Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005663.1 Kokia drynarioides strain JFW-HI SEQ_119836, 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: 67614
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Warning! 223 characters in sequence are not A, C, G, or T
Found at i:11066 original size:6 final size:6
Alignment explanation
Indices: 11055--11085 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
11045 AGGGAAGAAA
11055 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG A
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG A
11086 AGAGAGACGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.32, T:0.16
Consensus pattern (6 bp):
ATGAAG
Found at i:13017 original size:19 final size:19
Alignment explanation
Indices: 12993--13046 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 19
12983 TTAGAGGGTG
12993 ATAAAATTAAATGTCGACA
1 ATAAAATTAAATGTCGACA
*
13012 AT-AAA--AAATATCG-CAA
1 ATAAAATTAAATGTCGAC-A
*
13028 AGAAAATTAAATGTCGACA
1 ATAAAATTAAATGTCGACA
13047 GATTTTACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 10
0.68 0.08 0.25
Matches are distributed among these distances:
15 1 0.04
16 9 0.33
17 3 0.11
18 3 0.11
19 10 0.37
20 1 0.04
ACGTcount: A:0.56, C:0.11, G:0.11, T:0.22
Consensus pattern (19 bp):
ATAAAATTAAATGTCGACA
Found at i:27356 original size:150 final size:150
Alignment explanation
Indices: 27167--27468 Score: 561
Period size: 150 Copynumber: 2.0 Consensus size: 150
27157 AGCACAACCT
27167 TTGGCAAATTGCAAGGACTTGAAAATCCTAGATTTGGGAAACAATTACTTAATGATACAATTTTG
1 TTGGCAAATTGCAAGGACTTGAAAATCCTAGATTTGGGAAACAATTACTTAATGATACAATTTTG
27232 AATTGGGTCAGTATGAAAAGGACTTTGGTTGATTGAAACGTGTTTGATGGAGATCCTCAACTTAT
66 AATTGGGTCAGTATGAAAAGGACTTTGGTTGATTGAAACGTGTTTGATGGAGATCCTCAACTTAT
*
27297 TCTTCACGG-TTCCTCCCAAA
131 TCTTCAAGGCTT-CTCCCAAA
*
27317 TTGGCAAATTGCAAGGACTTGAAAATCCTAGATTTGGGAAACATTTACTTAATGATACAATTTTG
1 TTGGCAAATTGCAAGGACTTGAAAATCCTAGATTTGGGAAACAATTACTTAATGATACAATTTTG
*
27382 AATTGGGTCAGTATGAAAAGGACTTTGGTTGATTGAAACGTGTTTGATGGAGTTCCTCAACTTAT
66 AATTGGGTCAGTATGAAAAGGACTTTGGTTGATTGAAACGTGTTTGATGGAGATCCTCAACTTAT
27447 TCTTCAAGGCTTCTCCCAAA
131 TCTTCAAGGCTTCTCCCAAA
27467 TT
1 TT
27469 ATTTTATTAA
Statistics
Matches: 148, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
150 146 0.99
151 2 0.01
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.34
Consensus pattern (150 bp):
TTGGCAAATTGCAAGGACTTGAAAATCCTAGATTTGGGAAACAATTACTTAATGATACAATTTTG
AATTGGGTCAGTATGAAAAGGACTTTGGTTGATTGAAACGTGTTTGATGGAGATCCTCAACTTAT
TCTTCAAGGCTTCTCCCAAA
Found at i:27782 original size:22 final size:22
