Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004087.1 Kokia drynarioides strain JFW-HI SEQ_117257, 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: 73048
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:7742 original size:43 final size:43
Alignment explanation
Indices: 7689--7787 Score: 146
Period size: 43 Copynumber: 2.3 Consensus size: 43
7679 ACCTTGAAGG
* *
7689 ATTG-TTTAGGTAACTTTTCTGATTCTTTCTTATTTTAAATAT
1 ATTGTTTTAGGTAACTTTACTGATTCTTTCCTATTTTAAATAT
* *
7731 ATTGTTTTAGGTAAGTTTAGTGATTCTTTCCTATTTTAAATAT
1 ATTGTTTTAGGTAACTTTACTGATTCTTTCCTATTTTAAATAT
*
7774 ATTATTTTAGGTAA
1 ATTGTTTTAGGTAA
7788 AATGTCTTAC
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
42 4 0.08
43 47 0.92
ACGTcount: A:0.26, C:0.07, G:0.12, T:0.55
Consensus pattern (43 bp):
ATTGTTTTAGGTAACTTTACTGATTCTTTCCTATTTTAAATAT
Found at i:7802 original size:43 final size:43
Alignment explanation
Indices: 7693--7819 Score: 112
Period size: 43 Copynumber: 3.0 Consensus size: 43
7683 TGAAGGATTG
* * * * * *
7693 TTTAGGTAACTTTTCTGATTCTTTCTTATTTTAAATATATTGT
1 TTTAGGTAAATGTACTGACTCTTTCCTATTTTAAATATATTAT
* * * *
7736 TTTAGGTAAGTTTAGTGATTCTTTCCTATTTTAAATATATTAT
1 TTTAGGTAAATGTACTGACTCTTTCCTATTTTAAATATATTAT
* * * *
7779 TTTAGGTAAAATGT-CTTACTCTTTCCTGTTCTAAGTATATT
1 TTTAGGT-AAATGTACTGACTCTTTCCTATTTTAAATATATT
7820 CTAATGTGCC
Statistics
Matches: 70, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
43 66 0.94
44 4 0.06
ACGTcount: A:0.25, C:0.10, G:0.11, T:0.54
Consensus pattern (43 bp):
TTTAGGTAAATGTACTGACTCTTTCCTATTTTAAATATATTAT
Found at i:10326 original size:85 final size:85
Alignment explanation
Indices: 10189--10370 Score: 346
Period size: 85 Copynumber: 2.1 Consensus size: 85
10179 TAAGGTTCAA
10189 GTTTAGGGTTCAAGGGTTTGAAGTTATATGTTTTGGTTTCAATATTTTATGGTTTGTGGTTATAG
1 GTTT-GGGTTCAAGGGTTTGAAGTTATATGTTTTGGTTTCAATATTTTATGGTTTGTGGTTATAG
10254 ATTACGAGTTTGGGGTTTAGG
65 ATTACGAGTTTGGGGTTTAGG
10275 GTTTGGGTTCAAGGGTTTGAAGTTATATGTTTTGGTTTCAATATTTTATGGTTTGTGGTTATAGA
1 GTTTGGGTTCAAGGGTTTGAAGTTATATGTTTTGGTTTCAATATTTTATGGTTTGTGGTTATAGA
10340 TTACGAGTTTGGGGTTTAGG
66 TTACGAGTTTGGGGTTTAGG
*
10360 GTTTGAGTTCA
1 GTTTGGGTTCA
10371 TGGTTTTAGG
Statistics
Matches: 95, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
85 91 0.96
86 4 0.04
ACGTcount: A:0.19, C:0.04, G:0.30, T:0.47
Consensus pattern (85 bp):
GTTTGGGTTCAAGGGTTTGAAGTTATATGTTTTGGTTTCAATATTTTATGGTTTGTGGTTATAGA
TTACGAGTTTGGGGTTTAGG
Found at i:10752 original size:42 final size:43
Alignment explanation
Indices: 10705--10834 Score: 149
