Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001859.1 Hibiscus syriacus cultivar Beakdansim tig00003762_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: 126625
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:196 original size:9 final size:9
Alignment explanation
Indices: 184--208 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
174 ATTTTTTTAA
184 ATTTTATAT
1 ATTTTATAT
193 ATTTTATAT
1 ATTTTATAT
202 ATTTTAT
1 ATTTTAT
209 TGAAAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
ATTTTATAT
Found at i:2256 original size:12 final size:12
Alignment explanation
Indices: 2239--2263 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2229 TTATTTTTGA
2239 TAAAAAATTATT
1 TAAAAAATTATT
2251 TAAAAAATTATT
1 TAAAAAATTATT
2263 T
1 T
2264 TTTATCTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAAAAAATTATT
Found at i:7844 original size:18 final size:18
Alignment explanation
Indices: 7817--7857 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
7807 ATAATAGCAG
7817 TAAAAAATTAATAATAAT
1 TAAAAAATTAATAATAAT
*
7835 TAAAATATTAATAATAAT
1 TAAAAAATTAATAATAAT
7853 TAAAA
1 TAAAA
7858 CAACATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
TAAAAAATTAATAATAAT
Found at i:16927 original size:31 final size:32
Alignment explanation
Indices: 16892--16969 Score: 126
Period size: 31 Copynumber: 2.5 Consensus size: 32
16882 AACTCACATA
*
16892 CACATGCTTAAACC-CATTAATACTCATTTAT
1 CACATCCTTAAACCTCATTAATACTCATTTAT
16923 CACATCCTT-AACCTCATTAATACTCATTTAT
1 CACATCCTTAAACCTCATTAATACTCATTTAT
16954 CACATCCTT-AACCTCA
1 CACATCCTTAAACCTCA
16970 AAATCCTATC
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
30 4 0.09
31 41 0.91
ACGTcount: A:0.33, C:0.31, G:0.01, T:0.35
Consensus pattern (32 bp):
CACATCCTTAAACCTCATTAATACTCATTTAT
Found at i:19144 original size:3 final size:3
Alignment explanation
Indices: 19131--19225 Score: 154
Period size: 3 Copynumber: 31.7 Consensus size: 3
19121 AAGATACTAA
* * *
19131 TAT TTT TAT TAT TAT TAT TAT TAT TAT CAT TAT CAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
19179 TGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
19226 AATATTTAAA
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 84 1.00
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:19682 original size:22 final size:22
Alignment explanation
Indices: 19623--19683 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
19613 ACCCATCTGC
*
19623 GAAAGAAAGAAAAAAGAGACAGA
1 GAAAGAAA-AAAAAAAAGACAGA
* * * *
19646 GAACGGAGAAGAAAAAGACAGA
1 GAAAGAAAAAAAAAAAGACAGA
19668 GAAAGAAAAAAAAAAA
1 GAAAGAAAAAAAAAAA
19684 CAAACTAGTA
Statistics
Matches: 29, Mismatches: 9, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
22 24 0.83
23 5 0.17
ACGTcount: A:0.70, C:0.05, G:0.25, T:0.00
Consensus pattern (22 bp):
GAAAGAAAAAAAAAAAGACAGA
Found at i:20583 original size:20 final size:22
Alignment explanation
Indices: 20544--20585 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
20534 GATATTTTTA
*
20544 TTTTATTATATTGTATAAATAT
1 TTTTATTATATTGCATAAATAT
20566 TTTTA-TATATT-CATAAATAT
1 TTTTATTATATTGCATAAATAT
20586 ACTTATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 6 0.32
22 5 0.26
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (22 bp):
TTTTATTATATTGCATAAATAT
Found at i:20839 original size:17 final size:16
Alignment explanation
