Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009767.1 Kokia drynarioides strain JFW-HI SEQ_124487, 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: 569295
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 111 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:477622 original size:18 final size:18
Alignment explanation
Indices: 477567--477622 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
477557 GCAGGCACAT
* *
477567 CATGATCAGATGCAATCA
1 CATGCTCAGATGCAACCA
*
477585 CATGCTCAGATGCAATCA
1 CATGCTCAGATGCAACCA
* *
477603 CATGCTCATATGCAGCCA
1 CATGCTCAGATGCAACCA
477621 CA
1 CA
477623 GCAGACTGCA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.34, C:0.29, G:0.16, T:0.21
Consensus pattern (18 bp):
CATGCTCAGATGCAACCA
Found at i:488908 original size:23 final size:23
Alignment explanation
Indices: 488882--488930 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
488872 GGATTGTTAA
488882 TTGGAGTATGAGTTATTGAAGTT
1 TTGGAGTATGAGTTATTGAAGTT
488905 TTGGAGTATGAGTTATTGAAGTT
1 TTGGAGTATGAGTTATTGAAGTT
488928 TTG
1 TTG
488931 AGCAATTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.24, C:0.00, G:0.31, T:0.45
Consensus pattern (23 bp):
TTGGAGTATGAGTTATTGAAGTT
Found at i:509573 original size:18 final size:19
Alignment explanation
Indices: 509532--509576 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
509522 AAGTTGAAGA
509532 AGAAGAAGAAGAAGACCCT
1 AGAAGAAGAAGAAGACCCT
*
509551 A-AAGAAGAAGAAGATCC-
1 AGAAGAAGAAGAAGACCCT
509568 AGAAGAAGA
1 AGAAGAAGA
509577 TTTTGAGGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 1 0.04
18 22 0.92
19 1 0.04
ACGTcount: A:0.58, C:0.11, G:0.27, T:0.04
Consensus pattern (19 bp):
AGAAGAAGAAGAAGACCCT
Found at i:509589 original size:18 final size:18
Alignment explanation
Indices: 509568--509606 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
509558 AAGAAGATCC
**
509568 AGAAGAAGATTTTGAGGA
1 AGAAGAAGATCATGAGGA
509586 AGAAGAAGATCATGAGGA
1 AGAAGAAGATCATGAGGA
509604 AGA
1 AGA
509607 TCCTGTAGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.03, G:0.33, T:0.15
Consensus pattern (18 bp):
AGAAGAAGATCATGAGGA
Found at i:515665 original size:24 final size:24
Alignment explanation
Indices: 515594--515713 Score: 116
Period size: 24 Copynumber: 5.0 Consensus size: 24
515584 TTGATGCTCA
* **
515594 GTGCATTGCGAACTCTTGCAAACT
1 GTGCATTGTGAACTCTTGTGAACT
* *
515618 GTGCATTCTGAACTCTT-TCAAACT
1 GTGCATTGTGAACTCTTGT-GAACT
515642 GTGCATTGTGAACTCTTGTGAACT
1 GTGCATTGTGAACTCTTGTGAACT
* * * * **
515666 ATGCAATGCGAACTCTTTTGAGTT
1 GTGCATTGTGAACTCTTGTGAACT
*
515690 GTGCATTGTGAACTCTTTTGAACT
1 GTGCATTGTGAACTCTTGTGAACT
515714 ATTTGTAACC
Statistics
Matches: 78, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
24 77 0.99
25 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (24 bp):
GTGCATTGTGAACTCTTGTGAACT
Found at i:515679 original size:48 final size:48
Alignment explanation
Indices: 515594--515715 Score: 138
Period size: 48 Copynumber: 2.5 Consensus size: 48
515584 TTGATGCTCA