Period size: 42 Copynumber: 3.1 Consensus size: 43
10695 GCCTTGAACG
* * *
10705 ATTG-TTTAAGTAACTTTTCTGATTTTTTCCTATTTTAAATAT
1 ATTGTTTTAGGTAAATTTTCTTATTTTTTCCTATTTTAAATAT
* * **
10747 ATTGTTTTAGGTAAATTTACTTATTCTTTCCTA-TTTATGTAT
1 ATTGTTTTAGGTAAATTTTCTTATTTTTTCCTATTTTAAATAT
* *
10789 ATTGTTTTAGGTAAATTTTCTTATTCTTTT-CTATTATGAATAT
1 ATTGTTTTAGGTAAATTTTCTTATT-TTTTCCTATTTTAAATAT
10832 ATT
1 ATT
10835 CCAATGTGTC
Statistics
Matches: 72, Mismatches: 13, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
42 38 0.53
43 34 0.47
ACGTcount: A:0.25, C:0.08, G:0.08, T:0.58
Consensus pattern (43 bp):
ATTGTTTTAGGTAAATTTTCTTATTTTTTCCTATTTTAAATAT
Found at i:11215 original size:48 final size:48
Alignment explanation
Indices: 11160--11307 Score: 242
Period size: 48 Copynumber: 3.1 Consensus size: 48
11150 TCTTCCAATC
11160 TATCTTTTCGTAAAAATATATCTCATTTATCAATGTTGTCTAATAATA
1 TATCTTTTCGTAAAAATATATCTCATTTATCAATGTTGTCTAATAATA
* *
11208 TATCTTTTCGCAAAAATATATCTCATTTATCAGTGTTGTCTAATAATA
1 TATCTTTTCGTAAAAATATATCTCATTTATCAATGTTGTCTAATAATA
* * * *
11256 TATCTTTTCATAAAAATATATCTCATTTATCAATTTTTTCTAATAATT
1 TATCTTTTCGTAAAAATATATCTCATTTATCAATGTTGTCTAATAATA
11304 TATC
1 TATC
11308 ATTATTGCAA
Statistics
Matches: 92, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 92 1.00
ACGTcount: A:0.34, C:0.14, G:0.05, T:0.47
Consensus pattern (48 bp):
TATCTTTTCGTAAAAATATATCTCATTTATCAATGTTGTCTAATAATA
Found at i:11801 original size:24 final size:24
Alignment explanation
Indices: 11739--11802 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 24
11729 GTAGACTAAT
* **
11739 AAGAGTTTTACTCTAACAAATAAA
1 AAGAGTTTAACTGAAACAAATAAA
*
11763 AAGAGTTTAATTGAAACAAATAAA
1 AAGAGTTTAACTGAAACAAATAAA
*
11787 TAGAGTTTAACTGAAA
1 AAGAGTTTAACTGAAA
11803 GATTATTTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.52, C:0.08, G:0.12, T:0.28
Consensus pattern (24 bp):
AAGAGTTTAACTGAAACAAATAAA
Found at i:14700 original size:17 final size:17
Alignment explanation
Indices: 14650--14822 Score: 130
Period size: 17 Copynumber: 9.6 Consensus size: 17
14640 CCTATTTTGT
* *
14650 TTTAGATTTATCTTAAG
1 TTTAAATTTATTTTAAG
* *
14667 TTTGAATTTGTTTTTAAG
1 TTTAAATTT-ATTTTAAG
14685 TTTAAATTTATTTTAAG
1 TTTAAATTTATTTTAAG
*
14702 TTTAAGTTTAAGTTTATTTTAAA
1 TTT-A----AA-TTTATTTTAAG
*
14725 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAG
* *
14742 TTTAAATTTATTATCAAA
1 TTTAAATTTATT-TTAAG
** *
14760 TTTAAATTTATCCTAAA
1 TTTAAATTTATTTTAAG
* *
14777 TATAAATTTAATTTAAG
1 TTTAAATTTATTTTAAG
* *
14794 TTTAAATTTATTATCAAA
1 TTTAAATTTATT-TTAAG
