Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008110.1 Hibiscus syriacus cultivar Beakdansim tig00110646_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: 844371
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 5 of 5
Found at i:789737 original size:31 final size:30
Alignment explanation
Indices: 789676--789795 Score: 113
Period size: 31 Copynumber: 4.0 Consensus size: 30
789666 TTTTAAAATT
* *
789676 AAAATAAAAATATATATTTTTAAATT---AA
1 AAAACAAAAA-ATACATTTTTAAATTAAAAA
* *
789704 AAAA-ATAAAATATATTTTTAAATTAAAACA
1 AAAACAAAAAATACATTTTTAAATTAAAA-A
*
789734 AAAACAAAATATACATTTTTAAATTAAAATA
1 AAAACAAAAAATACATTTTTAAATTAAAA-A
* *
789765 AAAATAAAAATATACATTTTTAAGTTAAAAA
1 AAAACAAAAA-ATACATTTTTAAATTAAAAA
789796 TAAGAATAAA
Statistics
Matches: 78, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
26 15 0.19
27 4 0.05
28 4 0.05
29 1 0.01
30 5 0.06
31 31 0.40
32 18 0.23
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (30 bp):
AAAACAAAAAATACATTTTTAAATTAAAAA
Found at i:789794 original size:26 final size:26
Alignment explanation
Indices: 789663--789770 Score: 119
Period size: 26 Copynumber: 4.0 Consensus size: 26
789653 TATTCTTATA
*
789663 ATATTTTAAAATTAAAATAAAAATAT
1 ATATTTTTAAATTAAAATAAAAATAT
*
789689 ATATTTTTAAATTAAAA-AAATAAAAT
1 ATATTTTTAAATTAAAATAAA-AATAT
*
789715 ATATTTTTAAATTAAAACAAAAACAAAATAT
1 ATATTTTTAAATT---A-AAATA-AAAATAT
*
789746 ACATTTTTAAATTAAAATAAAAATA
1 ATATTTTTAAATTAAAATAAAAATA
789771 AAAATATACA
Statistics
Matches: 70, Mismatches: 5, Indels: 14
0.79 0.06 0.16
Matches are distributed among these distances:
25 3 0.04
26 39 0.56
27 4 0.06
28 1 0.01
29 1 0.01
30 3 0.04
31 17 0.24
32 2 0.03
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (26 bp):
ATATTTTTAAATTAAAATAAAAATAT
Found at i:789816 original size:30 final size:29
Alignment explanation
Indices: 789663--790073 Score: 244
Period size: 30 Copynumber: 14.0 Consensus size: 29
789653 TATTCTTATA
* * *
789663 ATATTTTAAAATTAAAAT-A-AA-AATAT
1 ATATTTTTAAGTTAAAATAAGAATAAAAT
*
789689 ATATTTTTAAATT-AAA-AA-AATAAAAT
1 ATATTTTTAAGTTAAAATAAGAATAAAAT
* * * *
789715 ATATTTTTAAATTAAAACAAAAACAAAAT
1 ATATTTTTAAGTTAAAATAAGAATAAAAT
* *
789744 ATACATTTTTAAATTAAAATAAAAATAAAAAT
1 AT--ATTTTTAAGTTAAAATAAGAAT-AAAAT
789776 ATACATTTTTAAGTTAAAAATAAGAATAAAAT
1 AT--ATTTTTAAGTT-AAAATAAGAATAAAAT
* * *
789808 ATATTTTTATGTTAAAATAAGGATAAATT
1 ATATTTTTAAGTTAAAATAAGAATAAAAT
* * ** * *
789837 ATATTTAATAATTTAATGTAAGACTATAAT
1 ATATTT-TTAAGTTAAAATAAGAATAAAAT
* * ** * *
789867 ATATTTAATAATTTAAGTTAAGAATATATT
1 ATATTT-TTAAGTTAAAATAAGAATAAAAT
** * *
789897 ATATGTAATAAGTTAAAATAAAAAATAAGAT
1 ATAT-TTTTAAGTTAAAAT-AAGAATAAAAT
* * * *
789928 ATACTTTTAAAATTTAAGATAAAAAGTAAAAT
1 ATA-TTTT-TAAGTTAAAATAAGAA-TAAAAT
** * *
789960 ATATTTTTAAGTTATGATAAGATTGAAAT
1 ATATTTTTAAGTTAAAATAAGAATAAAAT
* *
789989 ATA-TTTTAAGTTGAAATAAAAATAAAAT
1 ATATTTTTAAGTTAAAATAAGAATAAAAT
* * *
790017 ATATTTTTAGGTTAATACAAGAATAAAAT
1 ATATTTTTAAGTTAAAATAAGAATAAAAT
* *
790046 ATATTTAATAATTTAAAATAA-AATAAAA
1 ATATTT-TTAAGTTAAAATAAGAATAAAA
790074 AACATTTAAT
Statistics
Matches: 309, Mismatches: 59, Indels: 31
0.77 0.15 0.08
Matches are distributed among these distances:
25 6 0.02
26 29 0.09
27 3 0.01
28 24 0.08
29 70 0.23
30 83 0.27
31 41 0.13
32 43 0.14
33 10 0.03
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.38
Consensus pattern (29 bp):
ATATTTTTAAGTTAAAATAAGAATAAAAT
Found at i:789950 original size:32 final size:32
Alignment explanation
Indices: 789909--789969 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
789899 ATGTAATAAG
*
789909 TTAAAATAAAAAATAAGATATACTTTTAAAAT
1 TTAAAATAAAAAATAAAATATACTTTTAAAAT
* * *
789941 TTAAGATAAAAAGTAAAATATATTTTTAA
1 TTAAAATAAAAAATAAAATATACTTTTAA
789970 GTTATGATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (32 bp):
TTAAAATAAAAAATAAAATATACTTTTAAAAT
Found at i:790017 original size:57 final size:58
Alignment explanation
Indices: 789704--790073 Score: 226
Period size: 62 Copynumber: 6.2 Consensus size: 58
789694 TTTAAATTAA
* * * * * *
789704 AAAAATAAAATATATTTTTAAATTAAAACAAAAACAAAATATACATTTTTAAATTAAAAT
1 AAAAATAAAATATATTTTTAAGTTAATACAAGAATAAAATAT--ATTTATAAGTTAAAAT
* * * *
789764 AAAAATAAAAATATACATTTTTAAGTTAAAAATAAGAATAAAATATATTTTTATGTTAAAAT
1 AAAAAT-AAAATAT--ATTTTTAAGTT-AATACAAGAATAAAATATATTTATAAGTTAAAAT