* ** * *
515594 GTGCATTGCGAACTCTTGCAAACTGTGCATTCTGAACTCTTTCAAACT
1 GTGCATTGTGAACTCTTGTGAACTATGCATGCTGAACTCTTTCAAACT
** **
515642 GTGCATTGTGAACTCTTGTGAACTATGCAATGC-GAACTCTTTTGAGTT
1 GTGCATTGTGAACTCTTGTGAACTATGC-ATGCTGAACTCTTTCAAACT
*
515690 GTGCATTGTGAACTCTTTTGAACTAT
1 GTGCATTGTGAACTCTTGTGAACTAT
515716 TTGTAACCCC
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
48 60 0.95
49 3 0.05
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.37
Consensus pattern (48 bp):
GTGCATTGTGAACTCTTGTGAACTATGCATGCTGAACTCTTTCAAACT
Found at i:516594 original size:48 final size:48
Alignment explanation
Indices: 516526--516670 Score: 209
Period size: 48 Copynumber: 3.0 Consensus size: 48
516516 CACATAAACA
* * * * *
516526 AATCACTTTGCATATTAACTATCACATATTTTCCAATAATGACCACAT
1 AATCACTTTGCAAATAAACTATCACATAATTGCCAATAATGGCCACAT
*
516574 AATCACTTTGCAAATAAACTATCACATAATTGCCAATAATGGTCACAT
1 AATCACTTTGCAAATAAACTATCACATAATTGCCAATAATGGCCACAT
* **
516622 AATCACTTTGCAAATAAATTGCCACATAATTGCCAATAATGGCCACAT
1 AATCACTTTGCAAATAAACTATCACATAATTGCCAATAATGGCCACAT
516670 A
1 A
516671 TCTGCCACCT
Statistics
Matches: 87, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 87 1.00
ACGTcount: A:0.40, C:0.22, G:0.08, T:0.30
Consensus pattern (48 bp):
AATCACTTTGCAAATAAACTATCACATAATTGCCAATAATGGCCACAT
Found at i:516621 original size:21 final size:21
Alignment explanation
Indices: 516596--516670 Score: 69
Period size: 21 Copynumber: 3.3 Consensus size: 21
516586 AATAAACTAT
*
516596 CACATAATTGCCAATAATGGT
1 CACATAATTGCCAATAATGGC
* *
516617 CACATAATCACTTTGCAAATAAATTGC
1 CACAT-A--A--TTGCCAAT-AATGGC
516644 CACATAATTGCCAATAATGGC
1 CACATAATTGCCAATAATGGC
516665 CACATA
1 CACATA
516671 TCTGCCACCT
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
21 16 0.37
22 8 0.19
24 2 0.05
26 8 0.19
27 9 0.21
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.27
Consensus pattern (21 bp):
CACATAATTGCCAATAATGGC
Found at i:516652 original size:11 final size:11
Alignment explanation
Indices: 516638--516670 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
516628 TTTGCAAATA
516638 AATTGCCACAT
1 AATTGCCACAT
516649 AATTGCCA-AT
1 AATTGCCACAT
*
516659 AATGGCCACAT
1 AATTGCCACAT
516670 A
1 A
516671 TCTGCCACCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.24
Consensus pattern (11 bp):
AATTGCCACAT
Found at i:522061 original size:24 final size:25
Alignment explanation
Indices: 522028--522094 Score: 77
Period size: 24 Copynumber: 2.8 Consensus size: 25
522018 GTATTGCATA
*
522028 CTCTTG-TGAATTGTGCATTACAAG
1 CTCTTGCTGAAATGTGCATTACAAG
* * *
522052 CTGTT-CTGAACTGTGCATTGCAAG
1 CTCTTGCTGAAATGTGCATTACAAG
522076 CTCTTGC-GAAATGTGCATT
1 CTCTTGCTGAAATGTGCATT
522095 TCCAACCCCT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
24 35 0.97
25 1 0.03
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.36
Consensus pattern (25 bp):
CTCTTGCTGAAATGTGCATTACAAG
Found at i:525489 original size:21 final size:20
Alignment explanation
Indices: 525465--525530 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 20