14812 TTTAAATTTAT
1 TTTAAATTTAT
14823 CCTAAATATA
Statistics
Matches: 123, Mismatches: 24, Indels: 17
0.75 0.15 0.10
Matches are distributed among these distances:
17 62 0.50
18 45 0.37
22 3 0.02
23 13 0.11
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAG
Found at i:14705 original size:23 final size:23
Alignment explanation
Indices: 14679--14751 Score: 94
Period size: 23 Copynumber: 3.2 Consensus size: 23
14669 TGAATTTGTT
*
14679 TTTAAGTTTAAATTTATTTTAAG
1 TTTAAGTTTAAATTTATTTTAAA
*
14702 TTTAAGTTTAAGTTTATTTTAAA
1 TTTAAGTTTAAATTTATTTTAAA
* *
14725 TTTAAATTT-AATTTAAGTTTAAA
1 TTTAAGTTTAAATTT-ATTTTAAA
14748 TTTA
1 TTTA
14752 TTATCAAATT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
22 4 0.09
23 40 0.91
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (23 bp):
TTTAAGTTTAAATTTATTTTAAA
Found at i:14766 original size:6 final size:6
Alignment explanation
Indices: 14679--14821 Score: 81
Period size: 6 Copynumber: 24.7 Consensus size: 6
14669 TGAATTTGTT
* * * * * *
14679 TTTAAG TTTAAA TTT-AT TTTAAG TTTAAG TTTAAG TTT-AT TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
14725 TTTAAA TTT-AA TTTAAG TTTAAA TTT--A TTATCAAA TTTAAA TTT--A
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT-T-AAA TTTAAA TTTAAA
* * *
14770 TCCTAAA TATAAA TTT-AA TTTAAG TTTAAA TTT--A TTATCAAA TTTAAA
1 T-TTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT-T-AAA TTTAAA
14818 TTTA
1 TTTA
14822 TCCTAAATAT
Statistics
Matches: 110, Mismatches: 12, Indels: 30
0.72 0.08 0.20
Matches are distributed among these distances:
4 8 0.07
5 21 0.19
6 71 0.65
7 4 0.04
8 6 0.05
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:14770 original size:52 final size:52
Alignment explanation
Indices: 14721--14836 Score: 223
Period size: 52 Copynumber: 2.2 Consensus size: 52
14711 AAGTTTATTT
*
14721 TAAATTTAAATTTAATTTAAGTTTAAATTTATTATCAAATTTAAATTTATCC
1 TAAATATAAATTTAATTTAAGTTTAAATTTATTATCAAATTTAAATTTATCC
14773 TAAATATAAATTTAATTTAAGTTTAAATTTATTATCAAATTTAAATTTATCC
1 TAAATATAAATTTAATTTAAGTTTAAATTTATTATCAAATTTAAATTTATCC
14825 TAAATATAAATT
1 TAAATATAAATT
14837 AATAAAGTCC
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 63 1.00
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (52 bp):
TAAATATAAATTTAATTTAAGTTTAAATTTATTATCAAATTTAAATTTATCC
Found at i:14834 original size:17 final size:17
Alignment explanation
Indices: 14721--14836 Score: 92
Period size: 17 Copynumber: 6.7 Consensus size: 17
14711 AAGTTTATTT
*
14721 TAAATTTAAATTTAAT-T
1 TAAATTTAAATTT-ATCC
* **
14738 TAAGTTTAAATTTATTA
