Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006346.1 Hibiscus syriacus cultivar Beakdansim tig00015176_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: 89070
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:586 original size:306 final size:307
Alignment explanation
Indices: 1--722 Score: 1325
Period size: 306 Copynumber: 2.4 Consensus size: 307
1 GACTAATATAGAATAAAAAAATCAACA-TTGAGGATAAAATTAGAACAATTATAAGTTTAAGGAC
1 GACTAATATAGAAT--AAAAATCAACATTTGAGGATAAAATTAGAACAATTATAAGTTTAAGGAC
65 CAATTT-AAAAATTATCATTATTTAAATATGTTTAATGCAATTAACTACTGAAAACTCTCAAGGA
64 CAATTTAAAAAATTATCATTATTTAAATATGTTTAATGCAATTAACTACTGAAAACTCTCAAGGA
129 TCTAGCATTTTTGTCAAGATGGTCCTAATTTAAATTAGTCCCTAAATTTTTTAACATTTCAATAA
129 TCTAGCATTTTTGTCAAGATGGTCCTAATTTAAATTAGTCCCTAAATTTTTTAACATTTCAATAA
194 TGTTTGCAAAATCATTCAAGATTTTGTGGATTAAATTGGAACATTAATAAGTTTGGGGGATCAAT
194 TGTTTGCAAAATCATTCAAGATTTTGTGGATTAAATTGGAACATTAATAAGTTTGGGGGATCAAT
259 AGAATGAAAGTCATATTGGAGATGAATTTAGAATGTTCAAGAGTTTAGG
259 AGAATGAAAGTCATATTGGAGATGAATTTAGAATGTTCAAGAGTTTAGG
308 GACTAATATAGAATAAAAATCAACATTTGAGGAT-AAATTAGAACAATTA-AAGTTTAAGGACCA
1 GACTAATATAGAATAAAAATCAACATTTGAGGATAAAATTAGAACAATTATAAGTTTAAGGACCA
*
371 ATTTAAAAAAATTATCATTATTTAAATATGTTTAATGCAATTAACTCCTGAAAACTCTCAAGGAT
66 ATTT-AAAAAATTATCATTATTTAAATATGTTTAATGCAATTAACTACTGAAAACTCTCAAGGAT
436 CTAGCA-TTTTGTCAAGATGGTCCTAATTTAAATTAGTCCCTAAATTTTTTAACATTTC-ATAAT
130 CTAGCATTTTTGTCAAGATGGTCCTAATTTAAATTAGTCCCTAAATTTTTTAACATTTCAATAAT
499 GTTTGCAAAATCATTCAAGATTTTGTGGATTAAATTGGAACATTAATAAGTTTGGGGGATCAATA
195 GTTTGCAAAATCATTCAAGATTTTGTGGATTAAATTGGAACATTAATAAGTTTGGGGGATC-A-A
564 TAGAATG-AAGTCATATTTGGAGATGAATTTAGAATGTTCAAGAGTTTAGG
258 TAGAATGAAAGTCATA-TTGGAGATGAATTTAGAATGTTCAAGAGTTTAGG
614 GACTAATATAGAATAAAAATCAACATTTGAGGATAAAATTAGAACAATTATAAGTTTAAGGACCA
1 GACTAATATAGAATAAAAATCAACATTTGAGGATAAAATTAGAACAATTATAAGTTTAAGGACCA
679 ATTTAAAAAATTATCA-TATTTAAATATGTTTAATGCAATTAACT
66 ATTTAAAAAATTATCATTATTTAAATATGTTTAATGCAATTAACT
723 TTCTATATTA
Statistics
Matches: 406, Mismatches: 1, Indels: 17
0.96 0.00 0.04
Matches are distributed among these distances:
304 84 0.21
305 87 0.21
306 176 0.43
307 41 0.10
308 18 0.04
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (307 bp):
GACTAATATAGAATAAAAATCAACATTTGAGGATAAAATTAGAACAATTATAAGTTTAAGGACCA
ATTTAAAAAATTATCATTATTTAAATATGTTTAATGCAATTAACTACTGAAAACTCTCAAGGATC
TAGCATTTTTGTCAAGATGGTCCTAATTTAAATTAGTCCCTAAATTTTTTAACATTTCAATAATG
TTTGCAAAATCATTCAAGATTTTGTGGATTAAATTGGAACATTAATAAGTTTGGGGGATCAATAG
AATGAAAGTCATATTGGAGATGAATTTAGAATGTTCAAGAGTTTAGG
Found at i:1013 original size:23 final size:22
Alignment explanation
Indices: 982--1027 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
972 ATCTGAATTC
*
982 TATAGTATTTTGATAATATATATA
1 TATAGTATTGTG-TAATAT-TATA
1006 TATA-TATTGTGTAATATTATA
1 TATAGTATTGTGTAATATTATA
1027 T
1 T
1028 TTAAATTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 5 0.24
22 6 0.29
23 6 0.29
24 4 0.19
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (22 bp):
TATAGTATTGTGTAATATTATA
Found at i:1518 original size:2 final size:2
Alignment explanation
Indices: 1511--1557 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1501 CGGTGTTAAC