Indices: 20760--20838 Score: 63
Period size: 17 Copynumber: 4.8 Consensus size: 16
20750 TTCTTTTCTG
20760 ATATTTTTAAATAAAT
1 ATATTTTTAAATAAAT
*
20776 AAATATTTTAAATAAAT
1 ATAT-TTTTAAATAAAT
*
20793 ATAATTTTGAAA-ATAAT
1 AT-ATTTTTAAATA-AAT
* *
20810 AGGA-TTATAAATTAAAT
1 A-TATTTTTAAA-TAAAT
20827 ATATTTTTAAAT
1 ATATTTTTAAAT
20839 TTTTAAATTT
Statistics
Matches: 48, Mismatches: 8, Indels: 14
0.69 0.11 0.20
Matches are distributed among these distances:
16 11 0.23
17 34 0.71
18 3 0.06
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (16 bp):
ATATTTTTAAATAAAT
Found at i:23900 original size:22 final size:21
Alignment explanation
Indices: 23874--23923 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
23864 TAGTTAAAGA
* *
23874 AAAACAAGAATCTTATATCTAC
1 AAAACAA-AATCTTAGATCCAC
23896 AAAAC-AAATCTTAGATCCAC
1 AAAACAAAATCTTAGATCCAC
23916 AAAACAAA
1 AAAACAAA
23924 GGTTGGTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 17 0.68
21 3 0.12
22 5 0.20
ACGTcount: A:0.56, C:0.20, G:0.04, T:0.20
Consensus pattern (21 bp):
AAAACAAAATCTTAGATCCAC
Found at i:28837 original size:18 final size:17
Alignment explanation
Indices: 28815--28863 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
28805 TTAAAATTTT
28815 AAATTTAAATATTATAA
1 AAATTTAAATATTATAA
*
28832 ATAATTTAAAT-TTAGAA
1 A-AATTTAAATATTATAA
* *
28849 AAATATATATATTAT
1 AAATTTAAATATTAT
28864 TTTTTATTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 7 0.27
17 10 0.38
18 9 0.35
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (17 bp):
AAATTTAAATATTATAA
Found at i:28885 original size:16 final size:17
Alignment explanation
Indices: 28854--28888 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
28844 TAGAAAAATA
*
28854 TATATATTATTTTTTAT
1 TATATATTAATTTTTAT
28871 TATAT-TTAATTTTTAT
1 TATATATTAATTTTTAT
28887 TA
1 TA
28889 ATAAATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TATATATTAATTTTTAT
Found at i:30543 original size:3 final size:3
Alignment explanation
Indices: 30490--30530 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
30480 ACTCATTTTT
30490 TTA TTA TT- TATA TTA TTA TTA TTA TTA TTA TTA TT- TTA TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
30531 ATAAATATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 3 0.09
3 31 0.89
4 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:32673 original size:32 final size:29
Alignment explanation
Indices: 32605--32673 Score: 68
Period size: 30 Copynumber: 2.3 Consensus size: 29
32595 TTCTTTTCAA
32605 ATTTT-TTTTATATATACTTATTATTTTC
1 ATTTTATTTTATATATACTTATTATTTTC
** * *
32633 ATAGTATTTATATATTTTCTTATTAATATTTC
1 ATTTTATTT-TATATATACTTATT-AT-TTTC
32665 ATTTTATTT
1 ATTTTATTT
32674 GCAAGTATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
28 3 0.10
29 3 0.10
30 12 0.39
31 2 0.06
32 11 0.35
ACGTcount: A:0.28, C:0.06, G:0.01, T:0.65
Consensus pattern (29 bp):
ATTTTATTTTATATATACTTATTATTTTC
Found at i:33217 original size:16 final size:17
Alignment explanation
Indices: 33196--33233 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
33186 TAGGTAGATA
* *
33196 TTATTAT-TAAATTTAT
1 TTATTATGTAAACTAAT
33212 TTATTATGTAAACTAAT
1 TTATTATGTAAACTAAT
33229 TTATT
1 TTATT
33234 TCTTTTTGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.58
Consensus pattern (17 bp):
TTATTATGTAAACTAAT
Found at i:35942 original size:15 final size:15
Alignment explanation
