Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013432.1 Kokia drynarioides strain JFW-HI SEQ_128458, 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: 42561
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1227 original size:22 final size:22
Alignment explanation
Indices: 1201--1245 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1191 GTCAGCAATT
* *
1201 AAATATTTTTTTTAAATTTTAA
1 AAATATGTTTTATAAATTTTAA
*
1223 AAATATGTTTTATCAATTTTAA
1 AAATATGTTTTATAAATTTTAA
1245 A
1 A
1246 TGTGTATAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
AAATATGTTTTATAAATTTTAA
Found at i:3718 original size:62 final size:62
Alignment explanation
Indices: 3633--3749 Score: 180
Period size: 62 Copynumber: 1.9 Consensus size: 62
3623 GAGGTATGAA
*
3633 TTTTTTTTATCCAAGTTAGTCCCTAAACTTAACAATTGTTCTCACATTGGGGCTTCAAAACT
1 TTTTTTTTATCCAAGCTAGTCCCTAAACTTAACAATTGTTCTCACATTGGGGCTTCAAAACT
* * * * *
3695 TTTTTTTTATCTAAGCTAGTCCCTGAACTTAACGATTGTTTTCATATTGGGGCTT
1 TTTTTTTTATCCAAGCTAGTCCCTAAACTTAACAATTGTTCTCACATTGGGGCTT
3750 GAGCTTTTCT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
62 49 1.00
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.44
Consensus pattern (62 bp):
TTTTTTTTATCCAAGCTAGTCCCTAAACTTAACAATTGTTCTCACATTGGGGCTTCAAAACT
Found at i:5771 original size:31 final size:31
Alignment explanation
Indices: 5736--5794 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
5726 CAACTTAATC
** *
5736 TTTGAACTTCGTAATTGTTCTGACATTGAGA
1 TTTGAACTAAGTAATTATTCTGACATTGAGA
5767 TTTGAACTAAGTAATTATTCTGACATTG
1 TTTGAACTAAGTAATTATTCTGACATTG
5795 GGGCTTGACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (31 bp):
TTTGAACTAAGTAATTATTCTGACATTGAGA
Found at i:7341 original size:13 final size:12
Alignment explanation
Indices: 7323--7356 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
7313 CTGTTGCTAT
7323 TTGCTATTGTTTG
1 TTGCTATT-TTTG
7336 TTGCTA-TTTTG
1 TTGCTATTTTTG
7347 TTGCTATTTT
1 TTGCTATTTT
7357 ACTATTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 10 0.50
12 4 0.20
13 6 0.30
ACGTcount: A:0.09, C:0.09, G:0.18, T:0.65
Consensus pattern (12 bp):
TTGCTATTTTTG
Found at i:8560 original size:22 final size:23
Alignment explanation
Indices: 8533--8575 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
8523 CGAAACTACG
8533 AAAAAACTTA-CAAAT-TAAAATA
1 AAAAAAC-TACCAAATATAAAATA
8555 AAAAAACTACCAAATATAAAA
1 AAAAAACTACCAAATATAAAA
8576 ATTAAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 2 0.11
22 12 0.63
23 5 0.26
ACGTcount: A:0.70, C:0.12, G:0.00, T:0.19
Consensus pattern (23 bp):
AAAAAACTACCAAATATAAAATA
Found at i:9142 original size:22 final size:22
Alignment explanation
Indices: 9101--9143 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
9091 TATTTTACTG
* *
9101 TCATTTCGTTATTGTTTTGCTA
1 TCATTTCGTTATTATATTGCTA
*
9123 TCATTTCGTTGTTATATTGCT
1 TCATTTCGTTATTATATTGCT
9144 GCTATTTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.58
