Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014543.1 Kokia drynarioides strain JFW-HI SEQ_129582, 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: 69949
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 17 characters in sequence are not A, C, G, or T
Found at i:2955 original size:29 final size:29
Alignment explanation
Indices: 2923--3014 Score: 91
Period size: 29 Copynumber: 3.1 Consensus size: 29
2913 TGTAAACTTA
2923 TTTTATGTAAAATTTCATTTTTAACCTTT
1 TTTTATGTAAAATTTCATTTTTAACCTTT
*** *
2952 TTTT-T-T-TTTTTTCAATTTTTTTAAACTTAT
1 TTTTATGTAAAATTTC-A--TTTTTAACCTT-T
2982 TTTTATGTAAAATTTCATTTTTAACCTTT
1 TTTTATGTAAAATTTCATTTTTAACCTTT
3011 TTTT
1 TTTT
3015 TATTTTTTCA
Statistics
Matches: 48, Mismatches: 8, Indels: 14
0.69 0.11 0.20
Matches are distributed among these distances:
26 4 0.08
27 2 0.04
28 1 0.02
29 19 0.40
30 15 0.31
31 1 0.02
32 2 0.04
33 4 0.08
ACGTcount: A:0.24, C:0.09, G:0.02, T:0.65
Consensus pattern (29 bp):
TTTTATGTAAAATTTCATTTTTAACCTTT
Found at i:2979 original size:58 final size:60
Alignment explanation
Indices: 2915--3034 Score: 208
Period size: 59 Copynumber: 2.0 Consensus size: 60
2905 AAGAAATTTG
*
2915 TAAACTTA-TTTTATGTAAAATTTCATTTTTAACCTTTTTTTTTTTTTTTC-AATTTTTT
1 TAAACTTATTTTTATGTAAAATTTCATTTTTAACCTTTTTTTTATTTTTTCAAATTTTTT
2973 TAAACTTATTTTTATGTAAAATTTCATTTTTAACCTTTTTTTTATTTTTTCAAAATTTTTT
1 TAAACTTATTTTTATGTAAAATTTCATTTTTAACCTTTTTTTTATTTTTTC-AAATTTTTT
3034 T
1 T
3035 TTTTATATCT
Statistics
Matches: 58, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
58 8 0.14
59 41 0.71
61 9 0.16
ACGTcount: A:0.26, C:0.08, G:0.02, T:0.64
Consensus pattern (60 bp):
TAAACTTATTTTTATGTAAAATTTCATTTTTAACCTTTTTTTTATTTTTTCAAATTTTTT
Found at i:3047 original size:24 final size:23
Alignment explanation
Indices: 3008--3052 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
2998 ATTTTTAACC
*
3008 TTTTTTTTATTTTTTCAAAATTT
1 TTTTTTTTATTCTTTCAAAATTT
*
3031 TTTTTTTTATATCTTTCCAAAT
1 TTTTTTTTAT-TCTTTCAAAAT
3053 AATCAACTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.22, C:0.09, G:0.00, T:0.69
Consensus pattern (23 bp):
TTTTTTTTATTCTTTCAAAATTT
Found at i:9661 original size:6 final size:6
Alignment explanation
Indices: 9650--9706 Score: 55
Period size: 6 Copynumber: 9.5 Consensus size: 6
9640 AACAAATGAA
* * *
9650 TTTATG TTTATG TTTATG TTTATG TTCGTTTG TTTATT TTTAAG -TT-TG
1 TTTATG TTTATG TTTATG TTTATG TT--TATG TTTATG TTTATG TTTATG
9698 TTTATG TTT
1 TTTATG TTT
9707 CTTAAGAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
4 1 0.02
5 4 0.10
6 31 0.76
8 5 0.12
ACGTcount: A:0.14, C:0.02, G:0.16, T:0.68
Consensus pattern (6 bp):
TTTATG
Found at i:9700 original size:20 final size:20
Alignment explanation
Indices: 9660--9700 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
9650 TTTATGTTTA
*
9660 TGTTTATGTTTATGTTCGTT
1 TGTTTATGTTTAAGTTCGTT
* *
9680 TGTTTATTTTTAAGTTTGTT
1 TGTTTATGTTTAAGTTCGTT
9700 T
1 T