1511 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1553 AT AT A
1 AT AT A
1558 CATTATTTTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2422 original size:17 final size:17
Alignment explanation
Indices: 2388--2439 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
2378 ACCGGACAAA
* *
2388 TTTATTATTTTAGAGAG
1 TTTATTAATTTACAGAG
*
2405 TTTATTAATTTACCGAG
1 TTTATTAATTTACAGAG
*
2422 --TATTAATTTAAAGAG
1 TTTATTAATTTACAGAG
2437 TTT
1 TTT
2440 CTACTGTATT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 13 0.46
17 15 0.54
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.50
Consensus pattern (17 bp):
TTTATTAATTTACAGAG
Found at i:8356 original size:2 final size:2
Alignment explanation
Indices: 8351--8377 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
8341 GAGACACACA
8351 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 A
8378 AGGACTATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10908 original size:32 final size:32
Alignment explanation
Indices: 10843--10927 Score: 106
Period size: 32 Copynumber: 2.8 Consensus size: 32
10833 GTTCTACGGA
* **
10843 ACATATGGACAAAATTACC--TGTCTTTTGGG
1 ACATATGGACATAATTACCTATGTCTTTTAAG
10873 ACATATGGACATAATTACCTATGTCTTTTAAG
1 ACATATGGACATAATTACCTATGTCTTTTAAG
10905 ACATATGGACAGT-A-TACCTATGT
1 ACATATGGACA-TAATTACCTATGT
10928 TCTAATGAGC
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
30 18 0.37
31 9 0.18
32 21 0.43
33 1 0.02
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Consensus pattern (32 bp):
ACATATGGACATAATTACCTATGTCTTTTAAG
Found at i:10926 original size:31 final size:31
Alignment explanation
Indices: 10862--10955 Score: 95
Period size: 31 Copynumber: 3.0 Consensus size: 31
10852 CAAAATTACC
**
10862 TGTCTTTTGGGACATATGGACA-TAATTACCTA
1 TGTCTTTTAAGACATATGGACAGT-A-TACCTA
10894 TGTCTTTTAAGACATATGGACAGTATACCTA
1 TGTCTTTTAAGACATATGGACAGTATACCTA
* *
10925 TG--TTCTAATGAGCATATGGACAGTTTACCTA
1 TGTCTTTTAA-GA-CATATGGACAGTATACCTA
10956 GGTTCTTTGG
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
29 5 0.09
30 2 0.04
31 26 0.47
32 21 0.38
33 1 0.02
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (31 bp):
TGTCTTTTAAGACATATGGACAGTATACCTA
Found at i:11824 original size:21 final size:21
Alignment explanation
Indices: 11798--11848 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
11788 CTGTAGCAGT
* *
11798 ACTGTATCAGTGCATCGGTGC
1 ACTGTATCAATGCATCGATGC
* *
11819 ACTGTAGCAATGCATCGATGT
1 ACTGTATCAATGCATCGATGC
11840 ACTGTATCA
1 ACTGTATCA
11849 CTGTTCACAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (21 bp):
ACTGTATCAATGCATCGATGC
Found at i:13453 original size:6 final size:6
Alignment explanation
Indices: 13442--13469 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
13432 GCAACGACCC
13442 GGGTTA GGGTTA GGGTTA GGGTTA GGGT
1 GGGTTA GGGTTA GGGTTA GGGTTA GGGT
13470 CGTTTCTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.54, T:0.32
Consensus pattern (6 bp):
GGGTTA
Found at i:13695 original size:2 final size:2
Alignment explanation
Indices: 13690--13754 Score: 123
Period size: 2 Copynumber: 33.0 Consensus size: 2
13680 AATTTTTTAA
