Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001881.1 Kokia drynarioides strain JFW-HI SEQ_113653, 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: 103022
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 25 characters in sequence are not A, C, G, or T
Found at i:1469 original size:55 final size:54
Alignment explanation
Indices: 1385--1494 Score: 148
Period size: 55 Copynumber: 2.0 Consensus size: 54
1375 TGTGGGCCTC
* *
1385 CGAAAGCTTGCACCCATTTGTTTATCATTGACAACAAATGGGGTGTTTTCAGATG
1 CGAAAGCTTGCACCCATTTGTTCATCATTGACAAC-AATGAGGTGTTTTCAGATG
* * ** *
1440 CGAAAGCTTGCACCTATTTGTTCCTCATTGATGACAATGAGGTGTTTTGAGATG
1 CGAAAGCTTGCACCCATTTGTTCATCATTGACAACAATGAGGTGTTTTCAGATG
1494 C
1 C
1495 AAACTATGGT
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
54 18 0.38
55 30 0.62
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (54 bp):
CGAAAGCTTGCACCCATTTGTTCATCATTGACAACAATGAGGTGTTTTCAGATG
Found at i:4009 original size:21 final size:20
Alignment explanation
Indices: 3970--4009 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
3960 TACATCTTAT
* *
3970 GTAATTTACTTACCTTAATA
1 GTAATTTACTAACCATAATA
3990 GTAATTATACTAACCATAAT
1 GTAATT-TACTAACCATAAT
4010 GCAAGATCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.40, C:0.15, G:0.05, T:0.40
Consensus pattern (20 bp):
GTAATTTACTAACCATAATA
Found at i:4266 original size:24 final size:26
Alignment explanation
Indices: 4238--4285 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
4228 ATTATTTTAT
*
4238 TATAT-AAATA-ATTTTAAAATATGA
1 TATATCAAATACATTTAAAAATATGA
4262 TATATCAAATACATTTAAAAATAT
1 TATATCAAATACATTTAAAAATAT
4286 TAAAACAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.24
25 5 0.24
26 11 0.52
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (26 bp):
TATATCAAATACATTTAAAAATATGA
Found at i:4295 original size:12 final size:12
Alignment explanation
Indices: 4280--4305 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4270 ATACATTTAA
4280 AAATATTAAAAC
1 AAATATTAAAAC
4292 AAATATTAAAAC
1 AAATATTAAAAC
4304 AA
1 AA
4306 CAAATAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (12 bp):
AAATATTAAAAC
Found at i:4343 original size:41 final size:40
Alignment explanation
Indices: 4278--4374 Score: 119
Period size: 41 Copynumber: 2.5 Consensus size: 40
4268 AAATACATTT
* *
4278 AAAA-ATATTAAAACAAATATTAAAACAACAAATAAATTA
1 AAAATATATTAAAACAATTATTAAAACAACAAACAAATTA
* *
4317 AAAATGATATTAAAACAATTCA-TAAAACAATAAACAAATTG
1 AAAAT-ATATTAAAACAATT-ATTAAAACAACAAACAAATTA
4358 AAAAT-TATTAAAACAAT
1 AAAATATATTAAAACAAT
4375 AAAAAAACTA
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
39 16 0.31
41 34 0.67
42 1 0.02
ACGTcount: A:0.65, C:0.08, G:0.02, T:0.25
Consensus pattern (40 bp):
AAAATATATTAAAACAATTATTAAAACAACAAACAAATTA
Found at i:4843 original size:24 final size:23
Alignment explanation
Indices: 4804--4849 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
4794 TATTACAAGC
4804 AAAAAAAATTAGTATTAAAAATA
1 AAAAAAAATTAGTATTAAAAATA
* *
4827 AAAATAAAATTATTATTATAAAT
1 AAAA-AAAATTAGTATTAAAAAT
4850 TCGGGTCGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (23 bp):
AAAAAAAATTAGTATTAAAAATA
Found at i:5105 original size:22 final size:22
Alignment explanation
Indices: 5077--5144 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
5067 TGCATAAAAG
*
5077 AACGGAGAGCACTAAGGTGCTA
1 AACGGAGAGCACTAACGTGCTA
* *
5099 AACGGAGAGAACAAACGTGCTA
1 AACGGAGAGCACTAACGTGCTA
** *
5121 AACAAAGAGCACTACACGTACTA
1 AACGGAGAGCACTA-ACGTGCTA
5144 A
1 A
5145 TAACAGAGAA
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
22 29 0.78
23 8 0.22
