Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006220.1 Hibiscus syriacus cultivar Beakdansim tig00014820_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: 128125
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:5239 original size:17 final size:16
Alignment explanation
Indices: 5213--5246 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
5203 TTTCACTAAT
*
5213 AGAGGAAATATTACAA
1 AGAGGAAATAGTACAA
5229 AGAGAGAAATAGTACAA
1 AGAG-GAAATAGTACAA
5246 A
1 A
5247 TAGCCTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.59, C:0.06, G:0.21, T:0.15
Consensus pattern (16 bp):
AGAGGAAATAGTACAA
Found at i:6806 original size:12 final size:12
Alignment explanation
Indices: 6789--6813 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6779 AGGAACATGT
6789 AGTTCCAATTTG
1 AGTTCCAATTTG
6801 AGTTCCAATTTG
1 AGTTCCAATTTG
6813 A
1 A
6814 TCAAAATTGG
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:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (12 bp):
AGTTCCAATTTG
Found at i:21024 original size:28 final size:28
Alignment explanation
Indices: 20975--21031 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
20965 CGTTCTACAA
*
20975 AGGTTATTTCTACATTTGATTTTTTTTC
1 AGGTTATTTCTACATTTGATTTATTTTC
* *
21003 AGGTTATATTCTA-TTTTTATTTATTTTC
1 AGGTTAT-TTCTACATTTGATTTATTTTC
21031 A
1 A
21032 AAAAAAAGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 20 0.80
29 5 0.20
ACGTcount: A:0.21, C:0.09, G:0.09, T:0.61
Consensus pattern (28 bp):
AGGTTATTTCTACATTTGATTTATTTTC
Found at i:21386 original size:2 final size:2
Alignment explanation
Indices: 21381--21411 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
21371 TTTTACATGA
21381 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21412 ATTCATTATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:25600 original size:15 final size:15
Alignment explanation
Indices: 25580--25608 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
25570 GGATCAATAC
25580 ATTTTGCATACATTT
1 ATTTTGCATACATTT
25595 ATTTTGCATACATT
1 ATTTTGCATACATT
25609 CATTATTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.14, G:0.07, T:0.52
Consensus pattern (15 bp):
ATTTTGCATACATTT
Found at i:25620 original size:22 final size:22
Alignment explanation
Indices: 25595--25642 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
25585 GCATACATTT
25595 ATTTTGCATACATTCATTATTC
1 ATTTTGCATACATTCATTATTC
*
25617 ATTTTGCATACATTCATTGTTC
1 ATTTTGCATACATTCATTATTC
25639 ATTT
1 ATTT
25643 CATTATTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.25, C:0.17, G:0.06, T:0.52
Consensus pattern (22 bp):
ATTTTGCATACATTCATTATTC
Found at i:33240 original size:18 final size:18
Alignment explanation
Indices: 33217--33253 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
33207 TCCAAGTTTA
33217 TCTTTTCGAAACTCAATT
1 TCTTTTCGAAACTCAATT
* *
33235 TCTTTTTGAAATTCAATT
1 TCTTTTCGAAACTCAATT
33253 T
1 T
33254 ATTCTTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.27, C:0.16, G:0.05, T:0.51
Consensus pattern (18 bp):
TCTTTTCGAAACTCAATT
Found at i:34057 original size:122 final size:123
Alignment explanation
Indices: 33809--34092 Score: 435
Period size: 122 Copynumber: 2.3 Consensus size: 123
33799 TGAAGAAGAA
* * * * *
33809 GAAGAAGTTCATAATAAGAAAAAAATTATCTGAAGAGGAAGAAGAAGTTCATAATAAGAAGAATT
1 GAAG-AGTTCATAATGAG-AAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATAAGAAGAATC
* *
33874 TGTTCAACCTTTCGCTTGATTCTATCATAAAAGGAGATAGATCAGCATCAACATTGCCAG
64 TGTTCAACCTTTCGCTTGATTCTATCACAAAAGGAGATAGATCAACATCAACATTGCCAG
*
33934 GAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAA-CTG
1 GAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATAAGAAGAATCTG
* * **
33998 TTCAACCTTTCGCTTGATTCTATCACAGAAGGAGATATATCAACATCAACATTTTCAG
66 TTCAACCTTTCGCTTGATTCTATCACAAAAGGAGATAGATCAACATCAACATTGCCAG
34056 GAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGA
1 GAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGA
34093 TTAACATTTT
Statistics
Matches: 147, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
122 91 0.62
123 40 0.27
124 12 0.08
125 4 0.03
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.25
Consensus pattern (123 bp):
GAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATAAGAAGAATCTG
TTCAACCTTTCGCTTGATTCTATCACAAAAGGAGATAGATCAACATCAACATTGCCAG
