Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013722.1 Kokia drynarioides strain JFW-HI SEQ_128750, 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: 119798
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 78 characters in sequence are not A, C, G, or T
Found at i:321 original size:9 final size:9
Alignment explanation
Indices: 307--333 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
297 TTTGATGACC
307 TTAATTTTT
1 TTAATTTTT
316 TTAATTTTT
1 TTAATTTTT
325 TTAATTTTT
1 TTAATTTTT
334 ACCGTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (9 bp):
TTAATTTTT
Found at i:2940 original size:21 final size:21
Alignment explanation
Indices: 2914--2964 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 21
2904 TGTATTTATA
*
2914 AAATAATTATGTGTTAAATAT
1 AAATAATTATGTGATAAATAT
*
2935 AAATAAATTATTTGATAAATAT
1 AAAT-AATTATGTGATAAATAT
*
2957 AACTAATT
1 AAATAATT
2965 TTATAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 8 0.31
22 18 0.69
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.41
Consensus pattern (21 bp):
AAATAATTATGTGATAAATAT
Found at i:3532 original size:18 final size:19
Alignment explanation
Indices: 3492--3533 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
3482 TAAAATGCAT
*
3492 TTTTTTATATTTTTATTGA
1 TTTTTTATATTTTTATTAA
*
3511 -TTTTTATTTTTTTA-TAA
1 TTTTTTATATTTTTATTAA
3528 TTTTTT
1 TTTTTT
3534 TATCCCATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (19 bp):
TTTTTTATATTTTTATTAA
Found at i:5263 original size:9 final size:9
Alignment explanation
Indices: 5249--5317 Score: 71
Period size: 9 Copynumber: 8.4 Consensus size: 9
5239 TTTTGAAATA
5249 TAAAATTAT
1 TAAAATTAT
5258 TAAAATTA-
1 TAAAATTAT
*
5266 TGAAATTAT
1 TAAAATTAT
5275 T---ATT-T
1 TAAAATTAT
*
5280 TGAAA-TA-
1 TAAAATTAT
5287 TAAAATTAT
1 TAAAATTAT
5296 TAAAATTAT
1 TAAAATTAT
5305 TAAAATTAT
1 TAAAATTAT
5314 TAAA
1 TAAA
5318 TAATTTTAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
5 2 0.04
6 3 0.06
7 5 0.10
8 10 0.20
9 31 0.61
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (9 bp):
TAAAATTAT
Found at i:5290 original size:38 final size:39
Alignment explanation
Indices: 5226--5315 Score: 146
Period size: 38 Copynumber: 2.3 Consensus size: 39
5216 ACAAATTATT
*
5226 TTAAAATTATTTTTTTTGAAATATAAAATTATTAAAATTA
1 TTAAAATTA-TTATTTTGAAATATAAAATTATTAAAATTA
*
5266 -TGAAATTATTATTTTGAAATATAAAATTATTAAAATTA
1 TTAAAATTATTATTTTGAAATATAAAATTATTAAAATTA
5304 TTAAAATTATTA
1 TTAAAATTATTA
5316 AATAATTTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
38 29 0.63
39 17 0.37
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (39 bp):
TTAAAATTATTATTTTGAAATATAAAATTATTAAAATTA
Found at i:6047 original size:35 final size:35