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.12
Consensus pattern (22 bp):
AACGGAGAGCACTAACGTGCTA
Found at i:9676 original size:48 final size:48
Alignment explanation
Indices: 9605--9702 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
9595 CATATGTAAG
9605 AATGCGTAAAACAAGGATTAATTAATGCAATTACAGAATAGTCAAAAA
1 AATGCGTAAAACAAGGATTAATTAATGCAATTACAGAATAGTCAAAAA
9653 AATGCGTAAAACAAGGATTAATTAATGCAATTACAGAATAGTCAAAAA
1 AATGCGTAAAACAAGGATTAATTAATGCAATTACAGAATAGTCAAAAA
9701 AA
1 AA
9703 GAAAATTTAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.53, C:0.10, G:0.14, T:0.22
Consensus pattern (48 bp):
AATGCGTAAAACAAGGATTAATTAATGCAATTACAGAATAGTCAAAAA
Found at i:11741 original size:49 final size:49
Alignment explanation
Indices: 11707--11806 Score: 182
Period size: 49 Copynumber: 2.0 Consensus size: 49
11697 CCTGAAAACT
11707 TTAAGTTCCAATCCAACAATTTAAACCAATTAAAATACATCAAAAACCAC
1 TTAAG-TCCAATCCAACAATTTAAACCAATTAAAATACATCAAAAACCAC
*
11757 TTCAGTCCAATCCAACAATTTAAACCAATTAAAATACATCAAAAACCAC
1 TTAAGTCCAATCCAACAATTTAAACCAATTAAAATACATCAAAAACCAC
11806 T
1 T
11807 CCAGTAACTT
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
49 45 0.92
50 4 0.08
ACGTcount: A:0.49, C:0.25, G:0.02, T:0.24
Consensus pattern (49 bp):
TTAAGTCCAATCCAACAATTTAAACCAATTAAAATACATCAAAAACCAC
Found at i:11992 original size:33 final size:33
Alignment explanation
Indices: 11955--12020 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
11945 CATCTAAATC
11955 CTTTGACCTAGGGACACAATGAATAGCTTATGT
1 CTTTGACCTAGGGACACAATGAATAGCTTATGT
*
11988 CTTTGACTTAGGGACACAATGAATAGCTTATGT
1 CTTTGACCTAGGGACACAATGAATAGCTTATGT
12021 ACATGTCATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (33 bp):
CTTTGACCTAGGGACACAATGAATAGCTTATGT
Found at i:12469 original size:22 final size:22
Alignment explanation
Indices: 12441--12514 Score: 76
Period size: 22 Copynumber: 3.2 Consensus size: 22
12431 AAAAGAATGA
* *
12441 AGAGCACCAAGGTGCTAAACGG
1 AGAGCACAAACGTGCTAAACGG
* *
12463 AGAGCACAAATGTGTTAAACGG
1 AGAGCACAAACGTGCTAAACGG
*
12485 AGAGCACTACACGTGCTAATAACGG
1 AGAGCAC-AAACGTGCT-A-AACGG
12510 AGAGC
1 AGAGC
12515 GTGCTAAGGT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
22 26 0.60
23 6 0.14
24 1 0.02
25 10 0.23
ACGTcount: A:0.38, C:0.20, G:0.28, T:0.14
Consensus pattern (22 bp):
AGAGCACAAACGTGCTAAACGG
Found at i:19940 original size:14 final size:15
Alignment explanation
Indices: 19913--19946 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
19903 TTTTTTTAAA
19913 ATTATAATTAATATT
1 ATTATAATTAATATT
19928 ATTATAA-TAATATT
1 ATTATAATTAATATT
*
19942 TTTAT
1 ATTAT
19947 CTTTTCATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTATAATTAATATT
Found at i:21817 original size:16 final size:16
Alignment explanation
Indices: 21776--21817 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 16
21766 TTAAAAATTT
* *
21776 AAAAGTAAAATATTTA
1 AAAAATAAAATATTAA
21792 AAAAAT--AATATTAA
1 AAAAATAAAATATTAA
21806 AAAAATAAAATA
1 AAAAATAAAATA
21818 GAAAGAATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 13 0.59
16 9 0.41
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (16 bp):
AAAAATAAAATATTAA
Found at i:22399 original size:8 final size:8
Alignment explanation
Indices: 22374--22423 Score: 55
Period size: 8 Copynumber: 6.0 Consensus size: 8
22364 TTGTATTTTT
22374 AAATTCAAA
1 AAATT-AAA
* *
22383 AAGTAAAA
1 AAATTAAA
22391 AAATTAAA
1 AAATTAAA
22399 AAATTGAAA
1 AAATT-AAA
*
22408 AAAATAAA
1 AAATTAAA
22416 AAATTAAA
1 AAATTAAA
22424 TTTTAAATGT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
8 24 0.71
9 10 0.29
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.20
