Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003856.1 Hibiscus syriacus cultivar Beakdansim tig00008289_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: 822684
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:716705 original size:21 final size:21
Alignment explanation
Indices: 716675--716719 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
716665 ATTCTGTCGT
* *
716675 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
716696 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
716717 TTG
1 TTG
716720 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:726713 original size:21 final size:21
Alignment explanation
Indices: 726684--726755 Score: 83
Period size: 21 Copynumber: 3.4 Consensus size: 21
726674 AGAAGCAGCC
* *
726684 AGAGCAGCAGTGGAAGCAGAG
1 AGAGAAGCAGTGGAAGCACAG
* *
726705 AAAGAAGCAG-CGACAGCACAG
1 AGAGAAGCAGTGGA-AGCACAG
*
726726 AGAGAAGCAGTGGCAGCACAG
1 AGAGAAGCAGTGGAAGCACAG
726747 AGAGAAGCA
1 AGAGAAGCA
726756 ACATATGAGC
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
20 2 0.05
21 39 0.93
22 1 0.02
ACGTcount: A:0.43, C:0.18, G:0.36, T:0.03
Consensus pattern (21 bp):
AGAGAAGCAGTGGAAGCACAG
Found at i:727239 original size:43 final size:43
Alignment explanation
Indices: 727169--727414 Score: 176
Period size: 43 Copynumber: 5.7 Consensus size: 43
727159 CGTTTTTAGC
* **
727169 AAAAACGCCGTAAAACATCAATGCCTACTGC-AGCGTTTGTGAG
1 AAAAACGCCGCAAAACATCAACACCTACTGCGA-CGTTTGTGAG
* *
727212 AAAAACGCCACAAAACATCAACACCTACTACGACGTTTGTG-G
1 AAAAACGCCGCAAAACATCAACACCTACTGCGACGTTTGTGAG
* * *
727254 GAAAACACCGCAAAACATCAACACCTACTGCGACATTT-TAGAG
1 AAAAACGCCGCAAAACATCAACACCTACTGCGACGTTTGT-GAG
* * * * * * *
727297 AAAATCGTCGCTAAACATCAACACCTATTGTGGCGTTT-TTATG
1 AAAAACGCCGCAAAACATCAACACCTACTGCGACGTTTGTGA-G
* * * * * * * * **
727340 ACAAGCGCTGCGAAATATCAACACCTATTGCGGCGTTTTTCTG
1 AAAAACGCCGCAAAACATCAACACCTACTGCGACGTTTGTGAG
* * * *
727383 ATAAACGCCGCTAAATATCAACACCTATTGCG
1 AAAAACGCCGCAAAACATCAACACCTACTGCG
727415 GCATTTTTTT
Statistics
Matches: 165, Mismatches: 33, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
41 1 0.01
42 36 0.22
43 126 0.76
44 2 0.01
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.23
Consensus pattern (43 bp):
AAAAACGCCGCAAAACATCAACACCTACTGCGACGTTTGTGAG
Found at i:732050 original size:266 final size:266
Alignment explanation
Indices: 731530--732110 Score: 813
Period size: 266 Copynumber: 2.2 Consensus size: 266
731520 AAAGTTTCAC
*
731530 CCGACCCGACCCGACCCGAAATAATAAAAAAAATATTTTTATTCAATAAAAAACAGTGACTGAAT
1 CCGACCCGACCCGACCCGAAATAATAAAAAAAATATTTTTATTCAAT-AAAAACAATGACTGAAT
* * *
731595 TGGAAAAATATATATATAGAGAGAGGGGTATTATTATAATTATTCCTAAATATATAAGGTAAAAT
65 TGAAAAAAAATATATATAGAGAGA--GGAATTATTATAATTATTCCTAAATATATAAGGTAAAAT
* *
731660 TATATATTTTTTGGGTCGGGTCAGATATTTTTCTCCCTAAACCCGAACCTGACCCGACCTGAATA
128 TATATATTTTTTGGGTCGGGT-A-ATATTTTTCACCCTAAACCCGAACCTGACCCGACCCGAATA
* *
731725 TCACACTTAAAAAAAACCGACCCCACCCGACCCAAATAAAGTTTCACCCAACTCGACCCGAATAT
191 TCACACTTAAAAAAAACCGACCCCACCCGACCAAAATAAAGTTTCACCCAACACGACCCGAATAT
731790 ATGAATTAGAAA
256 ATGAATTAG-AA
* * *
731802 TCCGACCCCACCCGACCCGAAATAATAATAAAAAATATTTGTATTCAATAAAAACAATGACTTAA
1 -CCGACCCGACCCGACCCGAAATAATAA-AAAAAATATTTTTATTCAATAAAAACAATGACTGAA
* *
731867 TTGAAAAAAAAGTATATATAGAG-GA-GAATTATTGTAATTATTTCTAAATATATAAGGTAAAAT
64 TTGAAAAAAAA-TATATATAGAGAGAGGAATTATTATAATTATTCCTAAATATATAAGGTAAAAT
* *
731930 TATATATATTTTTGGGTCGGGT-AT-TTTTTCACCCTAAACCCGGA-CTCGATCCGACCCGAATA
128 TATATAT-TTTTTGGGTCGGGTAATATTTTTCACCCTAAACCCGAACCT-GACCCGACCCGAATA
** * * *
731992 TCACACTT-AAAAAAACCGACCTGATCTGACCAAAATAAAGTTTCACCCGACACGACCCGAATAT
191 TCACACTTAAAAAAAACCGACCCCACCCGACCAAAATAAAGTTTCACCCAACACGACCCGAATAT
732056 ATGAATTAGAA
256 ATGAATTAGAA
732067 ---ACCCGACCCGACCCGAAATAAT-AAAAAAATATTTTTATTCAATA
1 CCGACCCGACCCGACCCGAAATAATAAAAAAAATATTTTTATTCAATA
732111 TATAAATAAG
Statistics
Matches: 282, Mismatches: 22, Indels: 22
0.87 0.07 0.07
Matches are distributed among these distances:
259 20 0.07
260 1 0.00
261 21 0.07
265 2 0.01
266 60 0.21
267 39 0.14
268 2 0.01
270 42 0.15
271 14 0.05
273 51 0.18
274 30 0.11
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.27
Consensus pattern (266 bp):
CCGACCCGACCCGACCCGAAATAATAAAAAAAATATTTTTATTCAATAAAAACAATGACTGAATT
GAAAAAAAATATATATAGAGAGAGGAATTATTATAATTATTCCTAAATATATAAGGTAAAATTAT
ATATTTTTTGGGTCGGGTAATATTTTTCACCCTAAACCCGAACCTGACCCGACCCGAATATCACA
CTTAAAAAAAACCGACCCCACCCGACCAAAATAAAGTTTCACCCAACACGACCCGAATATATGAA
TTAGAA
Found at i:739148 original size:16 final size:16
Alignment explanation
Indices: 739114--739153 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
739104 TTTACTTCAT
* *
739114 AATGATT-AAGTGTTG
1 AATGATTCAAATGCTG
739129 AATGATTCAAATGCTG
1 AATGATTCAAATGCTG
739145 AATGATTCA
1 AATGATTCA
739154 GATGTTCTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (16 bp):
