Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008814.1 Hibiscus syriacus cultivar Beakdansim tig00111976_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: 1021170
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 5
Found at i:964641 original size:59 final size:59
Alignment explanation
Indices: 964547--964659 Score: 163
Period size: 59 Copynumber: 1.9 Consensus size: 59
964537 ACTGTCCACT
* *
964547 GGAGATGTTTATCCCTCGAGTGAGGCGACACTGATTCGAAATGTAATGAATCGAGCAAA
1 GGAGATGTTGATCCCTCAAGTGAGGCGACACTGATTCGAAATGTAATGAATCGAGCAAA
* ** **
964606 GGAGATGTTGATCCCTCAAGTGAGGCGTCGTTGATTCGAAATGTTGTGAATCGA
1 GGAGATGTTGATCCCTCAAGTGAGGCGACACTGATTCGAAATGTAATGAATCGA
964660 TCCAAGGTTA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 47 1.00
ACGTcount: A:0.28, C:0.16, G:0.29, T:0.27
Consensus pattern (59 bp):
GGAGATGTTGATCCCTCAAGTGAGGCGACACTGATTCGAAATGTAATGAATCGAGCAAA
Found at i:964761 original size:59 final size:59
Alignment explanation
Indices: 964700--965018 Score: 379
Period size: 59 Copynumber: 5.4 Consensus size: 59
964690 TCTCTACTGG
** * *
964700 AAATGTTGGTCCCTCATGTGAGGCGTTGCTGATTCGAAGTGTTGTGAATCGAGCAAAGG
1 AAATGTTAATCCCTCAAGTGAGGCGTTGCTGATTCGAAGTGTTGTGAATCGAGCAAAGA
** * * * *
964759 AAATGTCGATCCCTCAAGTGAGGCGTTGCTAATTCAAAGTGTTGTGAATCGAGAAAATA
1 AAATGTTAATCCCTCAAGTGAGGCGTTGCTGATTCGAAGTGTTGTGAATCGAGCAAAGA
* * * * * *
964818 AAATGTTGATCCCTCAAGTGAGGCATTGTTGATTCGAAGTATTTTGAATCGAGCACAGA
1 AAATGTTAATCCCTCAAGTGAGGCGTTGCTGATTCGAAGTGTTGTGAATCGAGCAAAGA
* * * * *
964877 AAATGTTAATCCATCAAGTGACGCGTTGCTGATTCGAAGTATTATGAATCGAGCATAGA
1 AAATGTTAATCCCTCAAGTGAGGCGTTGCTGATTCGAAGTGTTGTGAATCGAGCAAAGA
** * * * *
964936 AAATGTTAATCCCTCAAGTGAGGATTTGATGATTTGAAATGTTGAGAATCGAGCAAATG-
1 AAATGTTAATCCCTCAAGTGAGGCGTTGCTGATTCGAAGTGTTGTGAATCGAGCAAA-GA
964995 AAATGTTAATCCCTCAAGTGAGGC
1 AAATGTTAATCCCTCAAGTGAGGC
965019 TTAGTTTTTT
Statistics
Matches: 222, Mismatches: 37, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
59 221 1.00
60 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.29
Consensus pattern (59 bp):
AAATGTTAATCCCTCAAGTGAGGCGTTGCTGATTCGAAGTGTTGTGAATCGAGCAAAGA
Found at i:965132 original size:36 final size:36
Alignment explanation
Indices: 965028--965998 Score: 441
Period size: 38 Copynumber: 26.1 Consensus size: 36
965018 CTTAGTTTTT
*
965028 TTTAAGAAAAATAATCTCAAGTGAGATAAATCTTCTG
1 TTTAAGAAAAACAATCTCAAGTGAGATAAATCTTC-G
* ** * *
965065 TTTCGAGTGAAACTATCTCAAGCGAGATAAATCTT-G
1 TTT-AAGAAAAACAATCTCAAGTGAGATAAATCTTCG
* *
965101 CTTTAAGAAAAACAATCTCAAGTGCGCTAAATCTTCTG
1 -TTTAAGAAAAACAATCTCAAGTGAGATAAATCTTC-G
** *
965139 TTTCAAGTGAAACTAA-CTCAAGCGAGATAAAATCTTCTG
1 TTT-AAGAAAAAC-AATCTCAAGTGAGAT-AAATCTTC-G
* ** * *
965178 TTTCGAGTGAAACTATCTCAAGAT-AGATGAATCTT-G
1 TTT-AAGAAAAACAATCTCAAG-TGAGATAAATCTTCG
*
965214 TTTTAAGAAAAACAATCTCAAGTTAGATAAATCTTCTG