Alignment explanation
Indices: 5997--6068 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 35
5987 CAATGGAGAG
* *
5997 GGTGATAATGGTGAATGATGGAGAGAAATAATGGA
1 GGTGATAATGATGAATGATGGAGAGAAACAATGGA
*
6032 GGTGATGATGATGAATGATGGAGAGAAACAATGGA
1 GGTGATAATGATGAATGATGGAGAGAAACAATGGA
6067 GG
1 GG
6069 AGAAGAAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.39, C:0.01, G:0.39, T:0.21
Consensus pattern (35 bp):
GGTGATAATGATGAATGATGGAGAGAAACAATGGA
Found at i:14795 original size:23 final size:23
Alignment explanation
Indices: 14763--14810 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
14753 AGCATGTACT
* *
14763 TTGGTAAACTCGCAAGCTCACAC
1 TTGGTAAACTAGCAAACTCACAC
* *
14786 TTGGTCAACTAGCAAACTCATAC
1 TTGGTAAACTAGCAAACTCACAC
14809 TT
1 TT
14811 TGGGCGGCTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (23 bp):
TTGGTAAACTAGCAAACTCACAC
Found at i:15071 original size:22 final size:21
Alignment explanation
Indices: 15031--15071 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
15021 AATTATTCTT
*
15031 GATTAAAAAATAATCAAAAGA
1 GATTAAAAAATAAGCAAAAGA
*
15052 GATTAAAAAACTAAGGAAAA
1 GATTAAAAAA-TAAGCAAAA
15072 CATAGATGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.66, C:0.05, G:0.12, T:0.17
Consensus pattern (21 bp):
GATTAAAAAATAAGCAAAAGA
Found at i:18896 original size:7 final size:7
Alignment explanation
Indices: 18884--18918 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
18874 ATTTAAATAT
18884 TCAACAC
1 TCAACAC
18891 TCAACAC
1 TCAACAC
18898 TCAACAC
1 TCAACAC
18905 TCAACAC
1 TCAACAC
18912 TCAACAC
1 TCAACAC
18919 AATTAGATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.43, C:0.43, G:0.00, T:0.14
Consensus pattern (7 bp):
TCAACAC
Found at i:22928 original size:17 final size:16
Alignment explanation
Indices: 22906--22948 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
22896 AAAAACATAA
22906 TCATTTCTAAATGTTTC
1 TCATTTCTAAAT-TTTC
*
22923 TCATTTCTACATTTTC
1 TCATTTCTAAATTTTC
22939 TCTATTTCTA
1 TC-ATTTCTA
22949 TTCATTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 6 0.25
17 18 0.75
ACGTcount: A:0.21, C:0.21, G:0.02, T:0.56
Consensus pattern (16 bp):
TCATTTCTAAATTTTC
Found at i:31048 original size:20 final size:20
Alignment explanation
Indices: 31011--31049 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
31001 AAGACTAAGA
*
31011 AAAATAACTGAAATATAAAC
1 AAAATAACTGAAAAATAAAC
31031 AAAATAAACT-AAAAATAAA
1 AAAAT-AACTGAAAAATAAA
31050 TGATAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.72, C:0.08, G:0.03, T:0.18
Consensus pattern (20 bp):
AAAATAACTGAAAAATAAAC
Found at i:41029 original size:123 final size:122
Alignment explanation
Indices: 40750--41103 Score: 573