AATGATTCAAATGCTG
Found at i:741804 original size:54 final size:56
Alignment explanation
Indices: 741737--741976 Score: 211
Period size: 55 Copynumber: 4.4 Consensus size: 56
741727 AATACACATT
* ** * **
741737 TAGTGCCTATACGGAAATTCATCAACTCATCATGAATTCCATGGGT-TGCACAC-A
1 TAGTGCCTGTACGGTGATTCATCCACTCATCATGAATTCCATGAATATGCACACGA
* ** *
741791 TAGTGCCTGTACGGTGATTCATCCACCCATGTTGAATTCCGTGAATATGCACACGA
1 TAGTGCCTGTACGGTGATTCATCCACTCATCATGAATTCCATGAATATGCACACGA
** * * * * *
741847 -AGTGCCTGTACGGTGATTCATCCACTCAAGATAAATTACGTGATTATGCACATGA
1 TAGTGCCTGTACGGTGATTCATCCACTCATCATGAATTCCATGAATATGCACACGA
* * ** ** *
741902 -AGTGCATGTACGGTGATTCATCTACTCAGGATGAATTCTGTGATTATGCACAC-A
1 TAGTGCCTGTACGGTGATTCATCCACTCATCATGAATTCCATGAATATGCACACGA
* *
741956 AAGTGCATGTACGGTGATTCA
1 TAGTGCCTGTACGGTGATTCA
741977 CTCAGGATGA
Statistics
Matches: 159, Mismatches: 24, Indels: 5
0.85 0.13 0.03
Matches are distributed among these distances:
54 37 0.23
55 121 0.76
56 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (56 bp):
TAGTGCCTGTACGGTGATTCATCCACTCATCATGAATTCCATGAATATGCACACGA
Found at i:741858 original size:55 final size:55
Alignment explanation
Indices: 741783--741976 Score: 255
Period size: 55 Copynumber: 3.5 Consensus size: 55
741773 TTCCATGGGT
* * * * *
741783 TGCACAC-ATAGTGCCTGTACGGTGATTCATCCACCCATGTTGAATTCCGTGAATA
1 TGCACACGA-AGTGCATGTACGGTGATTCATCCACTCAAGATGAATTCCGTGATTA
* * *
741838 TGCACACGAAGTGCCTGTACGGTGATTCATCCACTCAAGATAAATTACGTGATTA
1 TGCACACGAAGTGCATGTACGGTGATTCATCCACTCAAGATGAATTCCGTGATTA
* * * *
741893 TGCACATGAAGTGCATGTACGGTGATTCATCTACTCAGGATGAATTCTGTGATTA
1 TGCACACGAAGTGCATGTACGGTGATTCATCCACTCAAGATGAATTCCGTGATTA
*
741948 TGCACACAAAGTGCATGTACGGTGATTCA
1 TGCACACGAAGTGCATGTACGGTGATTCA
741977 CTCAGGATGA
Statistics
Matches: 123, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
55 122 0.99
56 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (55 bp):
TGCACACGAAGTGCATGTACGGTGATTCATCCACTCAAGATGAATTCCGTGATTA
Found at i:741913 original size:27 final size:28
Alignment explanation
Indices: 741831--741974 Score: 77
Period size: 28 Copynumber: 5.2 Consensus size: 28
741821 GTTGAATTCC
* * *
741831 GTGAATATGCACACGAAGTGCCTGTACG
1 GTGATTATGCACATGAAGTGCATGTACG
* * **
741859 GTGATTCATCCAC-TCAAGATAAAT-TAC-
1 GTGATT-ATGCACATGAAG-TGCATGTACG
741886 GTGATTATGCACATGAAGTGCATGTACG
1 GTGATTATGCACATGAAGTGCATGTACG
* * * *
741914 GTGATTCAT-CTAC-TCAGGATGAAT-T-CT
1 GTGATT-ATGC-ACATGAAG-TGCATGTACG
**
741941 GTGATTATGCACACAAAGTGCATGTACG
1 GTGATTATGCACATGAAGTGCATGTACG
741969 GTGATT
1 GTGATT
741975 CACTCAGGAT
Statistics
Matches: 84, Mismatches: 20, Indels: 24
0.66 0.16 0.19
Matches are distributed among these distances:
26 16 0.19
27 24 0.29
28 29 0.35
29 15 0.18
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (28 bp):
GTGATTATGCACATGAAGTGCATGTACG
Found at i:742446 original size:11 final size:11
Alignment explanation
Indices: 742426--742661 Score: 67
Period size: 11 Copynumber: 21.9 Consensus size: 11
742416 GAAATAAAAG
742426 AAATAAAATAA
1 AAATAAAATAA
742437 ACAA-AAAATAA
1 A-AATAAAATAA
742448 AAATAAAATAA
1 AAATAAAATAA
*
742459 AACCT--AATAA
1 AA-ATAAAATAA
* **
742469 TAAT-AAATGCT
1 AAATAAAAT-AA
742480 AAAT-AAATAGA
1 AAATAAAATA-A
*
742491 ACA-AAAATAA
1 AAATAAAATAA
742501 AAAT-AAATAA
1 AAATAAAATAA
*
742511 GAAACAAAATAA
1 -AAATAAAATAA
*
742523 ATATAAAA-AA
1 AAATAAAATAA
** *
742533 AGGTGAAGAT--
1 AAAT-AAAATAA
*
742543 AAAGAAAATAA
1 AAATAAAATAA
*
742554 ATA-AAAATAA
1 AAATAAAATAA
*
742564 AAATATGAA-AA
1 AAATA-AAATAA
742575 AAATACAGAA-AA
1 AAATA-A-AATAA
*
742587 TAAAGAAAAT-A
1 -AAATAAAATAA
*
742598 AAA-GAAATAA
1 AAATAAAATAA
742608 AAATAGAAA-AA
1 AAATA-AAATAA
* *
742619 TAGA-AAAATGA
1 -AAATAAAATAA
*
742630 AAATGAAAATAG
1 AAAT-AAAATAA
742642 AAATAAAAT-A
1 AAATAAAATAA
742652 AAATAAAATA
1 AAATAAAATA
742662 TAAGTTAATA
Statistics
Matches: 164, Mismatches: 34, Indels: 54
0.65 0.13 0.21
Matches are distributed among these distances:
9 9 0.05
10 55 0.34
11 66 0.40
12 30 0.18
13 4 0.02
ACGTcount: A:0.73, C:0.03, G:0.07, T:0.17
Consensus pattern (11 bp):
AAATAAAATAA
Found at i:742450 original size:17 final size:17
Alignment explanation
Indices: 742404--742454 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
742394 CAAAAGAGAT
742404 ACAAAAAATAAGGAAAT-A
1 ACAAAAAATAA--AAATAA
*
742422 A-AAGAAAT-AAAATAA
1 ACAAAAAATAAAAATAA
742437 ACAAAAAATAAAAATAA
1 ACAAAAAATAAAAATAA
742454 A
1 A
742455 ATAAAACCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
14 4 0.14
15 2 0.07
16 7 0.25
17 14 0.50
18 1 0.04
ACGTcount: A:0.78, C:0.04, G:0.06, T:0.12
Consensus pattern (17 bp):
ACAAAAAATAAAAATAA
Found at i:742451 original size:6 final size:6
Alignment explanation
Indices: 742407--742664 Score: 50
Period size: 6 Copynumber: 40.3 Consensus size: 6
