Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002309.1 Hibiscus syriacus cultivar Beakdansim tig00004702_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: 77324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4733 original size:31 final size:31
Alignment explanation
Indices: 4698--4766 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
4688 GAGCTGCTCA
* *
4698 CGAGCTTCAGTTCAG-GATTTCGTGTTCGAGT
1 CGAGCTCCAGTTCAGAGATTTCGAG-TCGAGT
* *
4729 CGAGCTCCATTTCAGAGTTTTCGAGTCGAGT
1 CGAGCTCCAGTTCAGAGATTTCGAGTCGAGT
4760 CGAGCTC
1 CGAGCTC
4767 AGCAATACTC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 26 0.79
32 7 0.21
ACGTcount: A:0.17, C:0.23, G:0.28, T:0.32
Consensus pattern (31 bp):
CGAGCTCCAGTTCAGAGATTTCGAGTCGAGT
Found at i:22052 original size:16 final size:17
Alignment explanation
Indices: 22030--22068 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
22020 ATACATTCAA
*
22030 ATAATTATTATTAAAAT
1 ATAATTATTATAAAAAT
22047 -TAATTATTATAAAAAT
1 ATAATTATTATAAAAAT
22063 ATAATT
1 ATAATT
22069 CGAACTGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATAATTATTATAAAAAT
Found at i:23832 original size:31 final size:31
Alignment explanation
Indices: 23797--23859 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
23787 ATTTAAGATT
*
23797 ATTTTATA-ATATTTCAATAAGTTTAATGACA
1 ATTTTATATATATTTCAA-AACTTTAATGACA
* *
23828 ATTTTATATATTTTTTAAAACTTTAATGACA
1 ATTTTATATATATTTCAAAACTTTAATGACA
23859 A
1 A
23860 AAACCATATG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 21 0.75
32 7 0.25
ACGTcount: A:0.41, C:0.06, G:0.05, T:0.48
Consensus pattern (31 bp):
ATTTTATATATATTTCAAAACTTTAATGACA
Found at i:24293 original size:3 final size:3
Alignment explanation
Indices: 24280--24332 Score: 74
Period size: 3 Copynumber: 18.0 Consensus size: 3
24270 TTTTTTATCG
24280 TTA TT- TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
*
24324 TTA ATA TTA
1 TTA TTA TTA
24333 CATATTACAA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
2 4 0.09
3 38 0.84
4 3 0.07
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:24337 original size:16 final size:15
Alignment explanation
Indices: 24280--24339 Score: 65
Period size: 14 Copynumber: 4.2 Consensus size: 15
24270 TTTTTTATCG
*
24280 TTATT-TTATTATTA
1 TTATTATTATTAATA
24294 TTATTATTATT--TA
1 TTATTATTATTAATA
24307 TTATTATTATT-ATA
1 TTATTATTATTAATA
*
24321 TTATTAATATTACATA
1 TTATTATTATTA-ATA
24337 TTA
1 TTA
24340 CAATTTTTGC
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
13 13 0.32
14 17 0.41
15 5 0.12
16 6 0.15
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (15 bp):
TTATTATTATTAATA
Found at i:24339 original size:30 final size:30
Alignment explanation
Indices: 24280--24339 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
24270 TTTTTTATCG
* **
24280 TTATTTTATTATTATTATTATTATTTATTA
1 TTATTTTATTATTATTAATATTACATATTA
24310 TTATTATTA-TATTATTAATATTACATATTA
1 TTATT-TTATTATTATTAATATTACATATTA
24340 CAATTTTTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 23 0.88
31 3 0.12
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (30 bp):
TTATTTTATTATTATTAATATTACATATTA
Found at i:24434 original size:25 final size:25
Alignment explanation
Indices: 24405--24453 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
24395 CCCAACCCAT
24405 CAGATTAGGGTTTCAAACCCTAAAC