Found at i:34104 original size:50 final size:52
Alignment explanation
Indices: 34045--34144 Score: 152
Period size: 50 Copynumber: 2.0 Consensus size: 52
34035 TATCAACATC
34045 AACATTTTCAGGAAG-AGTTCATAATGAGAAG-A-ACTCATCTGAAGAGGATT
1 AACATTTTCA-GAAGAAGTTCATAATGAGAAGAACACTCATCTGAAGAGGATT
* *
34095 AACATTTTCAGAGGAAGTTCATAATGAGAAGAACACTTATCTGAAGAGGA
1 AACATTTTCAGAAGAAGTTCATAATGAGAAGAACACTCATCTGAAGAGGA
34145 AAAATAAGTT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
49 3 0.07
50 26 0.58
51 1 0.02
52 15 0.33
ACGTcount: A:0.41, C:0.12, G:0.22, T:0.25
Consensus pattern (52 bp):
AACATTTTCAGAAGAAGTTCATAATGAGAAGAACACTCATCTGAAGAGGATT
Found at i:34433 original size:16 final size:16
Alignment explanation
Indices: 34384--34425 Score: 68
Period size: 16 Copynumber: 2.6 Consensus size: 16
34374 GTTCATAATG
34384 AGAAGAACTCATCTGA
1 AGAAGAACTCATCTGA
34400 AGAAGAA-TCCATCTGA
1 AGAAGAACT-CATCTGA
34416 AGAAGAACTC
1 AGAAGAACTC
34426 GTCCGAAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 1 0.04
16 22 0.92
17 1 0.04
ACGTcount: A:0.45, C:0.19, G:0.19, T:0.17
Consensus pattern (16 bp):
AGAAGAACTCATCTGA
Found at i:42598 original size:31 final size:31
Alignment explanation
Indices: 42562--42620 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
42552 AACTTAAAAG
* *
42562 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
42593 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
42621 CTATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:42720 original size:32 final size:32
Alignment explanation
Indices: 42684--43360 Score: 295
Period size: 32 Copynumber: 21.5 Consensus size: 32
42674 CAATCGATAT
*
42684 TTTAAAATAAATCAATACATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
42716 TTTAAAATAAATCAATCCATACTAA-AAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
42747 TTTAAAATAAATCAAT---T-C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
42769 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
42801 TTTAAAATAAATCAATTCATATTTTAAAATAAATTAA
1 TTTAAAATAAATCAATCCATA--CT--AATAAATT-A
** * * * *
42838 TCCACACTAATAAAT-TAT--TTA-AAATAAATCAA
1 TTTA-A--AATAAATCAATCCATACTAATAAAT-TA
* * ** * * *
42870 TTCATACTAATAAA-CTATTTAAAATGAATCAATTCATA
1 TT--TA-AAATAAATCAATCCATACT-AAT-AAAT--TA
*
42908 TTTTAAAATAAATCAATTCATACTAATAAATTA
1 -TTTAAAATAAATCAATCCATACTAATAAATTA
* *
42941 TTTAAAATAAATCAATCTATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
42971 --T--AATAAATCAATCC--A-T-AT------
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
42989 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
43021 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
43053 TTTAAAATAAATCAATACATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
43085 TTTAAAATAAATCAATTCATACTTTAAAATAAATCAA
1 TTTAAAATAAATCAATCCATAC--T--AATAAAT-TA
* ** **
43122 TTCATACAACTACAAT-AATAAAT-C-AATCCA-TA
1 TT--TA-AAATA-AATCAATCCATACTAATAAATTA
* *
43154 TTTTAAAATAAATTAATTCATACTAATAAATTA
1 -TTTAAAATAAATCAATCCATACTAATAAATTA
43187 TTTAAAATAAATCAATCCATAC-AACTACAA-TA
1 TTTAAAATAAATCAATCCATACTAA-TA-AATTA
* ** * * *
43219 -AT-AAATAAATTCATATTTTAAAATAAATCAATCCATA
1 TTTAAAATAAA-TCA-A-TCCATACT-AATAAAT---TA
* *
43256 TTTTAAAATAAATCAATTCATACTAACAAATTA
1 -TTTAAAATAAATCAATCCATACTAATAAATTA
43289 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
43311 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
43343 TTTAAAAATAAATCAATC
1 TTT-AAAATAAATCAATC
43361 TATATTTTAT
Statistics
Matches: 499, Mismatches: 60, Indels: 171
0.68 0.08 0.23
Matches are distributed among these distances:
20 1 0.00
22 45 0.09
23 3 0.01
24 4 0.01
25 3 0.01
26 17 0.03
27 1 0.00
28 7 0.01
29 3 0.01
30 19 0.04
31 36 0.07
32 217 0.43
33 29 0.06
34 10 0.02
35 5 0.01
36 32 0.06
37 27 0.05
38 3 0.01
39 11 0.02
40 23 0.05
41 3 0.01
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:42727 original size:54 final size:54
Alignment explanation
Indices: 42636--42957 Score: 212
Period size: 54 Copynumber: 5.8 Consensus size: 54
42626 CAACTACAAT
*
42636 AATAAATCAAT-CTATACTAA-AAATTATTTAAAATAAATCAATCGATATTTTAA
1 AATAAATCAATAC-ATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAA
* *
42689 AATAAATCAATACATACTAATAAATTATTTAAAATAAATCAATCCATA-CTAAA
1 AATAAATCAATACATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAA
* * * * ** **
