Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014298.1 Kokia drynarioides strain JFW-HI SEQ_129333, 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: 107721
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:18843 original size:18 final size:18
Alignment explanation
Indices: 18808--18842 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
18798 ATTTTATTTT
18808 TATATAAATAAGTTAAAA
1 TATATAAATAAGTTAAAA
*
18826 TATAT-AATACGTTAAAA
1 TATATAAATAAGTTAAAA
18843 ACACTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.57, C:0.03, G:0.06, T:0.34
Consensus pattern (18 bp):
TATATAAATAAGTTAAAA
Found at i:20089 original size:27 final size:27
Alignment explanation
Indices: 20045--20097 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
20035 CCAGTATATA
* *
20045 AAATAGAACTTGAAATTTATAGGTGTC
1 AAATAGAACTCGAAATTTATAAGTGTC
*
20072 AAATAGAACTCGATATTTATAAGTGT
1 AAATAGAACTCGAAATTTATAAGTGT
20098 TGAGATCTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.34
Consensus pattern (27 bp):
AAATAGAACTCGAAATTTATAAGTGTC
Found at i:34709 original size:44 final size:44
Alignment explanation
Indices: 34645--34739 Score: 145
Period size: 44 Copynumber: 2.2 Consensus size: 44
34635 GATGACATCA
* * *
34645 TCGATGATGTCATTATGCTTATGTGGCACGCCACGTAGATTATT
1 TCGATGATATCATTATGCTTATGTGGCACGCCACATAGACTATT
* *
34689 TTGATGATATCATTATGCTTATGTGGCATGCCACATAGACTATT
1 TCGATGATATCATTATGCTTATGTGGCACGCCACATAGACTATT
34733 TCGATGA
1 TCGATGA
34740 CCTAGCATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.37
Consensus pattern (44 bp):
TCGATGATATCATTATGCTTATGTGGCACGCCACATAGACTATT
Found at i:36773 original size:17 final size:17
Alignment explanation
Indices: 36737--36776 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
36727 ATGGAAGCAT
* **
36737 TTAAGTTGATATTATGA
1 TTAAATTGATATTACAA
36754 TTAAATTGATATTACAA
1 TTAAATTGATATTACAA
36771 TTAAAT
1 TTAAAT
36777 CTAATTTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (17 bp):
TTAAATTGATATTACAA
Found at i:37896 original size:30 final size:31
Alignment explanation
Indices: 37860--37922 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
37850 TACATTTCAG
37860 TCCCTCAAC-TTTGAAAATATGACAAAACAA
1 TCCCTCAACTTTTGAAAATATGACAAAACAA
*
37890 TCCCTCAACTTTTGAAAATGTGACAAAACAA
1 TCCCTCAACTTTTGAAAATATGACAAAACAA
37921 TC
1 TC
37923 TTTTTCCGTC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 9 0.29
31 22 0.71
ACGTcount: A:0.43, C:0.24, G:0.08, T:0.25
Consensus pattern (31 bp):
TCCCTCAACTTTTGAAAATATGACAAAACAA
Found at i:57509 original size:124 final size:124
Alignment explanation
Indices: 57358--57603 Score: 363
Period size: 128 Copynumber: 2.0 Consensus size: 124
57348 AGGAAGTAAG
* *
57358 TTTTTTTTTTTTCATTCAAGTATAACTCACACACCTACAT-TCGT-A-CTAGATTATCACACAGG
1 TTTTTTTTTTTTCATTCAAGTACAACTCACACACCTACATAT-GTAATCTAGATTACCACACAGG
* *
57420 CTATGCTGCGGATCGGTCCCACGTATCGGGCAAGATGGGGTTCTAGGAGGAAGTAATTTT
65 CTATGCTGCGGATCGATCCCACCTATCGGGCAAGATGGGGTTCTAGGAGGAAGTAATTTT
*