1 CAGATTAGGGTTTCAAACCCTAAAC
24430 CAGATTAGGGTTTCAAACCCTAAA
1 CAGATTAGGGTTTCAAACCCTAAA
24454 TGTTCCAGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.24
Consensus pattern (25 bp):
CAGATTAGGGTTTCAAACCCTAAAC
Found at i:30039 original size:20 final size:20
Alignment explanation
Indices: 30014--30051 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
30004 AAGATCAAAC
30014 CAAAGAAAAAAAACAAAGAG
1 CAAAGAAAAAAAACAAAGAG
* *
30034 CAAAGAGAAAAATCAAAG
1 CAAAGAAAAAAAACAAAG
30052 CAAAAATCAA
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:0.71, C:0.11, G:0.16, T:0.03
Consensus pattern (20 bp):
CAAAGAAAAAAAACAAAGAG
Found at i:30050 original size:13 final size:12
Alignment explanation
Indices: 30034--30081 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
30024 AAACAAAGAG
30034 CAAAGAGAAAAAT
1 CAAAGA-AAAAAT
*
30047 CAAAGCAAAAAT
1 CAAAGAAAAAAT
*
30059 CAAAG-AAAAAG
1 CAAAGAAAAAAT
30070 CAAAGAACAAAA
1 CAAAGAA-AAAA
30082 GAGGACAAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
11 10 0.32
12 12 0.39
13 9 0.29
ACGTcount: A:0.71, C:0.12, G:0.12, T:0.04
Consensus pattern (12 bp):
CAAAGAAAAAAT
Found at i:30067 original size:11 final size:11
Alignment explanation
Indices: 30039--30076 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
30029 AAGAGCAAAG
30039 AGAAAAATCAA
1 AGAAAAATCAA
30050 AGCAAAAATCAA
1 AG-AAAAATCAA
*
30062 AGAAAAAGCAA
1 AGAAAAATCAA
30073 AGAA
1 AGAA
30077 CAAAAGAGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.71, C:0.11, G:0.13, T:0.05
Consensus pattern (11 bp):
AGAAAAATCAA
Found at i:31782 original size:36 final size:34
Alignment explanation
Indices: 31736--31805 Score: 86
Period size: 36 Copynumber: 2.0 Consensus size: 34
31726 ATTTTTCTAA
* * *
31736 AAAATAAATTTTGTCTCGCTTGAGACAATTTATTTC
1 AAAACAAATTTCGTCTCACTTGAGAC-ATTT-TTTC
*
31772 AAAACAAATTTCGTCTCATTTGAGACATTTTTTC
1 AAAACAAATTTCGTCTCACTTGAGACATTTTTTC
31806 CTTTGAGATC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 4 0.13
35 4 0.13
36 22 0.73
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (34 bp):
AAAACAAATTTCGTCTCACTTGAGACATTTTTTC
Found at i:31946 original size:196 final size:197
Alignment explanation
Indices: 31596--31996 Score: 607
Period size: 196 Copynumber: 2.0 Consensus size: 197
31586 ATTCAGTCCC
31596 TTGAGACATTTTTCCTTTGAGATCCAAATTTTGAATTTGTTTCACATTAAACAAAGTTGATCTCA
1 TTGAGACATTTTTCCTTTGAGATCCAAATTTTGAATTTGTTTCACATTAAACAAAGTTGATCTCA
** *
31661 TTTGAGATCGTATCTATTTCAAAACAAATTTTTGTCCCTTGAGACATTTTTCCACAAACTTTGAG
66 TTTGAGATCGTATCTATTTCAAAACAAATTTTTGTCCCGGGAGACAGTTTTCCACAAACTTTGAG
*
31726 ATTTTTCTAAAAAATAAATTTTGTCTC-GC-TTGAGACAATTTATTTCAAAACAAATTTCGTCTC
131 ATATTTCTAAAAAATAAATTTTGTCTCAGCTTTGAGACAATTTATTTCAAAACAAATTTCGTCTC
31789 -A
196 GA
31790 TTTGAGACATTTTTTCCTTTGAGATCCAAATTTTGAATTTGTTTCACATTAAACAAAGTTGATCT
1 -TTGAGACA-TTTTTCCTTTGAGATCCAAATTTTGAATTTGTTTCACATTAAACAAAGTTGATCT
* *
31855 CATTTGAGATCGTATCTATTTCAAAACAAAATTTTTGTCTCACGGGAGATAGTTTTCCACAAATT
64 CATTTGAGATCGTATCTATTTCAAAAC-AAATTTTTGTC-C-CGGGAGACAGTTTTCCACAAACT
* * * * * *
31920 TTGAGA-ATTT-TAAAACA-AATTTTTGTCTCATCTTTGAGACAATTTCTTTCAAAGCAAATTTT
126 TTGAGATATTTCTAAAAAATAAATTTTGTCTCAGCTTTGAGACAATTTATTTCAAAACAAATTTC
31982 GTCTCGA
191 GTCTCGA
31989 TTGAGACA
1 TTGAGACA
31997 GCTTTCTAAA
Statistics
Matches: 187, Mismatches: 12, Indels: 11
0.89 0.06 0.05