Indices: 35922--35953 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
35912 TCAATACCTT
35922 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
35937 TTTTGCATACATTCA
1 TTTTGCATACATGCA
35952 TT
1 TT
35954 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:43285 original size:1 final size:1
Alignment explanation
Indices: 43281--43332 Score: 50
Period size: 1 Copynumber: 52.0 Consensus size: 1
43271 AAGAAAGAAG
* * * * * *
43281 AAAAAGAAAAAAAAAAGAAAAAAAAGAAAAAAAAGAAGAAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
43333 TGGGGTCAAG
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (1 bp):
A
Found at i:43292 original size:20 final size:20
Alignment explanation
Indices: 43261--43332 Score: 96
Period size: 20 Copynumber: 3.7 Consensus size: 20
43251 ATGCTTGAAG
*
43261 AGAAAAAG--AAAAGAAAGA
1 AGAAAAAGAAAAAAAAAAGA
43279 AGAAAAAGAAAAAAAAAAGA
1 AGAAAAAGAAAAAAAAAAGA
*
43299 AAAAAAAGAAAAAAAAGAAGA
1 AGAAAAAGAAAAAAAA-AAGA
43320 A-AAAAAGAAAAAA
1 AGAAAAAGAAAAAA
43333 TGGGGTCAAG
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
18 8 0.16
20 36 0.73
21 5 0.10
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (20 bp):
AGAAAAAGAAAAAAAAAAGA
Found at i:43300 original size:29 final size:29
Alignment explanation
Indices: 43263--43332 Score: 113
Period size: 29 Copynumber: 2.4 Consensus size: 29
43253 GCTTGAAGAG
* *
43263 AAAAAGAAAAGAAAGAAGAAAAAGAAAAA
1 AAAAAGAAAAAAAAGAAAAAAAAGAAAAA
*
43292 AAAAAGAAAAAAAAGAAAAAAAAGAAGAA
1 AAAAAGAAAAAAAAGAAAAAAAAGAAAAA
43321 AAAAAGAAAAAA
1 AAAAAGAAAAAA
43333 TGGGGTCAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (29 bp):
AAAAAGAAAAAAAAGAAAAAAAAGAAAAA
Found at i:43331 original size:9 final size:9
Alignment explanation
Indices: 43263--43332 Score: 86
Period size: 9 Copynumber: 7.3 Consensus size: 9
43253 GCTTGAAGAG
43263 AAAAAGAAA
1 AAAAAGAAA
*
43272 AGAAAGAAGA
1 AAAAAGAA-A
*
43282 AAAAGAAAAA
1 AAAA-AGAAA
43292 AAAAAGAAA
1 AAAAAGAAA
43301 AAAAAGAAA
1 AAAAAGAAA
43310 AAAAAGAAGAA
1 AAAAAG-A-AA
43321 AAAAAGAAA
1 AAAAAGAAA
43330 AAA
1 AAA
43333 TGGGGTCAAG
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
9 31 0.58
10 11 0.21
11 11 0.21
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:44385 original size:93 final size:92
Alignment explanation
Indices: 44174--44415 Score: 403
Period size: 93 Copynumber: 2.6 Consensus size: 92
44164 GTCATAGACC
44174 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATATGAACCCCAAAAAACC
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG-TATGAA-CCCAAAAAACC
44239 AATCATTGAATTTGGAAGATGAATGTGCT
64 AATCATTGAATTTGGAAGATGAATGTGCT
* *
44268 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGTATGAACCCTAAAAACCA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT-GTATGAACCCAAAAAACCA
44333 ATCATTGAATTTGGAAGATGAATGTGCT
65 ATCATTGAATTTGGAAGATGAATGTGCT
* * *
44361 CATAGCATTTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGGAACC
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT-GTATGAACC
44416 ACAGAATCAA
Statistics
Matches: 140, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
93 89 0.64
94 50 0.36
95 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (92 bp):
CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGTATGAACCCAAAAAACCAA
TCATTGAATTTGGAAGATGAATGTGCT
Found at i:45123 original size:21 final size:20
Alignment explanation