42742 AATTATTTAA-A-ATAAATCAATTCA-TATTTTAAAATAAATCAATCCATACTAATAA
1 AATAAATCAATACAT-ACT-AATAAATTA-TTTAAAATAAATCAATCCATA-TTTTAA
* ** * * ** *
42797 ATTATTTAAAATAAAT-C-AATTCA-TATTTTAAAATAAATTAATCCACACTAATAAATTATTTA
1 AATAAAT-CAATACATACTAATAAATTA-TTTAAAATAAATCAAT---C-C--AT--A-T-TTTA
42859 A
54 A
* * * *
42860 AATAAATCAATTCATACTAATAAACTATTTAAAATGAATCAATTCATATTTTAA
1 AATAAATCAATACATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAA
*
42914 AATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATC
1 AATAAATCAATACATACTAATAAATTATTTAAAATAAATCAATC
42958 TATACAACTA
Statistics
Matches: 212, Mismatches: 35, Indels: 43
0.73 0.12 0.15
Matches are distributed among these distances:
51 2 0.01
52 5 0.02
53 53 0.25
54 97 0.46
55 7 0.03
56 3 0.01
57 2 0.01
58 5 0.02
60 3 0.01
62 7 0.03
63 8 0.04
64 18 0.08
65 2 0.01
ACGTcount: A:0.53, C:0.11, G:0.01, T:0.36
Consensus pattern (54 bp):
AATAAATCAATACATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAA
Found at i:42773 original size:22 final size:22
Alignment explanation
Indices: 42747--42789 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
42737 CTAAAAATTA
*
42747 TTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATCAATCCATAT
42769 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
42790 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:42798 original size:22 final size:22
Alignment explanation
Indices: 42749--42797 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
42739 AAAAATTATT
* **
42749 TAAAATAAATCAATTCATATTT
1 TAAAATAAATCAATCCATATAA
42771 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
42794 TAAA
1 TAAA
42798 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:42913 original size:22 final size:22
Alignment explanation
Indices: 42887--42929 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
42877 TAATAAACTA
*
42887 TTTAAAATGAATCAATTCATAT
1 TTTAAAATAAATCAATTCATAT
42909 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATTCATA
42930 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (22 bp):
TTTAAAATAAATCAATTCATAT
Found at i:42938 original size:22 final size:22
Alignment explanation
Indices: 42889--42937 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
42879 ATAAACTATT
* **
42889 TAAAATGAATCAATTCATATTT
1 TAAAATAAATCAATTCATATAA
42911 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATTCATA-TAA
42934 TAAA
1 TAAA
42938 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.53, C:0.10, G:0.02, T:0.35
Consensus pattern (22 bp):
TAAAATAAATCAATTCATATAA
Found at i:43018 original size:22 final size:23
Alignment explanation
Indices: 42943--43017 Score: 73
Period size: 22 Copynumber: 3.2 Consensus size: 23
42933 ATAAATTATT
42943 TAAAATAAATCAATCTATAC-AA
1 TAAAATAAATCAATCTATACTAA
* **
42965 CTACAATAATAAATCAATCCATA-TTT
1 -T--AA-AATAAATCAATCTATACTAA
42991 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCTATACTAA
43014 TAAA
1 TAAA
43018 TTATTTAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
22 15 0.37
23 8 0.20
25 3 0.07
26 15 0.37
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.31
Consensus pattern (23 bp):
TAAAATAAATCAATCTATACTAA
Found at i:43025 original size:166 final size:163
Alignment explanation
Indices: 42806--43360 Score: 614
Period size: 166 Copynumber: 3.4 Consensus size: 163
42796 AATTATTTAA
* * * *
42806 AATAAATCAATTCATATTTTAAAATAAATTAATCCACACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAAT
*
42871 TCATACTAATAAACTATTTAAAATGAATCAATTCATATTTTAAAATAAATCAATTCATACTAATA
66 CCATACTAATAAA-TATTTAAAAT-AATCAATTCATATTTTAAAATAAATCAATTCA-ACTAATA
42936 AATTATTTAAAATAAATCAATCTATACAACTACAAT
128 AATTATTTAAAATAAATCAATCTATACAACTACAAT
42972 AATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAAT
* * * * * *
43037 CCATACTAATAAATTATTTAAAATAAATCAATACATA--CT--AATAAATTATTTAAAATAAATC
66 CCATACTAATAAA-TATTTAAAAT-AATCAATTCATATTTTAAAATAAATCAATTCAACT-AAT-
*
43098 AATTCATACTTTAAAATAAATCAAT-TCATACAACTACAAT
127 AAAT--TA-TTTAAAATAAATCAATCT-ATACAACTACAAT
*
43138 AATAAATCAATCCATATTTTAAAATAAATTAAT-TCATACTAATAAATTATTTAAAATAAATCAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCT-ATACTAATAAATTATTTAAAATAAATCAA
*
43202 TCCATAC-AACTACAATA-AT-AAAT-A--AATTCATATTTTAAAATAAATCAA-TC--C--AT-
65 TCCATACTAA-TA-AATATTTAAAATAATCAATTCATATTTTAAAATAAATCAATTCAACTAATA
* *
