Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011454.1 Kokia drynarioides strain JFW-HI SEQ_126438, 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: 38273
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 20 characters in sequence are not A, C, G, or T
Found at i:4729 original size:10 final size:10
Alignment explanation
Indices: 4689--4721 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
4679 AACGTGTCAT
4689 AAAAA-TAAA
1 AAAAACTAAA
4698 TAAAAACTAAA
1 -AAAAACTAAA
4709 AAAAACTAAA
1 AAAAACTAAA
4719 AAA
1 AAA
4722 TAAAAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 18 0.82
11 4 0.18
ACGTcount: A:0.82, C:0.06, G:0.00, T:0.12
Consensus pattern (10 bp):
AAAAACTAAA
Found at i:4740 original size:16 final size:16
Alignment explanation
Indices: 4687--4743 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
4677 AAAACGTGTC
*
4687 ATAAAAATAAATAAAAA
1 ATAAAAA-AACTAAAAA
*
4704 CTAAAAAAAACTAAAAA
1 AT-AAAAAAACTAAAAA
* * *
4721 ATAAAAAAATTTAAAT
1 ATAAAAAAACTAAAAA
4737 ATAAAAA
1 ATAAAAA
4744 TTAAGAAGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
16 18 0.55
17 10 0.30
18 5 0.15
ACGTcount: A:0.77, C:0.04, G:0.00, T:0.19
Consensus pattern (16 bp):
ATAAAAAAACTAAAAA
Found at i:4743 original size:17 final size:17
Alignment explanation
Indices: 4687--4729 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
4677 AAAACGTGTC
4687 ATAAAAATAAA-TAAAAA
1 ATAAAAA-AAACTAAAAA
*
4704 CTAAAAAAAACTAAAAA
1 ATAAAAAAAACTAAAAA
4721 ATAAAAAAA
1 ATAAAAAAA
4730 TTTAAATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 20 0.87
ACGTcount: A:0.81, C:0.05, G:0.00, T:0.14
Consensus pattern (17 bp):
ATAAAAAAAACTAAAAA
Found at i:5074 original size:6 final size:6
Alignment explanation
Indices: 5063--5101 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
5053 ACAAATAATT
* *
5063 ATTTTA ATTTTA ATTTCA ATTTCA ATTTCA ATTTCA ATT
1 ATTTCA ATTTCA ATTTCA ATTTCA ATTTCA ATTTCA ATT
5102 GTTAAAAGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.56
Consensus pattern (6 bp):
ATTTCA
Found at i:5089 original size:18 final size:18
Alignment explanation
Indices: 5063--5106 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
5053 ACAAATAATT
*
5063 ATTTTAATTTTAATTTCA
1 ATTTTAATTTCAATTTCA
*
5081 ATTTCAATTTCAATTTCA
1 ATTTTAATTTCAATTTCA
5099 ATTGTTAA
1 ATT-TTAA
5107 AAGAAAACAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.34, C:0.09, G:0.02, T:0.55
Consensus pattern (18 bp):
ATTTTAATTTCAATTTCA
Found at i:7078 original size:25 final size:25
Alignment explanation
Indices: 7050--7099 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
7040 TAATTTTTTG
* *
7050 TAAAAAAACACAACCAATACAAATT
1 TAAAAAAAAAAAACCAATACAAATT
*
7075 TAAAAAAAAAAAATCAATACAAATT
1 TAAAAAAAAAAAACCAATACAAATT
7100 CAAGAGCTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.68, C:0.14, G:0.00, T:0.18
Consensus pattern (25 bp):
TAAAAAAAAAAAACCAATACAAATT
Found at i:7793 original size:49 final size:49
Alignment explanation
Indices: 7721--7817 Score: 176
