Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002115.1 Hibiscus syriacus cultivar Beakdansim tig00004338_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: 61615
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:1891 original size:32 final size:32
Alignment explanation
Indices: 1850--1910 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
1840 GAGGTGTGAA
*
1850 CGTTTAATGTCAAATGATTAAATTATCTTGAG
1 CGTTCAATGTCAAATGATTAAATTATCTTGAG
1882 CGTTCAATGTCAAATGATTAAATTATCTT
1 CGTTCAATGTCAAATGATTAAATTATCTT
1911 TAAATATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.41
Consensus pattern (32 bp):
CGTTCAATGTCAAATGATTAAATTATCTTGAG
Found at i:1951 original size:3 final size:3
Alignment explanation
Indices: 1943--1967 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1933 TTTTCCAAAT
1943 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
1968 GTTTTAACGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:7942 original size:23 final size:22
Alignment explanation
Indices: 7915--7993 Score: 95
Period size: 23 Copynumber: 3.4 Consensus size: 22
7905 ATTCAAGTCA
7915 AGTATCATATCAGAATCAGGTC
1 AGTATCATATCAGAATCAGGTC
* *
7937 ATGTATCAAATCAGAATCCATGTC
1 A-GTATCATATCAGAAT-CAGGTC
*
7961 AATATCATATCAGAATCTAGGTC
1 AGTATCATATCAGAATC-AGGTC
7984 AGTTATCATA
1 AG-TATCATA
7994 ATAGAATTCA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
22 2 0.04
23 32 0.68
24 13 0.28
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (22 bp):
AGTATCATATCAGAATCAGGTC
Found at i:7983 original size:47 final size:47
Alignment explanation
Indices: 7911--8000 Score: 132
Period size: 47 Copynumber: 1.9 Consensus size: 47
7901 CATAATTCAA
7911 GTCAAGTATCATATCAGAATCAGGTCA-TGTATCA-AATCAGAATCCAT
1 GTCAAGTATCATATCAGAATCAGGTCAGT-TATCATAAT-AGAATCCAT
7958 GTCAA-TATCATATCAGAATCTAGGTCAGTTATCATAATAGAAT
1 GTCAAGTATCATATCAGAATC-AGGTCAGTTATCATAATAGAAT
8001 TCAAATCAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
46 15 0.38
47 21 0.52
48 4 0.10
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (47 bp):
GTCAAGTATCATATCAGAATCAGGTCAGTTATCATAATAGAATCCAT
Found at i:12893 original size:18 final size:18
Alignment explanation
Indices: 12870--12915 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
12860 AACATTCTCA
*
12870 GTAATCTTATTCCCGCTG
1 GTAATCTTATTCCCACTG
* *
12888 GTAATCATATTCCCATTG
1 GTAATCTTATTCCCACTG
*
12906 ATAATCTTAT
1 GTAATCTTAT
12916 ATTTTGTTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.26, C:0.22, G:0.11, T:0.41
Consensus pattern (18 bp):
GTAATCTTATTCCCACTG
Found at i:14675 original size:31 final size:31
Alignment explanation
Indices: 14639--14698 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
14629 AACTTAAAAG
* *
14639 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
14670 AGTTTTACAATACTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
14699 CATACAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:15266 original size:21 final size:21
Alignment explanation
Indices: 15234--15286 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
15224 TTTTAATAAT
* *
15234 ATATAAAA--AAATTTATATG
1 ATATAAAATTAAATATATATA
*
15253 ATATAAAATTAAATATCTATA
1 ATATAAAATTAAATATATATA
*
15274 ATATAATATTAAA
1 ATATAAAATTAAA