Matches are distributed among these distances:
195 8 0.04
196 93 0.50
197 18 0.10
198 43 0.23
199 25 0.13
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.41
Consensus pattern (197 bp):
TTGAGACATTTTTCCTTTGAGATCCAAATTTTGAATTTGTTTCACATTAAACAAAGTTGATCTCA
TTTGAGATCGTATCTATTTCAAAACAAATTTTTGTCCCGGGAGACAGTTTTCCACAAACTTTGAG
ATATTTCTAAAAAATAAATTTTGTCTCAGCTTTGAGACAATTTATTTCAAAACAAATTTCGTCTC
GA
Found at i:32017 original size:35 final size:36
Alignment explanation
Indices: 31931--32050 Score: 129
Period size: 35 Copynumber: 3.3 Consensus size: 36
31921 TGAGAATTTT
**
31931 AAAACAAATTTTTGTCTC-ATCTTTGAGACAATTTCTTTC
1 AAAACAAA-TTTTGTCTCGA---TTGAGACAATTTCTTGA
* *
31970 AAAGCAAATTTTGTCTCGATTGAGACAGCTTTC-T-A
1 AAAACAAATTTTGTCTCGATTGAGACA-ATTTCTTGA
*
32005 AAAACAAATTTTGTCTCGTTTGAGACAATTTCTTGA
1 AAAACAAATTTTGTCTCGATTGAGACAATTTCTTGA
32041 AAAACAAATT
1 AAAACAAATT
32051 CCGCCTCACT
Statistics
Matches: 71, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
34 4 0.06
35 26 0.37
36 20 0.28
37 4 0.06
38 9 0.13
39 8 0.11
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.38
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCGATTGAGACAATTTCTTGA
Found at i:32066 original size:71 final size:73
Alignment explanation
Indices: 31931--32067 Score: 163
Period size: 71 Copynumber: 1.9 Consensus size: 73
31921 TGAGAATTTT
** * ** * *
31931 AAAACAAATTTTTGTCTCATCTTTGAGACAATTTCTTTCAAAGCAAATTTTGTCTCGATTGAGAC
1 AAAACAAATTTTTGTCTCA-CTTTGAGACAATTTCTTGAAAAACAAATTCCGCCTCGATGGAGAC
31996 AGCTTTCTA
65 AGCTTTCTA
*
32005 AAAACAAA-TTTTGTCTC-GTTTGAGACAATTTCTTGAAAAACAAATTCCGCCTC-ACTGGAGAC
1 AAAACAAATTTTTGTCTCACTTTGAGACAATTTCTTGAAAAACAAATTCCGCCTCGA-TGGAGAC
32067 A
65 A
32068 TTTTTCATTG
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
70 1 0.02
71 36 0.67
73 9 0.17
74 8 0.15
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (73 bp):
AAAACAAATTTTTGTCTCACTTTGAGACAATTTCTTGAAAAACAAATTCCGCCTCGATGGAGACA
GCTTTCTA
Found at i:32234 original size:36 final size:36
Alignment explanation
Indices: 32153--32234 Score: 87
Period size: 36 Copynumber: 2.3 Consensus size: 36
32143 ATTTTGTTTT
* *
32153 GCTTGAGACAATTTCTTTAAAAACAAAGTTTGTATC
1 GCTTGAGACAAATTCTTTAAAAACAAAGTTCGTATC
* * *
32189 ACTTAAGACAAATTCTCTT-AAAACAAA-TTGCGTCTC
1 GCTTGAGACAAATTCT-TTAAAAACAAAGTT-CGTATC
32225 GCTTGAGACA
1 GCTTGAGACA
32235 TTTTTCCTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
35 2 0.05
36 33 0.89
37 2 0.05
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (36 bp):
GCTTGAGACAAATTCTTTAAAAACAAAGTTCGTATC
Found at i:32800 original size:29 final size:28
Alignment explanation
Indices: 32747--33094 Score: 210
Period size: 29 Copynumber: 11.8 Consensus size: 28
32737 TCTTGAGACA
*
32747 GTTTCTCTTG-AAAAAATCTTTGAGTTT
1 GTTTCTTTTGAAAAAAATCTTTGAGTTT
* *
32774 GTTCCTTTTGAATAAAAATCTTGGAGTTT
1 GTTTCTTTTGAA-AAAAATCTTTGAGTTT
* *
32803 GTTCCTTTTGAATAAATATCTTTGAG-TT
1 GTTTCTTTTGAA-AAAAATCTTTGAGTTT
*
32831 GTTTCTTTTG-AAAAAATCTTTGAGTCT
1 GTTTCTTTTGAAAAAAATCTTTGAGTTT
* * ***
32858 ATTTATTTT-AAAACAAAGTTTTGTCTCTCTTGAGACA
1 GTTTCTTTTGAAAA-AAA--------TCT-TTGAGTTT
*
32895 GTTTCTCTTG-AAAAAATCTTTGAGTTT
1 GTTTCTTTTGAAAAAAATCTTTGAGTTT
* *
32922 GTTCCTTTTGAATAAAAATCTTGGAGTTT
1 GTTTCTTTTGAA-AAAAATCTTTGAGTTT
* * *
32951 GTTCCTTTTGAATAAATATCTTTGAG-TC
1 GTTTCTTTTGAA-AAAAATCTTTGAGTTT
32979 GTTTCTTTTG--AAAAATCTTTGAGTTT