** * * * ** * * * **
789826 AAGGATAAATTATATTTAATAATTTAATGTAAGACTATAATATATTTAATAATTTAAGTT
1 AAAAATAAAATATATTT-TTAAGTTAATACAAGAATAAAATATATTT-ATAAGTTAAAAT
* * * ** * * * * *
789886 AAGAATATATTATATGTAATAAGTTAAAATA-AAAAATAAGATATACTTTTAAAATTTAAGAT
1 AAAAATAAAATATAT-TTTTAAGTT--AATACAAGAATAAAATATA--TTTATAAGTTAAAAT
* * * *
789948 AAAAAGTAAAATATATTTTTAAGTT-ATGATAAGATTGAAATATATTT-TAAGTTGAAAT
1 AAAAA-TAAAATATATTTTTAAGTTAAT-ACAAGAATAAAATATATTTATAAGTTAAAAT
* *
790006 AAAAATAAAATATATTTTTAGGTTAATACAAGAATAAAATATATTTAATAATTTAAAAT
1 AAAAATAAAATATATTTTTAAGTTAATACAAGAATAAAATATATTT-ATAAGTTAAAAT
790065 -AAAATAAAA
1 AAAAATAAAA
790074 AACATTTAAT
Statistics
Matches: 243, Mismatches: 50, Indels: 36
0.74 0.15 0.11
Matches are distributed among these distances:
57 34 0.14
58 23 0.09
59 36 0.15
60 38 0.16
61 34 0.14
62 42 0.17
63 21 0.09
64 15 0.06
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.37
Consensus pattern (58 bp):
AAAAATAAAATATATTTTTAAGTTAATACAAGAATAAAATATATTTATAAGTTAAAAT
Found at i:790622 original size:20 final size:20
Alignment explanation
Indices: 790599--790636 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
790589 GTATTAATTC
790599 TATTGTCAT-TCTATTTTTGA
1 TATTG-CATCTCTATTTTTGA
790619 TATTGCATCTCTATTTTT
1 TATTGCATCTCTATTTTT
790637 CTTTTCTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.18, C:0.13, G:0.08, T:0.61
Consensus pattern (20 bp):
TATTGCATCTCTATTTTTGA
Found at i:794697 original size:20 final size:20
Alignment explanation
Indices: 794661--794698 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
794651 ATCCTATTCC
**
794661 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
794681 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
794699 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:794928 original size:12 final size:12
Alignment explanation
Indices: 794911--794935 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
794901 ATGATAGAAA
794911 AAATAATATTTT
1 AAATAATATTTT
794923 AAATAATATTTT
1 AAATAATATTTT
794935 A
1 A
794936 TCAAAAATAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AAATAATATTTT
Found at i:794932 original size:33 final size:34
Alignment explanation
Indices: 794893--794967 Score: 86
Period size: 33 Copynumber: 2.3 Consensus size: 34
794883 AATTTAATAT
794893 TAATATTTATGAT-AGAAAA-AAT-AATATTTTAAA
1 TAATATTTAT-ATCA-AAAATAATAAATATTTTAAA
*
794926 TAATATTT-TATCAAAAATATTAAATATTTTAAA
1 TAATATTTATATCAAAAATAATAAATATTTTAAA
*
794959 TAACATTTA
1 TAATATTTA
794968 ATATTAATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
31 6 0.17
32 4 0.11
33 26 0.72
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.43
Consensus pattern (34 bp):
TAATATTTATATCAAAAATAATAAATATTTTAAA
Found at i:795013 original size:14 final size:13
Alignment explanation
Indices: 794986--795020 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
794976 ATTTTTGATA
794986 AAAAATA-TTTTT
1 AAAAATATTTTTT
794998 AAAAATATTTTATT
1 AAAAATATTTT-TT
795012 AAAAATATT
1 AAAAATATT
795021 AAAAATATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 7 0.33
13 3 0.14
14 11 0.52
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AAAAATATTTTTT
Found at i:799584 original size:30 final size:30
Alignment explanation
Indices: 799512--799584 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 30
799502 CCCGAAGGAC
*
799512 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCAGTAA
**
799542 CTATTTAGAGGTCATAAAGATCCTCAGTAA
1 CTATCCAGAGGTCATAAAGATCCTCAGTAA
* *
799572 CTGTCCATAGGTC
1 CTATCCAGAGGTC
799585 CCGAAGAACC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCAGTAA
Found at i:804603 original size:30 final size:30
Alignment explanation
Indices: 804569--804641 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
804559 CCCGAATGAC
*
804569 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAAAGGTCATAAAGATCCTCGGTAA
804599 CTATCCAAAGGTCATAAAGATCCTCGGTAA
1 CTATCCAAAGGTCATAAAGATCCTCGGTAA
* *
804629 CTGTCCATAGGTC
1 CTATCCAAAGGTC
804642 CCAAAGAACC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.25
Consensus pattern (30 bp):
CTATCCAAAGGTCATAAAGATCCTCGGTAA
Found at i:804648 original size:30 final size:30
Alignment explanation
Indices: 804572--804668 Score: 113
Period size: 30 Copynumber: 3.2 Consensus size: 30