15287 AATTGATATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 8 0.29
21 20 0.71
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (21 bp):
ATATAAAATTAAATATATATA
Found at i:15324 original size:14 final size:14
Alignment explanation
Indices: 15305--15388 Score: 65
Period size: 14 Copynumber: 6.4 Consensus size: 14
15295 TTTAATTTAT
15305 TTAAAAAATTAATA
1 TTAAAAAATTAATA
15319 TT--AAAATTAATA
1 TTAAAAAATTAATA
* *
15331 TCTATAATA-TAATA
1 T-TAAAAAATTAATA
*
15345 TTAATAAATTAATA
1 TTAAAAAATTAATA
* *
15359 TT---TAATTTAT-
1 TTAAAAAATTAATA
15369 TTAAAAAATTAATA
1 TTAAAAAATTAATA
15383 TTAAAA
1 TTAAAA
15389 TTAAAATCAA
Statistics
Matches: 54, Mismatches: 8, Indels: 16
0.69 0.10 0.21
Matches are distributed among these distances:
10 2 0.04
11 6 0.11
12 11 0.20
13 11 0.20
14 21 0.39
15 3 0.06
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAAAATTAATA
Found at i:15360 original size:40 final size:37
Alignment explanation
Indices: 15277--15360 Score: 98
Period size: 40 Copynumber: 2.2 Consensus size: 37
15267 ATCTATAATA
* *
15277 TAATATTAAAAATTGATATTTAATTTATTTAAAAAAT
1 TAATATTAAAAATTAATATTTAATTAATTTAAAAAAT
*
15314 TAATATT-AAAATTAATATCTATAATATAATATTAATAAAT
1 TAATATTAAAAATTAATAT-T-TAAT-TAAT-TTAAAAAAT
15354 TAATATT
1 TAATATT
15361 TAATTTATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
36 10 0.25
37 8 0.20
38 4 0.10
39 3 0.08
40 15 0.38
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (37 bp):
TAATATTAAAAATTAATATTTAATTAATTTAAAAAAT
Found at i:15362 original size:64 final size:63
Alignment explanation
Indices: 15256--15415 Score: 256
Period size: 64 Copynumber: 2.6 Consensus size: 63
15246 TTATATGATA
*
15256 TAAAATTAAATATCTATAATATAATATTAAAAATTGATATTTAATTTATTTAAAAAATTAATAT
1 TAAAATT-AATATCTATAATATAATATTAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
15320 TAAAATTAATATCTATAATATAATATTAATAAATTAATATTTAATTTATTTAAAAAATTAATAT
1 TAAAATTAATATCTATAATATAATATTAA-AAATTAATATTTAATTTATTTAAAAAATTAATAT
*
15384 TAAAATTAAAATC-A-AATATAATA-T-AAAATTAA
1 TAAAATTAATATCTATAATATAATATTAAAAATTAA
15416 ATATAAAACC
Statistics
Matches: 93, Mismatches: 2, Indels: 7
0.91 0.02 0.07
Matches are distributed among these distances:
59 7 0.08
60 1 0.01
61 1 0.01
62 9 0.10
63 23 0.25
64 52 0.56
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.42
Consensus pattern (63 bp):
TAAAATTAATATCTATAATATAATATTAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
Found at i:15377 original size:24 final size:27
Alignment explanation
Indices: 15314--15385 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 27
15304 TTTAAAAAAT
15314 TAATATT--AAAATTAATATCTATAATA
1 TAATATTAAAAAATTAATAT-TATAATA
*
15340 TAATATTAATAAATTAATATT-TAAT-
1 TAATATTAAAAAATTAATATTATAATA
*
15365 TTAT-TTAAAAAATTAATATTA
1 TAATATTAAAAAATTAATATTA
15386 AAATTAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
24 15 0.38
25 3 0.08
26 11 0.28
27 1 0.03
28 10 0.25
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (27 bp):
TAATATTAAAAAATTAATATTATAATA
Found at i:15417 original size:64 final size:63
Alignment explanation
Indices: 15173--15417 Score: 223
Period size: 64 Copynumber: 3.7 Consensus size: 63
15163 ACAAATCCAA
* * * *
15173 AAAAAATATTATATTTAAACTT-AAATCAAA-ATAAT-TAAAATAAATATAAAATTTTAATAATA