9701 ATGTTTCTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.12, C:0.02, G:0.17, T:0.68
Consensus pattern (20 bp):
TGTTTATGTTTAAGTTCGTT
Found at i:10537 original size:30 final size:30
Alignment explanation
Indices: 10501--10569 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
10491 TTGAATTAAT
10501 TCGGTTAA-TCGATCGAATTCAGTTAACCGG
1 TCGGTTAACT-GATCGAATTCAGTTAACCGG
*
10531 TCGGTTAACTGATCGAATTCGGTTAACCGG
1 TCGGTTAACTGATCGAATTCAGTTAACCGG
*
10561 TCGATTAAC
1 TCGGTTAAC
10570 AAAATTAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 35 0.97
31 1 0.03
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.30
Consensus pattern (30 bp):
TCGGTTAACTGATCGAATTCAGTTAACCGG
Found at i:11442 original size:20 final size:20
Alignment explanation
Indices: 11414--11475 Score: 69
Period size: 20 Copynumber: 3.1 Consensus size: 20
11404 AAACCCTTTT
11414 AAAAA-CTTAAAAATTATTA
1 AAAAATCTTAAAAATTATTA
11433 AAAAATCTTAAAAATTA-TA
1 AAAAATCTTAAAAATTATTA
11452 AACACAAT-TTATAAAATT-TTA
1 AA-A-AATCTTA-AAAATTATTA
11473 AAA
1 AAA
11476 TTATAAATTC
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
19 9 0.24
20 16 0.42
21 13 0.34
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAAATCTTAAAAATTATTA
Found at i:17516 original size:30 final size:30
Alignment explanation
Indices: 17466--17695 Score: 195
Period size: 30 Copynumber: 7.8 Consensus size: 30
17456 GAAATTGTAT
* *
17466 TTTGACCTC-AAACTTCCCAAAAATTTAGA
1 TTTGACCCCTAAACTTTCCAAAAATTTAGA
*
17495 TTTGACCCCTAAACTTTCCAAAAATTTGGA
1 TTTGACCCCTAAACTTTCCAAAAATTTAGA
* *
17525 TTTAACCCCTAAACTTTCCAAAAATTTGGA
1 TTTGACCCCTAAACTTTCCAAAAATTTAGA
* *
17555 TTT-AACCCTCAAACTTTCCAAAAA-TTATGT
1 TTTGACCCCT-AAACTTTCCAAAAATTTA-GA
* * * *
17585 TTTGACCCTTAAAATTTCAAAAAATTAAG-
1 TTTGACCCCTAAACTTTCCAAAAATTTAGA
* * * *
17614 TTTGA-CCCTCGAATTTTTCAAAAATTAAGA
1 TTTGACCCCT-AAACTTTCCAAAAATTTAGA
* * * *
17644 TTTGACCTCTGAACTTTCTAAAAA-TTATGT
1 TTTGACCCCTAAACTTTCCAAAAATTTA-GA
*
17674 TTTGACACC-AAACTTTCCAAAA
1 TTTGACCCCTAAACTTTCCAAAA
17696 TTTCATTTTT
Statistics
Matches: 165, Mismatches: 27, Indels: 18
0.79 0.13 0.09
Matches are distributed among these distances:
28 3 0.02
29 48 0.29
30 105 0.64
31 9 0.05
ACGTcount: A:0.37, C:0.21, G:0.07, T:0.35
Consensus pattern (30 bp):
TTTGACCCCTAAACTTTCCAAAAATTTAGA
Found at i:26144 original size:30 final size:30
Alignment explanation
Indices: 25856--26149 Score: 298
Period size: 30 Copynumber: 9.8 Consensus size: 30
25846 GAGAATACAA
** *
25856 GGTTAAAACATAATTTTAGAAAAAGTTTAGG
1 GGTTAAAATGTAATTTTAG-AGAAGTTTAGG
* *
25887 GGTAAAAATGTAATTTTAG-GAAAATTTA-G
1 GGTTAAAATGTAATTTTAGAG-AAGTTTAGG
* *
25916 GGTTAAAATGTGATTTTAAAGAAGTTTA-G
1 GGTTAAAATGTAATTTTAGAGAAGTTTAGG
* *
25945 GGTTTAAATGTGATTTTAG-GAAAGTTTAGG
1 GGTTAAAATGTAATTTTAGAG-AAGTTTAGG
* *
25975 GGTTAAAACT-TGATTTTGGA-ATAGGTTTAGG
1 GGTTAAAA-TGTAATTTTAGAGA-A-GTTTAGG
* * *
26006 GGTTAAAATGTGATTTTGGAGAAGTTT-GA
1 GGTTAAAATGTAATTTTAGAGAAGTTTAGG
*
26035 GGTTAAAATGTAACTTTAGAGAAGTTTAGG
1 GGTTAAAATGTAATTTTAGAGAAGTTTAGG