525455 CTACTGGTAG
525465 AACTAAGGCTTCTACCGATAC
1 AACTAAGG-TTCTACCGATAC
* *
525486 AACTCTAGGTTCTACCGATAT
1 AACT-AAGGTTCTACCGATAC
**
525507 AACTCTGGGTTCTACCGATAC
1 AACT-AAGGTTCTACCGATAC
525528 AAC
1 AAC
525531 CCAGACTTCT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 37 0.93
22 3 0.08
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.27
Consensus pattern (20 bp):
AACTAAGGTTCTACCGATAC
Found at i:525540 original size:21 final size:20
Alignment explanation
Indices: 525472--525547 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 20
525462 TAGAACTAAG
*
525472 GCTTCTACCGATACAACTCTA
1 GCTTCTACCGATACAAC-CCA
* * **
525493 GGTTCTACCGATATAACTCTG
1 GCTTCTACCGATACAAC-CCA
*
525514 GGTTCTACCGATACAACCCA
1 GCTTCTACCGATACAACCCA
*
525534 GACTTCTATCGATA
1 G-CTTCTACCGATA
525548 TAACAGGCTC
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 2 0.04
21 44 0.96
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.29
Consensus pattern (20 bp):
GCTTCTACCGATACAACCCA
Found at i:541524 original size:31 final size:31
Alignment explanation
Indices: 541486--541562 Score: 127
Period size: 31 Copynumber: 2.5 Consensus size: 31
541476 ATAACCTATC
*
541486 GTTTCCAAGCAACCCGGAGTAATGGGTCATT
1 GTTTCCAAGCAACCCGGAGTAACGGGTCATT
* *
541517 GTTTCCAAGCAACCCGGGGTAGCGGGTCATT
1 GTTTCCAAGCAACCCGGAGTAACGGGTCATT
541548 GTTTCCAAGCAACCC
1 GTTTCCAAGCAACCC
541563 AAGATGACTT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.23, C:0.27, G:0.26, T:0.23
Consensus pattern (31 bp):
GTTTCCAAGCAACCCGGAGTAACGGGTCATT
Found at i:541889 original size:19 final size:20
Alignment explanation
Indices: 541850--541895 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
541840 ATCCGAAATG
541850 TTATGTGAAAATATGTGATA
1 TTATGTGAAAATATGTGATA
*
541870 -TATGTG-AAATATTTGAATA
1 TTATGTGAAAATATGTG-ATA
541889 TTATGTG
1 TTATGTG
541896 TGTTTATTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 8 0.35
19 9 0.39
20 6 0.26
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.43
Consensus pattern (20 bp):
TTATGTGAAAATATGTGATA
Found at i:542212 original size:151 final size:151
Alignment explanation
Indices: 541938--542239 Score: 532
Period size: 151 Copynumber: 2.0 Consensus size: 151
541928 CAGTGGGAAA
* *
541938 TCTCACACTGAGCCTTCAAAAGTTCACCCACTTTAGTTTAATGTGTTTCAGGAAATCTTCGTGAT
1 TCTCACACTGAGCCTTCAAAAGTTCACCCACGTTAGTTTAATGTGTTTCAGGAAATCTTCATGAT
542003 TAGTGCTCGGATTCGAATTCTCGGAGTGGACTCTCGATAATGCAAATGTTTTCACAAATTACGGC
66 TAGTGCTCGGATTCGAATTCTCGGAGTGGACTCTCGATAATGCAAATGTTTTCACAAATTACGGC
*
542068 ATTGGACCTTATCATAAATTT
131 ATTGGACCTCATCATAAATTT
* * *
542089 TCTCACACTGAGCCTTTAAAAGTTCACCCACGTTAGTTTAATGTGTTTTAGTAAATCTTCATGAT
1 TCTCACACTGAGCCTTCAAAAGTTCACCCACGTTAGTTTAATGTGTTTCAGGAAATCTTCATGAT
*
542154 TAGTGCTCGGATTCGAATTCTCGGAGTGGACTCTCGATAATGCAAATGTTTTCGCAAATTACGGC
66 TAGTGCTCGGATTCGAATTCTCGGAGTGGACTCTCGATAATGCAAATGTTTTCACAAATTACGGC
*
542219 ATTGGACCTCATCATAGATTT
131 ATTGGACCTCATCATAAATTT
542240 GATTAACTTG
Statistics
Matches: 143, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