1 AAAAAAT-TAATA-TTAAAATTAAAATCAAATATAATATAAAATAAAT-TAATA-TTTAAT-TTA
*
15235 TATA
61 T-TT
* *
15239 AAAAAATTTATATGATATAAAATTAAATATCTATAATATAATAT-TAA-AAATTGATATTTAATT
1 AAAAAA-TTA-AT-AT-TAAAATTAAA-ATC-A-AATATAATATAAAATAAATTAATATTTAATT
15302 TATTT
59 TATTT
* *
15307 AAAAAATTAATATTAAAATTAATATCTATAATATAATAT-TAATAAATTAATATTTAATTTATTT
1 AAAAAATTAATATTAAAATTAAAATC-A-AATATAATATAAAATAAATTAATATTTAATTTATTT
15371 AAAAAATTAATATTAAAATTAAAATCAAATATAATATAAAATTAAAT
1 AAAAAATTAATATTAAAATTAAAATCAAATATAATATAAAA-TAAAT
15418 ATAAAACCTC
Statistics
Matches: 155, Mismatches: 11, Indels: 28
0.80 0.06 0.14
Matches are distributed among these distances:
62 10 0.06
63 22 0.14
64 59 0.38
65 2 0.01
66 9 0.06
67 7 0.05
68 14 0.09
69 5 0.03
70 9 0.06
71 4 0.03
72 6 0.04
73 7 0.05
74 1 0.01
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (63 bp):
AAAAAATTAATATTAAAATTAAAATCAAATATAATATAAAATAAATTAATATTTAATTTATTT
Found at i:15418 original size:12 final size:12
Alignment explanation
Indices: 15373--15423 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
15363 ATTTATTTAA
15373 AAAATT-AATATT
1 AAAATTAAATA-T
15385 AAAATTAAA-AT
1 AAAATTAAATAT
*
15396 CAAA-TATAATAT
1 AAAATTA-AATAT
15408 AAAATTAAATAT
1 AAAATTAAATAT
15420 AAAA
1 AAAA
15424 CCTCATGTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
10 2 0.06
11 6 0.18
12 21 0.64
13 4 0.12
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (12 bp):
AAAATTAAATAT
Found at i:19521 original size:25 final size:25
Alignment explanation
Indices: 19487--19538 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
19477 GTATTGGTCC
*
19487 CCCGTCCCCGTCCCCGT-TTAAAAAA
1 CCCGTACCCGTCCCC-TCTTAAAAAA
19512 CCCGTACCCGTCCCCTCTTAAAAAA
1 CCCGTACCCGTCCCCTCTTAAAAAA
19537 CC
1 CC
19539 ACGGGGATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 1 0.04
25 24 0.96
ACGTcount: A:0.25, C:0.46, G:0.10, T:0.19
Consensus pattern (25 bp):
CCCGTACCCGTCCCCTCTTAAAAAA
Found at i:19837 original size:30 final size:30
Alignment explanation
Indices: 19801--19873 Score: 110
Period size: 30 Copynumber: 2.4 Consensus size: 30
19791 TTACTAAACT
* *
19801 CGTCCCCGTTTAACATAAACGGTTTTTTCC
1 CGTCCCCGTTTAACATAAACAGTTTTCTCC
* *
19831 CGTCCCCGTTTAGCATAAACAGTTTTCTCT
1 CGTCCCCGTTTAACATAAACAGTTTTCTCC
19861 CGTCCCCGTTTAA
1 CGTCCCCGTTTAA
19874 TTCGGTTTTC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.19, C:0.32, G:0.14, T:0.36
Consensus pattern (30 bp):
CGTCCCCGTTTAACATAAACAGTTTTCTCC
Found at i:20447 original size:2 final size:2
Alignment explanation
Indices: 20440--20496 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
20430 GTACGTGACA
20440 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
20482 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
20497 CATGATCATG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28753 original size:20 final size:20
Alignment explanation
Indices: 28728--28778 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
28718 TCACACTAAA
28728 TTCTCTCAAATTTTCTCAAT
1 TTCTCTCAAATTTTCTCAAT
28748 TTCTCTCAAATTTTCTCAAT
1 TTCTCTCAAATTTTCTCAAT
28768 TTCTCTCAAAT
1 TTCTCTCAAAT
28779 ACTCTATCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.49
Consensus pattern (20 bp):
TTCTCTCAAATTTTCTCAAT