1 TAAATTTAAATTTATCC
14755 TCAAATTTAAATTTATCC
1 T-AAATTTAAATTTATCC
* *
14773 TAAATATAAATTTAAT-T
1 TAAATTTAAATTT-ATCC
* **
14790 TAAGTTTAAATTTATTA
1 TAAATTTAAATTTATCC
14807 TCAAATTTAAATTTATCC
1 T-AAATTTAAATTTATCC
*
14825 TAAATATAAATT
1 TAAATTTAAATT
14837 AATAAAGTCC
Statistics
Matches: 80, Mismatches: 14, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
16 4 0.05
17 46 0.57
18 30 0.38
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (17 bp):
TAAATTTAAATTTATCC
Found at i:16643 original size:30 final size:29
Alignment explanation
Indices: 16563--16951 Score: 201
Period size: 30 Copynumber: 13.2 Consensus size: 29
16553 TGCCCAAAAG
* *
16563 ACCCCCAAACTCTTCAAAAA-T-CATATTTT
1 ACCCCTAAACT-TCCAAAAATTACAT-TTTT
* * *
16592 AACCCTCAAACTTCTAAAAATTACATTTTA
1 ACCCCT-AAACTTCCAAAAATTACATTTTT
16622 ACCCCTAAACTTCACAAAAATTACATTTTTT
1 ACCCCTAAACTTC-CAAAAATTACA-TTTTT
* *
16653 ACCTC-AAACTTCACAAAAATTACA-ATTT
1 ACCCCTAAACTTC-CAAAAATTACATTTTT
* * * *
16681 AACCTTAAATTTCCTAAAATTACATTTTT
1 ACCCCTAAACTTCCAAAAATTACATTTTT
* * **
16710 GA-CCTTAAACTTTTCAAAAATTATGTTTTT
1 -ACCCCTAAAC-TTCCAAAAATTACATTTTT
* *
16740 ACCCCCAAAC-ACCTAAAAATTACCA-TTTT
1 ACCCCTAAACTTCC-AAAAATTA-CATTTTT
* * * *
16769 ACCCTCGAACCTTCTAAAAATCACATTTTT
1 ACCC-CTAAACTTCCAAAAATTACATTTTT
*
16799 ACCCTTAAACTTTCC-AAAATTACCA-TTTT
1 ACCCCTAAAC-TTCCAAAAATTA-CATTTTT
* * *
16828 ACCCCAAAACCTTCAAAAAATAACATTTTT
1 ACCCCTAAA-CTTCCAAAAATTACATTTTT
* ***
16858 ACCCCCGATTTTTCCAGAAAATTACCA-TTTT
1 A-CCCCTAAACTTCCA-AAAATTA-CATTTTT
* * * *
16889 ACCCTTGAATTTCCAAAAATTCCATTTTTT
1 ACCCCTAAACTTCCAAAAATTACA-TTTTT
* *
16919 A-TCCTAAATTTCC-AAAATTACCA-TTTT
1 ACCCCTAAACTTCCAAAAATTA-CATTTTT
16946 ACCCCT
1 ACCCCT
16952 TGATATCTAA
Statistics
Matches: 275, Mismatches: 58, Indels: 55
0.71 0.15 0.14
Matches are distributed among these distances:
27 5 0.02
28 27 0.10
29 94 0.34
30 119 0.43
31 28 0.10
32 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.02, T:0.35
Consensus pattern (29 bp):
ACCCCTAAACTTCCAAAAATTACATTTTT
Found at i:16720 original size:58 final size:59
Alignment explanation
Indices: 16595--16732 Score: 172
Period size: 58 Copynumber: 2.3 Consensus size: 59
16585 ATATTTTAAC
* * *
16595 CCTCAAACTTCTAAAAATTACATTTTAACCCCTAAACTTCACAAAAATTACATTTTTTA
1 CCTCAAACTTCCAAAAATTACAATTTAACCCCTAAACTTCACAAAAATTACATTTTTGA
* * *
16654 CCTCAAACTTCACAAAAATTACAATTTAA-CCTTAAATTTC-CTAAAATTACATTTTTGA
1 CCTCAAACTTC-CAAAAATTACAATTTAACCCCTAAACTTCACAAAAATTACATTTTTGA
* *
16712 CCTTAAACTTTTCAAAAATTA
1 CCTCAAAC-TTCCAAAAATTA
16733 TGTTTTTACC