Alignment explanation
Indices: 27757--27812 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
27747 TTTTGGTTAT
* *
27757 TTAATTTTTAAATTTTTTAAAA
1 TTAATTTTTAAATTATTCAAAA
*
27779 TTAATTATTAAATTATTCAAAA
1 TTAATTTTTAAATTATTCAAAA
27801 TTAACTTTTTAA
1 TTAA-TTTTTAA
27813 TAGAAGTGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 23 0.79
23 6 0.21
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.54
Consensus pattern (22 bp):
TTAATTTTTAAATTATTCAAAA
Found at i:33472 original size:7 final size:7
Alignment explanation
Indices: 33460--33501 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
33450 AAATTAAATA
33460 ATATTTT
1 ATATTTT
33467 ATATTTT
1 ATATTTT
33474 ATATTTT
1 ATATTTT
* *
33481 AAATGTT
1 ATATTTT
33488 AT-TTTT
1 ATATTTT
33494 AGTATTTT
1 A-TATTTT
33502 TATAGAAACA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.14
7 21 0.72
8 4 0.14
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (7 bp):
ATATTTT
Found at i:36584 original size:24 final size:24
Alignment explanation
Indices: 36523--36585 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
36513 TAGACTAATA
* *
36523 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
* *
36547 AGAGTTTAATTGAAACAATTAAAC
1 AGAGTTTAACTGAAACAAATAAAC
36571 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
36586 GATTATTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.49, C:0.11, G:0.14, T:0.25
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:37464 original size:39 final size:39
Alignment explanation
Indices: 37410--37505 Score: 131
Period size: 39 Copynumber: 2.4 Consensus size: 39
37400 AAAATGCCGC
*
37410 AAAAAATAAAGTAATAACGACGTTTTT-TATAAACAACAT
1 AAAAAATAAA-TAATAACGACGTTTTTCCATAAACAACAT
*
37449 AAAAAATAAGATAATAACGACGTTTTTCCATAAACACCAT
1 AAAAAATAA-ATAATAACGACGTTTTTCCATAAACAACAT
*
37489 AAAATATAAAATAATAA
1 AAAAAAT-AAATAATAA
37506 TTAATATCAA
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
39 25 0.49
40 24 0.47
41 2 0.04
ACGTcount: A:0.56, C:0.11, G:0.06, T:0.26
Consensus pattern (39 bp):
AAAAAATAAATAATAACGACGTTTTTCCATAAACAACAT
Found at i:38294 original size:20 final size:20
Alignment explanation
Indices: 38250--38295 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
38240 TTATTTTTCG
*
38250 ATAAAAATACATAAAATTTT
1 ATAAAAATACATAAAATATT
*
38270 TTAAAAATACATACAAA-ATT
1 ATAAAAATACATA-AAATATT
38290 ATAAAA
1 ATAAAA
38296 TATTTATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 19 0.86
21 3 0.14
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (20 bp):
ATAAAAATACATAAAATATT
Found at i:38488 original size:25 final size:26
Alignment explanation