57480 TTTTTTTTTAATTTCATTCAAGTACAACTCACACACCTACATATGTACATTCTAGATTACCGCAC
1 TTTTTTTTT--TTTCATTCAAGTACAACTCACACACCTACATATGTA-A-TCTAGATTACCACAC
* *
57545 AGGCTATGCTGCGGATCGATCCCACCTATCGGGCAAGGTGGGGTTCTATGAGGAAGTAA
62 AGGCTATGCTGCGGATCGATCCCACCTATCGGGCAAGATGGGGTTCTAGGAGGAAGTAA
57604 GATGCTTAAG
Statistics
Matches: 110, Mismatches: 7, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
122 9 0.08
124 32 0.29
125 1 0.01
126 1 0.01
128 67 0.61
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (124 bp):
TTTTTTTTTTTTCATTCAAGTACAACTCACACACCTACATATGTAATCTAGATTACCACACAGGC
TATGCTGCGGATCGATCCCACCTATCGGGCAAGATGGGGTTCTAGGAGGAAGTAATTTT
Found at i:66775 original size:29 final size:29
Alignment explanation
Indices: 66741--66827 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
66731 GTTACAAATA
*
66741 TAGTCATGTTACAGATATAGTTATGGATG
1 TAGTCATGTTACAGATATAGTTACGGATG
* *
66770 CT-GTCATGTCACAAATATAGTTACGGATG
1 -TAGTCATGTTACAGATATAGTTACGGATG
* * * *
66799 TAGACATGATACAGATACAGTTACAGATG
1 TAGTCATGTTACAGATATAGTTACGGATG
66828 CAGACATGAT
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
28 1 0.02
29 45 0.96
30 1 0.02
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.31
Consensus pattern (29 bp):
TAGTCATGTTACAGATATAGTTACGGATG
Found at i:66832 original size:29 final size:29
Alignment explanation
Indices: 66724--66839 Score: 90
Period size: 29 Copynumber: 4.0 Consensus size: 29
66714 ATCATGTCGT
* ** * *
66724 AGATACAGTTACAAATATAGTCATGTTAC
1 AGATACAGTTACAGATGCAGACATGATAC
* ** * *
66753 AGATATAGTTATGGATGCTGTCATG-TCAC
1 AGATACAGTTACAGATGCAGACATGAT-AC
* * * *
66782 AAATATAGTTACGGATGTAGACATGATAC
1 AGATACAGTTACAGATGCAGACATGATAC
66811 AGATACAGTTACAGATGCAGACATGATAC
1 AGATACAGTTACAGATGCAGACATGATAC
66840 CCCCATTCGT
Statistics
Matches: 69, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
28 1 0.01
29 67 0.97
30 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (29 bp):
AGATACAGTTACAGATGCAGACATGATAC
Found at i:67030 original size:40 final size:40
Alignment explanation
Indices: 66926--67030 Score: 129
Period size: 40 Copynumber: 2.6 Consensus size: 40
66916 CACATCGTAG
* * ** *
66926 TGTTTACAGTGTCACTATCAATTCAGTTGTAATCTTGCAG
1 TGTTTACAGTGTCACTGTCAGTTCAGTTAAAATCTTGCAA
* *
66966 TGTTTACAGTGTCACGGTCGGTTCAGTTAAAATCTTGCAA
1 TGTTTACAGTGTCACTGTCAGTTCAGTTAAAATCTTGCAA
* *
67006 TGTTAACAGTGTCACTGCCAGTTCA
1 TGTTTACAGTGTCACTGTCAGTTCA
67031 ATAAATATTC
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 54 1.00
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (40 bp):
TGTTTACAGTGTCACTGTCAGTTCAGTTAAAATCTTGCAA
Found at i:67484 original size:41 final size:41
Alignment explanation
Indices: 67439--67529 Score: 101
Period size: 41 Copynumber: 2.2 Consensus size: 41
67429 TTATTACAGA
** * * * *
67439 CCATGTGTCTTAAAACAATATGCACACACCCTGACACACGC
1 CCATGTGTCCCAAAACAACATACACACACCCTAACACACAC
** *
67480 CCATGTACCCCAAAACAGCATACACACACCCTAACACACAC
1 CCATGTGTCCCAAAACAACATACACACACCCTAACACACAC
67521 CCATGTGTC
1 CCATGTGTC
67530 AGCACATGTG