804562 GAATGACCTA
* * *
804572 TCCAGAGGTCATAAAGATCCTCGGTAACTA
1 TCCATAGGTCACAAAGATCCTCGGTAACTG
* *
804602 TCCAAAGGTCATAAAGATCCTCGGTAACTG
1 TCCATAGGTCACAAAGATCCTCGGTAACTG
* * *
804632 TCCATAGGTCCCAAAGAACCTAGGTAAACTG
1 TCCATAGGTCACAAAGATCCTCGGT-AACTG
804663 TCCATA
1 TCCATA
804669 TGTTCCTTAG
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
30 48 0.81
31 11 0.19
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.23
Consensus pattern (30 bp):
TCCATAGGTCACAAAGATCCTCGGTAACTG
Found at i:804665 original size:31 final size:31
Alignment explanation
Indices: 804614--804691 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
804604 CAAAGGTCAT
* *
804614 AAAGATCCTCGGT-AACTGTCCATAGGTCCC
1 AAAGAACCTAGGTAAACTGTCCATAGGTCCC
* *
804644 AAAGAACCTAGGTAAACTGTCCATATGTTCC
1 AAAGAACCTAGGTAAACTGTCCATAGGTCCC
** *
804675 TTAGAACATAGGTAAAC
1 AAAGAACCTAGGTAAAC
804692 CCTCGACTCT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 11 0.28
31 29 0.73
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (31 bp):
AAAGAACCTAGGTAAACTGTCCATAGGTCCC
Found at i:809836 original size:19 final size:19
Alignment explanation
Indices: 809808--809856 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
809798 TGACCTCATT
*
809808 GGTCGTCAAGTGCTCCATA
1 GGTCGCCAAGTGCTCCATA
809827 GGTCGCCAAGTGCTCCATA
1 GGTCGCCAAGTGCTCCATA
809846 GGTCGCCAAGT
1 GGTCGCCAAGT
809857 ACTCATTGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.20, C:0.29, G:0.29, T:0.22
Consensus pattern (19 bp):
GGTCGCCAAGTGCTCCATA
Found at i:811943 original size:9 final size:9
Alignment explanation
Indices: 811929--811976 Score: 51
Period size: 9 Copynumber: 5.0 Consensus size: 9
811919 AAGGAAAAAG
811929 TGACCGGTT
1 TGACCGGTT
811938 TGACCGGTTT
1 TGACCGG-TT
* *
811948 TGGAACTGTTT
1 T-G-ACCGGTT
811959 TGACCGGTT
1 TGACCGGTT
811968 TGACCGGTT
1 TGACCGGTT
811977 ACAACCCGAC
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
9 21 0.66
10 4 0.12
11 4 0.12
12 3 0.09
ACGTcount: A:0.12, C:0.19, G:0.31, T:0.38
Consensus pattern (9 bp):
TGACCGGTT
Found at i:812003 original size:13 final size:13
Alignment explanation
Indices: 811984--812061 Score: 69
Period size: 13 Copynumber: 6.2 Consensus size: 13
811974 GTTACAACCC
811984 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
811997 TACCCGACTCGTT
1 GACCCGACCCGTT
812010 GACCCGACCC---
1 GACCCGACCCGTT
812020 GACCCGTTGACCC---
1 GACCC---GACCCGTT
812033 GACCCGACCCGTT
1 GACCCGACCCGTT
812046 GACCCGACCCGTT
1 GACCCGACCCGTT
812059 GAC
1 GAC
812062 AGTTGACCCG
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
10 10 0.18
13 45 0.82
ACGTcount: A:0.17, C:0.46, G:0.22, T:0.15
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:812003 original size:18 final size:18
Alignment explanation
Indices: 811998--812056 Score: 109
Period size: 18 Copynumber: 3.3 Consensus size: 18
811988 CGACCCGTTT
*
811998 ACCCGACTCGTTGACCCG
1 ACCCGACCCGTTGACCCG
812016 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
812034 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
812052 ACCCG
1 ACCCG
812057 TTGACAGTTG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.17, C:0.49, G:0.22, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGTTGACCCG
Found at i:812068 original size:7 final size:7
Alignment explanation
Indices: 812054--812092 Score: 60
Period size: 7 Copynumber: 5.4 Consensus size: 7
812044 TTGACCCGAC
812054 CCGTTGA
1 CCGTTGA
*
812061 CAGTTGA
1 CCGTTGA
812068 CCCGTTGA
1 -CCGTTGA
812076 CCGTTGA
1 CCGTTGA
812083 CCGTTGA
1 CCGTTGA
812090 CCG
1 CCG
812093 GAGTTGACCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 23 0.79
8 6 0.21
ACGTcount: A:0.15, C:0.31, G:0.28, T:0.26
Consensus pattern (7 bp):
CCGTTGA
Found at i:812071 original size:15 final size:15
Alignment explanation
Indices: 812051--812090 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
812041 CCGTTGACCC
812051 GACCCGTTGACAGTT
1 GACCCGTTGACAGTT
*
812066 GACCCGTTGACCGTT
1 GACCCGTTGACAGTT
812081 GA-CCGTTGAC
1 GACCCGTTGAC
812091 CGGAGTTGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 8 0.33
15 16 0.67
ACGTcount: A:0.17, C:0.30, G:0.28, T:0.25
Consensus pattern (15 bp):
GACCCGTTGACAGTT
Found at i:813435 original size:17 final size:18
Alignment explanation