Consensus pattern (22 bp):
TCATTTCGTTATTATATTGCTA
Found at i:10133 original size:60 final size:60
Alignment explanation
Indices: 10040--10160 Score: 242
Period size: 60 Copynumber: 2.0 Consensus size: 60
10030 CTGAGGCATT
10040 AAATATCAACTTAAATATGAGATATAACATAGTAAAGACTAGTGAATCAAATTGTAAATG
1 AAATATCAACTTAAATATGAGATATAACATAGTAAAGACTAGTGAATCAAATTGTAAATG
10100 AAATATCAACTTAAATATGAGATATAACATAGTAAAGACTAGTGAATCAAATTGTAAATG
1 AAATATCAACTTAAATATGAGATATAACATAGTAAAGACTAGTGAATCAAATTGTAAATG
10160 A
1 A
10161 GTATGCTTCT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.50, C:0.08, G:0.13, T:0.28
Consensus pattern (60 bp):
AAATATCAACTTAAATATGAGATATAACATAGTAAAGACTAGTGAATCAAATTGTAAATG
Found at i:11637 original size:23 final size:25
Alignment explanation
Indices: 11600--11646 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
11590 GAGCTGGCTG
11600 CTGGTCTGGTCTGCA-A-AAGGATA
1 CTGGTCTGGTCTGCAGAGAAGGATA
11623 CTGGTCTGTGT-TGCAGAGAAGGAT
1 CTGGTCTG-GTCTGCAGAGAAGGAT
11647 TTTCTGAGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 12 0.57
24 3 0.14
25 6 0.29
ACGTcount: A:0.23, C:0.15, G:0.34, T:0.28
Consensus pattern (25 bp):
CTGGTCTGGTCTGCAGAGAAGGATA
Found at i:13146 original size:4 final size:4
Alignment explanation
Indices: 13128--13198 Score: 51
Period size: 4 Copynumber: 18.2 Consensus size: 4
13118 TTGAAAAAAA
* * *
13128 AAAG AAAA AAGAG AAAG AAAG AAAG AATG AAAG -AAG -AAG GAAG AAGAG
1 AAAG AAAG AA-AG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AA-AG
* *
13176 GAAG AAAG --AG AAAG AAAA AAAG A
1 AAAG AAAG AAAG AAAG AAAG AAAG A
13199 TAATGTATTT
Statistics
Matches: 53, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
2 2 0.04
3 6 0.11
4 39 0.74
5 6 0.11
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.01
Consensus pattern (4 bp):
AAAG
Found at i:13172 original size:7 final size:7
Alignment explanation
Indices: 13128--13191 Score: 60
Period size: 7 Copynumber: 8.9 Consensus size: 7
13118 TTGAAAAAAA
*
13128 AAAGAAA
1 AAAGAAG
13135 AAAG-AG
1 AAAGAAG
13141 AAAGAAAG
1 AAAG-AAG
13149 AAAGAATG
1 AAAGAA-G
13157 AAAGAAG
1 AAAGAAG
*
13164 AAGGAAG
1 AAAGAAG
13171 AAGAGGAAG
1 AA-A-GAAG
13180 AAAG-AG
1 AAAGAAG
13186 AAAGAA
1 AAAGAA
13192 AAAAAGATAA
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
6 11 0.23
7 17 0.35
8 14 0.29
9 6 0.12
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.02
Consensus pattern (7 bp):
AAAGAAG
Found at i:13187 original size:22 final size:21
Alignment explanation
Indices: 13135--13198 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 21
13125 AAAAAAGAAA
13135 AAAGAGAAAGAAAGAAAGAATG
1 AAAGAG-AAGAAAGAAAGAATG
*
13157 AAAGAAGAAGGAAGAAGAGGAA-G
1 AAAG-AGAAGAAAGAA-A-GAATG
*
13180 AAAGAGAAAGAAAAAAAGA
1 AAAGAG-AAGAAAGAAAGA
13199 TAATGTATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
21 2 0.06
22 15 0.43
23 15 0.43
24 3 0.09
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.02