Period size: 123 Copynumber: 2.9 Consensus size: 122
40740 CCTTTCATTT
* * *
40750 TAATATCTCATATTAAAATGAAAATATATATCTTTAGAGAAATATATTGAAGGTTTATTAAAACA
1 TAATATCTCATATTAAAATGAAAATAT-T-CCTTTAAAGAAATATATGGAAGGTTTATTAAAACA
* * * *
40815 TTATATCCTTTTCAAAAGGCTATCATCTTCCATGTTTTAATATTCAATTTTCTTTTATA
64 TTATATCCTTTCCAAAAGGATATTATCTTCCATGTTTTAATATTCAATTTCCTTTTATA
* *
40874 TAATATCTCATATTAAAATGGAAATATTCCTTTAAAGAAGTATATGGAAGGTTTATTAAAACATT
1 TAATATCTCATATTAAAATGAAAATATTCCTTTAAAGAAATATATGGAAGGTTTATTAAAACATT
*
40939 ATATCCTTTCCAAAAGGATATTAACTTCCATGTTTTTAATATTCAATTTCCTTTTATA
66 ATATCCTTTCCAAAAGGATATTATCTTCCATG-TTTTAATATTCAATTTCCTTTTATA
*
40997 TAATATCTAATATTAAAATGAAAATATTCCTTTAAAGAAATATATGGAAGGTTTATTAAAACATT
1 TAATATCTCATATTAAAATGAAAATATTCCTTTAAAGAAATATATGGAAGGTTTATTAAAACATT
*
41062 ATATCCTTTCCAAAAGGATATTATCTTTCATGTTTTAATATT
66 ATATCCTTTCCAAAAGGATATTATCTTCCATGTTTTAATATT
41104 TAACAAAATT
Statistics
Matches: 214, Mismatches: 15, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
122 71 0.33
123 117 0.55
124 26 0.12
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.42
Consensus pattern (122 bp):
TAATATCTCATATTAAAATGAAAATATTCCTTTAAAGAAATATATGGAAGGTTTATTAAAACATT
ATATCCTTTCCAAAAGGATATTATCTTCCATGTTTTAATATTCAATTTCCTTTTATA
Found at i:48161 original size:119 final size:124
Alignment explanation
Indices: 47931--48167 Score: 317
Period size: 119 Copynumber: 1.9 Consensus size: 124
47921 ACTATCTTTC
* *
47931 CTTTTATTTTAATATCTCATATTAAAATGGAAATATATATCTTTAGAAAAATATATGGAAGGTTT
1 CTTTTATTATAATATCTAATATTAAAATGGAAATATATATCTTTAGAAAAATATATGGAAGG-TT
* *
47996 ATTAAAACATTATATCCTTTCCAAAATGATATTATCTTTAACGTTTTAATATTCAATTTT
65 ATTAAAACATTATATACTTTCCAAAAGGATATTATCTTTAACGTTTTAATATTCAATTTT
48056 CTTTTA-TATAATATCTAATATTAAAAT-GAAA-ATAT-TCCTTTA-AAGAAATATATGGAA-G-
1 CTTTTATTATAATATCTAATATTAAAATGGAAATATATAT-CTTTAGAA-AAATATATGGAAGGT
* * * * *
48114 TATTAAAATATTATATATTTTCCAAAAGGATATTATGTTTCATGTTTTAATATT
64 TATTAAAACATTATATACTTTCCAAAAGGATATTATCTTTAACGTTTTAATATT
48168 TAACAAAATC
Statistics
Matches: 101, Mismatches: 9, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
119 47 0.47
121 4 0.04
122 21 0.21
123 4 0.04
124 19 0.19
125 6 0.06
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (124 bp):
CTTTTATTATAATATCTAATATTAAAATGGAAATATATATCTTTAGAAAAATATATGGAAGGTTA
TTAAAACATTATATACTTTCCAAAAGGATATTATCTTTAACGTTTTAATATTCAATTTT
Found at i:50796 original size:40 final size:40
Alignment explanation
Indices: 50752--51044 Score: 217
Period size: 40 Copynumber: 7.4 Consensus size: 40
50742 CTCATGGTCG
*
50752 GGGTAAGAGATCT-GATGGTCTTCAATCTGCCCTCTAGTTA
1 GGGTAAAAGAT-TGGATGGTCTTCAATCTGCCCTCTAGTTA
* * * * *
50792 GGGTAAAAGACTAGATTG-CTTTAATCTGCCCTCTGGTTA