Indices: 38444--38504 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 26
38434 CCATTTTTAT
* *
38444 AAACCCAATTCAA-CTTTAAAAACCC
1 AAACCCAATTCAACCCTAAAAAACCC
* *
38469 AAACCCAATTGAACCCTAAAAAACTC
1 AAACCCAATTCAACCCTAAAAAACCC
*
38495 AAACCTAATT
1 AAACCCAATT
38505 ACCCAACAAG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 12 0.40
26 18 0.60
ACGTcount: A:0.49, C:0.30, G:0.02, T:0.20
Consensus pattern (26 bp):
AAACCCAATTCAACCCTAAAAAACCC
Found at i:39905 original size:29 final size:29
Alignment explanation
Indices: 39784--40033 Score: 201
Period size: 29 Copynumber: 8.6 Consensus size: 29
39774 TCCAAGTAGT
*
39784 CCCTAAACTTCTC-AAAATTACATTTTAA
1 CCCTAAACTTTTCTAAAATTACATTTTAA
*
39812 CCCTTAAACTTTTCTAAAATTACATTTTGA
1 CCC-TAAACTTTTCTAAAATTACATTTTAA
* *
39842 CCTCAAAACTTTTCTAAAATTACA-TTTGA
1 CC-CTAAACTTTTCTAAAATTACATTTTAA
* *
39871 CCCCAAACTTTTCTAAAATTACATTCTAA
1 CCCTAAACTTTTCTAAAATTACATTTTAA
* **
39900 TCCC-AAACTTTTCTAAAATTATATTTTTGT
1 -CCCTAAACTTTTCTAAAATTACA-TTTTAA
* * ** *
39930 CCCCAAACTTCTAAAAAATCACAATTTT-A
1 CCCTAAACTTTTCTAAAATTAC-ATTTTAA
* * *
39959 CCCTCAAAC-TTCCAAAAATTACATGTTTAC
1 CCCT-AAACTTTTCTAAAATTACAT-TTTAA
* *
39989 CCCTAAAC-TTCCAAAAATTACATTTT-A
1 CCCTAAACTTTTCTAAAATTACATTTTAA
40016 CCCTTAAAC-TTTCTAAAA
1 CCC-TAAACTTTTCTAAAA
40034 ATTATGTTTT
Statistics
Matches: 185, Mismatches: 25, Indels: 24
0.79 0.11 0.10
Matches are distributed among these distances:
27 3 0.02
28 40 0.22
29 74 0.40
30 66 0.36
31 2 0.01
ACGTcount: A:0.38, C:0.24, G:0.02, T:0.36
Consensus pattern (29 bp):
CCCTAAACTTTTCTAAAATTACATTTTAA
Found at i:39948 original size:87 final size:88
Alignment explanation
Indices: 39784--40014 Score: 224
Period size: 88 Copynumber: 2.6 Consensus size: 88
39774 TCCAAGTAGT
* *
39784 CCCT-AAACTTCTCAAAATTACATTTTAACCCTTAAACTTTTCTAAAATTACATTTTGACCTCAA
1 CCCTCAAACTTTTCAAAATTACATTCTAACCC-TAAACTTTTCTAAAATTACATTTTGACCTCAA
* ** *
39848 AACTTTTCTAAAATTAC-ATTTGA
65 AACTTCTAAAAAATCACAATTTGA
* *
39871 CCC-CAAACTTTTCTAAAATTACATTCTAATCCC-AAACTTTTCTAAAATTATATTTTTGTCC-C
1 CCCTCAAACTTTTC-AAAATTACATTCTAA-CCCTAAACTTTTCTAAAATTACA-TTTTGACCTC
* *
39933 CAAACTTCTAAAAAATCACAATTTTA
63 AAAACTTCTAAAAAATCACAATTTGA
* * * * *
39959 CCCTCAAAC-TTCCAAAAATTACATGTTTACCCCTAAAC-TTCCAAAAATTACATTTT
1 CCCTCAAACTTTTC-AAAATTACAT-TCTAACCCTAAACTTTTCTAAAATTACATTTT
40015 ACCCTTAAAC
Statistics
Matches: 119, Mismatches: 17, Indels: 16
0.78 0.11 0.11
Matches are distributed among these distances:
87 48 0.40
88 56 0.47
89 15 0.13
ACGTcount: A:0.37, C:0.24, G:0.02, T:0.37
Consensus pattern (88 bp):
CCCTCAAACTTTTCAAAATTACATTCTAACCCTAAACTTTTCTAAAATTACATTTTGACCTCAAA