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
58 32 0.46
59 22 0.32
60 15 0.22
ACGTcount: A:0.41, C:0.22, G:0.01, T:0.36
Consensus pattern (59 bp):
CCTCAAACTTCCAAAAATTACAATTTAACCCCTAAACTTCACAAAAATTACATTTTTGA
Found at i:16872 original size:59 final size:60
Alignment explanation
Indices: 16563--16949 Score: 211
Period size: 59 Copynumber: 6.6 Consensus size: 60
16553 TGCCCAAAAG
* * * * *
16563 ACCCCCAAACTCTT-CAAAAATCA-TATTTTAACCCTCAAA-CTTCTAAAAATTACATTTTA
1 ACCCCCAAACT-TTCCAAAAATTACCATTTT-ACCCTCAAACCTTCAAAAAATAACATTTTT
* * *
16622 ACCCCTAAAC-TTCACAAAAATTA-CATTTTTTA-CCTCAAA-CTTCACAAAAATTACA-ATTT
1 ACCCCCAAACTTTC-CAAAAATTACCA--TTTTACCCTCAAACCTTCA-AAAAATAACATTTTT
* ** * * * * **
16681 AACCTTAAA-TTTCCTAAAATTA-CATTTTTGA-CCTTAAACTTTTC-AAAAATTATGTTTTT
1 ACCCCCAAACTTTCCAAAAATTACCA-TTTT-ACCCTCAAAC-CTTCAAAAAATAACATTTTT
* * * *
16740 ACCCCCAAAC--ACCTAAAAATTACCATTTTACCCTCGAACCTTCTAAAAATCACATTTTT
1 ACCCCCAAACTTTCC-AAAAATTACCATTTTACCCTCAAACCTTCAAAAAATAACATTTTT
**
16799 ACCCTTAAACTTTCC-AAAATTACCATTTTACCC-CAAAACCTTCAAAAAATAACATTTTT
1 ACCCCCAAACTTTCCAAAAATTACCATTTTACCCTC-AAACCTTCAAAAAATAACATTTTT
* ** ** * * **
16858 ACCCCCGATTTTTCCAGAAAATTACCATTTTACCCTTGAA-TTTCCAAAAATTCCATTTTTT
1 ACCCCCAAACTTTCCA-AAAATTACCATTTTACCCTCAAACCTTCAAAAAATAACA-TTTTT
* *
16919 A-TCCTAAA-TTTCC-AAAATTACCATTTTACCC
1 ACCCCCAAACTTTCCAAAAATTACCATTTTACCC
16950 CTTGATATCT
Statistics
Matches: 260, Mismatches: 46, Indels: 46
0.74 0.13 0.13
Matches are distributed among these distances:
57 25 0.10
58 32 0.12
59 141 0.54
60 30 0.12
61 32 0.12
ACGTcount: A:0.37, C:0.26, G:0.02, T:0.35
Consensus pattern (60 bp):
ACCCCCAAACTTTCCAAAAATTACCATTTTACCCTCAAACCTTCAAAAAATAACATTTTT
Found at i:16917 original size:29 final size:29
Alignment explanation
Indices: 16754--17008 Score: 148
Period size: 29 Copynumber: 8.7 Consensus size: 29
16744 CCAAACACCT
* * *
16754 AAAAATTACCATTTTACCCTCGAACCTTCT
1 AAAAATTACCATTTTACCCTTGAA-TTTCC
* *
16784 AAAAATCA-CATTTTTACCCTTAAACTTTCC
1 AAAAATTACCA-TTTTACCCTTGAA-TTTCC
*** *
16814 -AAAATTACCATTTTACCCCAAAACCTT-C
1 AAAAATTACCATTTTACCCTTGAA-TTTCC
* * ** *
16842 AAAAAATAACATTTTTACCCCCGATTTTTCC
1 AAAAATTACCA-TTTTACCCTTGA-ATTTCC
16873 AGAAAATTACCATTTTACCCTTGAATTTCC
1 A-AAAATTACCATTTTACCCTTGAATTTCC
* *
16903 AAAAATT-CCATTTTTTATCC-TAAATTTCC
1 AAAAATTACCA--TTTTACCCTTGAATTTCC
* *
16932 -AAAATTACCATTTTACCCCTTG-ATATCT
1 AAAAATTACCATTTTA-CCCTTGAATTTCC
* * *
16960 AAAAATTACCATTTTACTCTTG-ATCCTCT
1 AAAAATTACCATTTTACCCTTGAAT-TTCC
* *
16989 AAAAATTATCGTTTTACCCT
1 AAAAATTACCATTTTACCCT
17009 CGGGCATCCA