Period size: 49 Copynumber: 2.0 Consensus size: 49
7711 AAAAAAATTG
*
7721 TTTTAAGTAAGTTTTTGGATGAGCGATTGGAGTGTTGTGGTAGAATCTA
1 TTTTAAGTAAGTCTTTGGATGAGCGATTGGAGTGTTGTGGTAGAATCTA
*
7770 TTTTAAGTATGTCTTTGGATGAGCGATTGGAGTGTTGTGGTAGAATCT
1 TTTTAAGTAAGTCTTTGGATGAGCGATTGGAGTGTTGTGGTAGAATCT
7818 TTTACTTTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.23, C:0.05, G:0.31, T:0.41
Consensus pattern (49 bp):
TTTTAAGTAAGTCTTTGGATGAGCGATTGGAGTGTTGTGGTAGAATCTA
Found at i:10134 original size:2 final size:2
Alignment explanation
Indices: 10127--10154 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
10117 CCATTAAGTG
10127 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
10155 TTGGTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10250 original size:61 final size:61
Alignment explanation
Indices: 10155--10277 Score: 210
Period size: 61 Copynumber: 2.0 Consensus size: 61
10145 ATATATATAT
* *
10155 TTGGTTTTTTCACAACCAACTCTTCAATTTTTGTAATCTTTTCTTATCATGTCATAAATGA
1 TTGGTTTTTTCACAACCAACTCTTCAATTATTGTAATCTTTTCTTACCATGTCATAAATGA
* *
10216 TTGGTTTTTTCAGAACCACCTCTTCAATTATTGTAATCTTTTCTTACCATGTCATAAATGA
1 TTGGTTTTTTCACAACCAACTCTTCAATTATTGTAATCTTTTCTTACCATGTCATAAATGA
10277 T
1 T
10278 CCATTAAGTG
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.26, C:0.19, G:0.09, T:0.46
Consensus pattern (61 bp):
TTGGTTTTTTCACAACCAACTCTTCAATTATTGTAATCTTTTCTTACCATGTCATAAATGA
Found at i:13918 original size:20 final size:20
Alignment explanation
Indices: 13839--13918 Score: 81
Period size: 20 Copynumber: 4.0 Consensus size: 20
13829 TGCCTGAAGC
*
13839 TATTTTGACTTGTTTGAAAAA
1 TATTTTGACTTGTTT-AAAAT
* **
13860 CATTTTGAAGTG-TTAAAAT
1 TATTTTGACTTGTTTAAAAT
* * *
13879 GATTTTGACTTGGTTCAAAT
1 TATTTTGACTTGTTTAAAAT
13899 TATTTTGACTTGTTTAAAAT
1 TATTTTGACTTGTTTAAAAT
13919 CATTATGTTA
Statistics
Matches: 47, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
19 13 0.28
20 25 0.53
21 9 0.19
ACGTcount: A:0.31, C:0.06, G:0.15, T:0.47
Consensus pattern (20 bp):
TATTTTGACTTGTTTAAAAT
Found at i:13932 original size:23 final size:24
Alignment explanation
Indices: 13897--13943 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
13887 CTTGGTTCAA
* *
13897 ATTATTTTGACTTG-TTTAAAATC
1 ATTATGTTAACTTGATTTAAAATC
13920 ATTATGTTAACTTGATTTTAAAAT
1 ATTATGTTAACTTGA-TTTAAAAT
13944 AGTTTCAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
25 8 0.40
ACGTcount: A:0.34, C:0.06, G:0.09, T:0.51
Consensus pattern (24 bp):
ATTATGTTAACTTGATTTAAAATC
Found at i:14196 original size:18 final size:18
Alignment explanation
Indices: 14163--14215 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
14153 GCTGAGATGA
14163 AAATAAATTT--TTAATT
1 AAATAAATTTAATTAATT
14179 AAATAAATTTAATTAATT
1 AAATAAATTTAATTAATT
* *
14197 GAA-AATTTTAAATTAATT
1 AAATAAATTT-AATTAATT
14215 A
1 A
14216 CAACTGAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
16 10 0.32
17 5 0.16
18 16 0.52
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
AAATAAATTTAATTAATT
Found at i:15359 original size:21 final size:21
Alignment explanation