Indices: 813402--813436 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
813392 TCGAAAGGAC
813402 TGAAGTAAATGATAAGAT
1 TGAAGTAAATGATAAGAT
*
813420 TGAATTAAAT-ATAAGAT
1 TGAAGTAAATGATAAGAT
813437 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.51, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATGATAAGAT
Found at i:814658 original size:24 final size:24
Alignment explanation
Indices: 814562--814670 Score: 85
Period size: 24 Copynumber: 4.5 Consensus size: 24
814552 GAATATTTTA
* *
814562 TCTGATTTCTGATTTGAATTATGT
1 TCTGATATCTGATCTGAATTATGT
* * * * *
814586 TTTGACATCCGATCTGAAATCTGT
1 TCTGATATCTGATCTGAATTATGT
* * * *
814610 TCTGAT-TCCTAACCTGGATTCTGT
1 TCTGATAT-CTGATCTGAATTATGT
814634 TCTGATATCTGATCTGAATTATGT
1 TCTGATATCTGATCTGAATTATGT
* *
814658 TTTGATTTCTGAT
1 TCTGATATCTGAT
814671 ATCTCCGTTT
Statistics
Matches: 63, Mismatches: 20, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
23 1 0.02
24 61 0.97
25 1 0.02
ACGTcount: A:0.21, C:0.16, G:0.17, T:0.47
Consensus pattern (24 bp):
TCTGATATCTGATCTGAATTATGT
Found at i:814838 original size:2 final size:2
Alignment explanation
Indices: 814831--814865 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
814821 CGGATGGGGG
814831 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
814866 GTTTTAAAAG
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:816853 original size:13 final size:13
Alignment explanation
Indices: 816837--816911 Score: 69
Period size: 13 Copynumber: 5.2 Consensus size: 13
816827 CCGTTGACCA
*
816837 ACCCGACCCGTTT
1 ACCCGACCCGTTG
816850 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTT-----G
816868 ACCCGACCCGTTG
1 ACCCGACCCGTTG
816881 ACCCGACCCGTTG
1 ACCCGACCCGTTG
*
816894 ACCGTTGACCCGTTG
1 ACC--CGACCCGTTG
816909 ACC
1 ACC
816912 GTTGACCGTT
Statistics
Matches: 53, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
13 29 0.55
15 12 0.23
18 12 0.23
ACGTcount: A:0.16, C:0.45, G:0.21, T:0.17
Consensus pattern (13 bp):
ACCCGACCCGTTG
Found at i:816871 original size:18 final size:18
Alignment explanation
Indices: 816815--816890 Score: 92
Period size: 18 Copynumber: 4.6 Consensus size: 18
816805 ACCGATCACA
816815 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
816833 A-CCAACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
*
816849 ----TACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
816863 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
816881 ACCCGACCCG
1 ACCCGACCCG
816891 TTGACCGTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
13 12 0.24
17 14 0.28
18 24 0.48
ACGTcount: A:0.18, C:0.50, G:0.20, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:816875 original size:31 final size:31
Alignment explanation
Indices: 816819--816896 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
816809 ATCACAACCC
816819 GACCCGACCCGTTGA-CCAACCCGACCCGTT
1 GACCCGACCCGTTGACCCAACCCGACCCGTT
* *
816849 TACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCAACCCGACCCGTT
816880 GACCCGACCCGTTGACC
1 GACCCGACCCGTTGACC
816897 GTTGACCCGT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
30 14 0.32
31 30 0.68
ACGTcount: A:0.18, C:0.47, G:0.21, T:0.14
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCAACCCGACCCGTT
Found at i:816900 original size:7 final size:7
Alignment explanation
Indices: 816888--816926 Score: 69
Period size: 7 Copynumber: 5.4 Consensus size: 7
816878 TTGACCCGAC
816888 CCGTTGA
1 CCGTTGA
816895 CCGTTGA
1 CCGTTGA
816902 CCCGTTGA
1 -CCGTTGA
816910 CCGTTGA
1 CCGTTGA
816917 CCGTTGA
1 CCGTTGA
816924 CCG
1 CCG
816927 GAGTTGACCA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 24 0.77
8 7 0.23
ACGTcount: A:0.13, C:0.33, G:0.28, T:0.26
Consensus pattern (7 bp):
CCGTTGA
Found at i:816905 original size:15 final size:15
Alignment explanation
Indices: 816872--816926 Score: 80
Period size: 15 Copynumber: 3.9 Consensus size: 15
816862 GACCCGACCC
*
816872 GACCCGTTGACC--C
1 GACCCGTTGACCGTT
816885 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
816900 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
816915 GA-CCGTTGACCG
1 GACCCGTTGACCG
816927 GAGTTGACCA
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
13 12 0.31
14 10 0.26
15 17 0.44
ACGTcount: A:0.15, C:0.36, G:0.27, T:0.22
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:818261 original size:18 final size:18