13690 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13732 AT AT AT A- AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
13755 TATCTCTGAG
Statistics
Matches: 62, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 61 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16474 original size:2 final size:2
Alignment explanation
Indices: 16467--16498 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
16457 TCACATATTT
16467 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16499 CACAGGCACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21193 original size:31 final size:32
Alignment explanation
Indices: 21155--21215 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
21145 ATGATTTTGA
*
21155 AAAACTAAAAGTTTAAGTATTAAA-ACATACT
1 AAAACTAAAAGTTTAAGTACTAAATACATACT
* *
21186 AAAACTAATAGTTTATGTACTAAATACATA
1 AAAACTAAAAGTTTAAGTACTAAATACATA
21216 GTTTATCCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 21 0.81
32 5 0.19
ACGTcount: A:0.52, C:0.10, G:0.07, T:0.31
Consensus pattern (32 bp):
AAAACTAAAAGTTTAAGTACTAAATACATACT
Found at i:22673 original size:32 final size:32
Alignment explanation
Indices: 22637--22702 Score: 96
Period size: 32 Copynumber: 2.1 Consensus size: 32
22627 GATTTTTGGC
*
22637 TTAATGTTAAAATAAGTGCCTAAAGTATACCT
1 TTAATATTAAAATAAGTGCCTAAAGTATACCT
* * *
22669 TTAATATTCAAATAAGTGCTTAAATTATACCT
1 TTAATATTAAAATAAGTGCCTAAAGTATACCT
22701 TT
1 TT
22703 TGTGTTGAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.39
Consensus pattern (32 bp):
TTAATATTAAAATAAGTGCCTAAAGTATACCT
Found at i:26139 original size:24 final size:24
Alignment explanation
Indices: 26107--26168 Score: 115
Period size: 24 Copynumber: 2.6 Consensus size: 24
26097 TGCATGGTAG
26107 TGCATCGATGCACCTGTTAAAGAA
1 TGCATCGATGCACCTGTTAAAGAA
*
26131 TGCATCGATGCACTTGTTAAAGAA
1 TGCATCGATGCACCTGTTAAAGAA
26155 TGCATCGATGCACC
1 TGCATCGATGCACC
26169 GATGCACTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.26
Consensus pattern (24 bp):
TGCATCGATGCACCTGTTAAAGAA
Found at i:26260 original size:2 final size:2
Alignment explanation
Indices: 26253--26280 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
26243 TACTGATAGC
26253 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26281 GATTGTGTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28778 original size:37 final size:36
Alignment explanation
Indices: 28719--28839 Score: 156
Period size: 36 Copynumber: 3.3 Consensus size: 36
28709 ATCCCATTAT
* *
28719 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAA
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
*
28754 CTATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 C-ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
* *
28791 CA-TTTTCAAAAAAAACATTTACCAAACTTTGAAAAT
1 CATTTTTC-AAAGAAACATTTACCAAACTTTGAAAAA
28827 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
28840 TTGGTTGCCA
Statistics
Matches: 75, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
35 6 0.08
36 36 0.48
37 28 0.37
38 5 0.07
ACGTcount: A:0.45, C:0.19, G:0.04, T:0.32
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
Found at i:28794 original size:21 final size:21
Alignment explanation