Indices: 15333--15381 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
15323 TGGTATTGTT
15333 ATTTTTAATTAAAGTTTTATA
1 ATTTTTAATTAAAGTTTTATA
15354 ATTTTTAATTAAAGTTTTATA
1 ATTTTTAATTAAAGTTTTATA
15375 ATTTTTA
1 ATTTTTA
15382 TATTTTTATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (21 bp):
ATTTTTAATTAAAGTTTTATA
Found at i:15386 original size:8 final size:9
Alignment explanation
Indices: 15347--15415 Score: 61
Period size: 9 Copynumber: 7.3 Consensus size: 9
15337 TTAATTAAAG
15347 TTTTATAAT
1 TTTTATAAT
*
15356 TTTTAATTAAAG
1 TTTT-A-T-AAT
15368 TTTTATAAT
1 TTTTATAAT
15377 TTTTAT-AT
1 TTTTATAAT
15385 TTTTATGATAT
1 TTTTAT-A-AT
*
15396 TTTAATAAT
1 TTTTATAAT
15405 TTTTA-AAT
1 TTTTATAAT
15413 TTT
1 TTT
15416 AAAATGATTT
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
8 14 0.28
9 18 0.36
10 3 0.06
11 9 0.18
12 6 0.12
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (9 bp):
TTTTATAAT
Found at i:15425 original size:28 final size:28
Alignment explanation
Indices: 15368--15450 Score: 73
Period size: 27 Copynumber: 2.9 Consensus size: 28
15358 TTAATTAAAG
* **
15368 TTTT-ATAATTTTTATATTTTTATGATA
1 TTTTAATAATTTTTATAATTTTAAAATA
15395 TTTTAATAATTTTTA-AATTTTAAAATGA
1 TTTTAATAATTTTTATAATTTTAAAAT-A
15423 -TTTAATTAATTTATTATCAATTATTAAA
1 TTTTAA-TAATTT-TTAT-AATT-TTAAA
15451 GTCTTTTTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
27 17 0.37
28 17 0.37
29 3 0.07
31 4 0.09
32 5 0.11
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.58
Consensus pattern (28 bp):
TTTTAATAATTTTTATAATTTTAAAATA
Found at i:17111 original size:13 final size:13
Alignment explanation
Indices: 17093--17117 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17083 GAATAACCAC
17093 TTTCTCTTGAAAA
1 TTTCTCTTGAAAA
17106 TTTCTCTTGAAA
1 TTTCTCTTGAAA
17118 GGATTTACAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.16, G:0.08, T:0.48
Consensus pattern (13 bp):
TTTCTCTTGAAAA
Found at i:19835 original size:26 final size:27
Alignment explanation
Indices: 19785--19838 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 27
19775 ACATACAAAG
19785 AAAATTAATTAATTAACTCATTTTAATA
1 AAAATTAATTAA-TAACTCATTTTAATA
19813 AAAATTAAATTAA-AA-TCATTTTAATA
1 AAAATT-AATTAATAACTCATTTTAATA
19839 CGCATGACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 11 0.44
27 2 0.08
28 6 0.24
29 6 0.24
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.41
Consensus pattern (27 bp):
AAAATTAATTAATAACTCATTTTAATA
Found at i:25063 original size:16 final size:17
Alignment explanation
Indices: 25042--25129 Score: 101
Period size: 17 Copynumber: 5.3 Consensus size: 17
25032 ATTTGTCTGG
* *
25042 ATTTATTGGAAA-TTGA
1 ATTTATTTGAAATTTAA
25058 ATTTATTT-AAATTTAA
1 ATTTATTTGAAATTTAA
* *
25074 GTTTATTTTAAATTTAA
1 ATTTATTTGAAATTTAA
25091 ATTTATTTGAAATTTAA
1 ATTTATTTGAAATTTAA
*
25108 ATTTATTAT-AAAATTAA
1 ATTTATT-TGAAATTTAA
25125 ATTTA
1 ATTTA
25130 GAAAGTCCAA
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
15 3 0.05
16 17 0.27
17 42 0.67
18 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (17 bp):