151 143 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (151 bp):
TCTCACACTGAGCCTTCAAAAGTTCACCCACGTTAGTTTAATGTGTTTCAGGAAATCTTCATGAT
TAGTGCTCGGATTCGAATTCTCGGAGTGGACTCTCGATAATGCAAATGTTTTCACAAATTACGGC
ATTGGACCTCATCATAAATTT
Found at i:543738 original size:29 final size:30
Alignment explanation
Indices: 543706--543787 Score: 112
Period size: 30 Copynumber: 2.8 Consensus size: 30
543696 TCCACTTAGC
* *
543706 TTAGATAGCCA-TAGGGCATCCACACATTA
1 TTAGATAGCCACAAAGGCATCCACACATTA
* *
543735 TTAGATAGCCACAAAGGCGTCTACACATTA
1 TTAGATAGCCACAAAGGCATCCACACATTA
*
543765 TTTGATAGCCACAAAGGCATCCA
1 TTAGATAGCCACAAAGGCATCCA
543788 AATACATTCA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
29 11 0.24
30 34 0.76
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.23
Consensus pattern (30 bp):
TTAGATAGCCACAAAGGCATCCACACATTA
Found at i:543977 original size:30 final size:30
Alignment explanation
Indices: 543915--543993 Score: 88
Period size: 30 Copynumber: 2.6 Consensus size: 30
543905 CATATAACAG
**
543915 AGAATAGCCAT-AATGGCTTACACATATCAA
1 AGAATAGCCATAAAT-GCTTACACATAAAAA
*
543945 AGAATAGCCATAAATGCTTTCACATAAAAA
1 AGAATAGCCATAAATGCTTACACATAAAAA
* * *
543975 AGAACAACCACAAATGCTT
1 AGAATAGCCATAAATGCTT
543994 CCATTTTTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
30 39 0.93
31 3 0.07
ACGTcount: A:0.47, C:0.20, G:0.11, T:0.22
Consensus pattern (30 bp):
AGAATAGCCATAAATGCTTACACATAAAAA
Found at i:544990 original size:20 final size:20
Alignment explanation
Indices: 544950--545019 Score: 77
Period size: 20 Copynumber: 3.4 Consensus size: 20
544940 AGTTTGAAAC
*
544950 AATTTTAAAATCAAGTTAAAAT
1 AATTTT-AAA-CAAGTCAAAAT
*
544972 GATTTTAAACAAGTCAAAAT
1 AATTTTAAACAAGTCAAAAT
* *
544992 AATTTGAACCAAGTCAAAAT
1 AATTTTAAACAAGTCAAAAT
*
545012 CATTTTAA
1 AATTTTAA
545020 CACTTCAAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 33 0.80
21 3 0.07
22 5 0.12
ACGTcount: A:0.50, C:0.10, G:0.07, T:0.33
Consensus pattern (20 bp):
AATTTTAAACAAGTCAAAAT
Found at i:546172 original size:27 final size:27
Alignment explanation
Indices: 546134--546214 Score: 99
Period size: 27 Copynumber: 3.0 Consensus size: 27
546124 CTCCGTAACG
* *
546134 GAGTATAGCTCATTCGATCCCAAAACA
1 GAGTTTAGCTCATTCGAGCCCAAAACA
* * *
546161 GAGTTTAGCTCATTTGAGCCTAAAATA
1 GAGTTTAGCTCATTCGAGCCCAAAACA
* *
546188 GAGTTTAGCTCATTTGAGCCCAGAACA
1 GAGTTTAGCTCATTCGAGCCCAAAACA
546215 AATTATTTCT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (27 bp):
GAGTTTAGCTCATTCGAGCCCAAAACA
Found at i:553044 original size:10 final size:10
Alignment explanation
Indices: 552988--553049 Score: 55
Period size: 10 Copynumber: 6.6 Consensus size: 10
552978 AAATGTTACA
552988 AAAAATTATAT
1 AAAAATTA-AT
552999 AAAAATTAA-
1 AAAAATTAAT
553008 ATAAAATTAA-
1 A-AAAATTAAT
*
553018 AAAACTT--T
1 AAAAATTAAT
553026 AAAAA--AAT
1 AAAAATTAAT
553034 AAAAATTAAT
1 AAAAATTAAT
553044 AAAAAT
1 AAAAAT
553050 CGTTTAAAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 13
0.74 0.03 0.22