742397 AAGAGATACA
* *
742407 AAAAAT AAGGAAAT AAAAGAA ATAAAAT AAACA- AAAAAT AAAAAT -AAAAT
1 AAAAAT AA--AAAT AAAA-AT A-AAAAT AAAAAT AAAAAT AAAAAT AAAAAT
* * ** *
742457 AAAACCT AATAAT AATAAAT GCTAAAT AAATAGAAC AAAAAT AAAAAT
1 AAAA-AT AAAAAT AA-AAAT -AAAAAT -AA-A-AAT AAAAAT AAAAAT
* ** * *
742505 AAATAAG AAACAA- AATAAAT ATAAAA- AAAGGT GAAGAT AAAGAA- AATAAAT
1 AAA-AAT AAA-AAT AA-AAAT A-AAAAT AAAAAT AAAAAT AAA-AAT AA-AAAT
* * *
742556 AAAAAT AAAAAT ATGAAAA- AAATAC AGAAAAT AAAGAA- AATAAA- AGAAAT
1 AAAAAT AAAAAT A--AAAAT AAAAAT A-AAAAT AAA-AAT AA-AAAT AAAAAT
* * *
742606 AAAAAT AGAAAAAT AGAAAAAT GAAAAT GAAAAT AGAAAT -AAAAT -AAAAT
1 AAAAAT --AAAAAT --AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
742656 AAAATAT AA
1 AAAA-AT AA
742665 GTTAATAATA
Statistics
Matches: 190, Mismatches: 32, Indels: 59
0.68 0.11 0.21
Matches are distributed among these distances:
5 26 0.14
6 87 0.46
7 44 0.23
8 31 0.16
9 2 0.01
ACGTcount: A:0.73, C:0.03, G:0.08, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:742561 original size:41 final size:41
Alignment explanation
Indices: 742516--742659 Score: 114
Period size: 45 Copynumber: 3.4 Consensus size: 41
742506 AATAAGAAAC
*** *
742516 AAAATAAATATAAAAAAA-GGTGAAGATAAAGAAAATAAATA
1 AAAATAAATATAAAAAAATACAGAAAATAAAGAAAATAAA-A
742557 AAAATAAAAATATGAAAAAAATACAGAAAATAAAGAAAATAAAA
1 AAAAT--AAATAT-AAAAAAATACAGAAAATAAAGAAAATAAAA
* * * *
742601 GAAATAAAAATAGAAAAATAGA-AAAATGAAAATGAAAATAGAAA
1 AAAATAAATATAAAAAAATACAGAAAAT--AAA-GAAAATA-AAA
742645 TAAAATAAA-ATAAAA
1 -AAAATAAATATAAAA
742660 TATAAGTTAA
Statistics
Matches: 84, Mismatches: 10, Indels: 15
0.77 0.09 0.14
Matches are distributed among these distances:
40 5 0.06
41 14 0.17
42 8 0.10
43 13 0.15
44 20 0.24
45 24 0.29
ACGTcount: A:0.74, C:0.01, G:0.10, T:0.15
Consensus pattern (41 bp):
AAAATAAATATAAAAAAATACAGAAAATAAAGAAAATAAAA
Found at i:742619 original size:8 final size:8
Alignment explanation
Indices: 742606--742644 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
742596 TAAAAGAAAT
742606 AAAAATAG
1 AAAAATAG
742614 AAAAATAG
1 AAAAATAG
742622 AAAAAT-G
1 AAAAATAG
742629 -AAAAT-G
1 AAAAATAG
742635 -AAAATAG
1 AAAAATAG
742642 AAA
1 AAA
742645 TAAAATAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 11 0.38
7 2 0.07
8 16 0.55
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (8 bp):
AAAAATAG
Found at i:742652 original size:5 final size:5
Alignment explanation
Indices: 742623--742661 Score: 51
Period size: 5 Copynumber: 7.2 Consensus size: 5
742613 GAAAAATAGA
742623 AAAAT GAAAAT GAAAAT AGAAAT AAAAT AAAAT AAAAT A
1 AAAAT -AAAAT -AAAAT A-AAAT AAAAT AAAAT AAAAT A
742662 TAAGTTAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 16 0.50
6 16 0.50
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:742654 original size:28 final size:27
Alignment explanation
Indices: 742583--742661 Score: 78
Period size: 28 Copynumber: 3.0 Consensus size: 27
742573 AAAAATACAG
*
742583 AAAATA-AAGAAAATAAAA-G-AAATA
1 AAAATAGAAAAAAATAAAATGAAAATA
*
742607 AAAATAGAAAAATAGA-AAAATGAAAATG
1 AAAATAGAAAAA-A-ATAAAATGAAAATA
742635 AAAATAGAAATAAAATAAAAT-AAAATA
1 AAAATAGAAA-AAAATAAAATGAAAATA
742662 TAAGTTAATA
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
24 6 0.13
25 4 0.09
26 5 0.11
27 8 0.18
28 20 0.44
29 2 0.04
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (27 bp):
AAAATAGAAAAAAATAAAATGAAAATA
Found at i:745017 original size:41 final size:42
Alignment explanation
Indices: 744910--745018 Score: 132
Period size: 41 Copynumber: 2.6 Consensus size: 42
744900 CGATATCTTT
* *
744910 CGTCGTGAAGTTGAAATCGTGGATGTGTGGGCATAATATCCTC
1 CGTCGTGGAGTTGAAATCGTGGATGTGTAGG-ATAATATCCTC
** *
744953 CGTCGTGGAGTTGAAATATTGGATTTGTAGG-T-ATGATCCTC
1 CGTCGTGGAGTTGAAATCGTGGATGTGTAGGATAAT-ATCCTC
*
744994 TGTCGTGGAGTTGAAATCGTGGATG
1 CGTCGTGGAGTTGAAATCGTGGATG
745019 GCCCATTCGT
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
40 2 0.04
41 28 0.50
43 26 0.46
ACGTcount: A:0.22, C:0.13, G:0.32, T:0.33
Consensus pattern (42 bp):
CGTCGTGGAGTTGAAATCGTGGATGTGTAGGATAATATCCTC
Found at i:745340 original size:14 final size:14
Alignment explanation
Indices: 745321--745347 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
745311 CGGTTGCCTG
745321 TCTGGAATCTTGAT
1 TCTGGAATCTTGAT
745335 TCTGGAATCTTGA
1 TCTGGAATCTTGA
745348 AGTTCTGATT
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:0.22, C:0.15, G:0.22, T:0.41
Consensus pattern (14 bp):
TCTGGAATCTTGAT
Found at i:752976 original size:18 final size:18
Alignment explanation
Indices: 752955--752996 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
752945 CATATGTCCC
752955 AGGACCACTATATCCCAA
1 AGGACCACTATATCCCAA
* *
752973 AGGACCACTATGTCCCGA
1 AGGACCACTATATCCCAA
752991 AGGACC
1 AGGACC
752997 GTGTAGATCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.33, C:0.33, G:0.19, T:0.14