1 -TTTAAGAAAAACAATCTCAAGTGAGATAAATCTTC-G
* ** * * *
965252 TTTCGAGTGAAACTACCTCAAGCGAGATAAAATCTTCTG
1 TTT-AAGAAAAACAATCTCAAGTGAGAT-AAATCTTC-G
** * * * **
965291 TTCGAGTAAAACTATCTCAAGCGAGACGAATC-TCG
1 TTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCG
965326 TTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTG
1 -TTTAAGAAAAACAATCTCAAGTGAGATAAATCTTC-G
* ** * *
965364 TTTCGAGTTAAACTATCTCAAATGAGATAAAATCTTCTG
1 TTT-AAGAAAAACAATCTCAAGTGAGAT-AAATCTTC-G
* ** * *
965403 TTTCGAGTGAAACTATCTCAAGTGAGATGAATCTT-G
1 TTT-AAGAAAAACAATCTCAAGTGAGATAAATCTTCG
965439 TTTTAAGAAAAA-AATCTCAAGTGAGATAAATCTTCTG
1 -TTTAAGAAAAACAATCTCAAGTGAGATAAATCTTC-G
** * * ** * *
965476 TTTCAAGTGAAACTATCTTAAACGAGATGAATC-TAG
1 TTT-AAGAAAAACAATCTCAAGTGAGATAAATCTTCG
*
965512 TTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTC
1 -TTTAAGAAAAACAATCTCAAGTGAGATAAATCTTC-G
* ** * * * * *
965550 TTTCGAGTGAAACTATCTTAAGCGCGATGAATCTT-G
1 TTT-AAGAAAAACAATCTCAAGTGAGATAAATCTTCG
* *
965586 TTTTAAGAAAATCAATCTCAAGTGAGATAAATCTATTG
1 -TTTAAGAAAAACAATCTCAAGTGAGATAAATCT-TCG
* ** * * * *
965624 TTTCGAGTGAAACTATCTCAAGCGATATGAATCTT-G
1 TTT-AAGAAAAACAATCTCAAGTGAGATAAATCTTCG
* * *
965660 CTTTAAGAAAAACAATTTTAAGTGAGATAAATCATCTG
1 -TTTAAGAAAAACAATCTCAAGTGAGATAAATCTTC-G
* ** * * * * *
965698 TTTCGAGTGAGACTATCTCAAGCGAGATGAAT-TTTG
1 TTT-AAGAAAAACAATCTCAAGTGAGATAAATCTTCG
* * *
965734 TTTTAAGACAAACAATATCAAGTGAGATAAATCATCTG
1 -TTTAAGAAAAACAATCTCAAGTGAGATAAATCTTC-G
* ** * * *
965772 TTTTGAGTGAAACTATCTCAAGCGAGATGAATCTT-G
1 -TTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCG
** *
965808 TTTTAAGAAAAACAATCTTGAGTGAAATGAAATGTCTT-G
1 -TTTAAGAAAAACAATCTCAAGTGAGAT-AAA--TCTTCG
* * * *
965847 TTTCGAGTAAAAATC-GTCTCAAGTTAGACAAAGT-TT-G
1 TTT-AAG-AAAAA-CAATCTCAAGTGAGATAAA-TCTTCG
* * *
965884 TTTAAGAAAAA-AATCTCAATTTAGATAAATCTTTTG
1 TTTAAGAAAAACAATCTCAAGTGAGATAAATC-TTCG
* ** *
965920 TTTCGAGTGAAACTATCTCAAGCT-AGATAAATCTT-G
1 TTT-AAGAAAAACAATCTCAAG-TGAGATAAATCTTCG
* * *
965956 TTTTAAGAAAAAGAATCTCAAGTTAGATAAGTCTTCG
1 -TTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCG
965993 TATTAA
1 T-TTAA
965999 ATTAGATTAT
Statistics
Matches: 705, Mismatches: 172, Indels: 114
0.71 0.17 0.12
Matches are distributed among these distances:
33 1 0.00
34 14 0.02
35 30 0.04
36 225 0.32
37 84 0.12
38 244 0.35
39 93 0.13
40 13 0.02
41 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.32
Consensus pattern (36 bp):
TTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCG
Found at i:965132 original size:74 final size:74
Alignment explanation
Indices: 965028--965478 Score: 371
Period size: 74 Copynumber: 6.0 Consensus size: 74
965018 CTTAGTTTTT
* *
965028 TTTAAGAAAAATAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGAT
1 TTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTAAAACTATCTCAAGCGAGAT
965093 AAATCTT-G
66 AAATCTTCG
* * * * *
965101 CTTTAAGAAAAACAATCTCAAGTGCGCTAAATCTTCTGTTTCAAGTGAAACTAACTCAAGCGAGA
1 -TTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTAAAACTATCTCAAGCGAGA
965166 TAAAATCTTCTG
65 T-AAATCTTC-G
* ** * * ** * * **
965178 TTTCGAGTGAAACTATCTCAAGAT-AGATGAATC-T-TGTTTTAAGAAAAACAATCTCAAGTTAG
1 TTT-AAGAAAAACAATCTCAAG-TGAGATAAATCTTCTGTTTCGAGTAAAACTATCTCAAGCGAG
965240 ATAAATCTTCTG
64 ATAAATCTTC-G
* ** * * *
965252 TTTCGAGTGAAACTACCTCAAGCGAGATAAAATCTTCTG-TTCGAGTAAAACTATCTCAAGCGAG
1 TTT-AAGAAAAACAATCTCAAGTGAGAT-AAATCTTCTGTTTCGAGTAAAACTATCTCAAGCGAG
**
965316 ACGAATC-TCG
64 ATAAATCTTCG
* **
965326 TTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTTAAACTATCTCAAATGAGA
1 -TTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTAAAACTATCTCAAGCGAGA
965391 TAAAATCTTCTG
65 T-AAATCTTC-G
* ** * * ** ** *
965403 TTTCGAGTGAAACTATCTCAAGTGAGATGAATC-T-TGTTTTAAG-AAAAAAATCTCAAGTGAGA
1 TTT-AAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTAAAACTATCTCAAGCGAGA
965465 TAAATCTTCTG
65 TAAATCTTC-G
965476 TTT
1 TTT
965479 CAAGTGAAAC
Statistics
Matches: 310, Mismatches: 52, Indels: 31
0.79 0.13 0.08
Matches are distributed among these distances:
73 23 0.07
74 153 0.49
75 50 0.16
76 35 0.11
77 48 0.15
78 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (74 bp):
TTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTAAAACTATCTCAAGCGAGAT
AAATCTTCG
Found at i:965354 original size:112 final size:112
Alignment explanation
Indices: 965041--965954 Score: 825
Period size: 112 Copynumber: 8.2 Consensus size: 112
965031 AAGAAAAATA
* * *
965041 ATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAATCTTGCTTTA
1 ATCTCAAGCGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTA
* *
965106 AGAAAAACAATCTCAAGTGCGCTAAATCTTCTGTTTCAAGTGAAACT
66 AGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCAAGTGAAACT
* **
965153 AACTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGATAGATGAATCTTGTTTT
1 ATCTCAAGCGAGAT-AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTT
* *
965218 AAGAAAAACAATCTCAAGTTAGATAAATCTTCTGTTTCGAGTGAAACT
65 AAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCAAGTGAAACT
* * * *
965266 ACCTCAAGCGAGATAAAATCTTCTG-TTCGAGTAAAACTATCTCAAGCGAGACGAATCTCGTTTT
1 ATCTCAAGCGAGAT-AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTT
* *
965330 AAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTTAAACT
65 AAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCAAGTGAAACT
** *
965378 ATCTCAAATGAGATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGTGAGATGAATCTTGTTTT
1 ATCTCAAGCGAGAT-AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTT
965443 AAGAAAAA-AATCTCAAGTGAGATAAATCTTCTGTTTCAAGTGAAACT
65 AAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCAAGTGAAACT
* * * * ** ** * * * *