* *
26065 GGTTGAAATGTAATTTTAGAAAAGTTTTA-G
1 GGTTAAAATGTAATTTTAGAGAAG-TTTAGG
*
26095 GTTTAAAATGTAATTTTAGAGAAGTTTAGG
1 GGTTAAAATGTAATTTTAGAGAAGTTTAGG
*
26125 GGTTAAAATATAATTTTAGAGAAGT
1 GGTTAAAATGTAATTTTAGAGAAGT
26150 CAAGGGTCAA
Statistics
Matches: 224, Mismatches: 26, Indels: 27
0.81 0.09 0.10
Matches are distributed among these distances:
28 1 0.00
29 78 0.35
30 97 0.43
31 47 0.21
32 1 0.00
ACGTcount: A:0.37, C:0.01, G:0.25, T:0.37
Consensus pattern (30 bp):
GGTTAAAATGTAATTTTAGAGAAGTTTAGG
Found at i:26169 original size:29 final size:30
Alignment explanation
Indices: 26039--26170 Score: 104
Period size: 30 Copynumber: 4.4 Consensus size: 30
26029 GTTTGAGGTT
* * * * *
26039 AAAATGTAACTTTAGAGAAGTTTAGGGGTT
1 AAAATATAATTTTAGAGAAGTTCAAGGGTC
* * * ** * *
26069 GAAATGTAATTTTAGAAAAGTTTTAGGTTT
1 AAAATATAATTTTAGAGAAGTTCAAGGGTC
* * * *
26099 AAAATGTAATTTTAGAGAAGTTTAGGGGTT
1 AAAATATAATTTTAGAGAAGTTCAAGGGTC
26129 AAAATATAATTTTAGAGAAG-TCAAGGGTC
1 AAAATATAATTTTAGAGAAGTTCAAGGGTC
*
26158 AAAATATGATTTT
1 AAAATATAATTTT
26171 TGGAAAGTTC
Statistics
Matches: 86, Mismatches: 16, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
29 18 0.21
30 68 0.79
ACGTcount: A:0.39, C:0.02, G:0.22, T:0.36
Consensus pattern (30 bp):
AAAATATAATTTTAGAGAAGTTCAAGGGTC
Found at i:26179 original size:119 final size:117
Alignment explanation
Indices: 25856--26170 Score: 339
Period size: 119 Copynumber: 2.6 Consensus size: 117
25846 GAGAATACAA
* * * *
25856 GGTTAAAACATAATTTTAGAAAAAGTTTAGGGGTAAAAATGTAATTTTAGGAAAATTTAGGGTTA
1 GGTTAAAACTTAATTTTAG--AAAGTTTAGGGGTTAAAATGTAATTTTA-GAGAAGTTAGGGTTA
* * * *
25921 AAATGTGATTTTAAAGAAGTTTA-GGGTTTAAATGTGATTTTAGGAAAGTTTAGG
63 AAATGTGATTTTAGAGAAGTTTAGGGGTTGAAATGTAATTTTAGAAAAGTTTAGG
* * * * *
25975 GGTTAAAACTTGATTTTGGAATAGGTTTAGGGGTTAAAATGTGATTTTGGAGAAGTTTGAGGTTA
1 GGTTAAAACTTAATTTTAGAA-A-GTTTAGGGGTTAAAATGTAATTTTAGAGAAGTTAG-GGTTA
* *
26040 AAATGTAACTTTAGAGAAGTTTAGGGGTTGAAATGTAATTTTAGAAAAGTTTTA-G
63 AAATGTGATTTTAGAGAAGTTTAGGGGTTGAAATGTAATTTTAGAAAAG-TTTAGG
* * * *
26095 GTTTAAAA-TGTAATTTTAGAGAAGTTTAGGGGTTAAAATATAATTTTAGAGAAGTCAAGGGTCA
1 GGTTAAAACT-TAATTTTAGA-AAGTTTAGGGGTTAAAATGTAATTTTAGAGAAGT-TAGGGTTA
*
26159 AAATATGATTTT
63 AAATGTGATTTT
26171 TGGAAAGTTC
Statistics
Matches: 161, Mismatches: 27, Indels: 16
0.79 0.13 0.08
Matches are distributed among these distances:
117 2 0.01
118 8 0.05
119 106 0.66
120 40 0.25
121 5 0.03
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.37
Consensus pattern (117 bp):
GGTTAAAACTTAATTTTAGAAAGTTTAGGGGTTAAAATGTAATTTTAGAGAAGTTAGGGTTAAAA
TGTGATTTTAGAGAAGTTTAGGGGTTGAAATGTAATTTTAGAAAAGTTTAGG
Found at i:27481 original size:15 final size:17
Alignment explanation
Indices: 27454--27486 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
27444 ATACCTTGAA
27454 TGGAAATTTGA-TTGCT
1 TGGAAATTTGATTTGCT
27470 TGGAAA-TTGATTTGCT
1 TGGAAATTTGATTTGCT
27486 T
1 T
27487 CTCTGTTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.24, C:0.06, G:0.24, T:0.45