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.35, C:0.38, G:0.10, T:0.16
Consensus pattern (41 bp):
CCATGTGTCCCAAAACAACATACACACACCCTAACACACAC
Found at i:67672 original size:94 final size:94
Alignment explanation
Indices: 67461--67675 Score: 231
Period size: 94 Copynumber: 2.3 Consensus size: 94
67451 AAACAATATG
* *
67461 CACACACCCTGACACACGCCCATGTACCCCAAAACAGCATACACACACCCTAACACACACCCATG
1 CACACACCCTGACACACGCCCGTGTGCCCCAAAACAGCATACACACACCCTAACACACACCCATG
*
67526 TGTCAGCACATGTGCCCTAGAACAGCATA
66 TGCCAGCACATGTGCCCTAGAACAGCATA
* * * * * * * *
67555 CATACACTCTGACACATAG-CCGTGTGCCTCC-AAACAGTATACACATACCCTGACACATACTCA
1 CACACACCCTGACACA-CGCCCGTGTGCC-CCAAAACAGCATACACACACCCTAACACACACCCA
* * * *
67618 TGTGCCAGC-CTGTGTGTCTCTA-AACTGTATA
64 TGTGCCAGCAC-ATGTG-CCCTAGAACAGCATA
67649 CACACACCCTGACACACGCCCGTGTGC
1 CACACACCCTGACACACGCCCGTGTGC
67676 TAGCCCATGT
Statistics
Matches: 98, Mismatches: 18, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
93 2 0.02
94 89 0.91
95 7 0.07
ACGTcount: A:0.31, C:0.37, G:0.14, T:0.18
Consensus pattern (94 bp):
CACACACCCTGACACACGCCCGTGTGCCCCAAAACAGCATACACACACCCTAACACACACCCATG
TGCCAGCACATGTGCCCTAGAACAGCATA
Found at i:67675 original size:53 final size:52
Alignment explanation
Indices: 67572--67706 Score: 162
Period size: 53 Copynumber: 2.6 Consensus size: 52
67562 TCTGACACAT
* * *
67572 AGCCGTGTGCCTCCAAACAGTATACACATACCCTGACACATACTCATGTGCC
1 AGCCGTGTGCCTCCAAACAGTATACACACACCCTGACACACACCCATGTGCC
* * * * * *
67624 AGCCTGTGTGTCTCTAAACTGTATACACACACCCTGACACACGCCCGTGTGCT
1 AGCC-GTGTGCCTCCAAACAGTATACACACACCCTGACACACACCCATGTGCC
*
67677 AGCCCATGTGCCTCCAAACAGTATACACAC
1 AG-CCGTGTGCCTCCAAACAGTATACACAC
67707 CTACACACCT
Statistics
Matches: 68, Mismatches: 13, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
52 4 0.06
53 62 0.91
54 2 0.03
ACGTcount: A:0.27, C:0.35, G:0.16, T:0.21
Consensus pattern (52 bp):
AGCCGTGTGCCTCCAAACAGTATACACACACCCTGACACACACCCATGTGCC
Found at i:67770 original size:43 final size:46
Alignment explanation
Indices: 67678--67780 Score: 122
Period size: 43 Copynumber: 2.3 Consensus size: 46
67668 CCGTGTGCTA
* * * *
67678 GCCCATGTGCCTCCAAACAGTATACACACCTACACACCTTGACATAT
1 GCCCGTGTGCCTCCAAACAG-ATACACACCTACACACCCTAACACAT
* *
67725 GCCTGTGTGCCTCCAAACAG-TACAC-TC-ACACACCCTAACACAT
1 GCCCGTGTGCCTCCAAACAGATACACACCTACACACCCTAACACAT
67768 GCCCGTGTGCCTC
1 GCCCGTGTGCCTC
67781 TTGCAACTCA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
43 25 0.51
44 1 0.02
45 5 0.10
47 18 0.37
ACGTcount: A:0.27, C:0.39, G:0.14, T:0.20
Consensus pattern (46 bp):
GCCCGTGTGCCTCCAAACAGATACACACCTACACACCCTAACACAT
Found at i:68847 original size:41 final size:41
Alignment explanation
Indices: 68790--68924 Score: 164
Period size: 43 Copynumber: 3.2 Consensus size: 41
68780 ATAGATACTG
*
68790 GTGCC-CCAGAACAGTATACACACACCCTGACACATGCCCGT
1 GTGCCTCCA-AACAGTATACACACACCCTGACACACGCCCGT
* *
68831 GTGCCTCCAAACAGTATACACACACATCTTGACACACGCCTGT
1 GTGCCTCCAAACAGTATACACACAC--CCTGACACACGCCCGT
* * *
68874 GTGCCTCTAAACAGTATACTGACACACCCTGACACACACTCGT