Matches are distributed among these distances:
8 10 0.23
9 6 0.14
10 19 0.44
11 8 0.19
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (10 bp):
AAAAATTAAT
Found at i:558810 original size:2 final size:2
Alignment explanation
Indices: 558797--558829 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
558787 TAAGGGCTTA
558797 AT AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
558830 TACCATACTC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:564811 original size:8 final size:8
Alignment explanation
Indices: 564798--564823 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
564788 TTAAAAGCCA
564798 AATAAAAC
1 AATAAAAC
564806 AATAAAAC
1 AATAAAAC
564814 AATAAAAC
1 AATAAAAC
564822 AA
1 AA
564824 ATTAAAACAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.77, C:0.12, G:0.00, T:0.12
Consensus pattern (8 bp):
AATAAAAC
Found at i:566828 original size:96 final size:96
Alignment explanation
Indices: 566656--566847 Score: 230
Period size: 96 Copynumber: 2.0 Consensus size: 96
566646 TTTTGGGAAA
** *
566656 AAGGATATTCGATTATCTCGATTTGAAGAAAGGTTACACCTAATAAGTTAAGGCGCAATATTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTACACCTAATAAGTTAAGGCACAATATTTCA
*
566721 GAATCGAAGAT-AAGGAAACATTGCCTCGATT
66 GAATCGAAGATAAAAGAAA-ATTGCCTCGATT
* * * * * *
566752 AAGGGTATTCGATTATTTCGATTTGAGGAAAAATTGCACCTAGTGAGTTAAGGCACAA-ATTTTC
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTACACCTAATAAGTTAAGGCACAATA-TTTC
566816 -GAAACTCG-AGATAAAAGAAAATTGCCTCGATT
65 AG-AA-TCGAAGATAAAAGAAAATTGCCTCGATT
566848 TTAAAGTTTT
Statistics
Matches: 82, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
95 2 0.02
96 71 0.87
97 9 0.11
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTACACCTAATAAGTTAAGGCACAATATTTCA
GAATCGAAGATAAAAGAAAATTGCCTCGATT
Found at i:567139 original size:59 final size:59
Alignment explanation
Indices: 567073--567622 Score: 548
Period size: 59 Copynumber: 9.4 Consensus size: 59
567063 CTTGGATACC
** *
567073 CGGGGGT-AAAATGGTAATTTTAGGAAAATTCAGGGTTAAAAATGGAATTTTTGAAAGTT
1 CGGGGGTAAAAATGG-AATTTTAGGAAGTTTCAGGGTTAAAAATGGGATTTTTGAAAGTT
* * *
567132 CGGGGGTAAAAATGGAATTTTTGGAAGTTTCAGGGTCAAAAATGGGATTTTTGGAAGTT
1 CGGGGGTAAAAATGGAATTTTAGGAAGTTTCAGGGTTAAAAATGGGATTTTTGAAAGTT
* * *
567191 CGAGGGTAAAAATAGAATTTT-GGAAGTTTC-GAGG-TCAAAATGGGATTTTT-AGAAGTT
1 CGGGGGTAAAAATGGAATTTTAGGAAGTTTCAG-GGTTAAAAATGGGATTTTTGA-AAGTT
** * * * * **
567248 TAGGGGTAAAAATGGAATTCTT-GGGAGTTTTAGGGTTAAAAATAGAATTTTCAAAAGTT
1 CGGGGGTAAAAATGGAATT-TTAGGAAGTTTCAGGGTTAAAAATGGGATTTTTGAAAGTT
* * * * * *
567307 CGAGGGTAAAAATGGAATTCTTA-AAAGTTTCGGGGTCAAAAATGGGATTTTCGTAAGTT
1 CGGGGGTAAAAATGGAATT-TTAGGAAGTTTCAGGGTTAAAAATGGGATTTTTGAAAGTT
* * *
567366 CGAGGGGTAAAAACGGAATTCTTAAG-AGTTTC-GAGGTCAAAAATGGGATTTTTGAAAGTT
1 CG-GGGGTAAAAATGGAATT-TTAGGAAGTTTCAG-GGTTAAAAATGGGATTTTTGAAAGTT
* *
567426 CGAGGGTAAAAATGGAATTTTTGGAAGTTTC-GAGGTTAAAAATGGGATTTTTGAAAGTT
1 CGGGGGTAAAAATGGAATTTTAGGAAGTTTCAG-GGTTAAAAATGGGATTTTTGAAAGTT
* * * ** *
567485 CGAGGGTAAAAAGGGAATTTTTAGG-AGTTTTAGGGTCGAAAATGGGATTTTTGGAAGTT