965490 ATCTTAAACGAGATGAATC-T-AGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTCTTT
1 ATCTCAAGCGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGT-TTT
* ** * * * * * * * *
965553 CGAGTGAAACTATCTTAAGCGCGATGAATC-T-TGTTTTAAG-AAAATCA
65 -AAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCAAGTGAAA-CT
* * *
965600 ATCTCAAGTGAGATAAATCTAT-TGTTTCGAGTGAAACTATCTCAAGCGATATGAATCTTGCTTT
1 ATCTCAAGCGAGATAAATCT-TCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTT
* * * * *
965664 AAGAAAAACAATTTTAAGTGAGATAAATCATCTGTTTCGAGTGAGACT
65 AAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCAAGTGAAACT
* ** ** * * * *
965712 ATCTCAAGCGAGATGAAT-TT-TGTTTTAAGACAAACAATATCAAGTGAGATAAATCATCTGTTT
1 ATCTCAAGCGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATC-T-TGTTT
* ** * * * * ** *
965775 TGAGTGAAACTATCTCAAGCGAGATGAATC-T-TGTTTTAAGAAAAACA
64 TAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCAAGTGAAACT
** * * * * * * ** **
965822 ATCTTGAGTGAAATGAAAT-GTCTTGTTTCGAGTAAAAATCGTCTCAAGTTAGACAAAGT-TTG-
1 ATCTCAAGCGAGAT-AAATCTTC-TGTTTCGAGTGAAACT-ATCTCAAGCGAGATGAA-TCTTGT
* * * *
965884 TTTAAGAAAAA-AATCTCAATTTAGATAAATCTTTTGTTTCGAGTGAAACT
62 TTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCAAGTGAAACT
*
965934 ATCTCAAGCTAGATAAATCTT
1 ATCTCAAGCGAGATAAATCTT
965955 GTTTTAAGAA
Statistics
Matches: 643, Mismatches: 138, Indels: 42
0.78 0.17 0.05
Matches are distributed among these distances:
109 34 0.05
110 111 0.17
111 34 0.05
112 280 0.44
113 170 0.26
114 13 0.02
115 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (112 bp):
ATCTCAAGCGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTA
AGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCAAGTGAAACT
Found at i:965541 original size:74 final size:74
Alignment explanation
Indices: 965155--965991 Score: 925
Period size: 74 Copynumber: 11.3 Consensus size: 74
965145 GTGAAACTAA
* **
965155 CTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGATAGATGAATCTTGTTTTAA
1 CTCAAGTGAGAT-AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAA
965220 GAAAAACAAT
65 GAAAAACAAT
* * * * **
965230 CTCAAGTTAGATAAATCTTCTGTTTCGAGTGAAACTACCTCAAGCGAGATAAAATCTTCTGTTCG
1 CTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGAT-GAATCTTGT-TTTA
* *
965295 AGTAAAACTAT
64 AGAAAAACAAT
* ** ** ** * * * **
965306 CTCAAGCGAGACGAATC-TC-GTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCG
1 CTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATC-T-TGTTTTA
** *
965369 AGTTAAACTAT
64 AGAAAAACAAT
* *
965380 CTCAAATGAGATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGTGAGATGAATCTTGTTTTAA
1 CTCAAGTGAGAT-AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAA
965445 GAAAAA-AAT
65 GAAAAACAAT
* * * *
965454 CTCAAGTGAGATAAATCTTCTGTTTCAAGTGAAACTATCTTAAACGAGATGAATCTAGTTTTAAG
1 CTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAG
965519 AAAAACAAT
66 AAAAACAAT
* * *
965528 CTCAAGTGAGATAAATCTTCTCTTTCGAGTGAAACTATCTTAAGCGCGATGAATCTTGTTTTAAG
1 CTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAG
*
965593 AAAATCAAT
66 AAAAACAAT
* *
965602 CTCAAGTGAGATAAATCTAT-TGTTTCGAGTGAAACTATCTCAAGCGATATGAATCTTGCTTTAA
1 CTCAAGTGAGATAAATCT-TCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAA
965666 GAAAAACAAT
65 GAAAAACAAT
* * * * *
965676 TTTAAGTGAGATAAATCATCTGTTTCGAGTGAGACTATCTCAAGCGAGATGAATTTTGTTTTAAG
1 CTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAG
*
965741 ACAAACAAT
66 AAAAACAAT
* * *
965750 ATCAAGTGAGATAAATCATCTGTTTTGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAG
1 CTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAG
965815 AAAAACAAT
66 AAAAACAAT
** * * * * * ** **
965824 CTTGAGTGAAATGAAAT-GTCTTGTTTCGAGTAAAAATCGTCTCAAGTTAGACAAAGT-TTG-TT
1 CTCAAGTGAGAT-AAATCTTC-TGTTTCGAGTGAAACT-ATCTCAAGCGAGATGAA-TCTTGTTT
965886 TAAGAAAAA-AAT
62 TAAGAAAAACAAT
* * * * *
965898 CTCAATTTAGATAAATCTTTTGTTTCGAGTGAAACTATCTCAAGCTAGATAAATCTTGTTTTAAG
1 CTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAG
*
965963 AAAAAGAAT
66 AAAAACAAT
* *
965972 CTCAAGTTAGATAAGTCTTC
1 CTCAAGTGAGATAAATCTTC
965992 GTATTAAATT
Statistics
Matches: 645, Mismatches: 99, Indels: 37
0.83 0.13 0.05
Matches are distributed among these distances:
71 1 0.00
72 17 0.03
73 88 0.14
74 404 0.63
75 64 0.10
76 42 0.07
77 29 0.04
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.32
Consensus pattern (74 bp):
CTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAG
AAAAACAAT
Found at i:971204 original size:26 final size:26
Alignment explanation
Indices: 971166--971245 Score: 133
Period size: 26 Copynumber: 3.1 Consensus size: 26
971156 AAATATGAGG
*
971166 TCTCTAGATTCTCCTTGCTTCTTTCT
1 TCTCTATATTCTCCTTGCTTCTTTCT
* *
971192 TTTCTATATTCTCCTTGTTTCTTTCT
1 TCTCTATATTCTCCTTGCTTCTTTCT
971218 TCTCTATATTCTCCTTGCTTCTTTCT
1 TCTCTATATTCTCCTTGCTTCTTTCT
971244 TC
1 TC
971246 CCCCCAAGCT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 49 1.00
ACGTcount: A:0.07, C:0.29, G:0.05, T:0.59
Consensus pattern (26 bp):
TCTCTATATTCTCCTTGCTTCTTTCT
Found at i:978657 original size:2 final size:2
Alignment explanation
Indices: 978650--978687 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
978640 TTATAATCAT
978650 TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
978688 TAAGAACTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:978687 original size:21 final size:21
Alignment explanation
Indices: 978650--978689 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
978640 TTATAATCAT
978650 TATATATATATATATATTATA
1 TATATATATATATATATTATA
978671 TATATATATATATATATTA
1 TATATATATATATATATTA
978690 AGAACTTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TATATATATATATATATTATA