ACTTCTAAAAAATCACAATTTGA
Found at i:40043 original size:29 final size:28
Alignment explanation
Indices: 39954--40043 Score: 101
Period size: 29 Copynumber: 3.1 Consensus size: 28
39944 AAAATCACAA
*
39954 TTTTACCCTCAAACTTCCAAAAATTACATG
1 TTTTACCCTTAAACTTCCAAAAATT--ATG
* **
39984 -TTTACCCCTAAACTTCCAAAAATTACA
1 TTTTACCCTTAAACTTCCAAAAATTATG
*
40011 TTTTACCCTTAAACTTTCTAAAAATTATG
1 TTTTACCCTTAAAC-TTCCAAAAATTATG
40040 TTTT
1 TTTT
40044 TACCTCAAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
27 1 0.02
28 12 0.24
29 37 0.74
ACGTcount: A:0.36, C:0.23, G:0.02, T:0.39
Consensus pattern (28 bp):
TTTTACCCTTAAACTTCCAAAAATTATG
Found at i:40046 original size:58 final size:59
Alignment explanation
Indices: 39903--40052 Score: 164
Period size: 58 Copynumber: 2.6 Consensus size: 59
39893 ATTCTAATCC
*
39903 CAAACTTTTCT-AAAATTATATTTTTGTCCCCAAACTTCTAAAAAATCACAATTTTACCCT
1 CAAAC-TTTCTAAAAATTATATTTTT-ACCCCAAACTTCTAAAAAATCACAATTTTACCCT
* * * * *
39963 CAAAC-TTCCAAAAATTACATGTTTACCCCTAAACTTC-CAAAAATTAC-ATTTTACCCT
1 CAAACTTTCTAAAAATTATATTTTTACCCC-AAACTTCTAAAAAATCACAATTTTACCCT
* * *
40020 TAAACTTTCTAAAAATTATGTTTTTACCTCAAA
1 CAAACTTTCTAAAAATTATATTTTTACCCCAAA
40053 ATCTTCGGAA
Statistics
Matches: 75, Mismatches: 12, Indels: 9
0.78 0.12 0.09
Matches are distributed among these distances:
57 17 0.23
58 34 0.45
59 19 0.25
60 5 0.07
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.37
Consensus pattern (59 bp):
CAAACTTTCTAAAAATTATATTTTTACCCCAAACTTCTAAAAAATCACAATTTTACCCT
Found at i:41797 original size:17 final size:17
Alignment explanation
Indices: 41774--41887 Score: 102
Period size: 17 Copynumber: 6.3 Consensus size: 17
41764 AAACCCATTT
41774 TTTAAATTTATTTTAAG
1 TTTAAATTTATTTTAAG
* *
41791 GTTAAATTTATTTTATG
1 TTTAAATTTATTTTAAG
*
41808 TTTAAATTTAAATTTGTTTTAAA
1 TTTAAATTT--A----TTTTAAG
41831 TTTAAATTTATTTTAAG
1 TTTAAATTTATTTTAAG
*
41848 TTTAAATTTATTTATAAA
1 TTTAAATTTATTT-TAAG
* * *
41866 TTTAAAATTATTCTAAA
1 TTTAAATTTATTTTAAG
41883 TTTAA
1 TTTAA
41888 TTAATAGTGT
Statistics
Matches: 81, Mismatches: 9, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
17 51 0.63
18 14 0.17
19 1 0.01
21 1 0.01
23 14 0.17
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (17 bp):
TTTAAATTTATTTTAAG
Found at i:41811 original size:23 final size:22
Alignment explanation
Indices: 41780--41828 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
41770 ATTTTTTAAA
*
41780 TTTATTTTAAGGTTAAATTTAT
1 TTTATTTTAAAGTTAAATTTAT
* *
41802 TTTATGTTTAAATTTAAATTTGT
1 TTTAT-TTTAAAGTTAAATTTAT
41825 TTTA
1 TTTA
41829 AATTTAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (22 bp):