Consensus pattern (21 bp):
AAAGAGAAGAAAGAAAGAATG
Found at i:13588 original size:20 final size:21
Alignment explanation
Indices: 13547--13589 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
13537 CAATTTACTT
13547 TAATTTAATTTTGCTAGTTAG
1 TAATTTAATTTTGCTAGTTAG
* *
13568 TAATTTTATTTTG-TTGTTAG
1 TAATTTAATTTTGCTAGTTAG
13588 TA
1 TA
13590 GTAGTAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.26, C:0.02, G:0.14, T:0.58
Consensus pattern (21 bp):
TAATTTAATTTTGCTAGTTAG
Found at i:13886 original size:21 final size:23
Alignment explanation
Indices: 13851--13893 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
13841 GGGTAAAATT
13851 AATTATATAATAAAATTATAAAA
1 AATTATATAATAAAATTATAAAA
*
13874 AATTA-AT-ATAAAATTTTAAA
1 AATTATATAATAAAATTATAAA
13894 TATTTTGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
22 2 0.11
23 5 0.26
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
AATTATATAATAAAATTATAAAA
Found at i:14108 original size:16 final size:16
Alignment explanation
Indices: 14063--14112 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
14053 TAAACCTAGT
*
14063 TAATTAATTACCAAAA
1 TAATTAATTATCAAAA
*
14079 T-A-TAA-TATAAAAAA
1 TAATTAATTAT-CAAAA
14093 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
14109 TAAT
1 TAAT
14113 ATCCCCATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
13 2 0.07
14 8 0.30
15 2 0.07
16 12 0.44
17 3 0.11
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Found at i:15449 original size:43 final size:43
Alignment explanation
Indices: 15367--15451 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
15357 ATTAACATGT
* *
15367 TAAATTATATTACTTGACTCGTGTTAATATGGTTGCATGTTAC
1 TAAATTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
* *
15410 TAAATTATATTACTTTACTCTTATTAATAT-CTTGACATGTTA
1 TAAATTATATTACTTGACTCGTATTAATATGCTTG-CATGTTA
15452 TTAATTGTGC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 3 0.08
43 34 0.92
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.47
Consensus pattern (43 bp):
TAAATTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
Found at i:15824 original size:17 final size:17
Alignment explanation
Indices: 15802--15851 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
15792 GCCCAACAAA
* *
15802 TTTAAAATTAAGTTTAT
1 TTTAAATTTAAATTTAT
15819 TTTAAATTTAAATTTAT
1 TTTAAATTTAAATTTAT
*
15836 TATAAATTTAAATTTA
1 TTTAAATTTAAATTTA
15852 AAATTTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (17 bp):
TTTAAATTTAAATTTAT
Found at i:15828 original size:6 final size:6
Alignment explanation
Indices: 15799--15858 Score: 54
Period size: 6 Copynumber: 10.2 Consensus size: 6
15789 TGGGCCCAAC
* * *
15799 AAATTT AAAATT AAGTTT -ATTTT AAATTT AAATTT --ATTAT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATT-T AAATTT
15845 AAATTT AAAATTT A
1 AAATTT -AAATTT A
15859 TTTAAATAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