Found at i:979490 original size:44 final size:45
Alignment explanation
Indices: 979360--979513 Score: 249
Period size: 45 Copynumber: 3.4 Consensus size: 45
979350 TAAGAATACA
979360 CCATATGCATTATTATTTTGGCAT-ACTTTCATGCCGGTAATGCAC
1 CCATATGCATTATTATTTTGGCATCA-TTTCATGCCGGTAATGCAC
*
979405 CCATATGCATTATTATTTTGGCATCCTTTCATGCCGGTAATGCAC
1 CCATATGCATTATTATTTTGGCATCATTTCATGCCGGTAATGCAC
* *
979450 CCATATGCATTATTA-TTTGGCATCATTTCATACCGATAATGCAC
1 CCATATGCATTATTATTTTGGCATCATTTCATGCCGGTAATGCAC
*
979494 CCATATCCATTATTATTTTG
1 CCATATGCATTATTATTTTG
979514 TTCATTCATT
Statistics
Matches: 102, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
44 40 0.39
45 62 0.61
ACGTcount: A:0.25, C:0.23, G:0.13, T:0.39
Consensus pattern (45 bp):
CCATATGCATTATTATTTTGGCATCATTTCATGCCGGTAATGCAC
Found at i:979935 original size:20 final size:21
Alignment explanation
Indices: 979910--979955 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
979900 CTGGCTCTTC
979910 GGTATCGATAC-CCCTACCAT
1 GGTATCGATACACCCTACCAT
*
979930 GGTATCGATACTACCCTACTAT
1 GGTATCGATAC-ACCCTACCAT
979952 GGTA
1 GGTA
979956 CTAACCCTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 11 0.48
22 12 0.52
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.28
Consensus pattern (21 bp):
GGTATCGATACACCCTACCAT
Found at i:980046 original size:19 final size:20
Alignment explanation
Indices: 980004--980070 Score: 93
Period size: 20 Copynumber: 3.4 Consensus size: 20
979994 ATTTGAAATG
980004 ATCGATACCTTCCCCTAGGT
1 ATCGATACCTTCCCCTAGGT
980024 ATCGATACCTTCCCCTA-GT
1 ATCGATACCTTCCCCTAGGT
* *
980043 ATCGATA-CTCCCCCTTCGGT
1 ATCGATACCTTCCCC-TAGGT
980063 ATCGATAC
1 ATCGATAC
980071 TGATTAAATC
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
18 6 0.14
19 10 0.24
20 26 0.62
ACGTcount: A:0.21, C:0.36, G:0.13, T:0.30
Consensus pattern (20 bp):
ATCGATACCTTCCCCTAGGT
Found at i:981757 original size:181 final size:181
Alignment explanation
Indices: 981453--981788 Score: 600
Period size: 181 Copynumber: 1.9 Consensus size: 181
981443 TTGGAGTCAT
* * * *
981453 CAACAGATGTATACGGCCTATAAATCCAACTGATCCCTAGTGCTTTCACATGTTAGTATTCCCTA
1 CAACAGATATATACCGCCTATAAATCCAACTGATCCCGAGTACTTTCACATGTTAGTATTCCCTA
*
981518 AAAAGAACAACGCCTTTGATTGAGAATTTTAGGATGATTTGAAAACTGTGTTATCTTTCACATTC
66 AAAAGAACAACGCCTTTGATTGAGAATTTTAGGATAATTTGAAAACTGTGTTATCTTTCACATTC
*
981583 CCTCTGGAAAGATCAATTATGATTTATCACTTTAGAGGACTTACATTATCA
131 CCTCTGAAAAGATCAATTATGATTTATCACTTTAGAGGACTTACATTATCA
*
981634 CAACAGATATATACCGCCTATAAATCCAACTGATCCCGAGTACTTTCACATGTTAGTATTCCTTA
1 CAACAGATATATACCGCCTATAAATCCAACTGATCCCGAGTACTTTCACATGTTAGTATTCCCTA
*
981699 AAAAGAACAACGCCTTTGATTGAGAATTTTAGGATAATTTGAAAACTGTGTTATCTTTCACATTG
66 AAAAGAACAACGCCTTTGATTGAGAATTTTAGGATAATTTGAAAACTGTGTTATCTTTCACATTC
981764 CCTCTGAAAAGATCAATTATGATTT
131 CCTCTGAAAAGATCAATTATGATTT
981789 CTCATAGGAG