1 GTTTCTTTTGAAAAAAATCTTTGAGTTT
* * * *
33005 GTTTCTTTGGAAACAAAATTTTTTCTCTCTTAAGATA
1 GTTTCTTTTGAAA-AAAA-------TCT-TTGAGTTT
33042 GTTTCTTTTGAAACAAAAATCTTTGAGTTT
1 GTTTCTTTTG-AA-AAAAATCTTTGAGTTT
33072 GTTTCTTTTGAAACAAAAT-TTTG
1 GTTTCTTTTGAAA-AAAATCTTTG
33095 TCTCTCTTAA
Statistics
Matches: 254, Mismatches: 35, Indels: 63
0.72 0.10 0.18
Matches are distributed among these distances:
25 12 0.05
26 22 0.09
27 33 0.13
28 35 0.14
29 89 0.35
30 15 0.06
31 3 0.01
36 9 0.04
37 29 0.11
38 6 0.02
39 1 0.00
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.47
Consensus pattern (28 bp):
GTTTCTTTTGAAAAAAATCTTTGAGTTT
Found at i:33047 original size:37 final size:36
Alignment explanation
Indices: 33005--33126 Score: 130
Period size: 37 Copynumber: 3.5 Consensus size: 36
32995 CTTTGAGTTT
*
33005 GTTTCTTTGGAAACAAAATTTTTTCTCTCTTAAGATA
1 GTTTCTTTTGAAACAAAA-TTTTTCTCTCTTAAGATA
* * * *
33042 GTTTCTTTTGAAACAAAA-----ATCT-TTGAGTTT
1 GTTTCTTTTGAAACAAAATTTTTCTCTCTTAAGATA
33072 GTTTCTTTTGAAACAAAATTTTGTCTCTCTTAAGATA
1 GTTTCTTTTGAAACAAAATTTT-TCTCTCTTAAGATA
*
33109 ATTTCTTTTGAAACAAAA
1 GTTTCTTTTGAAACAAAA
33127 ATCTTTGAAT
Statistics
Matches: 68, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
30 23 0.34
31 3 0.04
36 3 0.04
37 39 0.57
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.45
Consensus pattern (36 bp):
GTTTCTTTTGAAACAAAATTTTTCTCTCTTAAGATA
Found at i:33085 original size:67 final size:67
Alignment explanation
Indices: 32989--33144 Score: 267
Period size: 67 Copynumber: 2.3 Consensus size: 67
32979 GTTTCTTTTG
* *
32989 AAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTTTCTCTCTTAAGATAGTTTCTTTTGAA
1 AAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGAA
33054 AC
66 AC
*
33056 AAAAATCTTTGAGTTTGTTTCTTTTGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGAA
1 AAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGAA
33121 AC
66 AC
* *
33123 AAAAATCTTTGAATCTGTTTCT
1 AAAAATCTTTGAGTTTGTTTCT
33145 CTTAAAATGA
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 84 1.00
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.46
Consensus pattern (67 bp):
AAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGAA
AC
Found at i:33527 original size:28 final size:28
Alignment explanation
Indices: 33490--33557 Score: 102
Period size: 28 Copynumber: 2.4 Consensus size: 28
33480 CAATTTTGTG
*
33490 AAAAAATCTTTGAGATTGTTTCTTTTGA
1 AAAAAATCTTTGAGATTGTTTCCTTTGA
*
33518 AAAAAATCTTTGAGTTTGTTTCCTTTGA
1 AAAAAATCTTTGAGATTGTTTCCTTTGA
33546 AACAAAAT-TTTG
1 AA-AAAATCTTTG
33558 TCTCTCGAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 32 0.86
29 5 0.14
ACGTcount: A:0.34, C:0.09, G:0.13, T:0.44
Consensus pattern (28 bp):
AAAAAATCTTTGAGATTGTTTCCTTTGA
Found at i:33620 original size:40 final size:40
Alignment explanation
Indices: 33565--33644 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
33555 TTGTCTCTCG
*
33565 AGACAACTTCTTTTGAAAATACCCACCTTTGAGATCGTTT
1 AGACAACTTCTTTTGAAAATACCCACATTTGAGATCGTTT
*
33605 AGACAACTTCTTTTGAAAATACCCACATTTGATATCGTTT
1 AGACAACTTCTTTTGAAAATACCCACATTTGAGATCGTTT
33645 CTATTAAAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.36
Consensus pattern (40 bp):
AGACAACTTCTTTTGAAAATACCCACATTTGAGATCGTTT
Found at i:34086 original size:35 final size:36
Alignment explanation
Indices: 34020--34094 Score: 100