1 GGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTAGTTA
* * * *
50831 GGGTAAAAGATTGGATTGT-TTCAATTTGCCC-CATGGTTG
1 GGGTAAAAGATTGGATGGTCTTCAATCTGCCCTC-TAGTTA
* * *
50870 GGGTAATAGATTGGATTGTTTTCAATCTGCCCTCT-GATTA
1 GGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTAG-TTA
* * *
50910 GGGTAAAATATTGGATGGCCTTCAATCTACCCTCT-GATTA
1 GGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTAG-TTA
* * * * *
50950 TGGTAAAAGATTGGATAGTTTTCAATATG-CCTCATGAG-TG
1 GGGTAAAAGATTGGATGGTCTTCAATCTGCCCTC-T-AGTTA
* * *
50990 GGGTAAGAA-ATCGGATGGTCTTCAATCTACCCTCTAATTA
1 GGGTAA-AAGATTGGATGGTCTTCAATCTGCCCTCTAGTTA
* * *
51030 CGATAAGAGATTGGA
1 GGGTAAAAGATTGGA
51045 GGTTGTAACT
Statistics
Matches: 201, Mismatches: 39, Indels: 26
0.76 0.15 0.10
Matches are distributed among these distances:
38 1 0.00
39 76 0.38
40 116 0.58
41 7 0.03
42 1 0.00
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (40 bp):
GGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTAGTTA
Found at i:50819 original size:39 final size:39
Alignment explanation
Indices: 50713--50980 Score: 238
Period size: 40 Copynumber: 6.8 Consensus size: 39
50703 ATAACTTCAG
** * **
50713 GGGTAAAAGATTAAATTGTTTCAATTTG-CCTCATGGTCG
1 GGGTAAAAGATTGGATTGTTTCAATCTGCCCTC-TGGTTA
* * *
50752 GGGTAAGAGATCT-GATGGTCTTCAATCTGCCCTCTAGTTA
1 GGGTAAAAGAT-TGGATTGT-TTCAATCTGCCCTCTGGTTA
* *
50792 GGGTAAAAGACTAGATTGCTTT-AATCTGCCCTCTGGTTA
1 GGGTAAAAGATTGGATTG-TTTCAATCTGCCCTCTGGTTA
* *
50831 GGGTAAAAGATTGGATTGTTTCAATTTGCCC-CATGGTTG
1 GGGTAAAAGATTGGATTGTTTCAATCTGCCCTC-TGGTTA
* *
50870 GGGTAATAGATTGGATTGTTTTCAATCTGCCCTCTGATTA
1 GGGTAAAAGATTGGATTG-TTTCAATCTGCCCTCTGGTTA
* * * * *
50910 GGGTAAAATATTGGATGGCCTTCAATCTACCCTCTGATTA
1 GGGTAAAAGATTGGATTG-TTTCAATCTGCCCTCTGGTTA
* * *
50950 TGGTAAAAGATTGGATAGTTTTCAATATGCC
1 GGGTAAAAGATTGGATTG-TTTCAATCTGCC
50981 TCATGAGTGG
Statistics
Matches: 188, Mismatches: 32, Indels: 17
0.79 0.14 0.07
Matches are distributed among these distances:
38 4 0.02
39 77 0.41
40 101 0.54
41 6 0.03
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.35
Consensus pattern (39 bp):
GGGTAAAAGATTGGATTGTTTCAATCTGCCCTCTGGTTA
Found at i:51144 original size:50 final size:50
Alignment explanation
Indices: 51090--51225 Score: 155
Period size: 50 Copynumber: 2.7 Consensus size: 50
51080 TAAGATTCAT
*
51090 CCTTGTGACTTCAATCTATCCCTCTACAGCTTTAGGTGAATGAGATTTGC
1 CCTTGTGACTTCAATCTACCCCTCTACAGCTTTAGGTGAATGAGATTTGC
* * * * * *
51140 CCTTGCGACTTCATTTTGCCCCTTTACAGCTTTAGGTGTATGAGATTTGC
1 CCTTGTGACTTCAATCTACCCCTCTACAGCTTTAGGTGAATGAGATTTGC
* * * * * *
51190 CATTGTGATTTCAATCTGCACCTCCATAGCTTTAGG
1 CCTTGTGACTTCAATCTACCCCTCTACAGCTTTAGG
51226 GGTAAAAGAC
Statistics