43255 -A-T-TTTAAAATAAATCAATTCATACTAACAAATTATTTAA-
128 AATTATTTAAAATAAATCAA-TC-TA-T-AC-AACTA--CAAT
43294 AATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAAATAAATCAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTT-AAAATAAATCAA
43359 TC
65 TC
43361 TATATTTTAT
Statistics
Matches: 340, Mismatches: 26, Indels: 55
0.81 0.06 0.13
Matches are distributed among these distances:
150 15 0.04
151 1 0.00
152 2 0.01
153 2 0.01
154 2 0.01
155 4 0.01
156 49 0.14
157 17 0.05
158 2 0.01
160 7 0.02
161 2 0.01
162 16 0.05
163 4 0.01
164 13 0.04
165 7 0.02
166 195 0.57
167 2 0.01
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (163 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAAT
CCATACTAATAAATATTTAAAATAATCAATTCATATTTTAAAATAAATCAATTCAACTAATAAAT
TATTTAAAATAAATCAATCTATACAACTACAAT
Found at i:43036 original size:54 final size:53
Alignment explanation
Indices: 42972--43375 Score: 404
Period size: 54 Copynumber: 7.5 Consensus size: 53
42962 CAACTACAAT
42972 AATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAAT-TATACTAATAAATTATTTAA
*
43026 AATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATACATACTAATAAATTATTTAA
1 AATAAATCAAT-C---C--AT--A-T-TTTAAAATAAATCAAT-TATACTAATAAATTATTTAA
* * *
43090 AATAAATCAATTCATACTTTAAAATAAATCAATTCATAC-AACTACA--A--T--
1 AATAAATCAATCCATATTTTAAAATAAATCAATT-ATACTAA-TAAATTATTTAA
*
43138 AATAAATCAATCCATATTTTAAAATAAATTAATTCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATT-ATACTAATAAATTATTTAA
*** * **
43192 AATAAATCAATCCATACAACTACAAT-AAT-AA--ATA--AATTCA-TATTTTAA
1 AATAAATCAATCCATA-TTTTAAAATAAATCAATTATACTAATAAATTA-TTTAA
*
43240 AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAACAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATT-ATACTAATAAATTATTTAA
43294 AATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAA
1 AATAAATCAATCCATATTTTAAAATAAATCAAT-TATACTAATAAATTATTT-AA
* *
43349 AATAAATCAATCTATATTTTATAATAA
1 AATAAATCAATCCATATTTTAAAATAA
43376 TTTATTTTAA
Statistics
Matches: 293, Mismatches: 26, Indels: 61
0.77 0.07 0.16
Matches are distributed among these distances:
47 7 0.02
48 67 0.23
49 4 0.01
50 5 0.02
52 5 0.02
53 4 0.01
54 110 0.38
55 36 0.12
56 1 0.00
58 3 0.01
60 3 0.01
62 1 0.00
63 1 0.00
64 46 0.16
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (53 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATTATACTAATAAATTATTTAA
Found at i:43110 original size:22 final size:22
Alignment explanation
Indices: 43085--43177 Score: 105
Period size: 22 Copynumber: 4.0 Consensus size: 22
43075 TAATAAATTA
43085 TTTAAAATAAATCAATTCATAC
1 TTTAAAATAAATCAATTCATAC
43107 TTTAAAATAAATCAATTCATACAAC
1 TTTAAAATAAATCAATTCAT---AC
** * *
43132 TACAATAATAAATCAATCCATAT
1 TTTAA-AATAAATCAATTCATAC
*
43155 TTTAAAATAAATTAATTCATAC
1 TTTAAAATAAATCAATTCATAC
43177 T
1 T
43178 AATAAATTAT
Statistics
Matches: 58, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
22 35 0.60
23 4 0.07
25 5 0.09
26 14 0.24
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATTCATAC
Found at i:43180 original size:102 final size:98
Alignment explanation
Indices: 43053--43334 Score: 377
Period size: 102 Copynumber: 2.8 Consensus size: 98
43043 TAATAAATTA
* *
43053 TTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAATTCATACTTTAAAATAAA
1 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATACTTTAAAATAAA
43118 TCAATTCATACAACTACAATAATAAATCAATCCATAT
66 TCAATTCAT---ACTACAA-AATAAATCAATCCATAT
* **
43155 TTTAAAATAAATTAATTCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAA
1 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCAT---ACTTTAA-AA
* * **
43220 TAAATAAATTCATATTTTAAAATAAATCAATCCATAT
62 TAAATCAATTCATACTACAAAATAAATCAATCCATAT
* *
43257 TTTAAAATAAATCAATTCATACTAACAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
1 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATACTTTAAAATAAA
43322 TCAA-TCTATACTA
66 TCAATTC-ATACTA
43335 ATAAATTATT
Statistics
Matches: 158, Mismatches: 17, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
97 2 0.01
98 13 0.08
99 4 0.03
102 116 0.73
103 4 0.03
105 5 0.03
106 14 0.09
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (98 bp):
TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATACTTTAAAATAAA
TCAATTCATACTACAAAATAAATCAATCCATAT
Found at i:43246 original size:22 final size:22
Alignment explanation