Indices: 28767--28831 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
28757 TTTTTCAAAG
28767 AAACATTTACCAAACTTTGAA
1 AAACATTTACCAAACTTTGAA
* *
28788 AACCATTT-TCAAA-----AA
1 AAACATTTACCAAACTTTGAA
28803 AAACATTTACCAAACTTTGAA
1 AAACATTTACCAAACTTTGAA
*
28824 AATCATTT
1 AAACATTT
28832 TTTCAAAGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 12
0.66 0.10 0.24
Matches are distributed among these distances:
15 9 0.27
16 4 0.12
20 4 0.12
21 16 0.48
ACGTcount: A:0.48, C:0.18, G:0.03, T:0.31
Consensus pattern (21 bp):
AAACATTTACCAAACTTTGAA
Found at i:33172 original size:17 final size:18
Alignment explanation
Indices: 33152--33185 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
33142 TTTATAAAAT
33152 ATATTTTGTTA-TATTTA
1 ATATTTTGTTACTATTTA
33169 ATATTTTGTTACTATTT
1 ATATTTTGTTACTATTT
33186 TATTTAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTTGTTACTATTTA
Found at i:33204 original size:16 final size:15
Alignment explanation
Indices: 33185--33226 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
33175 TGTTACTATT
33185 TTATTTAATTATTGTA
1 TTATTTAATT-TTGTA
*
33201 TTATTTAATTTTTTA
1 TTATTTAATTTTGTA
*
33216 TTATTTTATTT
1 TTATTTAATTT
33227 AAATATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (15 bp):
TTATTTAATTTTGTA
Found at i:33222 original size:8 final size:8
Alignment explanation
Indices: 33153--33225 Score: 51
Period size: 8 Copynumber: 9.1 Consensus size: 8
33143 TTATAAAATA
*
33153 TATTTTGT
1 TATTTTAT
*
33161 TATATTTAA
1 TAT-TTTAT
*
33170 TATTTTGT
1 TATTTTAT
*
33178 TACTATT-T
1 TA-TTTTAT
*
33186 TATTTAAT
1 TATTTTAT
*
33194 TATTGTAT
1 TATTTTAT
*
33202 TATTTAAT
1 TATTTTAT
33210 T-TTTTAT
1 TATTTTAT
33217 TATTTTAT
1 TATTTTAT
33225 T
1 T
33226 TAAATATTTT
Statistics
Matches: 49, Mismatches: 12, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
7 8 0.16
8 32 0.65
9 9 0.18
ACGTcount: A:0.26, C:0.01, G:0.04, T:0.68
Consensus pattern (8 bp):
TATTTTAT
Found at i:33242 original size:20 final size:20
Alignment explanation
Indices: 33163--33242 Score: 53
Period size: 20 Copynumber: 4.0 Consensus size: 20
33153 TATTTTGTTA
33163 TATTTAATATTTTGTTACTATTT
1 TATTTAATA--TT-TTACTATTT
* *
33186 TATTTAAT-TATT-GTA--T
1 TATTTAATATTTTACTATTT
* *
33202 TATTTAATTTTTTATTATTT
1 TATTTAATATTTTACTATTT
33222 TATTTAAATATTTTACT-TTT
1 TATTT-AATATTTTACTATTT
33242 T
1 T
33243 TGCAGTTATA
Statistics
Matches: 46, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
16 9 0.20
17 3 0.07
18 4 0.09
19 2 0.04
20 11 0.24
21 9 0.20
23 8 0.17
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.68
Consensus pattern (20 bp):
TATTTAATATTTTACTATTT
Found at i:34100 original size:21 final size:21
Alignment explanation
Indices: 34070--34146 Score: 68
Period size: 21 Copynumber: 3.7 Consensus size: 21
34060 AAATACCTTG
*
34070 GTATCGATACCCCTATATGGA
1 GTATCAATACCCCTATATGGA
* ***
34091 GTATCAATA-CTC-ATACCCTA
1 GTATCAATACCCCTATA-TGGA
*
34111 GTATCGATACCCCTATATGGA
1 GTATCAATACCCCTATATGGA
*
34132 GTATCAATACTCCTA
1 GTATCAATACCCCTA
34147 CCATGGTATC
Statistics
Matches: 41, Mismatches: 12, Indels: 6
0.69 0.20 0.10
Matches are distributed among these distances:
19 3 0.07
20 11 0.27
21 24 0.59
22 3 0.07
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.30