1 GTGCCTCCAAACAGTATAC--ACACACCCTGACACACGCCCGT
68917 GTGCCTCC
1 GTGCCTCC
68925 TACAACTCAT
Statistics
Matches: 80, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
41 21 0.26
42 3 0.04
43 50 0.62
45 6 0.08
ACGTcount: A:0.28, C:0.37, G:0.16, T:0.19
Consensus pattern (41 bp):
GTGCCTCCAAACAGTATACACACACCCTGACACACGCCCGT
Found at i:81200 original size:7 final size:7
Alignment explanation
Indices: 81190--81214 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
81180 TTAAAAATTG
81190 AAAATAT
1 AAAATAT
81197 AAAATAT
1 AAAATAT
81204 AAAATAT
1 AAAATAT
81211 AAAA
1 AAAA
81215 AAATAAGTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
AAAATAT
Found at i:90708 original size:7 final size:7
Alignment explanation
Indices: 90698--90742 Score: 90
Period size: 7 Copynumber: 6.4 Consensus size: 7
90688 TCTTTTTACT
90698 TTTCAAA
1 TTTCAAA
90705 TTTCAAA
1 TTTCAAA
90712 TTTCAAA
1 TTTCAAA
90719 TTTCAAA
1 TTTCAAA
90726 TTTCAAA
1 TTTCAAA
90733 TTTCAAA
1 TTTCAAA
90740 TTT
1 TTT
90743 AATTGTCAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (7 bp):
TTTCAAA
Found at i:91167 original size:32 final size:33
Alignment explanation
Indices: 91122--91191 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 33
91112 ATCCTATTTT
91122 ATATATTAATTATAACAAAT-TAAAAAATAAAA
1 ATATATTAATTATAACAAATCTAAAAAATAAAA
** * * * *
91154 ATATATTTTTTATAAGAATTCTAGAAAATAATA
1 ATATATTAATTATAACAAATCTAAAAAATAAAA
91187 ATATA
1 ATATA
91192 AAATTGAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
32 16 0.52
33 15 0.48
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (33 bp):
ATATATTAATTATAACAAATCTAAAAAATAAAA
Found at i:91605 original size:25 final size:24
Alignment explanation
Indices: 91528--91606 Score: 68
Period size: 26 Copynumber: 3.1 Consensus size: 24
91518 ATTATTGAGT
*
91528 AAGAAGATAAATTTTTTGAAAAAGAAA
1 AAGAAGA-AAATTTTTT-AAGAAG-AA
* * *
91555 AAGAAGAAAACTCTTGAAGAATGAA
1 AAGAAGAAAATTTTTTAAGAA-GAA
*
91580 AGGAAGCAAAATTTTTTAAGAAGAA
1 AAGAAG-AAAATTTTTTAAGAAGAA
91605 AA
1 AA
91607 ATAAACAGAA
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
25 15 0.37
26 19 0.46
27 7 0.17
ACGTcount: A:0.57, C:0.04, G:0.18, T:0.22
Consensus pattern (24 bp):
AAGAAGAAAATTTTTTAAGAAGAA
Found at i:96143 original size:30 final size:31
Alignment explanation
Indices: 96102--96162 Score: 74
Period size: 33 Copynumber: 2.0 Consensus size: 31
96092 AAAATAAATA
96102 TTAATTTTTAAT-TAAT-TATT-TATTATTT
1 TTAATTTTTAATATAATATATTATATTATTT
*
96130 TTAATATTATTAATATAATATTTTATATTATTT
1 TTAAT-TT-TTAATATAATATATTATATTATTT
96163 GAGATAACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
28 5 0.19
29 2 0.07
30 5 0.19
31 4 0.15
32 3 0.11
33 8 0.30
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (31 bp):
TTAATTTTTAATATAATATATTATATTATTT
Found at i:97431 original size:18 final size:18
Alignment explanation
Indices: 97384--97438 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
97374 CATACCGATT
97384 TTTTTTATTTTTTTAA-A
1 TTTTTTATTTTTTTAATA
97401 TTAATTTTA--TTTTTAATA