ATTTATTTGAAATTTAA
Found at i:25085 original size:17 final size:17
Alignment explanation
Indices: 25057--25129 Score: 103
Period size: 17 Copynumber: 4.4 Consensus size: 17
25047 TTGGAAATTG
25057 AATTTA-TTTAAATTTA
1 AATTTATTTTAAATTTA
*
25073 AGTTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
*
25090 AATTTATTTGAAATTTA
1 AATTTATTTTAAATTTA
* *
25107 AATTTATTATAAAATTA
1 AATTTATTTTAAATTTA
25124 AATTTA
1 AATTTA
25130 GAAAGTCCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
16 5 0.10
17 45 0.90
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:25105 original size:7 final size:6
Alignment explanation
Indices: 25062--25129 Score: 56
Period size: 6 Copynumber: 11.8 Consensus size: 6
25052 AATTGAATTT
* *
25062 ATTTAA ATTTAA GTTT-A TTTTAA ATTTAA ATTT-- ATTTGAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA ATTTAA
*
25108 ATTT-- ATTATAA AATTAA ATTTA
1 ATTTAA ATT-TAA ATTTAA ATTTA
25130 GAAAGTCCAA
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
4 7 0.14
5 5 0.10
6 32 0.64
7 6 0.12
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (6 bp):
ATTTAA
Found at i:27130 original size:59 final size:59
Alignment explanation
Indices: 27038--27475 Score: 646
Period size: 59 Copynumber: 7.4 Consensus size: 59
27028 TCCCTAAACT
* *
27038 TTCTAAAAATTATCATTTTACCCCCGACCTTCCAAAAATCCCATTTTTGACCCCGAACC
1 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* *
27097 TTCTAAAAATTACCATTTTATCCCCGAACTTCCAAAAATCCCAATTTTGACCCCGAACC
1 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
** *
27156 TTCTAAATTTTACCA-TTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCCCGAACC
1 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
*
27214 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTTGGCCCCGAACC
1 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCA-TTTTTGACCCCGAACC
* * ** * *
27274 TTTTGAAAATTATGATTTTACCCACGAACTTCCAAAAATCCTATTTTTGACCCCGAACC
1 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * *
27333 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCTAATC
1 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* *
27392 TTCTAAAAATTACCATTTTACCTCCGAACTTCCAAAAATCCCATTTTTGACTCCGAACC
1 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * * *
27451 CTC-CAAAACTACCATTTTGCCCCCG
1 TTCTAAAAATTACCATTTTACCCCCG
27476 TGCATCCGAA
Statistics
Matches: 338, Mismatches: 39, Indels: 5
0.88 0.10 0.01
Matches are distributed among these distances:
58 71 0.21
59 215 0.64
60 52 0.15
ACGTcount: A:0.31, C:0.32, G:0.05, T:0.31
Consensus pattern (59 bp):
TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
Found at i:27445 original size:29 final size:30
Alignment explanation
Indices: 27059--27468 Score: 311
Period size: 30 Copynumber: 13.9 Consensus size: 30
27049 ATCATTTTAC
27059 CCCCG-ACCTTCCAAAAATCCCATTTTTGA
1 CCCCGAACCTTCCAAAAATCCCATTTTTGA
* *
27088 CCCCGAACCTTCTAAAAATTACCA-TTTT-A
1 CCCCGAACCTTCCAAAAA-TCCCATTTTTGA
*
27117 TCCCCGAA-CTTCCAAAAATCCCAATTTTGA
1 -CCCCGAACCTTCCAAAAATCCCATTTTTGA
* ** *
27147 CCCCGAACCTTCTAAATTTTACCA--TTT-A