Consensus pattern (17 bp):
TGGAAATTTGATTTGCT
Found at i:27898 original size:6 final size:6
Alignment explanation
Indices: 27884--27924 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
27874 GGGACATTAA
*
27884 TAAATT TAAACT TAAATT TAAA-- TAAATT TAAATT TAAATT T
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT T
27925 TGTTTGGGTC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 4 0.13
6 27 0.87
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (6 bp):
TAAATT
Found at i:27907 original size:22 final size:22
Alignment explanation
Indices: 27882--27924 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
27872 AAGGGACATT
27882 AATAAATTTAAACTTAAATTTA
1 AATAAATTTAAACTTAAATTTA
*
27904 AATAAATTTAAATTTAAATTT
1 AATAAATTTAAACTTAAATTT
27925 TGTTTGGGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
AATAAATTTAAACTTAAATTTA
Found at i:27914 original size:16 final size:16
Alignment explanation
Indices: 27890--27922 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
27880 TTAATAAATT
27890 TAAACTTAAATTTAAA
1 TAAACTTAAATTTAAA
*
27906 TAAATTTAAATTTAAA
1 TAAACTTAAATTTAAA
27922 T
1 T
27923 TTTGTTTGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAACTTAAATTTAAA
Found at i:28385 original size:82 final size:84
Alignment explanation
Indices: 28277--28440 Score: 287
Period size: 83 Copynumber: 2.0 Consensus size: 84
28267 TGACACTTCA
*
28277 GGTGTGTTGTGACTTTTCTTAGTTTACTTCTCAATA-CTCATCAGGAAGATGACTGCATTACTTG
1 GGTGTGTTGTGACTTTTCTTAGTTTACTTCTCAATATCTCATCAGGAAGATAACTGCATTACTTG
*
28341 TTTTAATTCGCTTCACTGT
66 TTTTAATCCGCTTCACTGT
*
28360 GGTGTGTTGT-ACTTTTCTTGGTTTACTTCTCAATATCTCATCAGGAAGATAACTGCATTACTTG
1 GGTGTGTTGTGACTTTTCTTAGTTTACTTCTCAATATCTCATCAGGAAGATAACTGCATTACTTG
28424 TTTTAATCCGCTTCACT
66 TTTTAATCCGCTTCACT
28441 ATATCTCATT
Statistics
Matches: 77, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
82 24 0.31
83 53 0.69
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.43
Consensus pattern (84 bp):
GGTGTGTTGTGACTTTTCTTAGTTTACTTCTCAATATCTCATCAGGAAGATAACTGCATTACTTG
TTTTAATCCGCTTCACTGT
Found at i:28729 original size:39 final size:39
Alignment explanation
Indices: 28686--29149 Score: 210
Period size: 39 Copynumber: 11.9 Consensus size: 39
28676 AATGGTTGCA
* * *
28686 ATCTGCCCCAGGCTTGGGGTAAGAGATAGGCTGATAGTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTG
* * ** * ***
28725 ATCTGCCCTAGGCTCGGGGTAAAAGATCAGATGACT-ACA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGA-TGGTG
* ** *
28764 ATTTGCCCCAGGCTTAGGTTAAGAGATTGGCTGATGGTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTG
* * * * * ** * * **
28803 ATCAGCCCTAGGATCGGGGTAAAAGATCGAATGGTTGCA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTG
*
28842 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTG
* * * ** * *
28881 ATTTGCCCTCAAGTTCTAGGTAAAAGA-T--C-GAATGGCTACA
1 ATCTGCCC-CAGGCTCGGGGTAAGAGATTGGCTG-ATGG-T--G
* * * * *
28921 ATTTACCCCAGGCTAGGGGTAAGAGATTGACTGATAGTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTG
* * * * * *
28960 AACTGCCCTAGACTCGAGGTAAGAAATTGGCTTATGGTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTG
* ** ** * * *
28999 ATTTGCCTTAGGCTTAGGGTAAAACA-T--CAGATGGTTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGG-TG
* * * * **
29036 CAGTCTGCCTCAGGCTCGGGGTAAAAGATCGGATGACT-GCA
1 -A-TCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGA-TGGTG
* * *
29077 ATCTG-CCTAGGCTTGGGGTAAGAGATTAGCTGATGGTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTG
29115 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGAT
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGAT
29150 TGAGTTTGAA
Statistics
Matches: 298, Mismatches: 107, Indels: 40
0.67 0.24 0.09
Matches are distributed among these distances:
36 6 0.02
37 8 0.03
38 31 0.10
39 219 0.73
40 24 0.08
41 1 0.00
42 7 0.02
43 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.25
Consensus pattern (39 bp):
ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTG
Found at i:28804 original size:78 final size:77
Alignment explanation
Indices: 28682--29141 Score: 360
Period size: 78 Copynumber: 5.9 Consensus size: 77
28672 ATCGAATGGT
* * *
28682 TGCAATCTGCCCCAGGCTTGGGGTAAGAGATAGGCTGATAGTGATCTGCCCTAGGCTCGGGGTAA
1 TGCAATCTGCCCCAGGCTTAGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAGGCTCGGGGTAA
28747 AAGATCAGATGAC
66 AAGATC-GATGAC
* * * * *
28760 TACAATTTGCCCCAGGCTTAGGTTAAGAGATTGGCTGATGGTGATCAGCCCTAGGATCGGGGTAA
1 TGCAATCTGCCCCAGGCTTAGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAGGCTCGGGGTAA
**
28825 AAGATCGAATGGT
66 AAGATCG-ATGAC
* ** * * * **
28838 TGCAATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATTTGCCCTCAAGTTCTAGGTA
1 TGCAATCTGCCCCAGGCTTAGGGTAAGAGATTGGCTGATGGTGATCTGCCCT-AGGCTCGGGGTA
*
28903 AAAGATCGAATGGC
65 AAAGATCG-ATGAC
* * * * * * * *
28917 TACAATTTACCCCAGGC-TAGGGGTAAGAGATTGACTGATAGTGAACTGCCCTAGACTCGAGGTA
1 TGCAATCTGCCCCAGGCTTA-GGGTAAGAGATTGGCTGATGGTGATCTGCCCTAGGCTCGGGGTA
* * *
28981 AGAA-ATTGGCTTA-
65 A-AAGA-TCGATGAC
** * ** * * *
28994 TGGTGATTTGCCTTAGGCTTAGGGTAAAACA-T--CAGATGGTTGCAGTCTG-CCTCAGGCTCGG
1 T-GCAATCTGCCCCAGGCTTAGGGTAAGAGATTGGCTGATGG-TG-A-TCTGCCCT-AGGCTCGG
29055 GGTAAAAGATCGGATGAC
61 GGTAAAAGATC-GATGAC
* * * *
29073 TGCAATCTG-CCTAGGCTTGGGGTAAGAGATTAGCTGATGGTGATCTGCCCCAGGCTCGGGGTAA
1 TGCAATCTGCCCCAGGCTTAGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAGGCTCGGGGTAA
*
29137 GAGAT
66 AAGAT
29142 TGGCTGATTG
Statistics
Matches: 297, Mismatches: 67, Indels: 37
0.74 0.17 0.09
Matches are distributed among these distances:
75 5 0.02
76 2 0.01
77 47 0.16
78 166 0.56
79 71 0.24
80 6 0.02
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.25
Consensus pattern (77 bp):
TGCAATCTGCCCCAGGCTTAGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAGGCTCGGGGTAA
AAGATCGATGAC
Found at i:37177 original size:30 final size:31
Alignment explanation
Indices: 37138--37492 Score: 152
Period size: 30 Copynumber: 12.1 Consensus size: 31