Indices: 45098--45136 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
45088 CATGTTGAAT
*
45098 TTTTAACAAGAATTTCAAAGA
1 TTTTAACAA-AAATTCAAAGA
*
45119 TTTTAGCAAAAATTCAAA
1 TTTTAACAAAAATTCAAA
45137 TCCATCATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.49, C:0.10, G:0.08, T:0.33
Consensus pattern (20 bp):
TTTTAACAAAAATTCAAAGA
Found at i:50292 original size:17 final size:18
Alignment explanation
Indices: 50258--50292 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
50248 TCAAAATATT
50258 AAAATAATTTATTCAAAA
1 AAAATAATTTATTCAAAA
*
50276 AAAATATTTTATT-AAAA
1 AAAATAATTTATTCAAAA
50293 TATAATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (18 bp):
AAAATAATTTATTCAAAA
Found at i:50331 original size:29 final size:32
Alignment explanation
Indices: 50291--50360 Score: 85
Period size: 29 Copynumber: 2.3 Consensus size: 32
50281 ATTTTATTAA
* *
50291 AATATAATTTC-AATAAGAATA-T-TAAAATT
1 AATATATTTTCAAATAAAAATATTATAAAATT
50320 AATATATTTTCATAATAAAAATATTATAAAATT
1 AATATATTTTCA-AATAAAAATATTATAAAATT
50353 AAT-TATTT
1 AATATATTT
50361 AAAATATTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 10 0.29
31 9 0.26
32 6 0.17
33 10 0.29
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (32 bp):
AATATATTTTCAAATAAAAATATTATAAAATT
Found at i:62137 original size:5 final size:5
Alignment explanation
Indices: 62129--62205 Score: 140
Period size: 5 Copynumber: 15.8 Consensus size: 5
62119 ATATTTATTT
62129 ATATA ATAT- A-ATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
62177 ATATA ATATA ATATA ATATA ATATA ATAT
1 ATATA ATATA ATATA ATATA ATATA ATAT
62206 GAGAAAAACA
Statistics
Matches: 70, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
3 2 0.03
4 2 0.03
5 66 0.94
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:62322 original size:18 final size:18
Alignment explanation
Indices: 62294--62333 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
62284 TTAAATATTG
62294 TTTTAAATAAT-TAATTT
1 TTTTAAATAATATAATTT
*
62311 TTTTACAATAATATTATTT
1 TTTTA-AATAATATAATTT
62330 TTTT
1 TTTT
62334 CATCACATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 5 0.25
18 6 0.30
19 9 0.45
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTTAAATAATATAATTT
Found at i:63471 original size:18 final size:16
Alignment explanation
Indices: 63436--63473 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
63426 TAGTTGACAA
63436 ATTT-AAATTAAATAT
1 ATTTAAAATTAAATAT
63451 ATTTAAAATATAAATTAT
1 ATTTAAAAT-TAAA-TAT
63469 ATTTA
1 ATTTA
63474 GTTATATCGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 4 0.20
16 4 0.20
17 4 0.20
18 8 0.40
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTTAAAATTAAATAT
Found at i:64087 original size:31 final size:29
Alignment explanation
Indices: 64047--64132 Score: 82
Period size: 31 Copynumber: 2.9 Consensus size: 29
64037 TGAAATGTTC
* *
64047 AAAAGTTTAAGGATTAATTTAAAATATTAGT
1 AAAAATTTAAGGATAAATTTAAAATATT--T
* * * *
64078 TATAATTTAAAGATAAAATTAAAATATTT
1 AAAAATTTAAGGATAAATTTAAAATATTT
* *
64107 AAAAATTTAAGAATCAATTTAAAATA
1 AAAAATTTAAGGATAAATTTAAAATA
64133 AAAATCATAC
Statistics
Matches: 43, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
29 21 0.49
31 22 0.51
ACGTcount: A:0.55, C:0.01, G:0.07, T:0.37
Consensus pattern (29 bp):
AAAAATTTAAGGATAAATTTAAAATATTT
Found at i:74322 original size:23 final size:23
Alignment explanation