1 CCCCGAACCTTCCAAA-AATCCCATTTTTGA
*
27175 CCCCCGAA-CTTCCAAAAATCTCATTTTTGA
1 -CCCCGAACCTTCCAAAAATCCCATTTTTGA
* *
27205 CCCCGAACCTTCTAAAAATTACCA-TTTT-A
1 CCCCGAACCTTCCAAAAA-TCCCATTTTTGA
*
27234 CCCCCGAA-CTTCCAAAAATCCCATTTTTTGG
1 -CCCCGAACCTTCCAAAAATCCCA-TTTTTGA
*** *
27265 CCCCGAACCTTTTGAAAAT--TATGATTTT-A
1 CCCCGAACCTTCCAAAAATCCCAT--TTTTGA
*
27294 CCCACGAA-CTTCCAAAAATCCTATTTTTGA
1 CCC-CGAACCTTCCAAAAATCCCATTTTTGA
* *
27324 CCCCGAACCTTCTAAAAATTACCA-TTTT-A
1 CCCCGAACCTTCCAAAAA-TCCCATTTTTGA
* *
27353 CCCCCAAACTTCCAAAAATCCCATTTTTGA
1 CCCCGAACCTTCCAAAAATCCCATTTTTGA
* * * *
27383 CCCCTAATCTTCTAAAAATTACCA-TTTT-A
1 CCCCGAACCTTCCAAAAA-TCCCATTTTTGA
27412 CCTCCGAA-CTTCCAAAAATCCCATTTTTGA
1 CC-CCGAACCTTCCAAAAATCCCATTTTTGA
* * * *
27442 CTCCGAACCCTCCAAAACTACCATTTT
1 CCCCGAACCTTCCAAAAATCCCATTTT
27469 GCCCCCGTGC
Statistics
Matches: 303, Mismatches: 45, Indels: 65
0.73 0.11 0.16
Matches are distributed among these distances:
27 3 0.01
28 25 0.08
29 117 0.39
30 129 0.43
31 29 0.10
ACGTcount: A:0.31, C:0.32, G:0.05, T:0.31
Consensus pattern (30 bp):
CCCCGAACCTTCCAAAAATCCCATTTTTGA
Found at i:35139 original size:28 final size:27
Alignment explanation
Indices: 35089--35149 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
35079 CAATTTTCAA
* **
35089 TTAATGATTGTTTCCTTTAATCCTCCTT
1 TTAATAATTGTTTCCTACAATCCT-CTT
*
35117 TTAATAATTGTTTCCTACGATCCTCTT
1 TTAATAATTGTTTCCTACAATCCTCTT
35144 TTAATA
1 TTAATA
35150 GAATTCTTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 9 0.31
28 20 0.69
ACGTcount: A:0.23, C:0.20, G:0.07, T:0.51
Consensus pattern (27 bp):
TTAATAATTGTTTCCTACAATCCTCTT
Found at i:35810 original size:37 final size:37
Alignment explanation
Indices: 35763--35852 Score: 119
Period size: 37 Copynumber: 2.4 Consensus size: 37
35753 TAGCTTCCTG
* *
35763 ATGAGATACTGAGAAGTGAACCGAATTCGTCTTCCAA
1 ATGAGATACTGAGAAGTGAACCAAATTCATCTTCCAA
* **
35800 ATGAGGTACTGAGAAGTGAACCAAATTCATCTTCCTG
1 ATGAGATACTGAGAAGTGAACCAAATTCATCTTCCAA
35837 ATGAGATA-TAGAGAAG
1 ATGAGATACT-GAGAAG
35853 CGGATTGAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
36 1 0.02
37 45 0.98
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.24
Consensus pattern (37 bp):
ATGAGATACTGAGAAGTGAACCAAATTCATCTTCCAA
Found at i:36028 original size:37 final size:37
Alignment explanation
Indices: 35930--36028 Score: 119
Period size: 37 Copynumber: 2.7 Consensus size: 37
35920 AAATGAGCAA
* * *
35930 ATCTTCCTGATGGGATACTGAGAAGTGAACCGAATTC
1 ATCTTCCTGATGAGATACAGAGAAGTGAACCAAATTC
* *
35967 ATCTTCCAGATGAGGTACTA-AGAAGTGAACCAAATTC
1 ATCTTCCTGATGAGATAC-AGAGAAGTGAACCAAATTC
* *
36004 GTCTTGCTGATGAGATACAGAGAAG
1 ATCTTCCTGATGAGATACAGAGAAG
36029 CGGATTGAAA
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
36 1 0.02
37 50 0.98
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.25
Consensus pattern (37 bp):
ATCTTCCTGATGAGATACAGAGAAGTGAACCAAATTC
Found at i:36161 original size:37 final size:37
Alignment explanation
Indices: 36106--36203 Score: 126
Period size: 37 Copynumber: 2.6 Consensus size: 37