4 3 0.07
5 5 0.11
6 27 0.61
7 9 0.20
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (6 bp):
AAATTT
Found at i:15829 original size:23 final size:24
Alignment explanation
Indices: 15799--15865 Score: 70
Period size: 23 Copynumber: 2.9 Consensus size: 24
15789 TGGGCCCAAC
*
15799 AAATTTAAAATTAAGTT-T-ATTTT
1 AAATTTAAAATTAA-TTATAAATTT
*
15822 AAATTT-AAATTTATTATAAATTT
1 AAATTTAAAATTAATTATAAATTT
*
15845 AAATTTAAAATTTATT-TAAAT
1 AAATTTAAAATTAATTATAAAT
15866 AATGCCCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
21 2 0.05
22 7 0.18
23 21 0.54
24 9 0.23
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (24 bp):
AAATTTAAAATTAATTATAAATTT
Found at i:16106 original size:22 final size:22
Alignment explanation
Indices: 16078--16124 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
16068 CTTGGACTGC
16078 CACCGCCACTGCTTCAAGCCTT
1 CACCGCCACTGCTTCAAGCCTT
16100 CACCGCCACTGCTTCAAGCCTT
1 CACCGCCACTGCTTCAAGCCTT
16122 CAC
1 CAC
16125 TGCCGAACCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.19, C:0.47, G:0.13, T:0.21
Consensus pattern (22 bp):
CACCGCCACTGCTTCAAGCCTT
Found at i:16830 original size:78 final size:77
Alignment explanation
Indices: 16695--16850 Score: 237
Period size: 78 Copynumber: 2.0 Consensus size: 77
16685 AGAAAATTGA
* *
16695 AAGGACAGAGGACTTATCCTCAGCCGGTTCTACCGTCGTCGGAGCTTCGCGCTGGAGTGCCGTCA
1 AAGGACAGAGGACTTATCCTCAGCCAGTTCTACCGTCGTCAGAGCTTCGCGCTGGAGTGCCGTCA
16760 TCGCCTTGTCGT
66 TCGCCTTGTCGT
16772 ANAGGACAGAGGACTTATCCTC-GACCAGTTCTACCGTCG-CTAGAGCTTCGCG-TCGGAGTGCC
1 A-AGGACAGAGGACTTATCCTCAG-CCAGTTCTACCGTCGTC-AGAGCTTCGCGCT-GGAGTGCC
16834 GTCATCGCCTTGTCGT
62 GTCATCGCCTTGTCGT
16850 A
1 A
16851 CATGGATCTG
Statistics
Matches: 73, Mismatches: 2, Indels: 7
0.89 0.02 0.09
Matches are distributed among these distances:
77 4 0.05
78 69 0.95
ACGTcount: A:0.17, C:0.29, G:0.28, T:0.24
Consensus pattern (77 bp):
AAGGACAGAGGACTTATCCTCAGCCAGTTCTACCGTCGTCAGAGCTTCGCGCTGGAGTGCCGTCA
TCGCCTTGTCGT
Found at i:17047 original size:14 final size:13
Alignment explanation
Indices: 17026--17067 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
17016 GGCAGGAATA
17026 GACAGACGCGCGT
1 GACAGACGCGCGT
17039 GATCAGACGCG-GT
1 GA-CAGACGCGCGT
17052 GAC-GACGCGCGAT
1 GACAGACGCGCG-T
17065 GAC
1 GAC
17068 GCGCGGTCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 6 0.23
12 2 0.08
13 10 0.38
14 8 0.31
ACGTcount: A:0.24, C:0.29, G:0.38, T:0.10
Consensus pattern (13 bp):
GACAGACGCGCGT
Found at i:17777 original size:30 final size:29
Alignment explanation
Indices: 17705--18143 Score: 398
Period size: 30 Copynumber: 14.9 Consensus size: 29
17695 GGAGGTTCCT
* *
17705 AAACTGTCTAAAAATTCTATTTTTACCCTCG
1 AAACT-TCCAAAAATTCCATTTTTACCC-CG
*
17736 -AACTTCCAAAAATCCCATTTTTGACCCCG
1 AAACTTCCAAAAATTCCATTTTT-ACCCCG
*
17765 AAACTTCTAAAAATTCCATTTTTACCCTCG
1 AAACTTCCAAAAATTCCATTTTTACCC-CG
**
17795 -AACTTCCAAAAATAACATTTTTAACCCCG