TTTATTTTAAAGTTAAATTTAT
Found at i:41817 original size:6 final size:6
Alignment explanation
Indices: 41808--41871 Score: 53
Period size: 6 Copynumber: 11.0 Consensus size: 6
41798 TTATTTTATG
** * *
41808 TTTAAA TTTAAA TTT-GT TTTAAA TTTAAA TTT-AT TTTAAG TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
41854 TTT-AT TTATAAA TTTAAA
1 TTTAAA TT-TAAA TTTAAA
41872 ATTATTCTAA
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
5 10 0.22
6 32 0.71
7 3 0.07
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:41829 original size:40 final size:40
Alignment explanation
Indices: 41774--41857 Score: 132
Period size: 40 Copynumber: 2.1 Consensus size: 40
41764 AAACCCATTT
* *
41774 TTTAAATTTATTTTAAGGTTAAATTTATTTTATGTTTAAA
1 TTTAAATTTATTTTAAAGTTAAATTTATTTTAAGTTTAAA
* *
41814 TTTAAATTTGTTTTAAATTTAAATTTATTTTAAGTTTAAA
1 TTTAAATTTATTTTAAAGTTAAATTTATTTTAAGTTTAAA
41854 TTTA
1 TTTA
41858 TTTATAAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (40 bp):
TTTAAATTTATTTTAAAGTTAAATTTATTTTAAGTTTAAA
Found at i:41834 original size:23 final size:23
Alignment explanation
Indices: 41792--41857 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 23
41782 TATTTTAAGG
**
41792 TTAAATTTATTTTATGTTTAAAT
1 TTAAATTTATTTTAAATTTAAAT
*
41815 TTAAATTTGTTTTAAATTTAAAT
1 TTAAATTTATTTTAAATTTAAAT
* *
41838 TT-ATTTTAAGTTTAAATTTA
1 TTAAATTT-ATTTTAAATTTA
41858 TTTATAAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
22 4 0.11
23 32 0.89
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (23 bp):
TTAAATTTATTTTAAATTTAAAT
Found at i:43721 original size:29 final size:29
Alignment explanation
Indices: 43667--43785 Score: 102
Period size: 28 Copynumber: 4.1 Consensus size: 29
43657 GCTCTAGAGG
* *
43667 CCTCTAAACTGTCCAGAAATAATATTTTGAC
1 CCTC-AAACTTTCCA-AAATTATATTTTGAC
*
43698 CCTCAAACTTTCCAAAATTTTATTTTGA-
1 CCTCAAACTTTCCAAAATTATATTTTGAC
* *
43726 CCT-AAATTTTCCAAAAATTACATTTT-AC
1 CCTCAAACTTTCC-AAAATTATATTTTGAC
* *
43754 CCTCGAACTTTCTAAAATTCACT-TTTTGAC
1 CCTCAAACTTTCCAAAATT-A-TATTTTGAC
43784 CC
1 CC
43786 CAATTTTTTC
Statistics
Matches: 72, Mismatches: 10, Indels: 13
0.76 0.11 0.14
Matches are distributed among these distances:
27 9 0.12
28 23 0.32
29 23 0.32
30 13 0.18
31 4 0.06
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.38
Consensus pattern (29 bp):
CCTCAAACTTTCCAAAATTATATTTTGAC
Found at i:43809 original size:29 final size:28
Alignment explanation
Indices: 43690--44047 Score: 111
Period size: 29 Copynumber: 12.4 Consensus size: 28
43680 CAGAAATAAT
** * **
43690 ATTTTGACCCTCAAACTTTCCAAAATTTT
1 ATTTTGACCC-CAATTTTTCAAAAATTAC