Alignment explanation
Indices: 818235--818270 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
818225 TCGAAAGGAC
*
818235 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
818253 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
818271 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:819494 original size:24 final size:24
Alignment explanation
Indices: 819398--819506 Score: 85
Period size: 24 Copynumber: 4.5 Consensus size: 24
819388 GAATATTTTA
* *
819398 TCTGATTTCTGATTTGAATTATGT
1 TCTGATATCTGATCTGAATTATGT
* * * * *
819422 TTTGACATCCGATCTGAAATCTGT
1 TCTGATATCTGATCTGAATTATGT
* * * *
819446 TCTGAT-TCCTAACCTGGATTCTGT
1 TCTGATAT-CTGATCTGAATTATGT
819470 TCTGATATCTGATCTGAATTATGT
1 TCTGATATCTGATCTGAATTATGT
* *
819494 TTTGATTTCTGAT
1 TCTGATATCTGAT
819507 ATCTCCGTTT
Statistics
Matches: 63, Mismatches: 20, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
23 1 0.02
24 61 0.97
25 1 0.02
ACGTcount: A:0.21, C:0.16, G:0.17, T:0.47
Consensus pattern (24 bp):
TCTGATATCTGATCTGAATTATGT
Found at i:819674 original size:2 final size:2
Alignment explanation
Indices: 819667--819691 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
819657 CGGATGGGGG
819667 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 T
819692 GTTTTAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:823469 original size:17 final size:17
Alignment explanation
Indices: 823449--823481 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
823439 ATAGTGTATT
823449 TTTTAATATTT-TTTATC
1 TTTTAAT-TTTATTTATC
823466 TTTTAATTTTATTTAT
1 TTTTAATTTTATTTAT
823482 TATGTCTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTAATTTTATTTATC
Found at i:825456 original size:22 final size:24
Alignment explanation
Indices: 825426--825485 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 24
825416 AACCATTTTT
*
825426 TTTATAAAACA-A-TTAAATGTTA
1 TTTAAAAAACAGATTTAAATGTTA
*
825448 TTTAAAAAA-AGATTTTAATGTTA
1 TTTAAAAAACAGATTTAAATGTTA
825471 TTTAAAAAAC-GATTT
1 TTTAAAAAACAGATTT
825486 TGTTCTAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
21 1 0.03
22 9 0.27
23 23 0.70
ACGTcount: A:0.48, C:0.03, G:0.07, T:0.42
Consensus pattern (24 bp):
TTTAAAAAACAGATTTAAATGTTA
Found at i:825467 original size:23 final size:23
Alignment explanation
Indices: 825441--825486 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
825431 AAAACAATTA
825441 AATGTTATTTAAAAAAAGATTTT
1 AATGTTATTTAAAAAAAGATTTT
*
825464 AATGTTATTTAAAAAACGATTTT
1 AATGTTATTTAAAAAAAGATTTT
825487 GTTCTAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.46, C:0.02, G:0.09, T:0.43
Consensus pattern (23 bp):
AATGTTATTTAAAAAAAGATTTT
Found at i:825496 original size:23 final size:23
Alignment explanation
Indices: 825447--825502 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
825437 ATTAAATGTT
* *
825447 ATTTAAAAAAAGATTTTAATGTT
1 ATTTAAAAAAAGATTTTAATCTA
* **
825470 ATTTAAAAAACGATTTTGTTCTA
1 ATTTAAAAAAAGATTTTAATCTA
*
825493 ATTTGAAAAA
1 ATTTAAAAAA
825503 TGGGCGAATT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.41
Consensus pattern (23 bp):
ATTTAAAAAAAGATTTTAATCTA
Found at i:826290 original size:22 final size:23
Alignment explanation
Indices: 826265--826308 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
826255 TATATTCACA
826265 TGAAGATTA-AAATAAAAATGAG
1 TGAAGATTACAAATAAAAATGAG
* *
826287 TGAATATTACAAATTAAAATGA
1 TGAAGATTACAAATAAAAATGA
826309 AATGACAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.57, C:0.02, G:0.14, T:0.27
Consensus pattern (23 bp):
TGAAGATTACAAATAAAAATGAG
Found at i:826433 original size:30 final size:29
Alignment explanation
Indices: 826330--826438 Score: 89
Period size: 29 Copynumber: 3.7 Consensus size: 29
826320 ATAAGTATTT
*
826330 GAAA-TTACAAGGACTAAAATAG-CAAATA
1 GAAACTTA-AAGGACTAAAATAGAAAAATA
* * * *
826358 CATAACTTAAAGGATTTAAATAACAAAAAATA
1 GA-AACTTAAAGGACTAAAAT-A-GAAAAATA
*
826390 GAAACTT-AGGGACTAAAATAGTAAAAATA
1 GAAACTTAAAGGACTAAAATAG-AAAAATA
*
826419 GAAACTTAAAGGACTGAAAT
1 GAAACTTAAAGGACTAAAAT
826439 GGTATTAACA
Statistics
Matches: 62, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
28 1 0.02
29 27 0.44
30 23 0.37
31 5 0.08
32 6 0.10
ACGTcount: A:0.56, C:0.09, G:0.14, T:0.21
Consensus pattern (29 bp):
GAAACTTAAAGGACTAAAATAGAAAAATA