Consensus pattern (18 bp):
AGGACCACTATATCCCAA
Found at i:753701 original size:24 final size:20
Alignment explanation
Indices: 753647--753684 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
753637 ATTCCCCTGA
753647 AGTGCATCGATACATTCTAC
1 AGTGCATCGATACATTCTAC
753667 AGTGCATCGATACATTCT
1 AGTGCATCGATACATTCT
753685 TTAAGATGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATACATTCTAC
Found at i:756246 original size:17 final size:17
Alignment explanation
Indices: 756221--756270 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
756211 TAAATACAAC
*
756221 AAAATAAAATAAAATGG
1 AAAATAAAATAAAATAG
*
756238 AAAAAAAAATGAAAATAG
1 AAAATAAAAT-AAAATAG
756256 -AAATAAAATAAAATA
1 AAAATAAAATAAAATA
756271 AAATATAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
16 6 0.21
17 17 0.59
18 6 0.21
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (17 bp):
AAAATAAAATAAAATAG
Found at i:756259 original size:6 final size:5
Alignment explanation
Indices: 756208--756289 Score: 67
Period size: 5 Copynumber: 15.4 Consensus size: 5
756198 TGTAAATACT
* * *
756208 AAAT- AAATA CAACA AAATA AAATA AAATGGA AAAAA AAATGA AAATA
1 AAATA AAATA AAATA AAATA AAATA AAAT--A AAATA AAAT-A AAATA
*
756255 GAAATA AAATA AAATA AAATA TAAGTA ATAATA AA
1 -AAATA AAATA AAATA AAATA -AAATA A-AATA AA
756290 GTTATAATGA
Statistics
Matches: 63, Mismatches: 8, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
4 4 0.06
5 37 0.59
6 18 0.29
7 4 0.06
ACGTcount: A:0.73, C:0.02, G:0.06, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:756330 original size:19 final size:19
Alignment explanation
Indices: 756308--756347 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
756298 GATAATAGAG
756308 AAATAGAATAATAAAAATA
1 AAATAGAATAATAAAAATA
* *
756327 AAATATAATAATAATAATA
1 AAATAGAATAATAAAAATA
756346 AA
1 AA
756348 TAACAAACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (19 bp):
AAATAGAATAATAAAAATA
Found at i:758089 original size:22 final size:23
Alignment explanation
Indices: 758051--758095 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
758041 CTAGTATCGA
758051 TACCCTTACCATGGTATCGATAC
1 TACCCTTACCATGGTATCGATAC
* *
758074 TACCCTT-CTATGGTATTGATAC
1 TACCCTTACCATGGTATCGATAC
758096 CCCTAACGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.24, C:0.27, G:0.13, T:0.36
Consensus pattern (23 bp):
TACCCTTACCATGGTATCGATAC
Found at i:758180 original size:17 final size:18
Alignment explanation
Indices: 758135--758185 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 18
758125 TTGATGTTTC
*
758135 TCGGTATCGATACCCCTCA
1 TCGGTATCGATACACCT-A
758154 TCATGGTATCGATACACCT-
1 TC--GGTATCGATACACCTA
758173 TCGGTATCGATAC
1 TCGGTATCGATAC
758186 TGATTGAATC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
17 11 0.38
19 4 0.14
21 14 0.48
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (18 bp):
TCGGTATCGATACACCTA
Found at i:760357 original size:53 final size:53
Alignment explanation
Indices: 760268--760596 Score: 274
Period size: 53 Copynumber: 6.1 Consensus size: 53
760258 ATATACATTT
* ** * * *
760268 AGTGCCTATACGGAAATTCATCAACTCATGATGAATTATGTGGGTTGCACACA
1 AGTGCCTGTACGGTGATTCATCCACTCAGGATGAATTATGTGAGTTGCACACA
* * *
760321 TAGTGCCTGTACGGTGA-TCATCCACCCAAGATGAATT-TCGTGAATTGCACACGA
1 -AGTGCCTGTACGGTGATTCATCCACTCAGGATGAATTAT-GTGAGTTGCACAC-A
* *** *
760375 AGTGCCTGTACGATGATTCATCCACTCAGGATGAATTCCATGATTGTGCACA-A
1 AGTGCCTGTACGGTGATTCATCCACTCAGGATGAATTATGTGAGT-TGCACACA
* * * *
760428 AGTTCATGTACGGTGATTCATCCACTCAGGATGAATTCTGTGATTATGC-CACGA
1 AGTGCCTGTACGGTGATTCATCCACTCAGGATGAATTATGTGAGT-TGCACAC-A
* ** ** *
760482 AGTGCCTGTACGGTGATT-ATCCACTCATGATGAATTCCGTGTTTATTCACACAA
1 AGTGCCTGTACGGTGATTCATCCACTCAGGATGAATTATGTGAGT-TGCACAC-A
* * **
760536 AGTGCATGTATGGTGATTCATCCACTCAGGATGAATTCCGTGA-TATGCACACGA
1 AGTGCCTGTACGGTGATTCATCCACTCAGGATGAATTATGTGAGT-TGCACAC-A
760590 AGTGCCT
1 AGTGCCT
760597 CAGTACGCAG
Statistics
Matches: 232, Mismatches: 34, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
52 3 0.01
53 113 0.49
54 88 0.38
55 28 0.12
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.29
Consensus pattern (53 bp):
AGTGCCTGTACGGTGATTCATCCACTCAGGATGAATTATGTGAGTTGCACACA
Found at i:760539 original size:54 final size:54
Alignment explanation
Indices: 760315--760596 Score: 297
Period size: 53 Copynumber: 5.3 Consensus size: 54
760305 ATGTGGGTTG
* * * * *
760315 CACACATAGTGCCTGTACGGTGA-TCATCCACCCAAGATGAATTTCGTG-AATT
1 CACACAAAGTGCCTGTACGGTGATTCATCCACTCAGGATGAATTCCGTGTTATT
* * *
760367 GCACACGAAGTGCCTGTACGATGATTCATCCACTCAGGATGAATTCCATG--ATT
1 -CACACAAAGTGCCTGTACGGTGATTCATCCACTCAGGATGAATTCCGTGTTATT
** * * * *
760420 GTGCACAAAGTTCATGTACGGTGATTCATCCACTCAGGATGAATTCTGTGATTATG
1 -CACACAAAGTGCCTGTACGGTGATTCATCCACTCAGGATGAATTCCGTG-TTATT
* *
760476 C-CACGAAGTGCCTGTACGGTGATT-ATCCACTCATGATGAATTCCGTGTTTATT