Indices: 74296--74340 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
74286 CACCACAGCT
*
74296 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
74319 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
74341 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:74507 original size:150 final size:149
Alignment explanation
Indices: 74308--74623 Score: 571
Period size: 150 Copynumber: 2.1 Consensus size: 149
74298 TATAAATGCA
74308 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
74372 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAAGACTTCACACATGT
65 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTT-CAAGACTTCACACATGT
* *
74437 TCCACAGAATATATATATATC
129 TCCAAAGAATATACATATATC
74458 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
74523 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
*
74588 CAAAGAATATACATATGTC
131 CAAAGAATATACATATATC
*
74607 CCGAAGGACCGTGTAGA
1 CCGAAGGACCGCGTAGA
74624 CCCTCTACCC
Statistics
Matches: 161, Mismatches: 4, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
149 52 0.32
150 109 0.68
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
CAAAGAATATACATATATC
Found at i:75211 original size:64 final size:63
Alignment explanation
Indices: 75078--75234 Score: 158
Period size: 64 Copynumber: 2.4 Consensus size: 63
75068 TAATGAGGGT
* * * ** *
75078 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATGTTGTATTATTACTGGG
1 ATGCATCGATGCA-TACTAATGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAAAGAG
* *
75142 ATGCATCGATGCATGACTTATGCATCGATGCACT-AATTGCATTCGATGTTTCTATT-TTAAA-A
1 ATGCATCGATGCAT-ACTAATGCATCGATGCA-TAAAATGCATTCGATG-TTCTATTATTAAAGA
75204 G
63 G
*
75205 AGTGCATCGATGCATTACCAATGCATCGAT
1 A-TGCATCGATGCA-TACTAATGCATCGAT
75235 ACACCTTCAA
Statistics
Matches: 79, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
63 3 0.04
64 68 0.86
65 8 0.10
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCATACTAATGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAAAGAG
Found at i:81375 original size:23 final size:23
Alignment explanation
Indices: 81349--81393 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
81339 CACCACAGCT
*
81349 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
81372 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
81394 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:82114 original size:64 final size:63
Alignment explanation
Indices: 81981--82137 Score: 158
Period size: 64 Copynumber: 2.4 Consensus size: 63
81971 TAATGAGGGT
* * * ** *
81981 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATGTTGTATTATTACTGGG
1 ATGCATCGATGCA-TACTAATGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAAAGAG
* *
82045 ATGCATCGATGCATGACTTATGCATCGATGCACT-AATTGCATTCGATGTTTCTATT-TTAAA-A
1 ATGCATCGATGCAT-ACTAATGCATCGATGCA-TAAAATGCATTCGATG-TTCTATTATTAAAGA
82107 G
63 G
*
82108 AGTGCATCGATGCATTACCAATGCATCGAT
1 A-TGCATCGATGCA-TACTAATGCATCGAT
82138 ACACCTTCAA
Statistics
Matches: 79, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
63 3 0.04
64 68 0.86
65 8 0.10
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCATACTAATGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAAAGAG
Found at i:83834 original size:23 final size:23
Alignment explanation
Indices: 83816--83868 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
83806 AATGCACCAA