1 TT--TTTTATTTTTTTAATA
97419 TTTTTTATTTTTTTAATA
1 TTTTTTATTTTTTTAATA
97437 TT
1 TT
97439 AAAAAATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
16 5 0.15
17 9 0.27
18 14 0.42
19 5 0.15
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTTTATTTTTTTAATA
Found at i:99214 original size:19 final size:20
Alignment explanation
Indices: 99176--99216 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
99166 TAGAAAAATC
99176 TTATTAAGTATAAATTATAA
1 TTATTAAGTATAAATTATAA
99196 TTATT-AGT-TAAATTTATAA
1 TTATTAAGTATAAA-TTATAA
99215 TT
1 TT
99217 TTCAAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 11 0.55
20 5 0.25
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (20 bp):
TTATTAAGTATAAATTATAA
Found at i:102564 original size:29 final size:29
Alignment explanation
Indices: 102490--102927 Score: 327
Period size: 29 Copynumber: 14.9 Consensus size: 29
102480 ACATCCGAGA
*
102490 GTAAAATGGTAATTTTTTGGAAGTATCGGG
1 GTAAAATGGTAA-TTTTTGGAAGTTTCGGG
*
102520 GTCAAAAAT-G-AGATTTTTGGAAGTTTAGGG
1 GT--AAAATGGTA-ATTTTTGGAAGTTTCGGG
* *
102550 GTAAAATGGTAATTTTTAGAAGTTTCGAG
1 GTAAAATGGTAATTTTTGGAAGTTTCGGG
102579 GTCAAAAATGGT-ATTTTTGGAAG-TTCGAGG
1 GT--AAAATGGTAATTTTTGGAAGTTTCG-GG
* *
102609 TTAAAATGGTAATTTTTGAAAGGTTT-GGG
1 GTAAAATGGTAATTTTTGGAA-GTTTCGGG
* *
102638 GTCAAAAAAGG-GA-TTTTGGAAG-TTCGGGG
1 GT--AAAATGGTAATTTTTGGAAGTTTC-GGG
*
102667 GTAAAATGGTAATTTTTGGAAGGTTCGGG
1 GTAAAATGGTAATTTTTGGAAGTTTCGGG
*
102696 GTCAAAAATGG-GA-TTTTGGAAG-TTCGGGG
1 GT--AAAATGGTAATTTTTGGAAGTTTC-GGG
* * * *
102725 GTAAAATGGTATTTTTTGAAAGTTTTGAG
1 GTAAAATGGTAATTTTTGGAAGTTTCGGG
102754 GTCAAAAATGG-AATTTTTGGAAG-TTCGGGG
1 GT--AAAATGGTAATTTTTGGAAGTTTC-GGG
* * * *
102784 GTTAAATGGTAATTTTTGAAAGGTTCGAG
1 GTAAAATGGTAATTTTTGGAAGTTTCGGG
*
102813 GTCAAAAATGG-GATTTTTGGAAG-TTCAGGG
1 GT--AAAATGGTAATTTTTGGAAGTTTC-GGG
*
102843 GTAAAATGGTAATTTATGGAAGTTTCGGG
1 GTAAAATGGTAATTTTTGGAAGTTTCGGG
*
102872 GTCAAAAATGGGT--TTTTTAGAAG-TTCAGGG
1 GT--AAAAT-GGTAATTTTTGGAAGTTTC-GGG
*
102902 GTAAAATGGTAATTTTTAGACAGTTT
1 GTAAAATGGTAATTTTTGGA-AGTTT
102928 AGGGACCTTC
Statistics
Matches: 330, Mismatches: 36, Indels: 83
0.73 0.08 0.18
Matches are distributed among these distances:
27 18 0.05
28 36 0.11
29 132 0.40
30 91 0.28
31 45 0.14
32 8 0.02
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.35
Consensus pattern (29 bp):
GTAAAATGGTAATTTTTGGAAGTTTCGGG
Found at i:102595 original size:59 final size:59
Alignment explanation
Indices: 102490--102927 Score: 578
Period size: 59 Copynumber: 7.4 Consensus size: 59
102480 ACATCCGAGA
* * *
102490 GTAAAATGGTAATTTTTTGGAAGTATCGGGGTCAAAAATGAGATTTTTGGAAGTTTAGGG
1 GTAAAATGGTAA-TTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCAGGG
* * *
102550 GTAAAATGGTAATTTTTAGAAGTTTCGAGGTCAAAAATGGTATTTTTGGAAGTTC-GAGG
1 GTAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCAG-GG
* * * *
102609 TTAAAATGGTAATTTTTGAAAGGTTT-GGGGTCAAAAAAGGGA-TTTTGGAAGTTCGGGG
1 GTAAAATGGTAATTTTTGGAA-GTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCAGGG
* *
102667 GTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGA-TTTTGGAAGTTCGGGG
1 GTAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCAGGG
* * * * * *
102725 GTAAAATGGTATTTTTTGAAAGTTTTGAGGTCAAAAATGGAATTTTTGGAAGTTCGGGG
1 GTAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCAGGG
* * * *
102784 GTTAAATGGTAATTTTTGAAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCAGGG
1 GTAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCAGGG
* * *
102843 GTAAAATGGTAATTTATGGAAGTTTCGGGGTCAAAAATGGGTTTTTTAGAAGTTCAGGG
1 GTAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCAGGG
*
102902 GTAAAATGGTAATTTTTAGACAGTTT
1 GTAAAATGGTAATTTTTGGA-AGTTT
102928 AGGGACCTTC
Statistics
Matches: 335, Mismatches: 37, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
57 3 0.01
58 101 0.30
59 210 0.63
60 21 0.06
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.35
Consensus pattern (59 bp):
GTAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCAGGG
Found at i:102699 original size:117 final size:117
Alignment explanation
Indices: 102485--102918 Score: 586
Period size: 117 Copynumber: 3.7 Consensus size: 117
102475 TTTGGACATC
* * * * *
102485 CGAGAGTAAAATGGTAATTTTTTGGAAGTATCGGGGTCAAAAATGAGATTTTTGGAAGTTTAGGG
1 CGAGGGTAAAATGGTAA-TTTTTGAAAGT-TTGGGGTCAAAAATGGGATTTTTGGAAGTTCAGGG
* * *
102550 GTAAAATGGTAATTTTTAGAAGTTTCGAGGTCAAAAATGGTATTTTTGGAAGTT
64 GTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTT
* * *
102604 CGAGGTTAAAATGGTAATTTTTGAAAGGTTTGGGGTCAAAAAAGGGA-TTTTGGAAGTTCGGGGG
1 CGAGGGTAAAATGGTAATTTTTGAAA-GTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCAGGGG
*
102668 TAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGA-TTTTGGAAGTT
65 TAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTT
* * * * *
102720 CGGGGGTAAAATGGTATTTTTTGAAAGTTTTGAGGTCAAAAATGGAATTTTTGGAAGTTCGGGGG
1 CGAGGGTAAAATGGTAATTTTTGAAAG-TTTGGGGTCAAAAATGGGATTTTTGGAAGTTCAGGGG
* *
102785 TTAAATGGTAATTTTTGAAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTT
65 TAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTT
* * * *
102838 C-AGGGGTAAAATGGTAATTTATGGAAGTTTCGGGGTCAAAAATGGGTTTTTTAGAAGTTCAGGG
1 CGA-GGGTAAAATGGTAATTTTTGAAAGTTT-GGGGTCAAAAATGGGATTTTTGGAAGTTCAGGG
102902 GTAAAATGGTAATTTTT
64 GTAAAATGGTAATTTTT
102919 AGACAGTTTA
Statistics
Matches: 278, Mismatches: 31, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
115 1 0.00
116 50 0.18
117 110 0.40
118 100 0.36
119 17 0.06
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.34
Consensus pattern (117 bp):
CGAGGGTAAAATGGTAATTTTTGAAAGTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCAGGGGT
AAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTT
Found at i:104642 original size:6 final size:6
Alignment explanation
Indices: 104618--104698 Score: 82
Period size: 6 Copynumber: 14.0 Consensus size: 6
104608 CTTTGGACTT
*
104618 TTTAAC TTTGAAA -TTAAA TTTAAA TTTAAA TTT-AA TTTAAA TTTAAGA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA-A
* *