Found at i:28762 original size:12 final size:11
Alignment explanation
Indices: 28728--28778 Score: 74
Period size: 10 Copynumber: 5.0 Consensus size: 11
28718 TCACACTAAA
28728 TTCTCTCAAAT
1 TTCTCTCAAAT
28739 TT-TCTC-AAT
1 TTCTCTCAAAT
28748 TTCTCTCAAAT
1 TTCTCTCAAAT
28759 TT-TCTC-AAT
1 TTCTCTCAAAT
28768 TTCTCTCAAAT
1 TTCTCTCAAAT
28779 ACTCTATCTA
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
9 10 0.28
10 16 0.44
11 10 0.28
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.49
Consensus pattern (11 bp):
TTCTCTCAAAT
Found at i:28783 original size:10 final size:10
Alignment explanation
Indices: 28725--28783 Score: 73
Period size: 10 Copynumber: 5.9 Consensus size: 10
28715 CAATCACACT
28725 AAATTCTCTC
1 AAATTCTCTC
*
28735 AAATTTTCTC
1 AAATTCTCTC
*
28745 AATTTCTCTC
1 AAATTCTCTC
*
28755 AAATTTTCTC
1 AAATTCTCTC
*
28765 AATTTCTCTC
1 AAATTCTCTC
*
28775 AAATACTCT
1 AAATTCTCT
28784 ATCTATTTAA
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
10 40 1.00
ACGTcount: A:0.29, C:0.25, G:0.00, T:0.46
Consensus pattern (10 bp):
AAATTCTCTC
Found at i:28863 original size:17 final size:18
Alignment explanation
Indices: 28826--28866 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
28816 ATATTATGTA
*
28826 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
28844 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
28861 TTTACT
1 TTTACT
28867 AATATAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:30910 original size:3 final size:3
Alignment explanation
Indices: 30902--30926 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
30892 ATCTGCTCAG
30902 GAC GAC GAC GAC GAC GAC GAC GAC G
1 GAC GAC GAC GAC GAC GAC GAC GAC G
30927 GTGATGATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.36, T:0.00
Consensus pattern (3 bp):
GAC
Found at i:38853 original size:21 final size:18
Alignment explanation
Indices: 38813--38853 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 18
38803 CAAAAATAAT
38813 ATTAAAAAAACATTAGTA
1 ATTAAAAAAACATTAGTA
38831 ATTAAAATAAACTATTAAGTA
1 ATTAAAA-AAAC-ATT-AGTA
38852 AT
1 AT
38854 AAGTTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 7 0.35
19 4 0.20
20 3 0.15
21 6 0.30
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTAAAAAAACATTAGTA
Found at i:46666 original size:20 final size:21
Alignment explanation
Indices: 46643--46682 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
46633 TATATTTTAA
46643 ATTTT-TATTAAAAATTTATT
1 ATTTTCTATTAAAAATTTATT
* *
46663 ATTTTCTTTTAAAAGTTTAT
1 ATTTTCTATTAAAAATTTAT
46683 AAGTTCATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (21 bp):
ATTTTCTATTAAAAATTTATT
Found at i:46703 original size:26 final size:26
Alignment explanation
Indices: 46669--46722 Score: 83
Period size: 27 Copynumber: 2.1 Consensus size: 26
46659 TATTATTTTC
46669 TTTTAAAAG-TTTATAAGTTCATCTCT
1 TTTTAAAAGTTTTATAAGTTCATC-CT
*
46695 TTTTTAAAGTTTTATAAGTTCATCCT
1 TTTTAAAAGTTTTATAAGTTCATCCT
46721 TT
1 TT
46723 AACATAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 12 0.46
27 14 0.54
ACGTcount: A:0.28, C:0.11, G:0.07, T:0.54
Consensus pattern (26 bp):
TTTTAAAAGTTTTATAAGTTCATCCT
Found at i:55732 original size:218 final size:220
Alignment explanation