83816 AGTGCCACATAGAATTGCACCGT
1 AGTGCCACATAGAATTGCACCGT
* *
83839 AGTGCCGCGTAGAATTGCACCGT
1 AGTGCCACATAGAATTGCACCGT
83862 AGTGCCA
1 AGTGCCA
83869 TATAATAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.21
Consensus pattern (23 bp):
AGTGCCACATAGAATTGCACCGT
Found at i:84002 original size:18 final size:18
Alignment explanation
Indices: 83979--84014 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
83969 GAATACATAT
83979 ATGTCCCGAAGGACCACA
1 ATGTCCCGAAGGACCACA
83997 ATGTCCCGAAGGACCACA
1 ATGTCCCGAAGGACCACA
84015 TATCATTCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.22, T:0.11
Consensus pattern (18 bp):
ATGTCCCGAAGGACCACA
Found at i:84089 original size:121 final size:121
Alignment explanation
Indices: 83875--84115 Score: 437
Period size: 121 Copynumber: 2.0 Consensus size: 121
83865 GCCATATAAT
* * *
83875 AATGTCCATAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGT
1 AATGTCCAGAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGT
83940 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
66 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
* *
83996 AATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGT
1 AATGTCCAGAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGT
84061 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCA
66 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCA
84116 TATAGACCCT
Statistics
Matches: 115, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
121 115 1.00
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.25
Consensus pattern (121 bp):
AATGTCCAGAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGT
GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
Found at i:84092 original size:62 final size:63
Alignment explanation
Indices: 83905--84100 Score: 164
Period size: 62 Copynumber: 3.2 Consensus size: 63
83895 ATCATTCCTT
* *
83905 AAGAAT-CATATACATATACTAGGGATCAAGTATGTGTCTCACCAGACTTCACACATGTTCCA
1 AAGAATACATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACTTCACACATGTTCCA
* * * * * *
83967 AAGAATACATAT--ATGTCCCGAAGGACCACA--A--TGTC-C-CGAAGGAC--CACATATCATT
1 AAGAATACATATACATATACC-AAGGATCA-AGTATGTGTCTCAC-CA-GACTTCACACAT-GTT
*
84022 CCTT
61 CC-A
*
84026 AAGAAT-CATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACTTCACACATGTTCCA
1 AAGAATACATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACTTCACACATGTTCCA
84088 AAGAATACATATA
1 AAGAATACATATA
84101 TGTCCCGAAG
Statistics
Matches: 100, Mismatches: 16, Indels: 35
0.66 0.11 0.23
Matches are distributed among these distances:
57 7 0.07
58 12 0.12
59 20 0.20
60 6 0.06
61 5 0.05
62 25 0.25
63 18 0.18
64 7 0.07
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.25
Consensus pattern (63 bp):
AAGAATACATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACTTCACACATGTTCCA
Found at i:85321 original size:21 final size:21
Alignment explanation
Indices: 85297--85341 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
85287 TTTTGTTCGT
* *
85297 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
85318 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
85339 TTG
1 TTG
85342 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:94265 original size:21 final size:21
Alignment explanation
Indices: 94236--94300 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
94226 AACAAGTTAG
*
94236 AAAATATTTATATATTTTTTA