36096 AACGAGCAAA
* *
36106 TCTTCCTGATG-GGATACTGAGAAGTGAACCGAATTCG
1 TCTTCCTGATGAGG-TACTGAGAAGTCAACCAAATTCG
*
36143 TCTTCCAGATGAGGTACTGAGAAGTCAACCAAATTCG
1 TCTTCCTGATGAGGTACTGAGAAGTCAACCAAATTCG
* * *
36180 TCTTGCTGATGAGATACAGAGAAG
1 TCTTCCTGATGAGGTACTGAGAAG
36204 CGGATTGAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
37 51 0.96
38 2 0.04
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.26
Consensus pattern (37 bp):
TCTTCCTGATGAGGTACTGAGAAGTCAACCAAATTCG
Found at i:36179 original size:175 final size:176
Alignment explanation
Indices: 35756--36342 Score: 1032
Period size: 176 Copynumber: 3.3 Consensus size: 176
35746 AAGTATTTAG
* *
35756 CTTCCTGATGAGATACTGAGAAGTGAACCGAATTCGTCTTCCAAATGAGGTACTGAGAAGTGAAC
1 CTTCCTGATGGGATACTGAGAAGTGAACCGAATTCGTCTTCCAGATGAGGTACTGAGAAGTGAAC
* * * *
35821 CAAATTCATCTTCCTGATGAGATATAGAGAAGCGGATTGAAACAGTGATAGGATCATCTTCCTGA
66 CAAATTCGTCTTGCTGATGAGATACAGAGAAGCGGATTGAAACAGTGATGGGATCATCTTCCTGA
* *
35886 TGAGACACTGAGAAGAAGAACCAAACGAGGCTCGAAATGAGCAAAT
131 TGAGACACTGAGAAGAAGACCCAAACGAGGCTCGAAACGAGCAAAT
* *
35932 CTTCCTGATGGGATACTGAGAAGTGAACCGAATTCATCTTCCAGATGAGGTACTAAGAAGTGAAC
1 CTTCCTGATGGGATACTGAGAAGTGAACCGAATTCGTCTTCCAGATGAGGTACTGAGAAGTGAAC
*
35997 CAAATTCGTCTTGCTGATGAGATACAGAGAAGCGGATTGAAACAGTGATGGGATCATCTTCTTGA
66 CAAATTCGTCTTGCTGATGAGATACAGAGAAGCGGATTGAAACAGTGATGGGATCATCTTCCTGA
36062 TGAGACACTGAGAAGAAGACCCAAACGA-GCTCGAAACGAGCAAAT
131 TGAGACACTGAGAAGAAGACCCAAACGAGGCTCGAAACGAGCAAAT
*
36107 CTTCCTGATGGGATACTGAGAAGTGAACCGAATTCGTCTTCCAGATGAGGTACTGAGAAGTCAAC
1 CTTCCTGATGGGATACTGAGAAGTGAACCGAATTCGTCTTCCAGATGAGGTACTGAGAAGTGAAC
36172 CAAATTCGTCTTGCTGATGAGATACAGAGAAGCGGATTGAAACAGTGATGGGATCATCTTCCTGA
66 CAAATTCGTCTTGCTGATGAGATACAGAGAAGCGGATTGAAACAGTGATGGGATCATCTTCCTGA
36237 TGAGACACTGAGAAGAAGACCCAAACGAGGCTCGAAACGAGCAAAT
131 TGAGACACTGAGAAGAAGACCCAAACGAGGCTCGAAACGAGCAAAT
* * *
36283 CTTCCTGATGGGATACTGAGAAGTGAACCAAATTCGTCTTCCAGATGAGATACAGAGAAG
1 CTTCCTGATGGGATACTGAGAAGTGAACCGAATTCGTCTTCCAGATGAGGTACTGAGAAG
36343 CGAGTTGAAA
Statistics
Matches: 392, Mismatches: 18, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
175 170 0.43
176 222 0.57
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (176 bp):
CTTCCTGATGGGATACTGAGAAGTGAACCGAATTCGTCTTCCAGATGAGGTACTGAGAAGTGAAC
CAAATTCGTCTTGCTGATGAGATACAGAGAAGCGGATTGAAACAGTGATGGGATCATCTTCCTGA
TGAGACACTGAGAAGAAGACCCAAACGAGGCTCGAAACGAGCAAAT
Found at i:36532 original size:37 final size:37
Alignment explanation
Indices: 36491--36580 Score: 144
Period size: 37 Copynumber: 2.4 Consensus size: 37
36481 TAGCTTCTTG
*
36491 ATGAGATACTGGGAAGTGAACCAAATTCGTCTTCCTA
1 ATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTA
* *
36528 ATGAGATACTGAGAAGTGAACCAAATTCGTCTTCTTG
1 ATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTA
*
36565 ATGAGATACAGAGAAG
1 ATGAGATACTGAGAAG
36581 CGAGTTGAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.26
Consensus pattern (37 bp):
ATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTA
Found at i:36875 original size:200 final size:198