Found at i:827895 original size:3 final size:3
Alignment explanation
Indices: 827887--828084 Score: 302
Period size: 3 Copynumber: 68.3 Consensus size: 3
827877 ATTAATAAAT
827887 ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
827934 ATA ATA ATA ATA ATA AT- ATA ATA CTA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
827981 ATA ATA CTA ATC ATA ATA ATA AT- ATA ATA ATA ATA ATA CT- ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
828027 ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA AT- ATA ATA ATA ATT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
828073 A-A ATA ATA ATA A
1 ATA ATA ATA ATA A
828085 AAGACCCGGA
Statistics
Matches: 178, Mismatches: 10, Indels: 14
0.88 0.05 0.07
Matches are distributed among these distances:
2 12 0.07
3 166 0.93
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:828597 original size:40 final size:41
Alignment explanation
Indices: 828502--828606 Score: 115
Period size: 40 Copynumber: 2.6 Consensus size: 41
828492 AGGAATGATA
*
828502 ACACGGTTCCTACGTGATGAGGACGATATATTATCTGGGGTG
1 ACACGGTTCCTACGTGATGAGGACGATATA-TATCGGGGGTG
** * * *
828544 ACACGACTCCTACGTGATGAGGA-GGTCTA-GTCGGGGGATG
1 ACACGGTTCCTACGTGATGAGGACGATATATATCGGGGG-TG
*
828584 ACACGGTTCCTACGCGATGAGGA
1 ACACGGTTCCTACGTGATGAGGA
828607 TGACATGCCA
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
39 6 0.11
40 22 0.42
41 4 0.08
42 21 0.40
ACGTcount: A:0.24, C:0.20, G:0.33, T:0.23
Consensus pattern (41 bp):
ACACGGTTCCTACGTGATGAGGACGATATATATCGGGGGTG
Found at i:828617 original size:130 final size:132
Alignment explanation
Indices: 828269--828603 Score: 437
Period size: 135 Copynumber: 2.5 Consensus size: 132
828259 GGTCTGGTCG
* * *
828269 TCTAAGGGTGACAC-AGCTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACTGCTCATACG
1 TCTAGGGGTGACACGA-CTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACAC-GTTCATACG
* * *
828333 TGATGAAGAGTTCTTGGCCATTTTTAGGTAGGGTGATAACTCGGTTCCTACGCGATGAGGACGAC
64 TGATGAAGAGTTC-TGGCCATCTTTAGGTA-GATGATAACACGGTTCCTACGCGATGAGGACGAC
*
828398 TGGTTA
127 TGATTA
* * *
828404 TCTAGGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCAGTGGATGACACGTCTCATACGT
1 TCTAGGGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGT-TCATACGT
* *
828469 GATGAAGAGTTCTGGCCATCTTTAGG-A-ATGATAACACGGTTCCTACGTGATGAGGACGA-TAT
65 GATGAAGAGTTCTGGCCATCTTTAGGTAGATGATAACACGGTTCCTACGCGATGAGGACGACT-G
828531 ATTA
129 ATTA
* * *
828535 TCT-GGGGTGACACGACTCCTACGTGATGAGGAGGTCTAGTCGGGGGATGACACGGTTCCTACGC
1 TCTAGGGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACAC-GTTCATACGT
828599 GATGA
65 GATGA
828604 GGATGACATG
Statistics
Matches: 178, Mismatches: 18, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
130 58 0.33
131 37 0.21
133 1 0.01
134 14 0.08
135 68 0.38
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.26
Consensus pattern (132 bp):
TCTAGGGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGTTCATACGTG
ATGAAGAGTTCTGGCCATCTTTAGGTAGATGATAACACGGTTCCTACGCGATGAGGACGACTGAT
TA
Found at i:828770 original size:31 final size:31
Alignment explanation
Indices: 828711--828771 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 31
828701 AAGGAAAACG
828711 ACTCAAAGATAGTTTTGTTTCAAGAGAAACAT
1 ACTCAAAGATA-TTTTGTTTCAAGAGAAACAT
828743 ACTCAAAGAT-TTTGTGTTTCCAA-AGAAAC
1 ACTCAAAGATATTT-TGTTT-CAAGAGAAAC
828772 CACCTCAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 3 0.11
31 11 0.41
32 13 0.48
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (31 bp):
ACTCAAAGATATTTTGTTTCAAGAGAAACAT
Found at i:831009 original size:40 final size:40
Alignment explanation
Indices: 830954--831155 Score: 368
Period size: 40 Copynumber: 5.0 Consensus size: 40
830944 TGCAGATTTA
830954 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
830994 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
831034 TAATACACTTCGGTGTATATGGTGGGAACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
831074 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
* * *
831114 TAATACACTTCGGTGTATATGATGGACACGACCTTACGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
831154 TA
1 TA
831156 GCACTACGGT
Statistics
Matches: 157, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 157 1.00
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.32