Period size: 35 Copynumber: 2.1 Consensus size: 36
34010 TATTTCTTTG
* *
34020 GAAACAAAATTTACCATCTTTGAATCTGTTTCCCTT
1 GAAACAAAATTAAACATCTTTGAATCTGTTTCCCTT
*
34056 GAAACAAAA-TAAACATCTTTGAGATC-GTTTCTCTT
1 GAAACAAAATTAAACATCTTTGA-ATCTGTTTCCCTT
34091 GAAA
1 GAAA
34095 TGAATTTTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
35 23 0.66
36 12 0.34
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.35
Consensus pattern (36 bp):
GAAACAAAATTAAACATCTTTGAATCTGTTTCCCTT
Found at i:34412 original size:28 final size:28
Alignment explanation
Indices: 34362--34415 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
34352 TCAAAATCCA
* *
34362 ATCTTTGAGTTTGTTTCTATTGAAACAC
1 ATCTTTGAGTTGGTTCCTATTGAAACAC
34390 ATCTTTGAGTTGGTCTCCT-TTGAAAC
1 ATCTTTGAGTTGGT-TCCTATTGAAAC
34416 CATTATCCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 20 0.87
29 3 0.13
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44
Consensus pattern (28 bp):
ATCTTTGAGTTGGTTCCTATTGAAACAC
Found at i:34578 original size:43 final size:43
Alignment explanation
Indices: 34518--34769 Score: 172
Period size: 43 Copynumber: 5.8 Consensus size: 43
34508 TCATTCCCCG
* *
34518 ACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCATAGATA
1 ACCAGACCTCCTCATCACGTAGGAGCCGTGTCAACCATAGATA
* * * * *
34561 ACCAG-CCGTCCTCATCACGTAGGAACCATGTTATCACCTTTAGATG
1 ACCAGACC-TCCTCATCACGTAGGAGCCGTGTCA--ACC-ATAGATA
* * * * * **
34607 GCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCAG---
1 ACCAGACCTCCTCATCACGTAGGAGCCGTGTCAACCATAGATA
*
34647 ACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCATAGATA
1 ACCAGACCTCCTCATCACGTAGGAGCCGTGTCAACCATAGATA
* * * * * *
34690 AACAG-CCGTCCTCGTCACGTAGGAACCGTGTTATCACCTTTAGATG
1 ACCAGACC-TCCTCATCACGTAGGAGCCGTGTCA--ACC-ATAGATA
* * *
34736 GCCAAGAACTCTTCATCACGTAGGAGCCGTGTCA
1 ACC-AGACCTCCTCATCACGTAGGAGCCGTGTCA
34770 CCTTTAGACG
Statistics
Matches: 157, Mismatches: 38, Indels: 24
0.72 0.17 0.11
Matches are distributed among these distances:
40 33 0.21
42 2 0.01
43 54 0.34
44 2 0.01
45 6 0.04
46 35 0.22
47 24 0.15
48 1 0.01
ACGTcount: A:0.27, C:0.30, G:0.20, T:0.23
Consensus pattern (43 bp):
ACCAGACCTCCTCATCACGTAGGAGCCGTGTCAACCATAGATA
Found at i:34662 original size:129 final size:129
Alignment explanation
Indices: 34427--34769 Score: 607
Period size: 129 Copynumber: 2.7 Consensus size: 129
34417 ATTATCCTAG
*
34427 AGATAACCAGCCGTCCTCGTCATGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCA
1 AGATAACCAGCCGTCCTCGTCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCA
*
34492 TCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCAT
66 TCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCAT
* *
34556 AGATAACCAGCCGTCCTCATCACGTAGGAACCATGTTATCACCTTTAGATGGCCAGAACTCTTCA
1 AGATAACCAGCCGTCCTCGTCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCA
34621 TCACGTATGAGCCGTGTCA-TCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCAT
66 TCACGTATGAGCCGTGTCATTCCCC-GACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCAT
*
34685 AGATAAACAGCCGTCCTCGTCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAAGAACTCTTC
1 AGATAACCAGCCGTCCTCGTCACGTAGGAACCGTGTTATCACCTTTAGATGGCC-AGAACTCTTC
*
34750 ATCACGTAGGAGCCGTGTCA
65 ATCACGTATGAGCCGTGTCA
34770 CCTTTAGACG
Statistics
Matches: 204, Mismatches: 8, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