Indices: 55095--55747 Score: 1136
Period size: 220 Copynumber: 3.0 Consensus size: 220
55085 CCTAAAGTCT
55095 TTAACTCTTGAAGAGCTAATCGGTTCCCTCCTCACTCATGAAATGATGCTTGAAGATGAGGTGGA
1 TTAACTCTTGAAGAGCTAATCGGTT-CCTCCTCACTCATGAAATGATGCTTGAAGATGAGGTGGA
* * *
55160 CATCGATAAGATTGACGAGACACCAAAGGAGAATGAGAAGAAGAAAAACATTGTAGTTGCTCTCA
65 CCTCGATAAGATTGACGAGACACCAAAGGAGAAGGAGAAGAAGAAAAACATTGGAGTTGCTCTCA
*
55225 AATCCATAAAAGATGAGAGTGATTCAGATGAAGATGACGATGACGAGAAAATGGCATTGTTTGCC
130 AATCCACAAAAGATGAGAGTGATTCAGATGAAGATGACGATGACGAGAAAATGGCATTGTTTGCC
55290 AAACGGTTCAG-AAAATGATGAGACC
195 AAACGGTTCAGAAAAATGATGAGACC
* * * *
55315 TTAACTCTTGAAGAGCTAATCGATTTCCTCCT--CTCATGAAATGATGATTAAAGATGAGGTGGG
1 TTAACTCTTGAAGAGCTAATCG-GTTCCTCCTCACTCATGAAATGATGCTTGAAGATGAGGTGGA
55378 CCTCGATAAGATTGACGAGACACCAAAGGAGAAGGAGAGAAGAAGAAAAACATTGGAGTTGCTCT
65 CCTCGATAAGATTGACGAGACACCAAAGGAGAA-G-GAGAAGAAGAAAAACATTGGAGTTGCTCT
*
55443 CAAATCCACAAAAGATGAGAGTGATTCAGATGAAGATGACGATGACGAGAAAATGGCATTGTTTT
128 CAAATCCACAAAAGATGAGAGTGATTCAGATGAAGATGACGATGACGAGAAAATGGCATTGTTTG
55508 CCAAACGGTTCAGAAAAATGATGAGACC
193 CCAAACGGTTCAGAAAAATGATGAGACC
55536 TTAACTCTTG-AGAGCTAATCGGTTCC-CCTCACTCATGAAATGATGCTTGAAGATGAGGTGGAC
1 TTAACTCTTGAAGAGCTAATCGGTTCCTCCTCACTCATGAAATGATGCTTGAAGATGAGGTGGAC
*
55599 CTCGATAAGATTGACGAGACACCAAAGGAGAAGGAGAAGAAGAAAAACATTGGAGTTGCTCTTAA
66 CTCGATAAGATTGACGAGACACCAAAGGAGAAGGAGAAGAAGAAAAACATTGGAGTTGCTCTCAA
*
55664 ATCCACAAAAGATGAGAGTGATTCAGATGAAGATGACGATGACGAGAAAATGACATTGTTTGCCA
131 ATCCACAAAAGATGAGAGTGATTCAGATGAAGATGACGATGACGAGAAAATGGCATTGTTTGCCA
55729 AACGGTTCAGAAAAATGAT
196 AACGGTTCAGAAAAATGAT
55748 CTTACTGAGG
Statistics
Matches: 411, Mismatches: 16, Indels: 14
0.93 0.04 0.03
Matches are distributed among these distances:
218 176 0.43
219 5 0.01
220 204 0.50
221 26 0.06
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (220 bp):
TTAACTCTTGAAGAGCTAATCGGTTCCTCCTCACTCATGAAATGATGCTTGAAGATGAGGTGGAC
CTCGATAAGATTGACGAGACACCAAAGGAGAAGGAGAAGAAGAAAAACATTGGAGTTGCTCTCAA
ATCCACAAAAGATGAGAGTGATTCAGATGAAGATGACGATGACGAGAAAATGGCATTGTTTGCCA
AACGGTTCAGAAAAATGATGAGACC
Found at i:56665 original size:23 final size:23
Alignment explanation
Indices: 56635--56682 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
56625 GGATGCTCAA
56635 GACACATGACCGAGACAAAAGTC
1 GACACATGACCGAGACAAAAGTC
56658 GACACATGACCGAGACAAAAGTC
1 GACACATGACCGAGACAAAAGTC
56681 GA
1 GA
56683 TTCATAGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (23 bp):
GACACATGACCGAGACAAAAGTC
Found at i:59977 original size:23 final size:21
Alignment explanation
Indices: 59932--60057 Score: 171
Period size: 21 Copynumber: 5.9 Consensus size: 21
59922 TTAGTACAGA
* *
59932 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATACCCCC-TGTAG
* * *
59954 GGGAACCAATTCCCCCTTTAAAG
1 GGGAACCGATACCCCCTGT--AG
*
59977 GGGAACCGATTCCCCCTGTAG
1 GGGAACCGATACCCCCTGTAG
59998 GGGAACCGATACCCCCTGTAG
1 GGGAACCGATACCCCCTGTAG
60019 GGGAACCGATACCCCCTGTAG
1 GGGAACCGATACCCCCTGTAG
60040 GGGAACCGATACCCCCTG
1 GGGAACCGATACCCCCTG
60058 AAGGTTCTGG
Statistics
Matches: 94, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
21 62 0.66
22 13 0.14
23 19 0.20
ACGTcount: A:0.25, C:0.33, G:0.26, T:0.17
Consensus pattern (21 bp):
GGGAACCGATACCCCCTGTAG
Done.