1 AAACTTCCAAAAATTCCATTTTT-ACCCCG
** **
17824 AAACTT--TTAAATT-TTTTTTTATCCCC-
1 AAACTTCCAAAAATTCCATTTTTA-CCCCG
*
17850 AAACTTCCAAAAA-TCCTATTTTTGAACCCG
1 AAACTTCCAAAAATTCC-ATTTTT-ACCCCG
* * *
17880 AAACTTCTAAAAATTTCGTTTTTACCCTCG
1 AAACTTCCAAAAATTCCATTTTTACCC-CG
* *
17910 AAA-TTCCAAAAATCCCATTTTTGATCCCG
1 AAACTTCCAAAAATTCCATTTTT-ACCCCG
*
17939 AAACTTCTAAAAATTCCATTTTTACCCTC-
1 AAACTTCCAAAAATTCCATTTTTACCC-CG
* * * *
17968 TAACTTCCAAAAATCCCATTTTTGATCCCA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCG
17998 AAACTTCCAAAAATTCCATTTTTACCCCCG
1 AAACTTCCAAAAATTCCATTTTTA-CCCCG
* *
18028 -AACTTCCAAAAAATCCCATTTTTACTCTCG
1 AAACTTCC-AAAAATTCCATTTTTAC-CCCG
*
18058 -AACTTCCAAAAATTCCATTTTTAATCCCG
1 AAACTTCCAAAAATTCCATTTTT-ACCCCG
* *
18087 AAACTTCTAAAAATTCCATTTTTAATCCCG
1 AAACTTCCAAAAATTCCATTTTT-ACCCCG
18117 AAACTTCCAAAAATTACCA-TTTTACCC
1 AAACTTCCAAAAATT-CCATTTTTACCC
18144 TTAGCAAAAA
Statistics
Matches: 337, Mismatches: 46, Indels: 52
0.77 0.11 0.12
Matches are distributed among these distances:
26 7 0.02
27 10 0.03
28 7 0.02
29 126 0.37
30 182 0.54
31 5 0.01
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCCG
Found at i:17803 original size:59 final size:59
Alignment explanation
Indices: 17705--18251 Score: 523
Period size: 59 Copynumber: 9.4 Consensus size: 59
17695 GGAGGTTCCT
*
17705 AAACTGTCTAAAAATTCTATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
1 AAACT-TCTAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
** *
17765 AAACTTCTAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATAACATTTTTAACCCCG
1 AAACTTCTAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
* ** * * *
17824 AAACTT-T-TAAATT-TTTTTTTATCCC-CAAACTTCCAAAAATCCTATTTTTGAACCCG
1 AAACTTCTAAAAATTCCATTTTTA-CCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
* * * *
17880 AAACTTCTAAAAATTTCGTTTTTACCCTCGAAATTCCAAAAATCCCATTTTTGATCCCG
1 AAACTTCTAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
* * *
17939 AAACTTCTAAAAATTCCATTTTTACCCTCTAACTTCCAAAAATCCCATTTTTGATCCCA
1 AAACTTCTAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
* * *
17998 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAAATCCCATTTTT-ACTCTCG
1 AAACTTCTAAAAATTCCATTTTTACCCTCGAACTTCC-AAAAATCCCATTTTTGAC-CCCG
* * * * * *
18058 -AACTTCCAAAAATTCCATTTTTAATCC-CGAAACTTCTAAAAATTCCATTTTTAATCCCG
1 AAACTTCTAAAAATTCCATTTTT-ACCCTCG-AACTTCCAAAAATCCCATTTTTGACCCCG
* ** * *
18117 AAACTTCCAAAAATTACCA-TTTTACCCT-----TAGCAAAAAACTCCATTTTTGACCCCA
1 AAACTTCTAAAAATT-CCATTTTTACCCTCGAACTTCCAAAAATC-CCATTTTTGACCCCG
* * * * * * *
18172 AAAC-TCTCAAAATTACC-CTTTTACCCCCGAA-TATCCAAAAATTCCATTTTTAATCCCT
1 AAACTTCTAAAAATT-CCATTTTTACCCTCGAACT-TCCAAAAATCCCATTTTTGACCCCG
**
18230 AATTTTCTAAAAATTACCATTT
1 AAACTTCTAAAAATT-CCATTT
18252 CACCCCCGAG
Statistics
Matches: 406, Mismatches: 59, Indels: 44
0.80 0.12 0.09
Matches are distributed among these distances:
54 25 0.06
55 16 0.04
56 37 0.09
57 9 0.02
58 24 0.06