37128 CGGAGAATAC
* * *
37138 GAGGTTAAAACATAATTTTAGAAAAAGTTTA
1 GAGGTCAAAATATAATTTTAGGAAAAGTTTA
* *
37169 GAGGTAAAAATGTAATTTTAGGAAAA-TTT-
1 GAGGTCAAAATATAATTTTAGGAAAAGTTTA
* * *
37198 GAGGTCAAAATGTGATTTT-GGAGAAGTTTA
1 GAGGTCAAAATATAATTTTAGGAAAAGTTTA
*
37228 G-GGTCAAAATATAATTTTAGGGAAAGTTTA
1 GAGGTCAAAATATAATTTTAGGAAAAGTTTA
* *
37258 G-GCGTCAAAACT-TGATTTT-GGAATAGGTTTA
1 GAG-GTCAAAA-TATAATTTTAGGAA-AAGTTTA
* * * *
37289 G-GAGTCAAAATGTGATTTT-GGAGAAG-TTC
1 GAG-GTCAAAATATAATTTTAGGAAAAGTTTA
*
37318 GGGGTCAAAATATAATTTTA-G---AG----
1 GAGGTCAAAATATAATTTTAGGAAAAGTTTA
** *
37341 GA-GTCAAAATGCAATTTT-GGAAAAGATTA
1 GAGGTCAAAATATAATTTTAGGAAAAGTTTA
* ** *
37370 -AGGTTCAAGATGGAATTTT-GAAAAAGTTT-
1 GAGG-TCAAAATATAATTTTAGGAAAAGTTTA
* * *
37399 GAGGGTTAAAATGTAATTTTA-GAGAAGTTT-
1 GA-GGTCAAAATATAATTTTAGGAAAAGTTTA
* * **
37429 GAGGGTTAAAATATAATTTTA-GAGAAGTCGA
1 GA-GGTCAAAATATAATTTTAGGAAAAGTTTA
* * * *
37460 GGGGTCAAAATATGATTTTTGG-AAAGTTCA
1 GAGGTCAAAATATAATTTTAGGAAAAGTTTA
37490 GAG
1 GAG
37493 ACCTATAAAA
Statistics
Matches: 257, Mismatches: 43, Indels: 49
0.74 0.12 0.14
Matches are distributed among these distances:
22 15 0.06
23 1 0.00
25 2 0.01
26 2 0.01
28 6 0.02
29 54 0.21
30 112 0.44
31 64 0.25
32 1 0.00
ACGTcount: A:0.38, C:0.04, G:0.25, T:0.32
Consensus pattern (31 bp):
GAGGTCAAAATATAATTTTAGGAAAAGTTTA
Found at i:37207 original size:29 final size:29
Alignment explanation
Indices: 37150--37248 Score: 103
Period size: 29 Copynumber: 3.3 Consensus size: 29
37140 GGTTAAAACA
* *
37150 TAATTTTAGAAAAAGTTTAGAGGTAAAAATG
1 TAATTTTAGGAAAA-TTT-GAGGTCAAAATG
37181 TAATTTTAGGAAAATTTGAGGTCAAAATG
1 TAATTTTAGGAAAATTTGAGGTCAAAATG
* * *
37210 TGATTTT-GGAGAAGTTT-AGGGTCAAAATA
1 TAATTTTAGGA-AAATTTGA-GGTCAAAATG
37239 TAATTTTAGG
1 TAATTTTAGG
37249 GAAAGTTTAG
Statistics
Matches: 59, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
28 4 0.07
29 37 0.63
30 5 0.08
31 13 0.22
ACGTcount: A:0.40, C:0.02, G:0.22, T:0.35
Consensus pattern (29 bp):
TAATTTTAGGAAAATTTGAGGTCAAAATG
Found at i:42057 original size:200 final size:200
Alignment explanation
Indices: 41714--42114 Score: 694
Period size: 200 Copynumber: 2.0 Consensus size: 200
41704 CCCTTGTTGC
* * *
41714 CAAAATGAACACCATTAGAATTTTGTTATCTTGTGTAGCCAACCTTGACTGGAACCTACAATAAT
1 CAAAATGAACACCATTAGAATTTTGTTATCTTGTGCAACCAACCTTGACTAGAACCTACAATAAT
* * * *
41779 TTTATGTGGAGAATGCATTCCTACCTGGAGACTTAGAAGAGGAAGTATATATGGAGATTCCTCCT
66 TTTATGTGAAGAATGCATTCCTACATGAAGACTTAGAAAAGGAAGTATATATGGAGATTCCTCCT
* * *
41844 GGATTTGATAATGCAAAAACGCAAGGGAAAGTATGCAGATTGAAGAAAGCCTTGTGTGGATTAAA
131 GGATTTGATAATGCAAAAACGCAAGGGAAAGTATGCAAATTGAAGAAAGCCTTGTATGAATTAAA
*
41909 ATAAT
196 ACAAT
41914 CAAAATGAACACCATTAGAATTTTGTTATCTTGTGCAACCAACCTTGACTAGAACCTACAATAAT
1 CAAAATGAACACCATTAGAATTTTGTTATCTTGTGCAACCAACCTTGACTAGAACCTACAATAAT
41979 TTTATGTGAAGAATGCATTCCTACATGAAGACTTAGAAAAGGAAGTATATATGGAGATTCCTCCT
66 TTTATGTGAAGAATGCATTCCTACATGAAGACTTAGAAAAGGAAGTATATATGGAGATTCCTCCT