1 CACACAAAGTGCCTGTACGGTGATTCATCCACTCAGGATGAATTCCGTG-TTATT
* * * *
760529 CACACAAAGTGCATGTATGGTGATTCATCCACTCAGGATGAATTCCGTGATATG
1 CACACAAAGTGCCTGTACGGTGATTCATCCACTCAGGATGAATTCCGTGTTATT
*
760583 CACACGAAGTGCCT
1 CACACAAAGTGCCT
760597 CAGTACGCAG
Statistics
Matches: 191, Mismatches: 32, Indels: 11
0.82 0.14 0.05
Matches are distributed among these distances:
53 91 0.48
54 76 0.40
55 22 0.12
56 2 0.01
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (54 bp):
CACACAAAGTGCCTGTACGGTGATTCATCCACTCAGGATGAATTCCGTGTTATT
Found at i:760562 original size:108 final size:108
Alignment explanation
Indices: 760315--760596 Score: 369
Period size: 108 Copynumber: 2.6 Consensus size: 108
760305 ATGTGGGTTG
* * * *
760315 CACACATAGTGCCTGTACGGTGA-TCATCCACCCAAGATGAATT-TCGTGA-ATTGCACACGAAG
1 CACACAAAGTGCATGTACGGTGATTCATCCACTCAGGATGAATTCT-GTGATA-TGCACACGAAG
760377 TGCCTGTACGATGATTCATCCACTCAGGATGAATTCCATGATTGT
64 TGCCTGTACGATGATTCATCCACTCAGGATGAATTCCATGATTGT
* *
760422 -GCACAAAGTTCATGTACGGTGATTCATCCACTCAGGATGAATTCTGTGATTATGC-CACGAAGT
1 CACACAAAGTGCATGTACGGTGATTCATCCACTCAGGATGAATTCTGTGA-TATGCACACGAAGT
* * * * *
760485 GCCTGTACGGTGATT-ATCCACTCATGATGAATTCCGTGTTTATT
65 GCCTGTACGATGATTCATCCACTCAGGATGAATTCCATGATT-GT
* *
760529 CACACAAAGTGCATGTATGGTGATTCATCCACTCAGGATGAATTCCGTGATATGCACACGAAGTG
1 CACACAAAGTGCATGTACGGTGATTCATCCACTCAGGATGAATTCTGTGATATGCACACGAAGTG
760594 CCT
66 CCT
760597 CAGTACGCAG
Statistics
Matches: 153, Mismatches: 15, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
106 41 0.27
107 50 0.33
108 61 0.40
109 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (108 bp):
CACACAAAGTGCATGTACGGTGATTCATCCACTCAGGATGAATTCTGTGATATGCACACGAAGTG
CCTGTACGATGATTCATCCACTCAGGATGAATTCCATGATTGT
Found at i:761049 original size:94 final size:96
Alignment explanation
Indices: 760950--761140 Score: 239
Period size: 94 Copynumber: 2.0 Consensus size: 96
760940 TACTTCTATA
* ** *
760950 CTATGGTAACGATAC-CCCT-TCGGATATCGATACCAATAATAGGTTCGATGTTGCCT-GGTATC
1 CTATGGTAACGATACTCCCTACCGG-TATCGATACCAA-AATAAATTCGATGTT-CCTAAGTATC
*
761012 GATACCCTT-ACCATGGTATCGATACTACC-CTT
63 GATACCCTTCACCATGGTATCGATACCACCTCTT
* * *
761044 CTATGGTACCGATACTCCCTACCGGTATCGATACCAAATTAAATTCGATGTTTCTAAGTATCGAT
1 CTATGGTAACGATACTCCCTACCGGTATCGATACCAAAATAAATTCGATGTTCCTAAGTATCGAT
*
761109 ACCCTTCATCATGGTATCGATACCACCTCTT
66 ACCCTTCACCATGGTATCGATACCACCTCTT
761140 C
1 C
761141 GGTATCGATA
Statistics
Matches: 83, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
93 2 0.02
94 40 0.48
95 34 0.41
96 7 0.08
ACGTcount: A:0.26, C:0.27, G:0.16, T:0.31
Consensus pattern (96 bp):
CTATGGTAACGATACTCCCTACCGGTATCGATACCAAAATAAATTCGATGTTCCTAAGTATCGAT
ACCCTTCACCATGGTATCGATACCACCTCTT
Found at i:761056 original size:22 final size:23
Alignment explanation
Indices: 761014--761063 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
761004 CTGGTATCGA
*
761014 TACCCTTACCATGGTATCGATAC
1 TACCCTTACCATGGTACCGATAC
*
761037 TACCCTT-CTATGGTACCGATAC
1 TACCCTTACCATGGTACCGATAC
761059 T-CCCT
1 TACCCT
761064 ACCGGTATCG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 4 0.16
22 14 0.56
23 7 0.28
ACGTcount: A:0.22, C:0.34, G:0.12, T:0.32
Consensus pattern (23 bp):
TACCCTTACCATGGTACCGATAC
Found at i:763499 original size:14 final size:14
Alignment explanation
Indices: 763480--763506 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
763470 TGAATTGAAT
763480 ATAAATGAACGAAC
1 ATAAATGAACGAAC
763494 ATAAATGAACGAA
1 ATAAATGAACGAA
763507 TTACTGGACG
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:0.59, C:0.11, G:0.15, T:0.15
Consensus pattern (14 bp):
ATAAATGAACGAAC
Found at i:763747 original size:21 final size:22
Alignment explanation
Indices: 763723--763768 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
763713 AAATGTGGGA
* *
763723 TCAATTTTTTTTTAAAG-GGTG
1 TCAATTATTTTTGAAAGTGGTG
763744 TCAATTATTTTTGAAAGTGGTG
1 TCAATTATTTTTGAAAGTGGTG
763766 TCA
1 TCA
763769 TTTCTTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.26, C:0.07, G:0.20, T:0.48
Consensus pattern (22 bp):
TCAATTATTTTTGAAAGTGGTG
Found at i:765055 original size:14 final size:14
Alignment explanation
Indices: 765036--765083 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
765026 TGTTCAGTAA
765036 TATGTTCGTTCATT
1 TATGTTCGTTCATT
*
765050 TATGTTCGTTCGTT
1 TATGTTCGTTCATT
*
765064 TATGTGT-GTTTATT
1 TATGT-TCGTTCATT
765078 TATGTT
1 TATGTT
765084 TAGCCCAATC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
13 1 0.03
14 28 0.93
15 1 0.03
ACGTcount: A:0.12, C:0.08, G:0.19, T:0.60
Consensus pattern (14 bp):
TATGTTCGTTCATT
Found at i:765265 original size:10 final size:10
Alignment explanation
Indices: 765250--765388 Score: 63
Period size: 10 Copynumber: 13.2 Consensus size: 10
765240 TATATTTTCA
765250 TTTATGTTCG
1 TTTATGTTCG
*