128 5 0.02
129 170 0.83
130 29 0.14
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.24
Consensus pattern (129 bp):
AGATAACCAGCCGTCCTCGTCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCA
TCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCAT
Found at i:34663 original size:40 final size:40
Alignment explanation
Indices: 34479--34679 Score: 163
Period size: 40 Copynumber: 4.8 Consensus size: 40
34469 CTTTAGATGG
*
34479 CCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCC-GA
1 CCAGAACTCTTCATCACGTAGGAGCCGTGTCA-TCCCCAGA
* * **
34519 CCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCATAGATAA
1 CCAGAACTCTTCATCACGTAGGAGCCGTGTCATCCCCAG---A
* * * * * *
34562 CCAG-CCGTCCTCATCACGTAGGAACCATGTTATCACCTTTAGA
1 CCAGAAC-TCTTCATCACGTAGGAGCCGTGTCATC-CC--CAGA
*
34605 TGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCAGA
1 ---CCAGAACTCTTCATCACGTAGGAGCCGTGTCATCCCCAGA
* *
34648 CCAGATCTCCTCATCACGTAGGAGCCGTGTCA
1 CCAGAACTCTTCATCACGTAGGAGCCGTGTCA
34680 ACCATAGATA
Statistics
Matches: 127, Mismatches: 22, Indels: 24
0.73 0.13 0.14
Matches are distributed among these distances:
39 2 0.02
40 60 0.47
42 1 0.01
43 31 0.24
44 1 0.01
45 2 0.02
46 29 0.23
47 1 0.01
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (40 bp):
CCAGAACTCTTCATCACGTAGGAGCCGTGTCATCCCCAGA
Found at i:34800 original size:43 final size:44
Alignment explanation
Indices: 34465--34811 Score: 163
Period size: 43 Copynumber: 8.0 Consensus size: 44
34455 AACCGTGTTA
* * *
34465 TCACCTTTAGATGGCC-AGAACTCTTCATCACGTATGAGCCGTG
1 TCACCTTTAGACGACCAAGAACTCTTCATCACGTAGGAGCCGTG
*** *
34508 TCA---TTCCCCGACC-AGATCTCTTCATCACGTAGGAGCCGTG
1 TCACCTTTAGACGACCAAGAACTCTTCATCACGTAGGAGCCGTG
* ** * * * *
34548 TCAACC-ATAGATAACC-AG-CCGTCCTCATCACGTAGGAACCATGTTA
1 TC-ACCTTTAGACGACCAAGAAC-TCTTCATCACGTAGGAGCC--G-TG
* * *
34594 TCACCTTTAGATGGCC-AGAACTCTTCATCACGTATGAGCCGTG
1 TCACCTTTAGACGACCAAGAACTCTTCATCACGTAGGAGCCGTG
** * *
34637 TCATCC---CCA-GACC-AGATCTCCTCATCACGTAGGAGCCGTG
1 TCA-CCTTTAGACGACCAAGAACTCTTCATCACGTAGGAGCCGTG
* ** * * * * *
34677 TCAACC-ATAGATAAAC-AG-CCGTCCTCGTCACGTAGGAACCGTG
1 TC-ACCTTTAGACGACCAAGAAC-TCTTCATCACGTAGGAGCCGTG
* *
34720 TTATCACCTTTAGATGGCCAAGAACTCTTCATCACGTAGGAGCCGTG
1 ---TCACCTTTAGACGACCAAGAACTCTTCATCACGTAGGAGCCGTG
* * *
34767 TCACCTTTAGACGACCCA-AACTCTTCATCACGTATGAGCAGTG
1 TCACCTTTAGACGACCAAGAACTCTTCATCACGTAGGAGCCGTG
34810 TC
1 TC
34812 GTCCCCAACA
Statistics
Matches: 232, Mismatches: 51, Indels: 42
0.71 0.16 0.13
Matches are distributed among these distances:
40 63 0.27
41 3 0.01
42 3 0.01
43 79 0.34
44 18 0.08
45 7 0.03
46 36 0.16
47 22 0.09
48 1 0.00
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (44 bp):
TCACCTTTAGACGACCAAGAACTCTTCATCACGTAGGAGCCGTG
Found at i:34981 original size:3 final size:3
Alignment explanation
Indices: 34968--35020 Score: 74
Period size: 3 Copynumber: 18.0 Consensus size: 3
34958 TTTTTTATCG
34968 TTA TT- TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
*
35012 TTA ATA TTA
1 TTA TTA TTA
35021 CATATTACAA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
2 4 0.09
3 38 0.84
4 3 0.07
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:35025 original size:16 final size:15
Alignment explanation
Indices: 34968--35027 Score: 65
Period size: 14 Copynumber: 4.2 Consensus size: 15
34958 TTTTTTATCG
*