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:832176 original size:27 final size:26
Alignment explanation
Indices: 832146--832216 Score: 79
Period size: 26 Copynumber: 2.6 Consensus size: 26
832136 CCTCAAAGCT
832146 GATTTTGTTAAGAGAAACAAACTCAAA
1 GATTTT-TTAAGAGAAACAAACTCAAA
* * * *
832173 GATTTTTCAAAAGGAACAGACTCAAA
1 GATTTTTTAAGAGAAACAAACTCAAA
832199 GATTTATTTCAAGAGAAA
1 GATTT-TTT-AAGAGAAA
832217 TTGTCTCAAG
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
26 21 0.60
27 8 0.23
28 6 0.17
ACGTcount: A:0.46, C:0.11, G:0.15, T:0.27
Consensus pattern (26 bp):
GATTTTTTAAGAGAAACAAACTCAAA
Found at i:832485 original size:36 final size:36
Alignment explanation
Indices: 832430--832528 Score: 135
Period size: 36 Copynumber: 2.8 Consensus size: 36
832420 TTGTATCTCA
* * * *
832430 GAGAAAAAATGTCTCAAGCGAGACGAAATTTGCTTT
1 GAGAGAAATTGTCTTAAGCGAGACAAAATTTGCTTT
*
832466 GAGAGAAATTGTCTTAAGCGAGACAAAATTTGTTTT
1 GAGAGAAATTGTCTTAAGCGAGACAAAATTTGCTTT
* *
832502 TAGAGAAATTGTCTTAAGAGAGACAAA
1 GAGAGAAATTGTCTTAAGCGAGACAAA
832529 GTTTATTTTT
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 56 1.00
ACGTcount: A:0.40, C:0.10, G:0.22, T:0.27
Consensus pattern (36 bp):
GAGAGAAATTGTCTTAAGCGAGACAAAATTTGCTTT
Found at i:832664 original size:35 final size:37
Alignment explanation
Indices: 832606--832683 Score: 88
Period size: 35 Copynumber: 2.2 Consensus size: 37
832596 TATCTTAAAG
* * **
832606 GGAAAATGTCTCAAGCGAAAC-AAA-TTTGTTTTGAA
1 GGAAACTGTCTCAAACGAAACAAAATTTTGTTTCAAA
* *
832641 GGAAACTGTCTCAAATGAGACAAAATTTTGTTTCAAA
1 GGAAACTGTCTCAAACGAAACAAAATTTTGTTTCAAA
832678 GGAAAC
1 GGAAAC
832684 AACTGTAAGA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
35 17 0.49
36 3 0.09
37 15 0.43
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (37 bp):
GGAAACTGTCTCAAACGAAACAAAATTTTGTTTCAAA
Found at i:832878 original size:33 final size:33
Alignment explanation
Indices: 832838--832906 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
832828 GTTGAATCCC
* * *
832838 CAAAGATGCCCCAATGTTCGATGTTGATTTCTT
1 CAAAGATGCCCCAATATTCAATGTTGATTGCTT
832871 CAAAGATGCCCCAATATTCAATGTTGATTGCTT
1 CAAAGATGCCCCAATATTCAATGTTGATTGCTT
832904 CAA
1 CAA
832907 CACTGATTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (33 bp):
CAAAGATGCCCCAATATTCAATGTTGATTGCTT
Found at i:833952 original size:13 final size:14
Alignment explanation
Indices: 833936--834045 Score: 79
Period size: 14 Copynumber: 7.8 Consensus size: 14
833926 CTCTTTGTCC
*
833936 TCTTTTTGTTTT-T
1 TCTTTTTCTTTTGT
833949 TCTTTTTCTTTTGT
1 TCTTTTTCTTTTGT
833963 TCTTTTT-TCTTTGAT
1 TCTTTTTCT-TTTG-T
833978 T-TTTTTCTCTTTGTT
1 TCTTTTTCT-TTTG-T
833993 TCTTTTTC-TTTGT
1 TCTTTTTCTTTTGT
*
834006 T-TTTTGTC-TTTGC
1 TCTTTT-TCTTTTGT
*
834019 TCTTTATTTTCTTTGT
1 TCTTT-TTCT-TTTGT
*
834035 TGTTTTTCTTT
1 TCTTTTTCTTT
834046 CTTTGTTTTT
Statistics
Matches: 80, Mismatches: 7, Indels: 19
0.75 0.07 0.18
Matches are distributed among these distances:
12 4 0.05
13 21 0.26
14 27 0.34
15 14 0.17
16 14 0.17
ACGTcount: A:0.02, C:0.13, G:0.08, T:0.77
Consensus pattern (14 bp):
TCTTTTTCTTTTGT
Found at i:833983 original size:29 final size:28
Alignment explanation
Indices: 833929--834099 Score: 107
Period size: 29 Copynumber: 5.8 Consensus size: 28
833919 GTCTGTGCTC
* *
833929 TTTGTCCTCTTTTTGTTT-TTTCTTTTTCT
1 TTTGTTCT-TTTTTCTTTGTTT-TTTTTCT
*
833958 TTTGTTCTTTTTTCTTTGATTTTTTTCT
1 TTTGTTCTTTTTTCTTTGTTTTTTTTCT
*
833986 CTTTGTT-TCTTTTTCTTTGTTTTTTGTC-
1 -TTTGTTCT-TTTTTCTTTGTTTTTTTTCT
* *
834014 TTTGCTCTTTATTTTCTTTGTTGTTTTTCT
1 TTTGTTC-TT-TTTTCTTTGTTTTTTTTCT
* * *
834044 TTCT-TTGTTTTTTCTCTTTTCTCTTTGTTTTT
1 TT-TGTTCTTTTTTCT-TTGT-T-TTT-TTTCT
*
834076 CTTTGTTTCTTTTCTCTTTGTTTT
1 -TTTG-TTCTTTTTTCTTTGTTTT
834100 GATTTGGTCT
Statistics
Matches: 111, Mismatches: 16, Indels: 28
0.72 0.10 0.18
Matches are distributed among these distances:
27 5 0.05
28 23 0.21
29 54 0.49
30 4 0.04
31 5 0.05
32 6 0.05
33 5 0.05
34 9 0.08
ACGTcount: A:0.01, C:0.15, G:0.08, T:0.76
Consensus pattern (28 bp):
TTTGTTCTTTTTTCTTTGTTTTTTTTCT
Found at i:834048 original size:17 final size:17
Alignment explanation
Indices: 834026--834079 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
834016 TGCTCTTTAT
834026 TTTCTTTGTTGTTTTTC
1 TTTCTTTGTTGTTTTTC
834043 TTTCTTTGTT-TTTTCTC
1 TTTCTTTGTTGTTTT-TC