59 240 0.59
60 52 0.13
61 3 0.01
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.35
Consensus pattern (59 bp):
AAACTTCTAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
Found at i:18212 original size:29 final size:29
Alignment explanation
Indices: 18180--18289 Score: 91
Period size: 28 Copynumber: 3.8 Consensus size: 29
18170 CAAAACTCTC
*
18180 AAAATTACCCTTTTACCCCCGAATATCCA
1 AAAATTACCATTTTACCCCCGAATATCCA
** * * *
18209 AAAATT-CCATTTTTAATCCCTAATTTTCTA
1 AAAATTACCA-TTTTACCCCCGAA-TATCCA
*
18239 AAAATTACCATTTCACCCCCGAGA-ATCC-
1 AAAATTACCATTTTACCCCCGA-ATATCCA
* *
18267 AAAATTACCATTTTGCCCTCGAA
1 AAAATTACCATTTTACCCCCGAA
18290 AAGTCTAATT
Statistics
Matches: 62, Mismatches: 15, Indels: 10
0.71 0.17 0.11
Matches are distributed among these distances:
27 1 0.02
28 21 0.34
29 18 0.29
30 18 0.29
31 4 0.06
ACGTcount: A:0.35, C:0.29, G:0.05, T:0.32
Consensus pattern (29 bp):
AAAATTACCATTTTACCCCCGAATATCCA
Found at i:31402 original size:21 final size:22
Alignment explanation
Indices: 31376--31427 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
31366 AACACATTAG
31376 CTTTCTTTCCTCTC-CTTCTTC
1 CTTTCTTTCCTCTCTCTTCTTC
* * *
31397 CTTTCTTT-CTTTCTTTTCTTT
1 CTTTCTTTCCTCTCTCTTCTTC
31418 CTTTCTTTCC
1 CTTTCTTTCC
31428 CGTTTATTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 4 0.15
21 21 0.81
22 1 0.04
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (22 bp):
CTTTCTTTCCTCTCTCTTCTTC
Found at i:31406 original size:4 final size:4
Alignment explanation
Indices: 31376--31426 Score: 57
Period size: 4 Copynumber: 12.2 Consensus size: 4
31366 AACACATTAG
* * *
31376 CTTT CTTT CCTCT CCTT CTTC CTTT CTTT CTTT CTTTT CTTT CTTT CTTT
1 CTTT CTTT -CTTT CTTT CTTT CTTT CTTT CTTT C-TTT CTTT CTTT CTTT
31426 C
1 C
31427 CCGTTTATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
4 32 0.82
5 7 0.18
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (4 bp):
CTTT
Found at i:31414 original size:13 final size:13
Alignment explanation
Indices: 31376--31426 Score: 61
Period size: 13 Copynumber: 4.1 Consensus size: 13
31366 AACACATTAG
*
31376 CTTTCTTTCCTCT
1 CTTTCTTTCCTTT
*
31389 CCTTC-TTCCTTT
1 CTTTCTTTCCTTT
*
31401 CTTTCTTTCTTTT
1 CTTTCTTTCCTTT
31414 CTTTCTTT-CTTT
1 CTTTCTTTCCTTT
31426 C
1 C
31427 CCGTTTATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
12 14 0.44
13 18 0.56
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (13 bp):
CTTTCTTTCCTTT
Found at i:31620 original size:26 final size:27
Alignment explanation
Indices: 31585--31636 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
31575 GCCAAGTGGC
31585 AAAACACTCC-TTAGTGCCGCCACTTA
1 AAAACACTCCATTAGTGCCGCCACTTA
* *
31611 AAAACCCTCCATTGGTGCCGCCACTT
1 AAAACACTCCATTAGTGCCGCCACTT
31637 CGTGTTCCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 9 0.39
27 14 0.61
ACGTcount: A:0.27, C:0.37, G:0.13, T:0.23
Consensus pattern (27 bp):
AAAACACTCCATTAGTGCCGCCACTTA
Done.