** *
43719 ATTTTGACCTAAATTTTCCAAAAATTAC
1 ATTTTGACCCCAATTTTTCAAAAATTAC
* *
43747 ATTTT-ACCCTCGAA-CTTTCTAAAATTCAC
1 ATTTTGACCC-C-AATTTTTCAAAAATT-AC
*
43776 TTTTTGACCCCAATTTTTTCAAAAATTAC
1 ATTTTGACCCCAA-TTTTTCAAAAATTAC
* * * * * *
43805 ATTTTTTATCCCTGAA-CTTCCCAAAATTCC
1 A-TTTTGA-CCC-CAATTTTTCAAAAATTAC
* *
43835 ATTTT-AACCCTATTTTTCCAAAAATTAC
1 ATTTTGACCCCAATTTTT-CAAAAATTAC
* ** *
43863 ATTTTTATCCCCAAACTTTCTAAAACTCTA-
1 ATTTTGA-CCCCAATTTTTC-AAAAAT-TAC
* * *
43893 TTTTTTACCCTAATTTTTCTAAAAATTACC
1 ATTTTGACCCCAATTTTTC-AAAAATTA-C
* ** * * *
43923 ATTTT-ACCCTAAACTTCCAAAGATTCC
1 ATTTTGACCCCAATTTTTCAAAAATTAC
**
43950 ATTTTTGACCCTGATTTTTCCAAAAATTATC
1 A-TTTTGACCCCAATTTTT-CAAAAATTA-C
** * * *
43981 ATTTT-ACCCCAAACTTCCAAAGATTCC
1 ATTTTGACCCCAATTTTTCAAAAATTAC
* *
44008 ATTTTTGACCTCGATTTTTCCAAAAATTATC
1 A-TTTTGACCCCAATTTTT-CAAAAATTA-C
44039 ATTTT-ACCC
1 ATTTTGACCC
44048 TTGAACTTCC
Statistics
Matches: 237, Mismatches: 67, Indels: 50
0.67 0.19 0.14
Matches are distributed among these distances:
26 1 0.00
27 11 0.05
28 64 0.27
29 76 0.32
30 74 0.31
31 9 0.04
32 2 0.01
ACGTcount: A:0.32, C:0.24, G:0.03, T:0.41
Consensus pattern (28 bp):
ATTTTGACCCCAATTTTTCAAAAATTAC
Found at i:44025 original size:116 final size:110
Alignment explanation
Indices: 43690--44133 Score: 387
Period size: 116 Copynumber: 3.8 Consensus size: 110
43680 CAGAAATAAT
** * *
43690 ATTTTGACCCTCAAACTTTCCAAAATTTTATTTTGACCTAAATTTTCCAAAAATTACATTTTACC
1 ATTTT-ACCCT-AAAC-TTCCAAAATTCCATTTTGACCTGATTTTTCCAAAAATTACATTTTACC
* *
43755 CTCGAACTTTCTAAAATT-CACTTTTTGACCCCAATTTTT-TCAAAAATTAC
63 C-CAAACTTTCCAAAATTCCA-TTTTTGA-CCCAATTTTTCT-AAAAATTAC
* *
43805 ATTTTTTATCCCTGAACTTCCCAAAATTCCATTTTAACCCT-ATTTTTCCAAAAATTACATTTTT
1 A--TTTTA-CCCTAAACTT-CCAAAATTCCATTTTGA-CCTGATTTTTCCAAAAATTACA-TTTT
* * * *
43869 ATCCCCAAACTTTCTAAAACTCTATTTTTTACCCTAATTTTTCTAAAAATTACC
60 A-CCCCAAACTTTCCAAAATTCCATTTTTGACCC-AATTTTTCTAAAAATTA-C
43923 ATTTTACCCTAAACTTCCAAAGATTCCATTTTTGACCCTGATTTTTCCAAAAATTATCATTTTAC
1 ATTTTACCCTAAACTTCCAAA-ATTCCA-TTTTGA-CCTGATTTTTCCAAAAATTA-CATTTTAC
* *
43988 CCCAAAC-TTCCAAAGATTCCATTTTTGACCTCGATTTTTCCAAAAATTATC
62 CCCAAACTTTCCAAA-ATTCCATTTTTGACC-CAATTTTTCTAAAAATTA-C
* * * * *
44039 ATTTTACCCTTGAACTTCC-AAAGTCCATTTTTGACCTCGATTCTTCCGAAAAGTACCATTTTAC
1 ATTTTACCC-TAAACTTCCAAAATTCCA-TTTTGACCT-GATTTTTCCAAAAATTA-CATTTTAC
** * *
44103 TCCCGGA-TGTCCAAAATTCCGTTTTTGACCC
62 -CCCAAACTTTCCAAAATTCCATTTTTGACCC
44134 CCAACTTTCC
Statistics
Matches: 280, Mismatches: 28, Indels: 43
0.80 0.08 0.12
Matches are distributed among these distances:
114 9 0.03
115 72 0.26
116 109 0.39