34968 TTATT-TTATTATTA
1 TTATTATTATTAATA
34982 TTATTATTATT--TA
1 TTATTATTATTAATA
34995 TTATTATTATT-ATA
1 TTATTATTATTAATA
*
35009 TTATTAATATTACATA
1 TTATTATTATTA-ATA
35025 TTA
1 TTA
35028 CAATTTTTGC
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
13 13 0.32
14 17 0.41
15 5 0.12
16 6 0.15
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (15 bp):
TTATTATTATTAATA
Found at i:35027 original size:30 final size:30
Alignment explanation
Indices: 34968--35027 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
34958 TTTTTTATCG
* **
34968 TTATTTTATTATTATTATTATTATTTATTA
1 TTATTTTATTATTATTAATATTACATATTA
34998 TTATTATTA-TATTATTAATATTACATATTA
1 TTATT-TTATTATTATTAATATTACATATTA
35028 CAATTTTTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 23 0.88
31 3 0.12
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (30 bp):
TTATTTTATTATTATTAATATTACATATTA
Found at i:35122 original size:25 final size:25
Alignment explanation
Indices: 35093--35141 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
35083 CCCAACCCAT
35093 CAGATTAGGGTTTCAAACCCTAAAC
1 CAGATTAGGGTTTCAAACCCTAAAC
35118 CAGATTAGGGTTTCAAACCCTAAA
1 CAGATTAGGGTTTCAAACCCTAAA
35142 TGTTCCAGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.24
Consensus pattern (25 bp):
CAGATTAGGGTTTCAAACCCTAAAC
Found at i:40275 original size:11 final size:11
Alignment explanation
Indices: 40261--40330 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
40251 ATAATATCTT
40261 ATATTATTATA
1 ATATTATTATA
*
40272 ATATAATTGA-A
1 ATATTATT-ATA
40283 CATATTATTATA
1 -ATATTATTATA
*
40295 ATATTA-GA-A
1 ATATTATTATA
*
40304 ATA-TATTATT
1 ATATTATTATA
*
40314 ATATTATTAAA
1 ATATTATTATA
40325 ATATTA
1 ATATTA
40331 ATAAATTTAT
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
8 2 0.04
9 5 0.11
10 4 0.09
11 26 0.57
12 9 0.20
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (11 bp):
ATATTATTATA
Found at i:40893 original size:30 final size:30
Alignment explanation
Indices: 40850--40925 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 30
40840 TTTTTTAACA
* *
40850 TTTTCGGTCATTTTTT-AGCGCCTAGTAATG
1 TTTTCAGTCATTTTTTGA-CGCCTAATAATG
*
40880 TTTTCAGTTATTTTTTGACGCCTAATAATG
1 TTTTCAGTCATTTTTTGACGCCTAATAATG
* *
40910 TTTCCGGTCATTTTTT
1 TTTTCAGTCATTTTTT
40926 CGAAAATCCA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 38 0.97
31 1 0.03
ACGTcount: A:0.17, C:0.16, G:0.16, T:0.51
Consensus pattern (30 bp):
TTTTCAGTCATTTTTTGACGCCTAATAATG
Found at i:45352 original size:20 final size:20
Alignment explanation
Indices: 45327--45367 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
45317 ATGAACCTGC
45327 AGATTATTGTGGAAGCTTTG
1 AGATTATTGTGGAAGCTTTG
45347 AGATTATTGTGGAAGCTTTG
1 AGATTATTGTGGAAGCTTTG
45367 A
1 A
45368 TGATCTTAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.27, C:0.05, G:0.29, T:0.39
Consensus pattern (20 bp):
AGATTATTGTGGAAGCTTTG
Found at i:58457 original size:21 final size:21
Alignment explanation
Indices: 58428--58473 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
58418 ATTTATCGTG
* *
58428 ATTGTGGCCGTCGCGAGCTCT
1 ATTGCGGCCGTCACGAGCTCT
*
58449 ATTGCGGCCGTCACGGGCTCT
1 ATTGCGGCCGTCACGAGCTCT
58470 ATTG
1 ATTG
58474 AACGTTATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.11, C:0.28, G:0.33, T:0.28
Consensus pattern (21 bp):
ATTGCGGCCGTCACGAGCTCT