*
42044 GGATTTGATAATGCAAAAATGCAAGGGAAAGTATGCAAATTGAAGAAAGCCTTGTATGAATTAAA
131 GGATTTGATAATGCAAAAACGCAAGGGAAAGTATGCAAATTGAAGAAAGCCTTGTATGAATTAAA
42109 ACAAT
196 ACAAT
42114 C
1 C
42115 TCCCAAAGCA
Statistics
Matches: 189, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
200 189 1.00
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (200 bp):
CAAAATGAACACCATTAGAATTTTGTTATCTTGTGCAACCAACCTTGACTAGAACCTACAATAAT
TTTATGTGAAGAATGCATTCCTACATGAAGACTTAGAAAAGGAAGTATATATGGAGATTCCTCCT
GGATTTGATAATGCAAAAACGCAAGGGAAAGTATGCAAATTGAAGAAAGCCTTGTATGAATTAAA
ACAAT
Found at i:45172 original size:16 final size:16
Alignment explanation
Indices: 45151--45184 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
45141 AACATAAGCA
45151 CTACCAGTTCCATTTT
1 CTACCAGTTCCATTTT
*
45167 CTACCAGTTTCATTTT
1 CTACCAGTTCCATTTT
45183 CT
1 CT
45185 CATTTCTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.29, G:0.06, T:0.47
Consensus pattern (16 bp):
CTACCAGTTCCATTTT
Found at i:54092 original size:49 final size:49
Alignment explanation
Indices: 54033--54216 Score: 167
Period size: 49 Copynumber: 3.8 Consensus size: 49
54023 ATATAGTGAT
* *
54033 TGAAAACCATTGTTGTGAGGCCATTCGGGATGGTAGATTAT-GCAAACAG
1 TGAAAACCATTGTTGTGAGGCCATCCGGGATGGTAGATTATCG-AAAAAG
* * * * *
54082 TGAAAGCCATTATTGTTAGGCCATCCAGGATGGTAG-TATATCGAAAAAA
1 TGAAAACCATTGTTGTGAGGCCATCCGGGATGGTAGAT-TATCGAAAAAG
* * * * * * *
54131 TGGAAGCCATTGTTGTCAGGCCATTCGAGATGGTAGAATATCGAAATAG
1 TGAAAACCATTGTTGTGAGGCCATCCGGGATGGTAGATTATCGAAAAAG
* * *
54180 TGAAAACCATAGTTCTTG-GACCATCCGGGATGGTAGA
1 TGAAAACCATTGTT-GTGAGGCCATCCGGGATGGTAGA
54217 ATTTGTAATT
Statistics
Matches: 107, Mismatches: 24, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
48 1 0.01
49 104 0.97
50 2 0.02
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.26
Consensus pattern (49 bp):
TGAAAACCATTGTTGTGAGGCCATCCGGGATGGTAGATTATCGAAAAAG
Found at i:54211 original size:98 final size:98
Alignment explanation
Indices: 54039--54215 Score: 243
Period size: 98 Copynumber: 1.8 Consensus size: 98
54029 TGATTGAAAA
* * * * *
54039 CCATTGTTGTGAGGCCATTCGGGATGGTAGATTATGCAAACAGTGAAAGCCATTATTGTTAGGCC
1 CCATTGTTGTCAGGCCATTCGAGATGGTAGAATATGCAAACAGTGAAAACCATTATTCTTAGGCC
54104 ATCCAGGATGGTAGTATATCGAAAAAATGGAAG
66 ATCCAGGATGGTAGTATATCGAAAAAATGGAAG
*
54137 CCATTGTTGTCAGGCCATTCGAGATGGTAGAATAT-CGAAATAGTGAAAACCA-TAGTTCTT-GG
1 CCATTGTTGTCAGGCCATTCGAGATGGTAGAATATGC-AAACAGTGAAAACCATTA-TTCTTAGG
*
54199 ACCATCCGGGATGGTAG
64 -CCATCCAGGATGGTAG
54216 AATTTGTAAT
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
97 5 0.07
98 64 0.93
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.27
Consensus pattern (98 bp):
CCATTGTTGTCAGGCCATTCGAGATGGTAGAATATGCAAACAGTGAAAACCATTATTCTTAGGCC
ATCCAGGATGGTAGTATATCGAAAAAATGGAAG
Found at i:54251 original size:49 final size:49
Alignment explanation
Indices: 54033--54287 Score: 158
Period size: 49 Copynumber: 5.2 Consensus size: 49
54023 ATATAGTGAT
* * * * * *