Consensus pattern (21 bp):
GTATCAATACCCCTATATGGA
Found at i:34177 original size:41 final size:41
Alignment explanation
Indices: 34062--34161 Score: 164
Period size: 41 Copynumber: 2.4 Consensus size: 41
34052 TTTTGAAAAA
*
34062 ATACCTTGGTATCGATACCCCTATATGGAGTATCAATACTC
1 ATACCATGGTATCGATACCCCTATATGGAGTATCAATACTC
* *
34103 ATACCCTAGTATCGATACCCCTATATGGAGTATCAATACTC
1 ATACCATGGTATCGATACCCCTATATGGAGTATCAATACTC
*
34144 CTACCATGGTATCGATAC
1 ATACCATGGTATCGATAC
34162 TCTATTAATG
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (41 bp):
ATACCATGGTATCGATACCCCTATATGGAGTATCAATACTC
Found at i:34838 original size:21 final size:21
Alignment explanation
Indices: 34812--34853 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
34802 CCAAAATGGG
*
34812 GGGAATCGGTACCCCTGCATA
1 GGGAATCGATACCCCTGCATA
*
34833 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTGCATA
34854 ATATTCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.29, G:0.24, T:0.21
Consensus pattern (21 bp):
GGGAATCGATACCCCTGCATA
Found at i:36146 original size:21 final size:21
Alignment explanation
Indices: 36120--36161 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
36110 CCAGAATGGG
*
36120 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
36141 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
36162 ATATTCAAAT
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:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:36239 original size:29 final size:31
Alignment explanation
Indices: 36207--36266 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
36197 AAATTTTGAA
*
36207 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
36236 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
36267 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:37586 original size:23 final size:23
Alignment explanation
Indices: 37556--37611 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
37546 ATTATTATAA
37556 TTTA-TTATTATTACATA-TTATT
1 TTTATTTATTATTACATATTTA-T
* *
37578 TTTATTTATTTTTACTTATTTAT
1 TTTATTTATTATTACATATTTAT
37601 TTTACTTTATT
1 TTTA-TTTATT
37612 TTGTTTTCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 4 0.14
23 16 0.55
24 9 0.31
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (23 bp):
TTTATTTATTATTACATATTTAT
Found at i:37587 original size:13 final size:13
Alignment explanation
Indices: 37545--37601 Score: 60
Period size: 13 Copynumber: 4.3 Consensus size: 13
37535 ATATGATATA
*
37545 TATTATTATAATT
1 TATTATTATTATT
**
37558 TATTATTATTACA
1 TATTATTATTATT
*
37571 TATTATTTTTATT
1 TATTATTATTATT
*
37584 TATTTTTACTTATT
1 TATTATTA-TTATT
37598 TATT
1 TATT
37602 TTACTTTATT
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
13 26 0.74
14 9 0.26
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.67
Consensus pattern (13 bp):
TATTATTATTATT
Found at i:37598 original size:14 final size:14
Alignment explanation
Indices: 37578--37612 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
37568 ACATATTATT
37578 TTTATTTATTTTTAC
1 TTTATTTA-TTTTAC
37593 -TTATTTATTTTAC
1 TTTATTTATTTTAC
37606 TTTATTT
1 TTTATTT
37613 TGTTTTCCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTATTTATTTTAC
Found at i:38912 original size:21 final size:21
Alignment explanation
Indices: 38886--38929 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
38876 GGCATGTTTC
38886 TTTATTTTGAAGTTTT-TTATT
1 TTTATTTTGAA-TTTTATTATT
*
38907 TTTATTTTTAATTTTATTATT
1 TTTATTTTGAATTTTATTATT
38928 TT
1 TT
38930 ATTATTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.75
Consensus pattern (21 bp):
TTTATTTTGAATTTTATTATT
Found at i:38929 original size:20 final size:21
Alignment explanation
Indices: 38886--38945 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 21
38876 GGCATGTTTC
*
38886 TTTATTTTGAAGTTTT-TTATT
1 TTTATTTTTAA-TTTTATTATT
38907 TTTATTTTTAATTTTATTA-T
1 TTTATTTTTAATTTTATTATT
*
38927 TTTATTATT-ATTATTATTA
1 TTTATTTTTAATT-TTATTA
38946 GTAGTATTAG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
19 3 0.09
20 19 0.54
21 13 0.37
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (21 bp):
TTTATTTTTAATTTTATTATT
Found at i:39507 original size:13 final size:13
Alignment explanation
Indices: 39489--39517 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
39479 ATTTTTTATT
39489 CCAATCTCTAAAC
1 CCAATCTCTAAAC
39502 CCAATCTCTAAAC
1 CCAATCTCTAAAC
39515 CCA
1 CCA
39518 TTTAAGTGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.41, G:0.00, T:0.21
Consensus pattern (13 bp):
CCAATCTCTAAAC
Found at i:42759 original size:30 final size:34
Alignment explanation
Indices: 42719--42780 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 34
42709 ATGCAATAAC
42719 TCATAACACACAT-ATAT-TAT-TT-CATACAAT
1 TCATAACACACATCATATATATATTACATACAAT
*
42749 TCATATCACACATCATATATATATTACATACA
1 TCATAACACACATCATATATATATTACATACA
42781 TTATATTCAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 12 0.44
31 4 0.15
32 3 0.11
33 2 0.07
34 6 0.22
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (34 bp):
TCATAACACACATCATATATATATTACATACAAT
Found at i:45333 original size:14 final size:15
Alignment explanation
Indices: 45314--45345 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
45304 GTGGTACTCT
45314 GCTGAAA-GTAATAA
1 GCTGAAAGGTAATAA
45328 GCTGAAAGGTAATAA
1 GCTGAAAGGTAATAA
45343 GCT
1 GCT
45346 ATTAATCTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.44, C:0.09, G:0.25, T:0.22
Consensus pattern (15 bp):
GCTGAAAGGTAATAA
Found at i:51963 original size:12 final size:12
Alignment explanation
Indices: 51920--51969 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
51910 CAAAGAATTT
51920 TTATTTTACTTG
1 TTATTTTACTTG
51932 TTTATTTT--TTG
1 -TTATTTTACTTG
51943 TATAGTTTTACTTG
1 T-TA-TTTTACTTG
*
51957 TTATTTTCCTTG
1 TTATTTTACTTG
51969 T
1 T
51970 CTTTTTCAGG
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
10 1 0.03
11 5 0.16
12 13 0.41
13 9 0.28
14 4 0.12
ACGTcount: A:0.14, C:0.08, G:0.10, T:0.68
Consensus pattern (12 bp):
TTATTTTACTTG
Found at i:53843 original size:19 final size:19
Alignment explanation
Indices: 53795--53832 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
53785 AATTATAAAC
53795 GAATTAAGGAATGAAATGG
1 GAATTAAGGAATGAAATGG
53814 GAATTAAGGAATGAAATGG
1 GAATTAAGGAATGAAATGG
53833 AGGTTAAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.32, T:0.21