Indices: 43218--43277 Score: 102
Period size: 22 Copynumber: 2.7 Consensus size: 22
43208 CAACTACAAT
*
43218 AATAAATAAATTCATATTTTAA
1 AATAAATCAATTCATATTTTAA
*
43240 AATAAATCAATCCATATTTTAA
1 AATAAATCAATTCATATTTTAA
43262 AATAAATCAATTCATA
1 AATAAATCAATTCATA
43278 CTAACAAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (22 bp):
AATAAATCAATTCATATTTTAA
Found at i:43286 original size:22 final size:22
Alignment explanation
Indices: 43190--43286 Score: 70
Period size: 22 Copynumber: 4.2 Consensus size: 22
43180 TAAATTATTT
*
43190 AAAATAAATCAATCCATACAACTA
1 AAAATAAATCAATCCAT--ATCTA
* * * *
43214 CAATAATAAATAAATTCATATTTT
1 -AA-AATAAATCAATCCATATCTA
* *
43238 AAAATAAATCAATCCATATTTT
1 AAAATAAATCAATCCATATCTA
*
43260 AAAATAAATCAATTCATA-CTA
1 AAAATAAATCAATCCATATCTA
43281 ACAAAT
1 A-AAAT
43287 TATTTAAAAT
Statistics
Matches: 60, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
21 2 0.03
22 39 0.65
23 2 0.03
24 2 0.03
25 2 0.03
26 13 0.22
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
AAAATAAATCAATCCATATCTA
Found at i:43340 original size:22 final size:22
Alignment explanation
Indices: 43291--43339 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
43281 ACAAATTATT
**
43291 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
43313 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCCATA-TAA
43336 TAAA
1 TAAA
43340 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:43351 original size:33 final size:31
Alignment explanation
Indices: 43308--43445 Score: 133
Period size: 30 Copynumber: 4.4 Consensus size: 31
43298 AATCAATCCA
43308 TATTTTAAAATAAATCAATCTATACTAATAAAT
1 TATTTTAAAATAAAT-AATCTATA-TAATAAAT
* *
43341 TATTTAAAAATAAATCAATCTATATTTTATAATAATT
1 TATTTTAAAATAAAT-AATC--TA---TATAATAAAT
* *
43378 TATTTTAAAATAAATTAT-TTTATAATAAAT
1 TATTTTAAAATAAATAATCTATATAATAAAT
43408 TATTTTAAAATAAATAATCT-TAT--TAAAT
1 TATTTTAAAATAAATAATCTATATAATAAAT
43436 TA-TTTAAAAT
1 TATTTTAAAAT
43446 TATTTTAATA
Statistics
Matches: 92, Mismatches: 7, Indels: 18
0.79 0.06 0.15
Matches are distributed among these distances:
27 8 0.09
28 7 0.08
30 29 0.32
31 1 0.01
33 20 0.22
35 2 0.02
36 2 0.02
37 21 0.23
38 2 0.02
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (31 bp):
TATTTTAAAATAAATAATCTATATAATAAAT
Found at i:43383 original size:15 final size:15
Alignment explanation
Indices: 43363--43422 Score: 93
Period size: 15 Copynumber: 4.0 Consensus size: 15
43353 AATCAATCTA
* *
43363 TATTTTATAATAATT
1 TATTTTAAAATAAAT
43378 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
*
43393 TATTTTATAATAAAT
1 TATTTTAAAATAAAT
43408 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
43423 AATCTTATTA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 41 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTTAAAATAAAT
Found at i:47518 original size:12 final size:13
Alignment explanation
Indices: 47480--47517 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
47470 TTTACTTTTT
*
47480 TATTTAAAAAAAA
1 TATTTTAAAAAAA
47493 TATTTTAAAAAAA
1 TATTTTAAAAAAA
47506 TATTTTAAAAAA
1 TATTTTAAAAAA
47518 TCCCCCAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
TATTTTAAAAAAA
Found at i:52622 original size:2 final size:2
Alignment explanation
Indices: 52615--52658 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
52605 AAATCATTCG
52615 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
52657 AT
1 AT
52659 TTCGAGCTCG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57655 original size:17 final size:17
Alignment explanation
Indices: 57635--57667 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
57625 CTCACTAACC
*
57635 CTTTTATTTTTTGTTCT
1 CTTTTATTTTGTGTTCT
57652 CTTTTATTTTGTGTTC
1 CTTTTATTTTGTGTTC
57668 ATCGTTTGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.12, G:0.09, T:0.73
Consensus pattern (17 bp):
CTTTTATTTTGTGTTCT
Found at i:58321 original size:19 final size:19
Alignment explanation
Indices: 58287--58331 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
58277 ATTTAGACAT
58287 TTTGCA-TTTCTTATTTTC
1 TTTGCATTTTCTTATTTTC
*
58305 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTCTTATTTTC
58324 TTTGCATT
1 TTTGCATT
58332 CACATTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.11, C:0.13, G:0.09, T:0.67
Consensus pattern (19 bp):
TTTGCATTTTCTTATTTTC