Matches: 70, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
50 70 1.00
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.38
Consensus pattern (50 bp):
CCTTGTGACTTCAATCTACCCCTCTACAGCTTTAGGTGAATGAGATTTGC
Found at i:62696 original size:30 final size:30
Alignment explanation
Indices: 62610--62698 Score: 110
Period size: 30 Copynumber: 3.0 Consensus size: 30
62600 ACAGTCTTAC
* *
62610 ACATGGCCATGTGCCCATG-TCGTGTGGCTT
1 ACATGGCCATGTGTCTA-GCTCGTGTGGCTT
* *
62640 ACATGGCCATGTGTTTAGC-CTATGTGGCTT
1 ACATGGCCATGTGTCTAGCTC-GTGTGGCTT
62670 ACATGGCCATGTGTCTAGCTCGTGTGGCT
1 ACATGGCCATGTGTCTAGCTCGTGTGGCT
62699 CCTAAAATAT
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
29 2 0.04
30 47 0.94
31 1 0.02
ACGTcount: A:0.15, C:0.24, G:0.29, T:0.33
Consensus pattern (30 bp):
ACATGGCCATGTGTCTAGCTCGTGTGGCTT
Found at i:63050 original size:13 final size:13
Alignment explanation
Indices: 63032--63056 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
63022 GTTAGGGTCG
63032 AATCTTATGTATT
1 AATCTTATGTATT
63045 AATCTTATGTAT
1 AATCTTATGTAT
63057 ATTATCATTT
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:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (13 bp):
AATCTTATGTATT
Found at i:67685 original size:24 final size:24
Alignment explanation
Indices: 67648--67704 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
67638 TTTCTAAAAG
* *
67648 ATTTAGTAGTATAATATATTTAAC
1 ATTTATTAGCATAATATATTTAAC
*
67672 ATTTATTAGCATAATATATTTTAC
1 ATTTATTAGCATAATATATTTAAC
*
67696 ATTGATTAG
1 ATTTATTAG
67705 AATTAGGATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.47
Consensus pattern (24 bp):
ATTTATTAGCATAATATATTTAAC
Found at i:68792 original size:24 final size:24
Alignment explanation
Indices: 68747--68793 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
68737 ATTTAGTAGT
*
68747 ATAATATATTTAGCATTTATTAGC
1 ATAATATATTTAGCATTGATTAGC
68771 ATAATATATTTTA-CATTGATTAG
1 ATAATATA-TTTAGCATTGATTAG
68794 AATTAGGCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (24 bp):
ATAATATATTTAGCATTGATTAGC
Found at i:73052 original size:2 final size:2
Alignment explanation
Indices: 73045--73071 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
73035 AATTTTGATA
73045 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
73072 ATCCCAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:79360 original size:22 final size:21
Alignment explanation
Indices: 79335--79382 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
79325 CAAATATTGA
*
79335 TTAATAATAGGATAAATTAAGG
1 TTAATAAGAGGATAAATTAA-G
* * *
79357 TTAAAAAGATGATTAATTAAG
1 TTAATAAGAGGATAAATTAAG
79378 TTAAT
1 TTAAT
79383 TATGAAAGTC
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (21 bp):