Statistics
Matches: 147, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
181 147 1.00
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (181 bp):
CAACAGATATATACCGCCTATAAATCCAACTGATCCCGAGTACTTTCACATGTTAGTATTCCCTA
AAAAGAACAACGCCTTTGATTGAGAATTTTAGGATAATTTGAAAACTGTGTTATCTTTCACATTC
CCTCTGAAAAGATCAATTATGATTTATCACTTTAGAGGACTTACATTATCA
Found at i:984632 original size:20 final size:18
Alignment explanation
Indices: 984596--984642 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 18
984586 GAAAGAAAAC
984596 AAAAAAAGAAAAAATTCA
1 AAAAAAAGAAAAAATTCA
984614 GAAAAAAA-AAAAGATATTCA
1 -AAAAAAAGAAAA-A-ATTCA
984634 AAAAGAAAG
1 AAAA-AAAG
984643 CAAAGCCAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
18 4 0.17
19 12 0.50
20 8 0.33
ACGTcount: A:0.74, C:0.04, G:0.11, T:0.11
Consensus pattern (18 bp):
AAAAAAAGAAAAAATTCA
Found at i:994430 original size:60 final size:60
Alignment explanation
Indices: 994336--994505 Score: 202
Period size: 60 Copynumber: 2.8 Consensus size: 60
994326 AGTTTGAGAG
* *
994336 GAAATTTAAATATTCAAAAAGTTT-GGGA-TCAATTTAGAATGAAGGTCATAGTTTGGGGAT
1 GAAATTGAAATATTC-AAAAGTTTAGGGACT-AATTTAGAATGAAGGTCATAGTTTAGGGAT
* *
994396 GAAATTGAAATATTCAAAAGTTTAAGGACTAATTTAGAATCATA-GTCATAGTTTAGGGAT
1 GAAATTGAAATATTCAAAAGTTTAGGGACTAATTTAGAATGA-AGGTCATAGTTTAGGGAT
* * * * * *
994456 GAAATTGGAATATTTAAAAGTTTAGGGACCAATTGAAAATGAGGGTCATA
1 GAAATTGAAATATTCAAAAGTTTAGGGACTAATTTAGAATGAAGGTCATA
994506 TTGTGAGTAC
Statistics
Matches: 94, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
59 8 0.09
60 84 0.89
61 2 0.02
ACGTcount: A:0.41, C:0.06, G:0.22, T:0.32
Consensus pattern (60 bp):
GAAATTGAAATATTCAAAAGTTTAGGGACTAATTTAGAATGAAGGTCATAGTTTAGGGAT
Found at i:994479 original size:29 final size:29
Alignment explanation
Indices: 994385--994483 Score: 83
Period size: 29 Copynumber: 3.3 Consensus size: 29
994375 TGAAGGTCAT
* * *
994385 AGTTTGGGGATGAAATTGAAATATTCAAA
1 AGTTTAGGGATGAAATTGGAATATTTAAA
* * * * * *
994414 AGTTTAAGGACT-AATTTAGAATCATAGTCAT
1 AGTTTAGGGA-TGAAATTGGAAT-AT-TTAAA
994445 AGTTTAGGGATGAAATTGGAATATTTAAA
1 AGTTTAGGGATGAAATTGGAATATTTAAA
994474 AGTTTAGGGA
1 AGTTTAGGGA
994484 CCAATTGAAA
Statistics
Matches: 51, Mismatches: 15, Indels: 8
0.69 0.20 0.11
Matches are distributed among these distances:
29 27 0.53
30 6 0.12
31 18 0.35
ACGTcount: A:0.39, C:0.04, G:0.23, T:0.33
Consensus pattern (29 bp):
AGTTTAGGGATGAAATTGGAATATTTAAA
Found at i:994827 original size:13 final size:13
Alignment explanation
Indices: 994809--994833 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
994799 TTTTACAATT
994809 ATAAATAATTTTA
1 ATAAATAATTTTA
994822 ATAAATAATTTT
1 ATAAATAATTTT
994834 TTCAGAAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATAAATAATTTTA
Found at i:995036 original size:2 final size:2
Alignment explanation