117 81 0.29
118 9 0.03
ACGTcount: A:0.30, C:0.25, G:0.05, T:0.40
Consensus pattern (110 bp):
ATTTTACCCTAAACTTCCAAAATTCCATTTTGACCTGATTTTTCCAAAAATTACATTTTACCCCA
AACTTTCCAAAATTCCATTTTTGACCCAATTTTTCTAAAAATTAC
Found at i:44099 original size:57 final size:57
Alignment explanation
Indices: 43732--44102 Score: 314
Period size: 58 Copynumber: 6.4 Consensus size: 57
43722 TTGACCTAAA
* * * * *
43732 TTTTCCAAAAATTA-CATTTTACCCTCGAACTTTCTAAA-ATTCACTTTTTGACCCCAAT
1 TTTTCCAAAAATTACCATTTTACCCT-AAAC-TTCCAAAGATCCA-TTTTTGACCTCGAT
* * * *
43790 TTTTTCAAAAATTA-CATTTTTTATCCCTGAACTTCCCAAA-ATTCCA-TTTTAACC-CTAT
1 TTTTCCAAAAATTACCA--TTTTA-CCCTAAACTT-CCAAAGA-TCCATTTTTGACCTCGAT
* * * * *
43848 TTTTCCAAAAATTA-CATTTTTATCCCCAAACTTTCTAAA-ACTCTATTTTTTACC-CTAAT
1 TTTTCCAAAAATTACCA-TTTTA-CCCTAAAC-TTCCAAAGA-TCCATTTTTGACCTC-GAT
*
43907 TTTTCTAAAAATTACCATTTTACCCTAAACTTCCAAAGATTCCATTTTTGACC-CTGAT
1 TTTTCCAAAAATTACCATTTTACCCTAAACTTCCAAAGA-TCCATTTTTGACCTC-GAT
* *
43965 TTTTCCAAAAATTATCATTTTACCCCAAACTTCCAAAGATTCCATTTTTGACCTCGAT
1 TTTTCCAAAAATTACCATTTTACCCTAAACTTCCAAAGA-TCCATTTTTGACCTCGAT
* *
44023 TTTTCCAAAAATTATCATTTTACCCTTGAACTTCCAAAG-TCCATTTTTGACCTCGAT
1 TTTTCCAAAAATTACCATTTTACCC-TAAACTTCCAAAGATCCATTTTTGACCTCGAT
* * *
44080 TCTTCCGAAAAGTACCATTTTAC
1 TTTTCCAAAAATTACCATTTTAC
44103 TCCCGGATGT
Statistics
Matches: 272, Mismatches: 29, Indels: 25
0.83 0.09 0.08
Matches are distributed among these distances:
57 64 0.24
58 144 0.53
59 41 0.15
60 16 0.06
61 7 0.03
ACGTcount: A:0.31, C:0.25, G:0.04, T:0.40
Consensus pattern (57 bp):
TTTTCCAAAAATTACCATTTTACCCTAAACTTCCAAAGATCCATTTTTGACCTCGAT
Found at i:44129 original size:115 final size:115
Alignment explanation
Indices: 43734--44157 Score: 327
Period size: 115 Copynumber: 3.7 Consensus size: 115
43724 GACCTAAATT
* * * * * *
43734 TTCCAAAAATTA-CATTTTACCCTCGAACTTTCTAAA-ATT-CACTTTTTGACCCCAATTTTTTC
1 TTCCAAAAAGTACCATTTTACCC-CAAAC-TTCCAAAGATTCCA-TTTTTGACCTCGATTTTTCC
* * *
43796 AAAAATTA-CATTTTTTATCCCTGAACTTCCCAAA-ATTCCA-TTTTAACCCT-ATTT
63 AAAAATTACCA--TTTTA-CCCTAAACTT-CCAAAGA-TCCATTTTTGACCCTGATTC
* * * * * *
43850 TTCCAAAAATTA-CATTTTTATCCCCAAACTTTCTAAA-ACTCTATTTTTTACC-CTAATTTTTC
1 TTCCAAAAAGTACCA-TTTTA-CCCCAAAC-TTCCAAAGATTCCATTTTTGACCTC-GATTTTTC
* *
43912 TAAAAATTACCATTTTACCCTAAACTTCCAAAGATTCCATTTTTGACCCTGATTT
62 CAAAAATTACCATTTTACCCTAAACTTCCAAAGA-TCCATTTTTGACCCTGATTC
* *
43967 TTCCAAAAATTATCATTTTACCCCAAACTTCCAAAGATTCCATTTTTGACCTCGATTTTTCCAAA
1 TTCCAAAAAGTACCATTTTACCCCAAACTTCCAAAGATTCCATTTTTGACCTCGATTTTTCCAAA
* *
44032 AATTATCATTTTACCCTTGAACTTCCAAAG-TCCATTTTTGA-CCTCGATTC
66 AATTACCATTTTACCC-TAAACTTCCAAAGATCCATTTTTGACCCT-GATTC