1 CGGGGGTAAAAATGGAA-TTTTAGGAAGTTTCAGGGTTAAAAATGGGATTTTTGAAAGTT
* * * * * **
567544 TGGGGGTAAAAATGGAATTTTTGGGAGTTTTAGGG-TCAAAATGGGATTTTCAAAAGTT
1 CGGGGGTAAAAATGGAATTTTAGGAAGTTTCAGGGTTAAAAATGGGATTTTTGAAAGTT
*
567602 CGGGGGTAAAAAGGGAATTTT
1 CGGGGGTAAAAATGGAATTTT
567623 TGGACAATTT
Statistics
Matches: 416, Mismatches: 60, Indels: 31
0.82 0.12 0.06
Matches are distributed among these distances:
57 35 0.08
58 68 0.16
59 247 0.59
60 66 0.16
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (59 bp):
CGGGGGTAAAAATGGAATTTTAGGAAGTTTCAGGGTTAAAAATGGGATTTTTGAAAGTT
Found at i:567506 original size:29 final size:29
Alignment explanation
Indices: 567076--567624 Score: 313
Period size: 29 Copynumber: 18.7 Consensus size: 29
567066 GGATACCCGG
* * * *
567076 GGGTAAAATGGTAATTTTAGGAAAATTC-A
1 GGGTAAAAAGGGAATTTT-TGAAAGTTCGA
* *
567105 GGGTTAAAAATGGAATTTTTGAAAGTTCGG
1 GGG-TAAAAAGGGAATTTTTGAAAGTTCGA
* *
567135 GGGTAAAAATGGAATTTTTGGAAGTTTC-A
1 GGGTAAAAAGGGAATTTTTGAAAG-TTCGA
*
567164 GGGTCAAAAATGGG-ATTTTTGGAAGTTCGA
1 GGGT-AAAAA-GGGAATTTTTGAAAGTTCGA
** *
567194 GGGTAAAAATAGAA-TTTTGGAAGTTTCGA
1 GGGTAAAAAGGGAATTTTTGAAAG-TTCGA
* *
567223 -GGTCAAAATGGG-ATTTTT-AGAAGTT-TA
1 GGGT-AAAAAGGGAATTTTTGA-AAGTTCGA
* * ** **
567250 GGGGTAAAAATGGAATTCTTGGGAGTTTTA
1 -GGGTAAAAAGGGAATTTTTGAAAGTTCGA
** **
567280 GGGTTAAAAATAGAATTTTCAAAAGTTCGA
1 GGG-TAAAAAGGGAATTTTTGAAAGTTCGA
* * *
567310 GGGTAAAAATGGAATTCTTAAAAGTTTCG-
1 GGGTAAAAAGGGAATTTTTGAAAG-TTCGA
* *
567339 GGGTCAAAAATGGG-ATTTTCGTAAGTTCGA
1 GGGT-AAAAA-GGGAATTTTTGAAAGTTCGA
* *
567369 GGGGTAAAAACGGAATTCTT-AAGAGTTTCGA
1 -GGGTAAAAAGGGAATTTTTGAA-AG-TTCGA
567400 -GGTCAAAAATGGG-ATTTTTGAAAGTTCGA
1 GGGT-AAAAA-GGGAATTTTTGAAAGTTCGA
* *
567429 GGGTAAAAATGGAATTTTTGGAAGTTTCGA
1 GGGTAAAAAGGGAATTTTTGAAAG-TTCGA
*
567459 GGTTAAAAATGGG-ATTTTTGAAAGTTCGA
1 GGGTAAAAA-GGGAATTTTTGAAAGTTCGA
* **
567488 GGGTAAAAAGGGAATTTTT-AGGAGTTTTA
1 GGGTAAAAAGGGAATTTTTGA-AAGTTCGA
* * * *
567517 GGGTCGAAAATGGG-ATTTTTGGAAGTTTGG
1 GGGT--AAAAAGGGAATTTTTGAAAGTTCGA
* ** **
567547 GGGTAAAAATGGAATTTTTGGGAGTTTTA
1 GGGTAAAAAGGGAATTTTTGAAAGTTCGA
* ** *
567576 GGGTCAAAATGGG-ATTTTCAAAAGTTCGG
1 GGGT-AAAAAGGGAATTTTTGAAAGTTCGA
567605 GGGTAAAAAGGGAATTTTTG
1 GGGTAAAAAGGGAATTTTTG
567625 GACAATTTAG
Statistics
Matches: 406, Mismatches: 74, Indels: 80
0.73 0.13 0.14
Matches are distributed among these distances:
27 1 0.00
28 41 0.10
29 190 0.47
30 148 0.36
31 26 0.06
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (29 bp):
GGGTAAAAAGGGAATTTTTGAAAGTTCGA
Found at i:568586 original size:18 final size:17
Alignment explanation
Indices: 568554--568606 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 17
568544 ATTTTCCTTT
*
568554 TATTATTATTTTATTAA
1 TATTATTGTTTTATTAA
568571 TATTATTGTATTTATT-A
1 TATTATTGT-TTTATTAA
568588 TATTTATTGTTATTATTAA
1 TA-TTATTGTT-TTATTAA
568607 AACATTCTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
17 12 0.39
18 18 0.58
19 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (17 bp):
TATTATTGTTTTATTAA
Done.