765260 TTTATGTTCA
1 TTTATGTTCG
765270 TTTAT-TGT-G
1 TTTATGT-TCG
* *
765279 TTCAT-TGACG
1 TTTATGT-TCG
765289 -TT-TGTTCG
1 TTTATGTTCG
*
765297 TTTGTGTTCG
1 TTTATGTTCG
*
765307 TTTACGTTCG
1 TTTATGTTCG
*
765317 TTTATTGTGTTTG
1 TTTA---TGTTCG
765330 TTTATGTTCG
1 TTTATGTTCG
*
765340 TTCATTTGTGTTCG
1 ----TTTATGTTCG
*
765354 TTTACGTTCG
1 TTTATGTTCG
765364 TTTATTGTGTTCG
1 TTTA---TGTTCG
765377 TTTATGTTCG
1 TTTATGTTCG
765387 TT
1 TT
765389 CATTTGTGTT
Statistics
Matches: 99, Mismatches: 15, Indels: 30
0.69 0.10 0.21
Matches are distributed among these distances:
8 3 0.03
9 11 0.11
10 59 0.60
13 17 0.17
14 9 0.09
ACGTcount: A:0.09, C:0.11, G:0.21, T:0.59
Consensus pattern (10 bp):
TTTATGTTCG
Found at i:765308 original size:47 final size:47
Alignment explanation
Indices: 765246--765404 Score: 237
Period size: 47 Copynumber: 3.4 Consensus size: 47
765236 AAAATATATT
* * * * * * *
765246 TTCATTTATGTTCGTTTATGTTCATTTATTGTGTTCATTGACGTTTG
1 TTCATTTGTGTTCGTTTACGTTCGTTTATTGTGTTCGTTTATGTTCG
* *
765293 TTCGTTTGTGTTCGTTTACGTTCGTTTATTGTGTTTGTTTATGTTCG
1 TTCATTTGTGTTCGTTTACGTTCGTTTATTGTGTTCGTTTATGTTCG
765340 TTCATTTGTGTTCGTTTACGTTCGTTTATTGTGTTCGTTTATGTTCG
1 TTCATTTGTGTTCGTTTACGTTCGTTTATTGTGTTCGTTTATGTTCG
765387 TTCATTTGTGTTCGTTTA
1 TTCATTTGTGTTCGTTTA
765405 TCATTTAAAT
Statistics
Matches: 101, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 101 1.00
ACGTcount: A:0.10, C:0.11, G:0.20, T:0.58
Consensus pattern (47 bp):
TTCATTTGTGTTCGTTTACGTTCGTTTATTGTGTTCGTTTATGTTCG
Found at i:765461 original size:31 final size:31
Alignment explanation
Indices: 765423--765503 Score: 144
Period size: 31 Copynumber: 2.6 Consensus size: 31
765413 ATGAACGAAC
765423 ATGAACGAACACGAACAAGCTACATTCCTTA
1 ATGAACGAACACGAACAAGCTACATTCCTTA
765454 ATGAACGAACACGAACAAGCTACATTCCTTA
1 ATGAACGAACACGAACAAGCTACATTCCTTA
**
765485 ACAAACGAACACGAACAAG
1 ATGAACGAACACGAACAAG
765504 AAATTTTTTG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.46, C:0.26, G:0.14, T:0.15
Consensus pattern (31 bp):
ATGAACGAACACGAACAAGCTACATTCCTTA
Found at i:765729 original size:6 final size:6
Alignment explanation
Indices: 765718--765763 Score: 65
Period size: 6 Copynumber: 7.7 Consensus size: 6
765708 AATTCATATT
* * *
765718 ATATAA ATATAA ATATAA ACATAA ACATAA ACATAA ATATAA ATAT
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATAT
765764 TTTAATTTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (6 bp):
ATATAA
Found at i:773950 original size:115 final size:116
Alignment explanation
Indices: 773734--773968 Score: 409
Period size: 115 Copynumber: 2.0 Consensus size: 116
773724 CTTATTGAAG
* * *
773734 ACACATGCAGTGCAGGCAGCCATTCATGTTATCTGTTCTTAACCAACACGAAATGAAAATGACTT
1 ACACATGCAGAGCAGGCAGCCATTCATGTTATCCGTTCTTAACCAACAC-AAACGAAAATGACTT
*
773799 GAATTCTCTTCATGGTTTTCAAGCTTCCTTCTCAATTTACCTTGCATGGAAA
65 GAATTCTCTACATGGTTTTCAAGCTTCCTTCTCAATTTACCTTGCATGGAAA
773851 ACACATGCAGAGCAGGCAGCCATTCATGTTATCCGTTCTTAACCAACAC-AACGAAAATGACTTG
1 ACACATGCAGAGCAGGCAGCCATTCATGTTATCCGTTCTTAACCAACACAAACGAAAATGACTTG
*
773915 AATTCTCTACATGGTTTTCAAGCTTCCTTCTCAATTTATCTTGCATGGAAA
66 AATTCTCTACATGGTTTTCAAGCTTCCTTCTCAATTTACCTTGCATGGAAA
773966 ACA
1 ACA
773969 TAATTCATCT
Statistics
Matches: 113, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
115 66 0.58
117 47 0.42
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (116 bp):
ACACATGCAGAGCAGGCAGCCATTCATGTTATCCGTTCTTAACCAACACAAACGAAAATGACTTG
AATTCTCTACATGGTTTTCAAGCTTCCTTCTCAATTTACCTTGCATGGAAA
Found at i:776351 original size:5 final size:4
Alignment explanation
Indices: 776315--776372 Score: 55
Period size: 4 Copynumber: 14.0 Consensus size: 4
776305 ATGTTAGAAA
* * *
776315 AAAT AAAT AAAT AAAT AAA- ATACT AAAT AAAT CAAAT GAAAG GAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT -AAAT -AAAT AAAT AAAT
776365 AAAT AAAT
1 AAAT AAAT
776373 TAAAAAAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
3 1 0.02
4 35 0.80
5 8 0.18
ACGTcount: A:0.69, C:0.03, G:0.05, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:778081 original size:5 final size:5
Alignment explanation
Indices: 778071--778269 Score: 361
Period size: 5 Copynumber: 40.4 Consensus size: 5
778061 GTACATTATG
778071 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA T-ATA -AATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
778119 TAATA TAATA TAAATA TAATA TAATA TAATA T-ATA TAATA TAATA TAATA
1 TAATA TAATA T-AATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
778169 TAATA TAATA T-ATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
778218 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
778268 TA
1 TA
778270 CATTACATGA
Statistics
Matches: 189, Mismatches: 0, Indels: 10
0.95 0.00 0.05
Matches are distributed among these distances:
4 14 0.07
5 170 0.90
6 5 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:778949 original size:107 final size:106