Statistics
Matches: 180, Mismatches: 31, Indels: 29
0.75 0.13 0.12
Matches are distributed among these distances:
27 5 0.03
28 23 0.13
29 83 0.46
30 49 0.27
31 12 0.07
32 8 0.04
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.37
Consensus pattern (29 bp):
AAAAATTACCATTTTACCCTTGAATTTCC
Found at i:24479 original size:33 final size:33
Alignment explanation
Indices: 24403--24485 Score: 87
Period size: 33 Copynumber: 2.5 Consensus size: 33
24393 AAGCTATGCC
* * *
24403 AATAGATGTTCCAATCAATGATGAAGTTGCTTT
1 AATAGATGTTCCAATCAATCATGAAGCTGCTCT
* * *
24436 GATAGTTGTTCCAATCATTCATGAAGCTG-TCCT
1 AATAGATGTTCCAATCAATCATGAAGCTGCT-CT
*
24469 AATAGATGTTCCCATCA
1 AATAGATGTTCCAATCA
24486 CTTATGTTGA
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
32 1 0.03
33 39 0.98
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (33 bp):
AATAGATGTTCCAATCAATCATGAAGCTGCTCT
Found at i:50246 original size:17 final size:17
Alignment explanation
Indices: 50224--50263 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
50214 AAGCACAAGG
*
50224 AGGAAGGAGAGCGTCCA
1 AGGAAGGAGAGCATCCA
* *
50241 AGGAAGGATAGCATCCG
1 AGGAAGGAGAGCATCCA
50258 AGGAAG
1 AGGAAG
50264 AAGAAAAAGA
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:0.38, C:0.15, G:0.40, T:0.07
Consensus pattern (17 bp):
AGGAAGGAGAGCATCCA
Found at i:50363 original size:16 final size:18
Alignment explanation
Indices: 50342--50379 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
50332 TGTAGTTGGA
50342 TGCATTG-TA-TTGTCGT
1 TGCATTGTTATTTGTCGT
50358 TGCATTGTTATTTGTCGT
1 TGCATTGTTATTTGTCGT
50376 TGCA
1 TGCA
50380 ATTTTCATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 7 0.35
17 2 0.10
18 11 0.55
ACGTcount: A:0.13, C:0.13, G:0.24, T:0.50
Consensus pattern (18 bp):
TGCATTGTTATTTGTCGT
Found at i:57358 original size:67 final size:67
Alignment explanation
Indices: 57250--57384 Score: 252
Period size: 67 Copynumber: 2.0 Consensus size: 67
57240 ACTATCTCTA
* *
57250 GACTACTAGGACTATTCCTTAATTGCTCCTCTTGCGTTGCATTGAGCACTTCTCTTCAGAAGTGA
1 GACTACTAGGACTATTCCTTAATTGCTACTCTTGCGTTGCATTGAGCACTTCTCTTCAGAAATGA
57315 TT
66 TT
57317 GACTACTAGGACTATTCCTTAATTGCTACTCTTGCGTTGCATTGAGCACTTCTCTTCAGAAATGA
1 GACTACTAGGACTATTCCTTAATTGCTACTCTTGCGTTGCATTGAGCACTTCTCTTCAGAAATGA
57382 TT
66 TT
57384 G
1 G
57385 CTCCTCTGCT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.37
Consensus pattern (67 bp):
GACTACTAGGACTATTCCTTAATTGCTACTCTTGCGTTGCATTGAGCACTTCTCTTCAGAAATGA
TT
Found at i:66156 original size:333 final size:330
Alignment explanation