Consensus pattern (19 bp):
GAATTAAGGAATGAAATGG
Found at i:59157 original size:147 final size:148
Alignment explanation
Indices: 58882--59172 Score: 426
Period size: 147 Copynumber: 2.0 Consensus size: 148
58872 AAAATCGGAT
* * * *
58882 GAAATCTCGTGTCTTTTTATATTTGCTCTATTGTCGTTACATGACAATGAACAATGAGGGACAAC
1 GAAAACTCGTGTCTTTTTATATTTGCCCTATTATCGTTACACGACAATGAACAATGAGGGACAAC
* * * *
58947 TGTAGACACTCATATTCGTCCGGAGTTGTTCCAAGTGTTTTTATATTTATGATATATATTGTTTA
66 TGTAGACACACATATTCATCCGGAGTTGTTCCAAGGGTTTTTATATTTATGATATATAGTGTTTA
59012 TAA-TATATATATAGGAC
131 TAATTATATATATAGGAC
* * * *
59029 GAAAACTCGTGTCTTTTTATCTTTTCCCTATTATCGTTACACGACAATGGAGAATGAAGGG-CAA
1 GAAAACTCGTGTCTTTTTATATTTGCCCTATTATCGTTACACGACAATGAACAATG-AGGGACAA
*
59093 CTGTAGACACACATATTCATCTGGAGTTGTTCCAAGGGTTTTTATATTTATGCA-ATATAGTGTT
65 CTGTAGACACACATATTCATCCGGAGTTGTTCCAAGGGTTTTTATATTTATG-ATATATAGTGTT
59157 TATAATTATATATATA
129 TATAATTATATATATA
59173 ATATAAATAG
Statistics
Matches: 128, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
147 113 0.88
148 15 0.12
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (148 bp):
GAAAACTCGTGTCTTTTTATATTTGCCCTATTATCGTTACACGACAATGAACAATGAGGGACAAC
TGTAGACACACATATTCATCCGGAGTTGTTCCAAGGGTTTTTATATTTATGATATATAGTGTTTA
TAATTATATATATAGGAC
Found at i:59192 original size:12 final size:13
Alignment explanation
Indices: 59177--59207 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
59167 TATATAATAT
59177 AAATAGTTTTTAA
1 AAATAGTTTTTAA
59190 AATATAGTTTTTAA
1 AA-ATAGTTTTTAA
59204 AAAT
1 AAAT
59208 GCGTATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (13 bp):
AAATAGTTTTTAA
Found at i:59207 original size:15 final size:14
Alignment explanation
Indices: 59179--59205 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
59169 TATAATATAA
59179 ATAGTTTTTAAAAT
1 ATAGTTTTTAAAAT
59193 ATAGTTTTTAAAA
1 ATAGTTTTTAAAA
59206 ATGCGTATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (14 bp):
ATAGTTTTTAAAAT
Found at i:59432 original size:14 final size:14
Alignment explanation
Indices: 59413--59446 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
59403 TTTACTATTA
59413 TTATTTATTTTTAC-
1 TTATTTA-TTTTACT
59427 TTATTTATTTTACT
1 TTATTTATTTTACT
59441 TTATTT
1 TTATTT
59447 TGTTTTCAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (14 bp):
TTATTTATTTTACT
Found at i:60588 original size:18 final size:18
Alignment explanation
Indices: 60561--60598 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
60551 GTGAAGTATG
60561 AATGGCGTTGTCGTGGCA
1 AATGGCGTTGTCGTGGCA
* *
60579 AATGGTGTTGTTGTGGCA
1 AATGGCGTTGTCGTGGCA
60597 AA
1 AA
60599 GTGTATAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.11, G:0.37, T:0.32
Consensus pattern (18 bp):
AATGGCGTTGTCGTGGCA
Found at i:69863 original size:19 final size:19
Alignment explanation
Indices: 69839--69882 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
69829 GTTTGGATCA
* **
69839 AGGAATATGGGATTTTCAT
1 AGGAATATGAGATTCCCAT
*
69858 AGGAATGTGAGATTCCCAT
1 AGGAATATGAGATTCCCAT
69877 AGGAAT
1 AGGAAT
69883 GGAATCCACA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.34, C:0.09, G:0.27, T:0.30
Consensus pattern (19 bp):
AGGAATATGAGATTCCCAT