TTAATAAGAGGATAAATTAAG
Found at i:80276 original size:41 final size:41
Alignment explanation
Indices: 80229--80481 Score: 346
Period size: 41 Copynumber: 6.1 Consensus size: 41
80219 GTACAAATGC
* *
80229 AAGACTCATGTCTAGAAATGAGAATGAGATTTTGATTAAGG
1 AAGACTCATGTCTCGAAATGAGAATGAGATTATGATTAAGG
* *
80270 AAGACTCATGTCTCGAGATGAGAATGAGATTATGAATAAGG
1 AAGACTCATGTCTCGAAATGAGAATGAGATTATGATTAAGG
* * *
80311 AAGACTCATGTTTCGAAATGAGAATGAGATTTTGATTAAAG
1 AAGACTCATGTCTCGAAATGAGAATGAGATTATGATTAAGG
*
80352 AAGACTCATGTCTCGAGATGAGAATGAGATTATG-TATAAGG
1 AAGACTCATGTCTCGAAATGAGAATGAGATTATGAT-TAAGG
* * * *
80393 AATACTTATGTCTCGAAATGAGAATGATATTTTGATTAAGG
1 AAGACTCATGTCTCGAAATGAGAATGAGATTATGATTAAGG
* * *
80434 AAGACTCATGTCTCGACATGAGAATGAGAATATGGTTAAAGG
1 AAGACTCATGTCTCGAAATGAGAATGAGATTATGATT-AAGG
80476 AAGACT
1 AAGACT
80482 TATGACTTGA
Statistics
Matches: 184, Mismatches: 25, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
40 1 0.01
41 172 0.93
42 11 0.06
ACGTcount: A:0.38, C:0.09, G:0.24, T:0.28
Consensus pattern (41 bp):
AAGACTCATGTCTCGAAATGAGAATGAGATTATGATTAAGG
Found at i:80329 original size:82 final size:82
Alignment explanation
Indices: 80229--80481 Score: 398
Period size: 82 Copynumber: 3.1 Consensus size: 82
80219 GTACAAATGC
*
80229 AAGACTCATGTCTAGAAATGAGAATGAGATTTTGATTAAGGAAGACTCATGTCTCGAGATGAGAA
1 AAGACTCATGTCTCGAAATGAGAATGAGATTTTGATTAAGGAAGACTCATGTCTCGAGATGAGAA
80294 TGAGATTATGAATAAGG
66 TGAGATTATGAATAAGG
* *
80311 AAGACTCATGTTTCGAAATGAGAATGAGATTTTGATTAAAGAAGACTCATGTCTCGAGATGAGAA
1 AAGACTCATGTCTCGAAATGAGAATGAGATTTTGATTAAGGAAGACTCATGTCTCGAGATGAGAA
*
80376 TGAGATTATGTATAAGG
66 TGAGATTATGAATAAGG
* * * *
80393 AATACTTATGTCTCGAAATGAGAATGATATTTTGATTAAGGAAGACTCATGTCTCGACATGAGAA
1 AAGACTCATGTCTCGAAATGAGAATGAGATTTTGATTAAGGAAGACTCATGTCTCGAGATGAGAA
* **
80458 TGAGAATATGGTTAAAGG
66 TGAGATTATGAAT-AAGG
80476 AAGACT
1 AAGACT
80482 TATGACTTGA
Statistics
Matches: 156, Mismatches: 14, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
82 147 0.94
83 9 0.06
ACGTcount: A:0.38, C:0.09, G:0.24, T:0.28
Consensus pattern (82 bp):
AAGACTCATGTCTCGAAATGAGAATGAGATTTTGATTAAGGAAGACTCATGTCTCGAGATGAGAA
TGAGATTATGAATAAGG
Found at i:87510 original size:41 final size:41
Alignment explanation
Indices: 87456--87722 Score: 322
Period size: 41 Copynumber: 6.5 Consensus size: 41
87446 TTGTATAAAT
* *
87456 GGAAGACTTATGTCTCGAAATGAGAATGAGATTTTGATTAA
1 GGAAGACTCATGTCTCGAAATGAGAATGAGATTATGATTAA
* *
87497 GGAAGACTCATGTCTCGAGATGAGAATGAGATTATGAATAA
1 GGAAGACTCATGTCTCGAAATGAGAATGAGATTATGATTAA
* * *
87538 GGAAGACTCATGT-TCCGAAATGAGAATGATATTTTGATTGA
1 GGAAGACTCATGTCT-CGAAATGAGAATGAGATTATGATTAA
* *
87579 GAAAGACTCATGTCTCGAGATGAGAATGAGATTATG-TATAA