Indices: 65550--66205 Score: 992
Period size: 333 Copynumber: 2.0 Consensus size: 330
65540 AAATTAGGTG
*
65550 GAAACACCAGCTTATCAACTTGAACAAGGACATCTTTGACCTGTCCTTCCAGTTGTGCTAGAGAT
1 GAAACACCAGCTTATCAACTTGAACAAGGACATCTTTGACCTATCCTTCCAGTTGTGCTAGAGAT
* * * * * * *
65615 TTTTCTGTCGGTTGTAATGTCACTACAATAGGCTTTATCGTCCCGATTCCTAACTTCTTAAAAGT
66 CTATCTGTCAGTTGTAATGTCACCACAATAGGCTTCATCATCCCGACTCCTAACTTCTTAAAAGT
* *
65680 AGACAGAGGCATTAAGTTAATACTAGCTCCTAAATCACACAAAGCTTTACCTAAGTAATGATTTT
131 AAACAGAGGCACTAAGTTAATACTAGCTCCTAAATCACACAAAGCTTTACCTAAGTAATGATTTT
* * *
65745 CGATGGAGCATGGGATTGTGAAGTTGCCAGGATCTTTCATCTTGGTTGGCGACTTGTTTGTGATT
196 CGATGGAGCATGGGATTGTGAAGCTGCCAGGATCTTTCATCTTGGTTAGCAACTTGTTTGTGATT
* *
65810 ACAACACTGCATCCCTCTGTGAGCGCAATCATCTCGATATCGGATACCTTCTTTTCTTTGATAAA
261 ACAACACTGCATCCCTCTATGAGCGCAATCATCTCGATATCGGATAAC--CTTTT-TTTGATAAA
65875 ATCAGCAA
323 ATCAGCAA
* * * *
65883 GAAACACCAGCTTATCGACTTGGACAAGGACATCTTTGATCTATCCTTTC-GATTGTGCTAGAGA
1 GAAACACCAGCTTATCAACTTGAACAAGGACATCTTTGACCTATCCTTCCAG-TTGTGCTAGAGA
** * *
65947 TCTATCTG-CTAGTTGTAATGTCACCGTAGTAGGCTTCATCATCTCGACTCCTAACTTCTTAAAA
65 TCTATCTGTC-AGTTGTAATGTCACCACAATAGGCTTCATCATCCCGACTCCTAACTTCTTAAAA
* * *
66011 GTAAATAGAGGCACTAAGTTAATACTTGCTCCTAAATCACACAAAGTTTTACCTAAGTAATGATT
129 GTAAACAGAGGCACTAAGTTAATACTAGCTCCTAAATCACACAAAGCTTTACCTAAGTAATGATT
*
66076 TTCGATGGAGCATGGGATTGTGAAGCTGCCAGGATCTTTCATTTTGGTTAGCAACTTGTTTGTGA
194 TTCGATGGAGCATGGGATTGTGAAGCTGCCAGGATCTTTCATCTTGGTTAGCAACTTGTTTGTGA
* *
66141 TTACAACATTGCATCCCTCTATGAGCGTAATCATCTCGATATCGGATAACCTTTTTTTGATAAAA
259 TTACAACACTGCATCCCTCTATGAGCGCAATCATCTCGATATCGGATAACCTTTTTTTGATAAAA
66206 GCTCCTTCAT
Statistics
Matches: 292, Mismatches: 29, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
330 10 0.03
331 5 0.02
332 2 0.01
333 275 0.94
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (330 bp):
GAAACACCAGCTTATCAACTTGAACAAGGACATCTTTGACCTATCCTTCCAGTTGTGCTAGAGAT
CTATCTGTCAGTTGTAATGTCACCACAATAGGCTTCATCATCCCGACTCCTAACTTCTTAAAAGT
AAACAGAGGCACTAAGTTAATACTAGCTCCTAAATCACACAAAGCTTTACCTAAGTAATGATTTT
CGATGGAGCATGGGATTGTGAAGCTGCCAGGATCTTTCATCTTGGTTAGCAACTTGTTTGTGATT
ACAACACTGCATCCCTCTATGAGCGCAATCATCTCGATATCGGATAACCTTTTTTTGATAAAATC
AGCAA
Found at i:71296 original size:11 final size:11
Alignment explanation
Indices: 71282--71306 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
71272 AATTTTTGAA
71282 AAATCTTTTAT
1 AAATCTTTTAT
71293 AAATCTTTTAT
1 AAATCTTTTAT
71304 AAA
1 AAA
71307 AACCAGCATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (11 bp):
AAATCTTTTAT
Done.