54033 TGAAAACCATTGTTGTGAGGCCATTCGGGATGGTAGATTAT-GCAAACAG
1 TGAAAACCATTGTTGTCAGACCATCCGAGATGGTAGAATATCG-AAATAG
* * * * * * *
54082 TGAAAGCCATTATTGTTAGGCCATCC-AGGATGGTAGTATATCGAAAAAA
1 TGAAAACCATTGTTGTCAGACCATCCGA-GATGGTAGAATATCGAAATAG
* * * *
54131 TGGAAGCCATTGTTGTCAGGCCATTCGAGATGGTAGAATATCGAAATAG
1 TGAAAACCATTGTTGTCAGACCATCCGAGATGGTAGAATATCGAAATAG
* * ** * * * *
54180 TGAAAACCATAGTTCTTGGACCATCCGGGATGGTAGAAT-TTGTAATTTG
1 TGAAAACCATTGTTGTCAGACCATCCGAGATGGTAGAATATCG-AAATAG
* * * * ** *
54229 TGAAAATCATTGTTGTCAGACCA-CTTGAGATGGTAAAATGTTTATATAG
1 TGAAAACCATTGTTGTCAGACCATC-CGAGATGGTAGAATATCGAAATAG
54278 TGAAAACCAT
1 TGAAAACCAT
54288 CATTGTCGGG
Statistics
Matches: 159, Mismatches: 41, Indels: 12
0.75 0.19 0.06
Matches are distributed among these distances:
48 3 0.02
49 152 0.96
50 4 0.03
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (49 bp):
TGAAAACCATTGTTGTCAGACCATCCGAGATGGTAGAATATCGAAATAG
Found at i:55580 original size:19 final size:20
Alignment explanation
Indices: 55533--55570 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
55523 TTTCTGTTTG
55533 AATCGATTCATTACTATTTA
1 AATCGATTCATTACTATTTA
*
55553 AATCGATTCTTTACTATT
1 AATCGATTCATTACTATT
55571 AATCTGATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.16, G:0.05, T:0.47
Consensus pattern (20 bp):
AATCGATTCATTACTATTTA
Found at i:56071 original size:19 final size:20
Alignment explanation
Indices: 56047--56090 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
56037 CAAAACACAC
56047 CATGAAAAAG-AAATACAAA
1 CATGAAAAAGAAAATACAAA
* *
56066 CATGAATATGAAAATACAAA
1 CATGAAAAAGAAAATACAAA
*
56086 AATGA
1 CATGA
56091 TGTTATATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.64, C:0.09, G:0.11, T:0.16
Consensus pattern (20 bp):
CATGAAAAAGAAAATACAAA
Found at i:56234 original size:2 final size:2
Alignment explanation
Indices: 56225--56257 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
56215 CACCAAAAAA
56225 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
56258 TATGTTATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:68747 original size:23 final size:23
Alignment explanation
Indices: 68721--68773 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
68711 ACATTATTTG
*
68721 AAAGAAAATATTTAATTAAGACT
1 AAAGAAAATAATTAATTAAGACT
* *
68744 AAAGAAATTAATTAATTAATACT
1 AAAGAAAATAATTAATTAAGACT
68767 AAAGAAA
1 AAAGAAA
68774 GAAATTGCCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.60, C:0.04, G:0.08, T:0.28
Consensus pattern (23 bp):
AAAGAAAATAATTAATTAAGACT
Found at i:68779 original size:23 final size:23
Alignment explanation
Indices: 68732--68779 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
68722 AAGAAAATAT
**
68732 TTAATTAAGACTAAAGAAATTAA
1 TTAATTAAGACTAAAGAAAGAAA
*
68755 TTAATTAATACTAAAGAAAGAAA
1 TTAATTAAGACTAAAGAAAGAAA
68778 TT
1 TT
68780 GCCACATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.56, C:0.04, G:0.08, T:0.31
Consensus pattern (23 bp):
TTAATTAAGACTAAAGAAAGAAA
Done.