* ** * * * ** *
44082 TTCCGAAAAGTACCATTTTACTCCCGGA-TGTCCAAA-ATTCCGTTTTTGACCCCCAACTTTCCC
1 TTCCAAAAAGTACCATTTTAC-CCCAAACT-TCCAAAGATTCCATTTTTGACCTCGATTTTTCCA
44145 AAAATTACCATTT
64 AAAATTACCATTT
44158 GTCCCCGAGT
Statistics
Matches: 264, Mismatches: 29, Indels: 31
0.81 0.09 0.10
Matches are distributed among these distances:
114 8 0.03
115 88 0.33
116 84 0.32
117 76 0.29
118 8 0.03
ACGTcount: A:0.30, C:0.26, G:0.05, T:0.39
Consensus pattern (115 bp):
TTCCAAAAAGTACCATTTTACCCCAAACTTCCAAAGATTCCATTTTTGACCTCGATTTTTCCAAA
AATTACCATTTTACCCTAAACTTCCAAAGATCCATTTTTGACCCTGATTC
Found at i:45764 original size:18 final size:21
Alignment explanation
Indices: 45726--45764 Score: 57
Period size: 18 Copynumber: 2.0 Consensus size: 21
45716 GAAGGTTTAA
45726 ATTCTAAGTCTTATAAATTAT
1 ATTCTAAGTCTTATAAATTAT
45747 ATTC-AAGT-TTAT-AATTAT
1 ATTCTAAGTCTTATAAATTAT
45765 TTAAAAGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 4 0.22
20 4 0.22
21 4 0.22
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.49
Consensus pattern (21 bp):
ATTCTAAGTCTTATAAATTAT
Found at i:49834 original size:18 final size:18
Alignment explanation
Indices: 49811--49849 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
49801 GGTGTGTAAT
49811 AATTTTAAA-ATATTTTAA
1 AATTTTAAATAT-TTTTAA
*
49829 AATTTTGAATATTTTTAA
1 AATTTTAAATATTTTTAA
49847 AAT
1 AAT
49850 ACTAGTATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
AATTTTAAATATTTTTAA
Found at i:56509 original size:16 final size:18
Alignment explanation
Indices: 56490--56522 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
56480 AAAATTAATA
56490 ATTA-ATAAA-ATATTAG
1 ATTATATAAATATATTAG
56506 ATTATATAAATATATTA
1 ATTATATAAATATATTA
56523 TTTATAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 5 0.33
18 6 0.40
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (18 bp):
ATTATATAAATATATTAG
Found at i:56672 original size:15 final size:16
Alignment explanation
Indices: 56645--56674 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
56635 GGAAACATAA
56645 TAATTTAAATATAAAT
1 TAATTTAAATATAAAT
56661 TAATTT-AATATAAA
1 TAATTTAAATATAAA
56675 GCTTAAACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TAATTTAAATATAAAT
Found at i:67119 original size:21 final size:21
Alignment explanation
Indices: 67093--67135 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
67083 AGGTTATATA
*
67093 CCTCCATCAAAAAGCGGTGGT
1 CCTCCATCAAAAAGCAGTGGT
67114 CCTCCATCAAAAAGCAGTGGT
1 CCTCCATCAAAAAGCAGTGGT
67135 C
1 C
67136 GTATCTCGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (21 bp):
CCTCCATCAAAAAGCAGTGGT
Done.