*
834060 TTTTCTCT-TTGTTTTTC
1 -TTTCTTTGTTGTTTTTC
834077 TTT
1 TTT
834080 GTTTCTTTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
16 7 0.21
17 16 0.48
18 10 0.30
ACGTcount: A:0.00, C:0.15, G:0.07, T:0.78
Consensus pattern (17 bp):
TTTCTTTGTTGTTTTTC
Found at i:834051 original size:46 final size:47
Alignment explanation
Indices: 833970--834099 Score: 144
Period size: 46 Copynumber: 2.8 Consensus size: 47
833960 TGTTCTTTTT
* * *
833970 TCTTTGATTTTTTTCTCTTTGTTTCTT-TTTCTTTGTTTTTTGTCTTTGC
1 TCTTTGATTTTCTT-T-GTTGTTT-TTCTTTCTTTGTTTTTTCTCTTTGC
*
834019 TCTTT-ATTTTCTTTGTTGTTTTTCTTTCTTTGTTTTTTCTCTTTTC
1 TCTTTGATTTTCTTTGTTGTTTTTCTTTCTTTGTTTTTTCTCTTTGC
*
834065 TCTTTGTTTTTCTTTGTT-TCTTTTC--TCTTTGTTTT
1 TCTTTGATTTTCTTTGTTGT-TTTTCTTTCTTTGTTTT
834100 GATTTGGTCT
Statistics
Matches: 73, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
45 12 0.16
46 32 0.44
47 17 0.23
48 7 0.10
49 5 0.07
ACGTcount: A:0.02, C:0.15, G:0.08, T:0.75
Consensus pattern (47 bp):
TCTTTGATTTTCTTTGTTGTTTTTCTTTCTTTGTTTTTTCTCTTTGC
Found at i:834085 original size:20 final size:20
Alignment explanation
Indices: 833980--834075 Score: 67
Period size: 20 Copynumber: 4.8 Consensus size: 20
833970 TCTTTGATTT
*
833980 TTTTCTCTTTGTTTCTTTTTC
1 TTTTCTCTTTGTTT-TTTCTC
* * *
834001 TTTGT-TTTTTGTCTTTGCTC
1 TTT-TCTCTTTGTTTTTTCTC
*
834021 TTTATTTTCTTTGTTGTTTT-TC
1 -TT-TTCTCTTTGTT-TTTTCTC
834043 --TT-TCTTTGTTTTTTCTC
1 TTTTCTCTTTGTTTTTTCTC
834060 TTTTCTCTTTGTTTTT
1 TTTTCTCTTTGTTTTT
834076 CTTTGTTTCT
Statistics
Matches: 59, Mismatches: 7, Indels: 19
0.69 0.08 0.22
Matches are distributed among these distances:
16 4 0.07
17 10 0.17
18 2 0.03
19 2 0.03
20 15 0.25
21 13 0.22
22 10 0.17
23 3 0.05
ACGTcount: A:0.01, C:0.15, G:0.08, T:0.76
Consensus pattern (20 bp):
TTTTCTCTTTGTTTTTTCTC
Found at i:834105 original size:25 final size:23
Alignment explanation
Indices: 833987--834099 Score: 96
Period size: 25 Copynumber: 5.0 Consensus size: 23
833977 TTTTTTTCTC
833987 TTTGTTTCTTTT-TCTTTG-TTT
1 TTTGTTTCTTTTCTCTTTGTTTT
* *
834008 TTTG--TCTTTGCTCTTTATTTT
1 TTTGTTTCTTTTCTCTTTGTTTT
* *
834029 CTTTG-TTGTTTT-TCTTTCTTTGT
1 -TTTGTTTCTTTTCTCTTTGTTT-T
834052 TTT-TTCTCTTTTCTCTTTGTTTTT
1 TTTGTT-TCTTTTCTCTTTG-TTTT
834076 CTTTGTTTCTTTTCTCTTTGTTTT
1 -TTTGTTTCTTTTCTCTTTGTTTT
834100 GATTTGGTCT
Statistics
Matches: 74, Mismatches: 7, Indels: 19
0.74 0.07 0.19
Matches are distributed among these distances:
19 5 0.07
20 5 0.07
21 7 0.09
22 16 0.22
23 10 0.14
24 10 0.14
25 19 0.26
26 2 0.03
ACGTcount: A:0.01, C:0.14, G:0.09, T:0.76
Consensus pattern (23 bp):
TTTGTTTCTTTTCTCTTTGTTTT
Found at i:837779 original size:29 final size:29
Alignment explanation
Indices: 837664--837782 Score: 94
Period size: 30 Copynumber: 4.0 Consensus size: 29
837654 TTGAATTTAC
* * * *
837664 AAGGACCAAAATAGCAAATACAATAACTT
1 AAGGACTAAAATAGTAAAAACAAAAACTT
* ** *
837693 AAAGGACTTAAATAACAAAAAAATAGAAACTT
1 -AAGGACTAAAATAGTAAAAACA-A-AAACTT
*
837725 AGGGACTAAAATAGTAAAAACAAAAACTT
1 AAGGACTAAAATAGTAAAAACAAAAACTT
* **
837754 AAAGGACTAAAATGGTATTAACAAAAACT
1 -AAGGACTAAAATAGTAAAAACAAAAACT
837783 AGAACCTAAT
Statistics
Matches: 71, Mismatches: 15, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
29 6 0.08
30 42 0.59
31 18 0.25
32 5 0.07
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.18
Consensus pattern (29 bp):
AAGGACTAAAATAGTAAAAACAAAAACTT
Found at i:839176 original size:3 final size:3
Alignment explanation
Indices: 839161--839214 Score: 51
Period size: 3 Copynumber: 19.0 Consensus size: 3
839151 CAAAATGTAT
* * * *
839161 TAA TAA AAA TAA TAA TAC TAA T-A TAT TAA TAA TAA -AA TTA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
839206 TAA TAA TAA
1 TAA TAA TAA
839215 AAGACCAGGA
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
2 5 0.12
3 35 0.88
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:840232 original size:20 final size:21
Alignment explanation
Indices: 840190--840234 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
840180 ATACAGGGCG
840190 GACTATAGGGTATGCTAAATT
1 GACTATAGGGTATGCTAAATT
840211 GACTATAGGGTATGCT-AATT
1 GACTATAGGGTATGCTAAATT
840231 GACT
1 GACT
840235 GTAAAATGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.31, C:0.11, G:0.24, T:0.33
Consensus pattern (21 bp):
GACTATAGGGTATGCTAAATT
Done.