Found at i:61881 original size:165 final size:164
Alignment explanation
Indices: 61702--62577 Score: 937
Period size: 165 Copynumber: 5.3 Consensus size: 164
61692 ACCTGCCACC
*
61702 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAG
*
61767 AAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAG
66 AAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAG
* *
61832 CATAACTCAAGGCTAGAAGGGTTATCTGTGACCAA
131 CATAACTTAAGTCTAGAAGGGTTATCTGTGACC-A
61867 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAG
* *
61932 AAGGGCTATCTGCCAAAGACCCCCAAGTTCGATTACACTCAGCTTCGAGGGCACGTCATTTGCAG
66 AAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAG
* **
61997 CATAACTTAAGTCGAGAAGGGTTATCTGCCAACCA
131 CATAACTTAAGTCTAGAAGGGTTATCTG-TGACCA
* * * * *
62032 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAC
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAG
* * *** * * * *
62097 AAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGC-TCAACGGCACATCATTT
66 AAGGGCTATCTG-C--C-AAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTT
* * * *
62161 GCAGCATAGCTTAAGTCGAGAAGAGCTATC--TG-CCA
127 GCAGCATAACTTAAGTCTAGAAGGGTTATCTGTGACCA
** * * * * * ** * * **
62196 AAGACCCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTCACAGCATAACTCAAGTTT
1 AAGA-CCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAGCTTAAGTCG
* ** * ** * * *
62261 AGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGTTCAACTTC-AAGGCATATCATT
64 AGAAGGGCTATCTG---CCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATT
* * ** *
62325 TGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAA
126 TGCAGCATAACTTAAGTCTAGAAGGGTTATCTG-TGACCA
* * *
62365 AAGACCTTTGAGTTCGACTACGCTCA-----ACGGCACATCATTTGCAGTATAGCTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAG
* * * * * * *
62425 AAGGGCTATATGCCAAA-AACCCCAAGTTCGATTACACTCAGCTTCGAGGGCATATCATGTACAA
66 AAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAG
* * *
62489 CATAACTCAAGGCTAGGAGGGTTATCTGTGACCA
131 CATAACTTAAGTCTAGAAGGGTTATCTGTGACCA
* * *
62523 AAGACCTTCAAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAACATAGC
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGC
62578 CTAAAGCAAG
Statistics
Matches: 591, Mismatches: 100, Indels: 42
0.81 0.14 0.06
Matches are distributed among these distances:
158 47 0.08
159 42 0.07
162 35 0.06
163 20 0.03
164 7 0.01
165 304 0.51
166 47 0.08
168 60 0.10
169 29 0.05
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (164 bp):
AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAG
AAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAG
CATAACTTAAGTCTAGAAGGGTTATCTGTGACCA
Found at i:61918 original size:84 final size:83
Alignment explanation
Indices: 61702--62567 Score: 771
Period size: 84 Copynumber: 10.5 Consensus size: 83
61692 ACCTGCCACC
* *
61702 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAG
*
61767 AAGGGCTATC--TG-CCA
66 AAGGGTTATCTGTGACCA
** * * * * * * * *
61782 AAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTA
1 AAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTCGA
61847 GAAGGGTTATCTGTGACCAA
65 GAAGGGTTATCTGTGACC-A
*
61867 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAG
*
61932 AAGGGCTATC--TG-CCA
66 AAGGGTTATCTGTGACCA
** * * * * * *
61947 AAGACCCCCAAGTTCGATTACACTCAGCTTCGAGGGCACGTCATTTGCAGCATAACTTAAGTCGA
1 AAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTCGA
**
62012 GAAGGGTTATCTGCCAACCA
65 GAAGGGTTATCTG-TGACCA
* * * *
62032 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAC
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAG
* ** *
62097 AAGGGTTGTCTGCCAACAA
66 AAGGGTTATCTG-TGACCA
* *
62116 AAGACCTTTGAGTTCGACTACGCTCAGCT-CAACGGCACATCATTTGCAGCATAGCTTAAGTCGA
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAACTTAAGTCGA
* *
62180 GAAGAGCTATC--TG-CCA
65 GAAGGGTTATCTGTGACCA
** * * * * * ** * **
62196 AAGACCCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTCACAGCATAACTCAAGTTT
1 AAGA-CCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTCG
*
62261 AGAAGGGTTATCTGTCACCA
64 AGAAGGGTTATCTGTGACCA
* * * * * *
62281 AAGACCTTCGAGTTCGACTACGTTCAACTTCAAGGCATATCATTTGCAGCACAACTTAAGTCTAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAG
* ** *
62346 AAGGGTTGTCTGCCAACAA
66 AAGGGTTATCTG-TGACCA
* * * *