1 GGAAGACTCATGTCTCGAAATGAGAATGAGATTATGAT-TAA
* *
87620 GGAAGACTCATGTCTCGAAATAAGAATGAGATTTTGATTAA
1 GGAAGACTCATGTCTCGAAATGAGAATGAGATTATGATTAA
* * * * * *
87661 GCAAGACTCATGTCTTGAGATGAGAATAAGAATATGGTTAAA
1 GGAAGACTCATGTCTCGAAATGAGAATGAGATTATGATT-AA
* *
87703 GGAAGACTTATGACTCGAAA
1 GGAAGACTCATGTCTCGAAA
87723 GAGCATAAGG
Statistics
Matches: 190, Mismatches: 31, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
40 2 0.01
41 169 0.89
42 19 0.10
ACGTcount: A:0.38, C:0.10, G:0.24, T:0.28
Consensus pattern (41 bp):
GGAAGACTCATGTCTCGAAATGAGAATGAGATTATGATTAA
Found at i:87562 original size:82 final size:82
Alignment explanation
Indices: 87456--87722 Score: 383
Period size: 82 Copynumber: 3.2 Consensus size: 82
87446 TTGTATAAAT
* *
87456 GGAAGACTTATGTCTCGAAATGAGAATGAGATTTTGATTAAGGAAGACTCATGTCTCGAGATGAG
1 GGAAGACTCATGTCTCGAAATGAGAATGAGATTTTGATTAAGAAAGACTCATGTCTCGAGATGAG
87521 AATGAGATTATGAATAA
66 AATGAGATTATGAATAA
* *
87538 GGAAGACTCATGT-TCCGAAATGAGAATGATATTTTGATTGAGAAAGACTCATGTCTCGAGATGA
1 GGAAGACTCATGTCT-CGAAATGAGAATGAGATTTTGATTAAGAAAGACTCATGTCTCGAGATGA
*
87602 GAATGAGATTATGTATAA
65 GAATGAGATTATGAATAA
* * *
87620 GGAAGACTCATGTCTCGAAATAAGAATGAGATTTTGATTAAGCAAGACTCATGTCTTGAGATGAG
1 GGAAGACTCATGTCTCGAAATGAGAATGAGATTTTGATTAAGAAAGACTCATGTCTCGAGATGAG
* * **
87685 AATAAGAATATGGTTAAA
66 AATGAGATTATGAAT-AA
* *
87703 GGAAGACTTATGACTCGAAA
1 GGAAGACTCATGTCTCGAAA
87723 GAGCATAAGG
Statistics
Matches: 166, Mismatches: 16, Indels: 5
0.89 0.09 0.03
Matches are distributed among these distances:
81 1 0.01
82 144 0.87
83 21 0.13
ACGTcount: A:0.38, C:0.10, G:0.24, T:0.28
Consensus pattern (82 bp):
GGAAGACTCATGTCTCGAAATGAGAATGAGATTTTGATTAAGAAAGACTCATGTCTCGAGATGAG
AATGAGATTATGAATAA
Found at i:98321 original size:9 final size:9
Alignment explanation
Indices: 98303--98346 Score: 61
Period size: 9 Copynumber: 4.7 Consensus size: 9
98293 CTCAAACACA
98303 TTTTTTTTC
1 TTTTTTTTC
*
98312 TTTTTCTTC
1 TTTTTTTTC
98321 TTTTTTTTGAC
1 TTTTTTTT--C
98332 TTTTTTTTC
1 TTTTTTTTC
98341 TTTTTT
1 TTTTTT
98347 CGAACAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 22 0.71
11 9 0.29
ACGTcount: A:0.02, C:0.11, G:0.02, T:0.84
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:98328 original size:20 final size:20
Alignment explanation
Indices: 98303--98346 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
98293 CTCAAACACA
98303 TTTTTTTT--CTTTTTCTTC
1 TTTTTTTTGACTTTTTCTTC
*
98321 TTTTTTTTGACTTTTTTTTC
1 TTTTTTTTGACTTTTTCTTC
98341 TTTTTT
1 TTTTTT
98347 CGAACAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.35
20 15 0.65
ACGTcount: A:0.02, C:0.11, G:0.02, T:0.84
Consensus pattern (20 bp):
TTTTTTTTGACTTTTTCTTC