Found at i:71740 original size:20 final size:21
Alignment explanation
Indices: 71707--71769 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
71697 CCTTTAACTG
*
71707 AATTGTACTAATTAATATAAA
1 AATTATACTAATTAATATAAA
* * *
71728 AATT-TATTAATTAAAATTTAA
1 AATTATACTAATTAATA-TAAA
*
71749 TATTATACTAATTAATATAAA
1 AATTATACTAATTAATATAAA
71770 GGTCAATATA
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
20 10 0.30
21 13 0.39
22 10 0.30
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (21 bp):
AATTATACTAATTAATATAAA
Found at i:73418 original size:70 final size:70
Alignment explanation
Indices: 73330--73471 Score: 266
Period size: 70 Copynumber: 2.0 Consensus size: 70
73320 AAATTTTCCC
*
73330 TCGTACCAATAGATAATAACTTGAAAATGATCAAATTAATAATTATAAAATGATACCAACCACTA
1 TCGTACCAATAGATAATAACTTGAAAATGATCAAATTAATAATTATAAAATGATACCAACAACTA
73395 ATTTG
66 ATTTG
*
73400 TCGTACCATTAGATAATAACTTGAAAATGATCAAATTAATAATTATAAAATGATACCAACAACTA
1 TCGTACCAATAGATAATAACTTGAAAATGATCAAATTAATAATTATAAAATGATACCAACAACTA
73465 ATTTG
66 ATTTG
73470 TC
1 TC
73472 TAATAAGACG
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.31
Consensus pattern (70 bp):
TCGTACCAATAGATAATAACTTGAAAATGATCAAATTAATAATTATAAAATGATACCAACAACTA
ATTTG
Found at i:77274 original size:20 final size:20
Alignment explanation
Indices: 77252--77290 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
77242 TTTAAATATT
77252 TTTTA-TTTTTATAAATTTA
1 TTTTACTTTTTATAAATTTA
77271 TTTTACTTTTTATAAATTTA
1 TTTTACTTTTTATAAATTTA
77291 AATTTTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTACTTTTTATAAATTTA
Found at i:85788 original size:3 final size:3
Alignment explanation
Indices: 85780--85826 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
85770 TTTAGGAGTG
85780 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GG
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GG
85827 GTTAACTGCC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:86814 original size:61 final size:60
Alignment explanation
Indices: 86708--86862 Score: 177
Period size: 61 Copynumber: 2.6 Consensus size: 60
86698 TTTGGATGAA
* *** *
86708 TTTAGGGATAAAATTGGAATATTCAAAAGTTTGGGGACAAATTTAGAATAAGAGTCATAG
1 TTTAGGGATAAAATTAGAATATTCAAAAGTTTAAAGACAAATTTAGAATAAGAGTAATAG
* * * *
86768 TTT-GAGGATAAAAATTAGAATGTTCAAAAGTTTAAAGACTAGTTTAGAATGAGAGTAATAG
1 TTTAG-GGAT-AAAATTAGAATATTCAAAAGTTTAAAGACAAATTTAGAATAAGAGTAATAG
* * *
86829 TTTAGGGATGAAATTAAAATATTTAAAAGTTTAA
1 TTTAGGGATAAAATTAGAATATTCAAAAGTTTAA
86863 GGATTATTTT
Statistics
Matches: 79, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
59 1 0.01
60 28 0.35
61 49 0.62
62 1 0.01
ACGTcount: A:0.44, C:0.03, G:0.21, T:0.32
Consensus pattern (60 bp):
TTTAGGGATAAAATTAGAATATTCAAAAGTTTAAAGACAAATTTAGAATAAGAGTAATAG
Found at i:87525 original size:22 final size:23
Alignment explanation
Indices: 87499--87543 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
87489 AAATCATAAA
87499 ATATCA-AAAGACAAAGAAAAAC
1 ATATCATAAAGACAAAGAAAAAC
* *
87521 ATATCATAAAGACAGAGATAAAC
1 ATATCATAAAGACAAAGAAAAAC
87544 GTGCCATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.62, C:0.13, G:0.11, T:0.13
Consensus pattern (23 bp):
ATATCATAAAGACAAAGAAAAAC
Done.