1 AAAAAATTTATATATTTTTTA
94257 AAAAAATTTA-A-A----TTA
1 AAAAAATTTATATATTTTTTA
*
94272 ATAAAATTTATATATTTTTTA
1 AAAAAATTTATATATTTTTTA
*
94293 ATAAAATT
1 AAAAAATT
94301 GAAAATATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
15 12 0.33
16 1 0.03
17 1 0.03
19 1 0.03
20 1 0.03
21 20 0.56
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AAAAAATTTATATATTTTTTA
Found at i:94319 original size:38 final size:35
Alignment explanation
Indices: 94236--94319 Score: 105
Period size: 36 Copynumber: 2.3 Consensus size: 35
94226 AACAAGTTAG
* *
94236 AAAATATTTATATATTTTTTAAAAAAATTTAAATT
1 AAAAAATTTATATATTTTTTAAAAAAATTAAAATT
*
94271 AATAAAATTTATATATTTTTTAATAAAATTGAAAATAT
1 AA-AAAATTTATATATTTTTTAAAAAAATT-AAAAT-T
94309 AAAAAGATTTA
1 AAAAA-ATTTA
94320 ATGAAAGGGT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
35 2 0.05
36 25 0.60
37 7 0.17
38 8 0.19
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (35 bp):
AAAAAATTTATATATTTTTTAAAAAAATTAAAATT
Found at i:95471 original size:23 final size:23
Alignment explanation
Indices: 95440--95499 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
95430 TCCTCTTGCC
95440 CTCGGATGCCCTCGCATAGCTCG
1 CTCGGATGCCCTCGCATAGCTCG
* *
95463 GTCGGATGCTCTCGCATAGCTCG
1 CTCGGATGCCCTCGCATAGCTCG
* *
95486 CTCGAATGGCCTCG
1 CTCGGATGCCCTCG
95500 GATGCCCAGC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.13, C:0.35, G:0.28, T:0.23
Consensus pattern (23 bp):
CTCGGATGCCCTCGCATAGCTCG
Found at i:103607 original size:20 final size:21
Alignment explanation
Indices: 103582--103620 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
103572 ATTACAATGT
*
103582 TGATGT-GTGATTCACGATGA
1 TGATGTGGCGATTCACGATGA
103602 TGATGTGGCGATTCACGAT
1 TGATGTGGCGATTCACGAT
103621 ATATAATATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.23, C:0.13, G:0.31, T:0.33
Consensus pattern (21 bp):
TGATGTGGCGATTCACGATGA
Found at i:110331 original size:62 final size:62
Alignment explanation
Indices: 110239--110362 Score: 239
Period size: 62 Copynumber: 2.0 Consensus size: 62
110229 TCCATAAATT
110239 CAACATGTTATGTTATCAATCAACGTGATAAGCATACGATCATTATTAATTGTACTCTTCAA
1 CAACATGTTATGTTATCAATCAACGTGATAAGCATACGATCATTATTAATTGTACTCTTCAA
*
110301 CAACATGTTATGTTATCAATCAACGTGATAAGCATATGATCATTATTAATTGTACTCTTCAA
1 CAACATGTTATGTTATCAATCAACGTGATAAGCATACGATCATTATTAATTGTACTCTTCAA
110363 TGAAAAATAT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.36
Consensus pattern (62 bp):
CAACATGTTATGTTATCAATCAACGTGATAAGCATACGATCATTATTAATTGTACTCTTCAA
Found at i:111601 original size:27 final size:25
Alignment explanation
Indices: 111546--111623 Score: 95
Period size: 27 Copynumber: 3.1 Consensus size: 25
111536 AAATAAGTCT
111546 ACATTGCTCTTATTCAATGAAAATA
1 ACATTGCTCTTATTCAATGAAAATA
* *
111571 ACATTGCTCTTATTGGAGGTGAAAATA
1 ACATTGCTCTTATT-CA-ATGAAAATA
* *
111598 ACATTACTC-TATTCAATGGAAATA
1 ACATTGCTCTTATTCAATGAAAATA
111622 AC
1 AC
111624 TAAGCAAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
24 9 0.20
25 15 0.33
26 5 0.11
27 16 0.36
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.33
Consensus pattern (25 bp):
ACATTGCTCTTATTCAATGAAAATA
Found at i:115180 original size:2 final size:2
Alignment explanation
Indices: 115169--115352 Score: 96
Period size: 2 Copynumber: 97.5 Consensus size: 2
115159 TCTGGGATAG
* *