Found at i:100776 original size:25 final size:25
Alignment explanation
Indices: 100737--100921 Score: 208
Period size: 25 Copynumber: 7.4 Consensus size: 25
100727 GACATTGAAG
*
100737 GATATTTTGTCTGGCTCGTAAGAGC
1 GATATTCTGTCTGGCTCGTAAGAGC
* * * *
100762 TATATTCTTTTTGGCTCGCAAGAGC
1 GATATTCTGTCTGGCTCGTAAGAGC
*
100787 GATATTCTGTCTAGCTCGTAAGAGC
1 GATATTCTGTCTGGCTCGTAAGAGC
* * *
100812 AATATTCTGTCTGGCTCATAAGAGT
1 GATATTCTGTCTGGCTCGTAAGAGC
*
100837 GATATTCTGTTTGGCTCGTAAGAGC
1 GATATTCTGTCTGGCTCGTAAGAGC
* * * * *
100862 GATATTTTATCTTGCTTGTGAGAGC
1 GATATTCTGTCTGGCTCGTAAGAGC
* * *
100887 GATATTTTGTCTGACTCATAAGAGC
1 GATATTCTGTCTGGCTCGTAAGAGC
100912 GATATTCTGT
1 GATATTCTGT
100922 TAGGGCTCGA
Statistics
Matches: 129, Mismatches: 31, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 129 1.00
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.38
Consensus pattern (25 bp):
GATATTCTGTCTGGCTCGTAAGAGC
Found at i:100861 original size:75 final size:75
Alignment explanation
Indices: 100738--100922 Score: 246
Period size: 75 Copynumber: 2.5 Consensus size: 75
100728 ACATTGAAGG
* * *
100738 ATATTTTGTCTGGCTCGTAAGAGCT-ATATTCTTTTTGGCTCGCAAGAGCGATATTCTGTCTAGC
1 ATATTTTGTCTGGCTCATAAGAG-TGATATTCTGTTTGGCTCGCAAGAGCGATATTCTATCTAGC
100802 TCGTAAGAGCA
65 TCGTAAGAGCA
* * * *
100813 ATATTCTGTCTGGCTCATAAGAGTGATATTCTGTTTGGCTCGTAAGAGCGATATTTTATCTTGCT
1 ATATTTTGTCTGGCTCATAAGAGTGATATTCTGTTTGGCTCGCAAGAGCGATATTCTATCTAGCT
* * *
100878 TGTGAGAGCG
66 CGTAAGAGCA
* *
100888 ATATTTTGTCTGACTCATAAGAGCGATATTCTGTT
1 ATATTTTGTCTGGCTCATAAGAGTGATATTCTGTT
100923 AGGGCTCGAA
Statistics
Matches: 96, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
74 1 0.01
75 95 0.99
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.38
Consensus pattern (75 bp):
ATATTTTGTCTGGCTCATAAGAGTGATATTCTGTTTGGCTCGCAAGAGCGATATTCTATCTAGCT
CGTAAGAGCA
Found at i:105513 original size:15 final size:16
Alignment explanation
Indices: 105481--105512 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
105471 ATGCACGGTG
105481 TTTTTTCTTCCTTCTC
1 TTTTTTCTTCCTTCTC
105497 TTTTTCTCTTCCTTCT
1 TTTTT-TCTTCCTTCT
105513 TGCGCTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTTTTCTTCCTTCTC
Found at i:113445 original size:21 final size:20
Alignment explanation
Indices: 113414--113471 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 20
113404 TTGAAGAGTT
*
113414 TTGTGGTTGCATCTGATTCTG
1 TTGTGGATGCATCTGATT-TG
*
113435 ATT-TGGATGCATCTGGCTTTG
1 -TTGTGGATGCATCT-GATTTG
113456 TTGTGGATGCATCTGA
1 TTGTGGATGCATCTGA
113472 GTATGCTGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 3 0.10
21 23 0.74
22 5 0.16
ACGTcount: A:0.14, C:0.14, G:0.29, T:0.43
Consensus pattern (20 bp):
TTGTGGATGCATCTGATTTG
Done.