Alignment explanation
Indices: 778739--778949 Score: 262
Period size: 107 Copynumber: 2.0 Consensus size: 106
778729 TATTGTTCCT
* * *
778739 AGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGTTTTGGAACTGGAAAATTGTTTATTGACAAC
1 AGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGAAAATTGTTTATTGACAAC
* * *
778804 TAGCGGTCCCTTCGTCGTAAAGTTGAACTTGCGTTGTCTCG
66 CAGCGGCCCCTTCGTCGTAAAGTTGAACTTGCGCTGTCTCG
* * * * *
778845 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGGAAGTCT-TTTGTTGACA
1 AGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGCTCTGAAACT-GGAAAAT-TGTTTATTGACA
* * * *
778909 GCCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCT
64 ACCAGCGGCCCCTTCGTCGTAAAGTTGAACTTGCGCTGTCT
778950 TAAACTGGGA
Statistics
Matches: 88, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
106 39 0.44
107 48 0.55
108 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (106 bp):
AGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGAAAATTGTTTATTGACAAC
CAGCGGCCCCTTCGTCGTAAAGTTGAACTTGCGCTGTCTCG
Found at i:778981 original size:65 final size:65
Alignment explanation
Indices: 778855--779208 Score: 500
Period size: 65 Copynumber: 5.5 Consensus size: 65
778845 AGTCCAATAT
* * * * * *
778855 CCTTCGCTGTGAAGTTGAAATTG-G--CTCTGAAATTGGGGAAGTCTTTTGTTGACAGCCAGCGG
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGAAACT-GGGAAAT-TTTTGTTGACAACCAGCGG
778917 CC
64 CC
* *
778919 CCTTCGTTGTGAAGTTGAACTTGTGCTGTCTTAAACTGGGAAATTTTTGTTGACAACCAGCGGCC
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGAAACTGGGAAATTTTTGTTGACAACCAGCGGCC
* * * *
778984 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGATACTGAGAAATTTTCGTCGACAACCAGCGGCC
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGAAACTGGGAAATTTTTGTTGACAACCAGCGGCC
* * *
779049 CCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGACACTGAGAAATTTTTGTTGACAACCAGCGGCC
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGAAACTGGGAAATTTTTGTTGACAACCAGCGGCC
* *
779114 CATTCGTTGTGAAGTTGAACTTGTGTTGTCTGATACTGGGAAA-TTTTGTTGACAACCAGCGGCC
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGAAACTGGGAAATTTTTGTTGACAACCAGCGGCC
*
779178 CCTTCGTCGTGAAGTTGAACTTGTGTTGTCT
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
779209 TGAGTGGCAC
Statistics
Matches: 264, Mismatches: 23, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
64 71 0.27
65 180 0.68
66 6 0.02
67 7 0.03
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (65 bp):
CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGAAACTGGGAAATTTTTGTTGACAACCAGCGGCC
Found at i:790683 original size:5 final size:4
Alignment explanation
Indices: 790647--790704 Score: 55
Period size: 4 Copynumber: 14.0 Consensus size: 4
790637 ATGTTAGAAG
* * *
790647 AAAT AAAT AAAT AAAT AAA- ATACT AAAT AAAT CAAAT GAAAG GAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT -AAAT -AAAT AAAT AAAT
790697 AAAT AAAT
1 AAAT AAAT
790705 TTAAAAAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
3 1 0.02
4 35 0.80
5 8 0.18
ACGTcount: A:0.69, C:0.03, G:0.05, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:790720 original size:10 final size:9
Alignment explanation
Indices: 790706--790730 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
790696 TAAATAAATT
790706 TAAAAAAAA
1 TAAAAAAAA
790715 TAAAAAAAA
1 TAAAAAAAA
790724 TAAAAAA
1 TAAAAAA
790731 TGATGATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:790752 original size:35 final size:31
Alignment explanation
Indices: 790711--790792 Score: 83
Period size: 35 Copynumber: 2.5 Consensus size: 31
790701 AAATTTAAAA
*
790711 AAAATAAAAAAAATAAAAAATGATGATAAAACT
1 AAAATAAAAAAAATAAAAAAT-AAGAT-AAACT
***
790744 ATTAAATAAACCGAATAAAAAATAAGATAAACT
1 A--AAATAAAAAAAATAAAAAATAAGATAAACT
790777 AAAATGAAAAAAAATA
1 AAAAT-AAAAAAAATA
790793 TATATATAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
31 4 0.10
32 7 0.18
33 7 0.18
34 4 0.10
35 17 0.44
ACGTcount: A:0.71, C:0.05, G:0.06, T:0.18
Consensus pattern (31 bp):
AAAATAAAAAAAATAAAAAATAAGATAAACT
Found at i:795995 original size:16 final size:16
Alignment explanation
Indices: 795976--796014 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
795966 TATAATTTTC
795976 TTTTATAAA-TTTAAT
1 TTTTATAAATTTTAAT
795991 TTTT-TAAAATTTTAAT
1 TTTTAT-AAATTTTAAT
796007 TTTTATAA
1 TTTTATAA
796015 CAACTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 1 0.05
15 7 0.33
16 12 0.57
17 1 0.05
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTATAAATTTTAAT
Found at i:802721 original size:118 final size:118
Alignment explanation
Indices: 802582--802821 Score: 446
Period size: 118 Copynumber: 2.0 Consensus size: 118
802572 TTTTTAAATA
802582 TTATTTATATATTTTATCAAAAATGATTTTTAAATAATAATAAATAAAAATAAAAATGATCATAA
1 TTATTTATATATTTTATCAAAAATGATTTTTAAATAATAATAAATAAAAATAAAAATGATCATAA