62365 AAGACCTTTGAGTTCGACTACGCTCA-----ACGGCACATCATTTGCAGTATAGCTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAG
* *
62425 AAGGGCTA--TATG-CCA
66 AAGGGTTATCTGTGACCA
* * * * * * * * * * * * * *
62440 AAAACC-CCAAGTTCGATTACACTCAGCTTCGAGGGCATATCATGTACAACATAACTCAAGGCTA
1 AAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTCGA
*
62504 GGAGGGTTATCTGTGACCA
65 GAAGGGTTATCTGTGACCA
*
62523 AAGACCTTCAAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
62568 ACAACATAGC
Statistics
Matches: 619, Mismatches: 139, Indels: 53
0.76 0.17 0.07
Matches are distributed among these distances:
74 14 0.02
75 7 0.01
77 1 0.00
79 34 0.05
80 84 0.14
81 101 0.16
82 39 0.06
83 67 0.11
84 214 0.35
85 58 0.09
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.24
Consensus pattern (83 bp):
AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAG
AAGGGTTATCTGTGACCA
Found at i:62135 original size:249 final size:246
Alignment explanation
Indices: 61661--62567 Score: 1137
Period size: 249 Copynumber: 3.7 Consensus size: 246
61651 TAAACAAACT
* * * * * ** * * *
61661 ATTTGCAGCTTAGCTCAAGGCCAGAAGGGCTACCTGCCACCAAGACCTTCGAGTTCGACTACGCT
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCA--AAGACCCCCAAGTTCGATTACACT
* * * * * * *
61726 CAGC-TCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTG--CCAAAGACC
64 CAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGTCGAGAAGGGTTATCTGCACCAAAGACC
** * * * * * * * *
61788 CCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGG
129 TTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCACAACTTAAGTCTAGAAGGG
* ** * *
61853 TTATCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
193 TTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCT-CAAGGCACATC
61908 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCAAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCAAGTTCGATTACACTCA
* * *
61973 GCTTCGAGGGCACGTCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACC
66 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGTCGAGAAGGGTTATCTG-C-ACCAAAGACC
* *
62038 TTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTACAAGGGT
129 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCACAACTTAAGTCTAGAAGGGT
62103 TGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATC
194 TGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAA-GGCACATC
* *
62157 ATTTGCAGCATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGACCCCCCGAGTTCGATTACACTC
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA-CCCCCAAGTTCGATTACACTC
* * **
62222 AGCTTCGAGGGCATATCATTCACAGCATAACTCAAGTTTAGAAGGGTTATCTGTCACCAAAGACC
65 AGCTTCGAGGGCACATCATTTACAGCATAACTCAAGTCGAGAAGGGTTATCTG-CACCAAAGACC
* * * *
62287 TTCGAGTTCGACTACGTTCAACTTCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGT
129 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCACAACTTAAGTCTAGAAGGGT
*
62352 TGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCA----ACGGCACATC
194 TGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAAGGCACATC
* * *
62401 ATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATATGCCAAA-AACCCCAAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCAAGTTCGATTACACTCA
* * * * * * *
62465 GCTTCGAGGGCATATCATGTACAACATAACTCAAGGCTAGGAGGGTTATCTGTGACCAAAGACCT
66 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGTCGAGAAGGGTTATCTG-CACCAAAGACCT
*
62530 TCAAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
130 TCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
62568 ACAACATAGC
Statistics
Matches: 588, Mismatches: 65, Indels: 19
0.88 0.10 0.03
Matches are distributed among these distances:
242 111 0.19
243 1 0.00
244 46 0.08
245 24 0.04
246 43 0.07
247 34 0.06
248 3 0.01
249 232 0.39
250 94 0.16
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.23
Consensus pattern (246 bp):
ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCAAGTTCGATTACACTCA
GCTTCGAGGGCACATCATTTACAGCATAACTCAAGTCGAGAAGGGTTATCTGCACCAAAGACCTT
CGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTG
TCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAAGGCACATC
Found at i:64677 original size:12 final size:11
Alignment explanation
Indices: 64641--64701 Score: 50
Period size: 12 Copynumber: 5.2 Consensus size: 11
64631 GAATCTAACC
*
64641 TTTTGTTATTA
1 TTTTTTTATTA
*
64652 TTTTTTTTTATA
1 TTTTTTTAT-TA
64664 TTTTTTTATCTA