Found at i:64562 original size:5 final size:5
Alignment explanation
Indices: 64552--64614 Score: 126
Period size: 5 Copynumber: 12.6 Consensus size: 5
64542 TCTTGATTTT
64552 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA
64602 TTTAA TTTAA TTT
1 TTTAA TTTAA TTT
64615 TTCGGTTATG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 58 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTTAA
Found at i:67138 original size:22 final size:22
Alignment explanation
Indices: 67113--67161 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
67103 AGTATAATTT
67113 TATGAGGAAGAATTAGGTGTTA
1 TATGAGGAAGAATTAGGTGTTA
***
67135 TATGATTTAGAATTAGGTGTTA
1 TATGAGGAAGAATTAGGTGTTA
67157 TATGA
1 TATGA
67162 TTTAGGTATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.35, C:0.00, G:0.27, T:0.39
Consensus pattern (22 bp):
TATGAGGAAGAATTAGGTGTTA
Found at i:67162 original size:22 final size:22
Alignment explanation
Indices: 67121--67166 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
67111 TTTATGAGGA
67121 AGAATTAGGTGTTATATGATTT
1 AGAATTAGGTGTTATATGATTT
67143 AGAATTAGGTGTTATATGATTT
1 AGAATTAGGTGTTATATGATTT
67165 AG
1 AG
67167 GTATGATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.24, T:0.43
Consensus pattern (22 bp):
AGAATTAGGTGTTATATGATTT
Found at i:69380 original size:31 final size:30
Alignment explanation
Indices: 69330--69390 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
69320 GTTATATAAG
69330 TTATGTGATACAAAGATGGAACATGATATGT
1 TTATGTGATACAAAGATGGAA-ATGATATGT
* *
69361 TTATGTGATA-AAGGTATGGAAATTATATGT
1 TTATGTGATACAAAG-ATGGAAATGATATGT
69391 CTATACAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 11 0.41
31 16 0.59
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.36
Consensus pattern (30 bp):
TTATGTGATACAAAGATGGAAATGATATGT
Found at i:69681 original size:23 final size:23
Alignment explanation
Indices: 69613--69681 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
69603 CAATCTTATA
69613 TGGCACTACGGTGCATTTCTACG
1 TGGCACTACGGTGCATTTCTACG
* * * * *
69636 CGGCACTTCTGTGAAATTCTACG
1 TGGCACTACGGTGCATTTCTACG
* *
69659 TGGCACTCCGGTGCATTTATACG
1 TGGCACTACGGTGCATTTCTACG
69682 AGTTGTGGTG
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.19, C:0.26, G:0.25, T:0.30
Consensus pattern (23 bp):
TGGCACTACGGTGCATTTCTACG
Found at i:73524 original size:24 final size:24
Alignment explanation
Indices: 73492--73547 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
73482 CTATTCTTTC
73492 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
73516 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
73540 GCTTCAAT
1 GCTTCAAT
73548 CGAACTTCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (24 bp):
GCTTCAATTGAGCTCAAATTTTAG
Found at i:74063 original size:31 final size:30
Alignment explanation
Indices: 74028--74111 Score: 80
Period size: 30 Copynumber: 2.8 Consensus size: 30
74018 ATGTGAAGGG
* * *
74028 AGATGCTGACGTGGCATGTCCATATCATAGT
1 AGATGCTGACGTGGCATGTCCACAT-AGACT
* * *
74059 AGATGATGATGTGGCA-GATCCACGTAGACT
1 AGATGCTGACGTGGCATG-TCCACATAGACT
*
74089 AAATGCTGACGTGGCATGTCCAC
1 AGATGCTGACGTGGCATGTCCAC
74112 GTGTGATGCC
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
30 22 0.52
31 20 0.48
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.25
Consensus pattern (30 bp):
AGATGCTGACGTGGCATGTCCACATAGACT
Done.