802647 AAAATTAGTAAGAGAAAAATTTTATGAGAC-AAAAGTAGTACTTTTTTGTCTT
66 AAAATTAGTAAGAGAAAAATTTTATGAGACAAAAAGTAGTACTTTTTTGTCTT
802699 TTATTTATATATTTTTATCAAAAATGATTTTTAAATAATAATAAATAAAAATAAAAATGATCATA
1 TTATTTATATA-TTTTATCAAAAATGATTTTTAAATAATAATAAATAAAAATAAAAATGATCATA
* *
802764 AAAAATTAGTAAGAGACAAATTTTATGAGACAAAAAGTAGTATTTTTTTGTCTT
65 AAAAATTAGTAAGAGAAAAATTTTATGAGACAAAAAGTAGTACTTTTTTGTCTT
802818 TTAT
1 TTAT
802822 GTCTGCAGCT
Statistics
Matches: 119, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
117 11 0.09
118 83 0.70
119 25 0.21
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (118 bp):
TTATTTATATATTTTATCAAAAATGATTTTTAAATAATAATAAATAAAAATAAAAATGATCATAA
AAAATTAGTAAGAGAAAAATTTTATGAGACAAAAAGTAGTACTTTTTTGTCTT
Found at i:803833 original size:16 final size:16
Alignment explanation
Indices: 803812--803842 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
803802 ATAAATAAAT
803812 GAACATAAACGAACAC
1 GAACATAAACGAACAC
*
803828 GAACATAAATGAACA
1 GAACATAAACGAACA
803843 AATTTTTTTT
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:0.58, C:0.19, G:0.13, T:0.10
Consensus pattern (16 bp):
GAACATAAACGAACAC
Found at i:805873 original size:36 final size:36
Alignment explanation
Indices: 805823--805898 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
805813 GTTATAGCAA
*
805823 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
805859 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
805895 AAAA
1 AAAA
805899 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:810344 original size:15 final size:15
Alignment explanation
Indices: 810326--810355 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
810316 CCACGGTGCT
810326 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
810341 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
810356 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:810827 original size:36 final size:36
Alignment explanation
Indices: 810777--810852 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
810767 GTTATAGCAA
*
810777 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
810813 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
810849 AAAA
1 AAAA
810853 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:815236 original size:15 final size:15
Alignment explanation
Indices: 815218--815247 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
815208 CCACGGTGCT
815218 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
815233 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
815248 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:815718 original size:35 final size:36
Alignment explanation
Indices: 815669--815743 Score: 134
Period size: 35 Copynumber: 2.1 Consensus size: 36
815659 GTTATAGCAA
*
815669 AAAAATCGTCTTTATTCGAATTTTGCC-AAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
815704 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
815740 AAAA
1 AAAA
815744 TCCTGAAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 26 0.68
36 12 0.32
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:820212 original size:15 final size:15
Alignment explanation
Indices: 820194--820223 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
820184 CCACGGTGCT
820194 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
820209 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
820224 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:820690 original size:35 final size:36
Alignment explanation
Indices: 820635--820715 Score: 137
Period size: 35 Copynumber: 2.2 Consensus size: 36
820625 CCGGACTGTT
*
820635 ATAGCAAAAAATCGTCTTTATTCGAATTTTGCC-AAA
1 ATAGC-AAAAATCGTATTTATTCGAATTTTGCCAAAA
820671 ATAGCAAAAATCGTATTTATTCGAATTTTGCCAAAA
1 ATAGCAAAAATCGTATTTATTCGAATTTTGCCAAAA
820707 ATAGCAAAA
1 ATAGCAAAA
820716 TCCCGAAAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
35 26 0.60
36 17 0.40
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.31
Consensus pattern (36 bp):
ATAGCAAAAATCGTATTTATTCGAATTTTGCCAAAA
Found at i:821872 original size:65 final size:65
Alignment explanation
Indices: 821797--821950 Score: 281
Period size: 65 Copynumber: 2.4 Consensus size: 65
821787 TCAATATATT
* *
821797 TTATCTTCCAATTATATAACTTCAAATCTTTTATATTGAAATATTAACAAATGATACACAAAAAA
1 TTATCCTCCAATCATATAACTTCAAATCTTTTATATTGAAATATTAACAAATGATACACAAAAAA
*
821862 TTATCCTCCAATCATATAACTTCAAATCTTTTATATTGAAATATTAACAAATGATACACATAAAA
1 TTATCCTCCAATCATATAACTTCAAATCTTTTATATTGAAATATTAACAAATGATACACAAAAAA
821927 TTATCCTCCAATCATATAACTTCA
1 TTATCCTCCAATCATATAACTTCA
821951 CATTTTGAAT
Statistics
Matches: 86, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 86 1.00
ACGTcount: A:0.44, C:0.18, G:0.03, T:0.36
Consensus pattern (65 bp):
TTATCCTCCAATCATATAACTTCAAATCTTTTATATTGAAATATTAACAAATGATACACAAAAAA
Done.