Indices: 995031--995065 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
995021 TTTATTTTTT
995031 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
995066 TAGCTATTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:999827 original size:2 final size:2
Alignment explanation
Indices: 999820--999875 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
999810 TTTATGTGAT
999820 TA TA TA TA TA 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 TA TA TA TA TA
999862 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
999876 GTAATAAAAG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1001958 original size:2 final size:2
Alignment explanation
Indices: 1001951--1001979 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1001941 TATCTGGTTT
1001951 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1001980 GATTCAGTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1005416 original size:15 final size:15
Alignment explanation
Indices: 1005396--1005426 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1005386 GATTGTATGC
1005396 TAAATTGAGCAAATG
1 TAAATTGAGCAAATG
1005411 TAAATTGAGCAAATG
1 TAAATTGAGCAAATG
1005426 T
1 T
1005427 CTCTGAGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.06, G:0.19, T:0.29
Consensus pattern (15 bp):
TAAATTGAGCAAATG
Found at i:1008331 original size:22 final size:22
Alignment explanation
Indices: 1008305--1008366 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
1008295 TTGACCGAAC
1008305 CAAACCATTGACTTTGACAGGT
1 CAAACCATTGACTTTGACAGGT
*
1008327 CAAACCGTTGACTTTGACAGGT
1 CAAACCATTGACTTTGACAGGT
**
1008349 CTGACCATTGACTTTGAC
1 CAAACCATTGACTTTGAC
1008367 TAAAAAATTC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.29
Consensus pattern (22 bp):
CAAACCATTGACTTTGACAGGT
Found at i:1012748 original size:16 final size:16
Alignment explanation
Indices: 1012724--1012754 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1012714 GGACATGTTG
1012724 ATATATATACACATAT
1 ATATATATACACATAT
*
1012740 ATATTTATACACATA
1 ATATATATACACATA
1012755 CACATACATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (16 bp):
ATATATATACACATAT
Found at i:1015470 original size:55 final size:54
Alignment explanation
Indices: 1015386--1015502 Score: 207
Period size: 55 Copynumber: 2.1 Consensus size: 54
1015376 ATTGTGAAAA
1015386 AGAAATATGGGTATATGCAATTATGCATGGATTATCGTCAGTTAAATAAGGTAAT
1 AGAAATATGGGTATATGCAATTATGCATGGATTATCGTCAGTT-AATAAGGTAAT
*
1015441 AGAAATATGGGTATATGCAATTATGCATGGATTATCGTTAGTTAATAAGGTAAT
1 AGAAATATGGGTATATGCAATTATGCATGGATTATCGTCAGTTAATAAGGTAAT
1015495 AGAGAATA
1 AGA-AATA
1015503 ACAAGTATAT
Statistics
Matches: 60, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
54 14 0.23
55 46 0.77
ACGTcount: A:0.39, C:0.06, G:0.22, T:0.32
Consensus pattern (54 bp):
AGAAATATGGGTATATGCAATTATGCATGGATTATCGTCAGTTAATAAGGTAAT
Done.