCATTTTGTTACAAATAGGTAAAGTT
1 AGTGATCATTTTGTTACAAATAGATAAAGTC
12858789 AGTGA
1 AGTGA
12858794 CTAATTTGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.36
Consensus pattern (31 bp):
AGTGATCATTTTGTTACAAATAGATAAAGTC
Found at i:12860287 original size:2 final size:2
Alignment explanation
Indices: 12860280--12860305 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12860270 AGAATGTTAC
12860280 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
12860306 TGACCGAAGG
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:12861079 original size:31 final size:31
Alignment explanation
Indices: 12861044--12861110 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
12861034 AACAAATTAG
* * *
12861044 TCACTAACTTTACCTATTTGTAACAAAATGA
1 TCACTAACGTTACCGATTTCTAACAAAATGA
* *
12861075 TCACTGACGTTATCGATTTCTAACAAAATGA
1 TCACTAACGTTACCGATTTCTAACAAAATGA
12861106 TCACT
1 TCACT
12861111 CTATCGTTAC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.34
Consensus pattern (31 bp):
TCACTAACGTTACCGATTTCTAACAAAATGA
Done.