115169 TA TA TA -A TA TA TA T- TT TG TA TA T- TA TA T- TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
115206 TA TA TCA TA TA GTA TA TA T- TA TA TA TA T- TA TA -A TA TA TA T-
1 TA TA T-A TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
115246 TA TA AA AA TA TA TA T- TA TA GTG T- TA TA TT TA TA T- TA TA AA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* * *
115286 TA TGG TA TA T- TA TA TGG TA TA T- TA TA TA CTC TA T- TA TA TA
1 TA T-A TA TA TA TA TA T-A TA TA TA TA TA TA -TA TA TA TA TA TA
*
115326 TA TA TA TA TA TA TA T- TA TT TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
115353 CATGTTATTA
Statistics
Matches: 142, Mismatches: 17, Indels: 46
0.69 0.08 0.22
Matches are distributed among these distances:
1 17 0.12
2 117 0.82
3 8 0.06
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (2 bp):
TA
Found at i:115200 original size:21 final size:21
Alignment explanation
Indices: 115171--115351 Score: 118
Period size: 21 Copynumber: 8.2 Consensus size: 21
115161 TGGGATAGTA
* *
115171 TATAATATATATTTTGTATAT
1 TATAATATATATTATATATAT
*
115192 TATATTATATATTATATATCA-
1 TATAATATATATTATATAT-AT
*
115213 TATAGTATATATTATATATAT
1 TATAATATATATTATATATAT
* *
115234 TATAATATATATTATAAAAAT
1 TATAATATATATTATATATAT
* *
115255 ATATATTATAGTGTTATATTTATAT
1 -TATAATATA-TATTATA--TATAT
**
115280 TATAA-ATATGGTATATTATAT
1 TATAATATATATTATA-TATAT
*
115301 GGTATATTATATACTCTATTATATAT
1 --TATAATATATA-T-TA-TATATAT
115327 ATATATATATATATTAT-T-TAT
1 -TATA-ATATATATTATATATAT
115348 TATA
1 TATA
115352 TCATGTTATT
Statistics
Matches: 129, Mismatches: 18, Indels: 27
0.74 0.10 0.16
Matches are distributed among these distances:
20 5 0.04
21 61 0.47
22 16 0.12
23 14 0.11
24 10 0.08
25 8 0.06
26 13 0.10
27 2 0.02
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (21 bp):
TATAATATATATTATATATAT
Found at i:115204 original size:12 final size:12
Alignment explanation
Indices: 115169--115387 Score: 116
Period size: 12 Copynumber: 18.2 Consensus size: 12
115159 TCTGGGATAG
*
115169 TATATAATATA-
1 TATATTATATAT
* *
115180 TATTTTGTATAT
1 TATATTATATAT
115192 TATATTATATAT
1 TATATTATATAT
115204 TATATATCATATAGT
1 TATAT-T-ATATA-T
115219 ATATATTATATATAT
1 -TATA-T-TATATAT
*
115234 TATAATATATAT
1 TATATTATATAT
* *
115246 TATA-AAAATA-
1 TATATTATATAT
*
115256 TATATTATAGTGT
1 TATATTATA-TAT
115269 TATATT-TATAT
1 TATATTATATAT
* **
115280 TATA-AATATGG
1 TATATTATATAT
**
115291 TATATTATATGG
1 TATATTATATAT
*
115303 TATATTATATAC
1 TATATTATATAT
*
115315 TCTATTATATA-
1 TATATTATATAT
115326 TATA-TATATA-
1 TATATTATATAT
*
115336 TATATTATTTAT
1 TATATTATATAT
* *
115348 TATATCATGTTAT
1 TATATTAT-ATAT
*
115361 TAGTATTTATTTAT
1 TA-TA-TTATATAT
115375 T-TATTA-ATAT
1 TATATTATATAT
115385 TAT
1 TAT
115388 TTTCGGTTTT
Statistics
Matches: 167, Mismatches: 24, Indels: 34
0.74 0.11 0.15
Matches are distributed among these distances:
10 18 0.11
11 39 0.23
12 64 0.38
13 13 0.08
14 16 0.10
15 5 0.03
16 9 0.05
17 3 0.02
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (12 bp):
TATATTATATAT
Found at i:122199 original size:18 final size:19
Alignment explanation
Indices: 122167--122203 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
122157 AAGTTTTTAA
*
122167 ATAAAAAATTATATAATTT
1 ATAAAAAAATATATAATTT
122186 ATAAAAAAAT-TATAATTT
1 ATAAAAAAATATATAATTT
122204 TTTAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
ATAAAAAAATATATAATTT
Done.