104666 -TT-AA TTTAAA TTTAAA -ATAAA TCTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
104699 ATAAATTAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
4 1 0.02
5 15 0.23
6 45 0.70
7 3 0.05
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:104654 original size:11 final size:11
Alignment explanation
Indices: 104631--104697 Score: 64
Period size: 11 Copynumber: 5.9 Consensus size: 11
104621 AACTTTGAAA
104631 TTAAATTTAAAT
1 TTAAATTT-AAT
104643 TTAAATTTAAT
1 TTAAATTTAAT
*
104654 TTAAATTTAAGA
1 TTAAATTTAA-T
104666 TT-AATTTAAAT
1 TTAAATTT-AAT
* *
104677 TTAAAATAAAT
1 TTAAATTTAAT
*
104688 CTAAATTTAA
1 TTAAATTTAA
104698 AATAAATTAA
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
11 30 0.67
12 15 0.33
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:104654 original size:17 final size:17
Alignment explanation
Indices: 104618--104705 Score: 106
Period size: 17 Copynumber: 5.1 Consensus size: 17
104608 CTTTGGACTT
*
104618 TTTAACTTTGAAATTAAA
1 TTTAAATTT-AAATTAAA
*
104636 TTTAAATTTAAATTTAA
1 TTTAAATTTAAATTAAA
104653 TTTAAATTTAAGATT-AA
1 TTTAAATTTAA-ATTAAA
*
104670 TTTAAATTTAAAATAAA
1 TTTAAATTTAAATTAAA
* *
104687 TCTAAATTTAAAATAAA
1 TTTAAATTTAAATTAAA
104704 TT
1 TT
104706 AAAAAGGGCC
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
16 2 0.03
17 50 0.79
18 11 0.17
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (17 bp):
TTTAAATTTAAATTAAA
Found at i:105720 original size:201 final size:200
Alignment explanation
Indices: 105429--105796 Score: 524
Period size: 201 Copynumber: 1.8 Consensus size: 200
105419 CGTGGGTTTG
* ** * * *
105429 ATTTGGTTTTCTTCTCAGTATCTCATTGGGAAGATGACTGCGTCGTTTCTTTCAATCTGCTTCTC
1 ATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATAACCGCGTCGCTTCTTTCAATCTGCTTCTC
* *
105494 TATATCTCATCAAGAAGATGAATTTGGTCCACTTCTCAGTATTTCATCAGGAA-TAAACCTTTTT
66 TATATCTCATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGTAAACC-TTTT
* *
105558 ATCACTTCGACTTGCTTTTCAGTGTCTCATCAAGAAGCCAGAGTTCGAAGATTTTGCTCATATCG
130 ATCACTTCGACCTGCTTCTCAGTGTCTCATCAAGAAGCCAGAGTTCGAAGATTTTGCTCATATCG
105623 AGCCTC
195 AGCCTC
* *
105629 ATTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGATAACCGCGTCGCTTGTTTCAA-CTCGCTTC
1 ATTT-GGTCTTCTTCTCAGTATCTCATCAGGAAGATAACCGCGTCGCTTCTTTCAATCT-GCTTC
* * * *
105693 TCTGTATCTCATCAGGAAGGCGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGTTAACCTTT
64 TCTATATCTCATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGTAAACCTTT
* * *
105758 TATCGCTTCGACCTGCTTCTCGGTGTCTCATCAGGAAGC
129 TATCACTTCGACCTGCTTCTCAGTGTCTCATCAAGAAGC
105797 TGGTCACATC
Statistics
Matches: 146, Mismatches: 19, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
200 6 0.04
201 135 0.92
202 5 0.03
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (200 bp):
ATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATAACCGCGTCGCTTCTTTCAATCTGCTTCTC
TATATCTCATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGTAAACCTTTTA
TCACTTCGACCTGCTTCTCAGTGTCTCATCAAGAAGCCAGAGTTCGAAGATTTTGCTCATATCGA
GCCTC
Done.