1 TTTTTTTAT-TA
64676 TTTTCTTTAATTA
1 TTTT-TTT-ATTA
* *
64689 TATTATTATTA
1 TTTTTTTATTA
64700 TT
1 TT
64702 ATTATACTAA
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
11 12 0.30
12 18 0.45
13 8 0.20
14 2 0.05
ACGTcount: A:0.21, C:0.03, G:0.02, T:0.74
Consensus pattern (11 bp):
TTTTTTTATTA
Found at i:64704 original size:27 final size:23
Alignment explanation
Indices: 64641--64704 Score: 65
Period size: 27 Copynumber: 2.6 Consensus size: 23
64631 GAATCTAACC
*
64641 TTTTGTTATTATTTTTTTTTATA
1 TTTTATTATTATTTTTTTTTATA
*
64664 TTTTTTTATCTATTTTCTTTAATTATA
1 TTTTATTAT-TATTTT-TTT--TTATA
64691 TTATTATTATTATT
1 TT-TTATTATTATT
64705 ATACTAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
23 8 0.24
24 6 0.18
25 3 0.09
27 11 0.32
28 6 0.18
ACGTcount: A:0.22, C:0.03, G:0.02, T:0.73
Consensus pattern (23 bp):
TTTTATTATTATTTTTTTTTATA
Found at i:86443 original size:17 final size:16
Alignment explanation
Indices: 86421--86454 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
86411 TAAAAACAGT
86421 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
86438 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
86454 A
1 A
86455 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:86973 original size:24 final size:24
Alignment explanation
Indices: 86929--86975 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
86919 ATAAAGAACC
*
86929 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
86953 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
86976 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:91915 original size:17 final size:16
Alignment explanation
Indices: 91893--91926 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
91883 TAAAAACAGT
91893 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
91910 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
91926 A
1 A
91927 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:92445 original size:24 final size:24
Alignment explanation
Indices: 92401--92447 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
92391 ATAAAGAACC
*
92401 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
92425 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
92448 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:95764 original size:19 final size:20
Alignment explanation
Indices: 95742--95785 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
95732 GAGAAAAGGT
95742 AAAAGTTAA-AATGAAAGAG
1 AAAAGTTAATAATGAAAGAG
* *
95761 AAAAATTAATAATGAAAGAT
1 AAAAGTTAATAATGAAAGAG
95781 AAAAG
1 AAAAG
95786 AAAAAGTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.18
Consensus pattern (20 bp):
AAAAGTTAATAATGAAAGAG
Found at i:100630 original size:19 final size:19
Alignment explanation
Indices: 100603--100644 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
100593 AAAACCGAAA
* *
100603 TCGGTTTTTTTGGTTCGGT
1 TCGGGTTTTTCGGTTCGGT
100622 TCGGGTTTTTCGGTTCGGT
1 TCGGGTTTTTCGGTTCGGT
100641 TCGG
1 TCGG
100645 TTCGGTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.00, C:0.14, G:0.36, T:0.50
Consensus pattern (19 bp):
TCGGGTTTTTCGGTTCGGT
Found at i:100655 original size:23 final size:24
Alignment explanation
Indices: 100614--100659 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 24
100604 CGGTTTTTTT
100614 GGTTCGGTTCGGGTTTTTCGGTTC
1 GGTTCGGTTCGGGTTTTTCGGTTC
100638 GGTTCGGTTC-GGTTTTTCGGTT
1 GGTTCGGTTCGGGTTTTTCGGTT
100660 TTTCAATGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.00, C:0.15, G:0.37, T:0.48
Consensus pattern (24 bp):
GGTTCGGTTCGGGTTTTTCGGTTC
Found at i:103076 original size:24 final size:24
Alignment explanation
Indices: 103032--103078 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
103022 ATAAAGAACC
*
103032 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
103056 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
103079 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:114542 original size:20 final size:20
Alignment explanation
Indices: 114517--114563 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
114507 TTTTAAAGCC
*
114517 CATTTAGAA-TCATGTAGATG
1 CATTTAGAAGT-ATGTAGAAG
*
114537 CATTTAGAAGTATTTAGAAG
1 CATTTAGAAGTATGTAGAAG
114557 CATTTAG
1 CATTTAG
114564 TTGCATGTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (20 bp):
CATTTAGAAGTATGTAGAAG
Done.