Alignment explanation
Indices: 36521--37030 Score: 679
Period size: 200 Copynumber: 2.6 Consensus size: 198
36511 CCAAATTCGT
* * *
36521 CTTCCTAATGAGATACTGAGAAGTGAACCAAATTCGTCTTCTTGATGAGATACAGAGAAGC-GAG
1 CTTCCTGATGAGATACTGGGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGA-
* * *
36585 TTGAAACAAACGACGCAGTCATCTCCCTGATGAGACATTGAGGAGAAGACCCAAACAAGGCTCAA
65 TTGAAACAAACGACGCAGCCATCTCCCAGATGAGACACTGAGGAGAAGACCCAAACAAGGCTCAA
36650 AGCAAGCAAAATCTTTGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTGGAAGCAATAAAT
130 AGCAAGCAAAATCTTTGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTGGAAGC--TAAAT
*
36715 GGTTAG
193 GGCTAG
*
36721 CTTCCTGATGAGATACTGGGAAGTGAACCAAATTCGTCTTCCTGATAAGATACAGAGAAGCGGAT
1 CTTCCTGATGAGATACTGGGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGAT
* * * * * *
36786 TGAAAC-GATGATG-GGACCATCTTCCAGATGAGACACTGAGGAGAAGACCCAAACGAGGCTCAA
66 TGAAACAAACGACGCAG-CCATCTCCCAGATGAGACACTGAGGAGAAGACCCAAACAAGGCTCAA
** * **
36849 AGTGAGCAAAATCTTTGAACCCCAGCTTCCTGATGAGACACTGAGAAGCATGTGTTAGCTAAATG
130 AGCAAGCAAAATCTTTGAA-CCCAGCTTCCTGATGAGACACTGAGAAGCAGGTGGAAGCTAAATG
36914 GCTAG
194 GCTAG
* * *
36919 CTTCCTGATGAGATACTAGGAAGTGAACTAAATTCATCTTCCTGATGAGATACAGAGAAGCGGAT
1 CTTCCTGATGAGATACTGGGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGAT
** * * *
36984 TGAAACAGGCGACGC-GATCATTCTCCCA-ATGAGATACTGAGAAGAAG
66 TGAAACAAACGACGCAG-CCA-TCTCCCAGATGAGACACTGAGGAGAAG
37031 GCCAAGTCAA
Statistics
Matches: 274, Mismatches: 30, Indels: 13
0.86 0.09 0.04
Matches are distributed among these distances:
198 78 0.28
199 88 0.32
200 106 0.39
201 2 0.01
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.21
Consensus pattern (198 bp):
CTTCCTGATGAGATACTGGGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGAT
TGAAACAAACGACGCAGCCATCTCCCAGATGAGACACTGAGGAGAAGACCCAAACAAGGCTCAAA
GCAAGCAAAATCTTTGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTGGAAGCTAAATGGC
TAG
Found at i:37369 original size:17 final size:17
Alignment explanation
Indices: 37341--37413 Score: 103
Period size: 17 Copynumber: 4.4 Consensus size: 17
37331 TTGGAAATTG
37341 AATTTA-TTTAAATTTA
1 AATTTATTTTAAATTTA
*
37357 AGTTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
*
37374 AATTTATTTGAAATTTA
1 AATTTATTTTAAATTTA
* *
37391 AATTTATTATAAAATTA
1 AATTTATTTTAAATTTA
37408 AATTTA
1 AATTTA
37414 GAAAGTCCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
16 5 0.10
17 45 0.90
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:37389 original size:7 final size:6
Alignment explanation
Indices: 37346--37413 Score: 56
Period size: 6 Copynumber: 11.8 Consensus size: 6
37336 AATTGAATTT
* *
37346 ATTTAA ATTTAA GTTT-A TTTTAA ATTTAA ATTT-- ATTTGAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA ATTTAA
*
37392 ATTT-- ATTATAA AATTAA ATTTA
1 ATTTAA ATT-TAA ATTTAA ATTTA
37414 GAAAGTCCAA
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
4 7 0.14
5 5 0.10
6 32 0.64
7 6 0.12
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (6 bp):
ATTTAA
Done.