Consensus pattern (8 bp):
AAATTAAA
Found at i:22400 original size:17 final size:17
Alignment explanation
Indices: 22374--22423 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
22364 TTGTATTTTT
* *
22374 AAATTCAAAAAGTAAAA
1 AAATTAAAAAATTAAAA
22391 AAATTAAAAAATTGAAAA
1 AAATTAAAAAATT-AAAA
22409 AAA-TAAAAAATTAAA
1 AAATTAAAAAATTAAA
22424 TTTTAAATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
16 3 0.10
17 20 0.67
18 7 0.23
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.20
Consensus pattern (17 bp):
AAATTAAAAAATTAAAA
Found at i:22403 original size:25 final size:25
Alignment explanation
Indices: 22374--22423 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
22364 TTGTATTTTT
*
22374 AAATTC-AAAAAGTAAAAAAATTAAA
1 AAATTCAAAAAAAT-AAAAAATTAAA
*
22399 AAATTGAAAAAAATAAAAAATTAAA
1 AAATTCAAAAAAATAAAAAATTAAA
22424 TTTTAAATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.20
Consensus pattern (25 bp):
AAATTCAAAAAAATAAAAAATTAAA
Found at i:22649 original size:22 final size:20
Alignment explanation
Indices: 22617--22659 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
22607 TATATTTAAT
*
22617 ATTTATTAATTTAAAGTATTTG
1 ATTTATAAATTT-AA-TATTTG
22639 ATTTATAAATTTAATATTTG
1 ATTTATAAATTTAATATTTG
22659 A
1 A
22660 ATTTCGAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
21 2 0.10
22 11 0.55
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (20 bp):
ATTTATAAATTTAATATTTG
Found at i:26688 original size:2 final size:2
Alignment explanation
Indices: 26681--26714 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
26671 GTTGTATGGA
26681 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
26715 GGATAATGGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:27376 original size:2 final size:2
Alignment explanation
Indices: 27369--27399 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
27359 ACAACTCCAT
27369 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
27400 TATGTTCGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:33705 original size:4 final size:4
Alignment explanation
Indices: 33696--33720 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
33686 CTCCCCCGCC
33696 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
33721 CAATAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:34991 original size:16 final size:15
Alignment explanation
Indices: 34970--35003 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
34960 ATATCCATTT
34970 ATTTTAAAATAAAGTA
1 ATTTTAAAATAAA-TA
*
34986 ATTTTAATATAAATA
1 ATTTTAAAATAAATA
35001 ATT
1 ATT
35004 AAAAAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (15 bp):
ATTTTAAAATAAATA
Found at i:41628 original size:5 final size:5
Alignment explanation
Indices: 41620--41646 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
41610 CTATAAAAGA
41620 GAAGG GAAGG GAAGG GAAGG GAAGG GA
1 GAAGG GAAGG GAAGG GAAGG GAAGG GA
41647 GAGCTTTCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (5 bp):
GAAGG
Found at i:46078 original size:19 final size:18
Alignment explanation
Indices: 46056--46111 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
46046 AAAAAACAAA
*
46056 AAAAATCAAAATAATTTTT
1 AAAAATCAAAAT-ATTTAT
* *
46075 AAAATTTAAAATATTTAT
1 AAAAATCAAAATATTTAT
*
46093 AAAAATTCTAAA-ATTTAT
1 AAAAA-TCAAAATATTTAT
46111 A
1 A
46112 TATTTTTTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
18 16 0.53
19 14 0.47
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (18 bp):
AAAAATCAAAATATTTAT
Found at i:68262 original size:23 final size:23
Alignment explanation
Indices: 68231--68336 Score: 106
Period size: 23 Copynumber: 4.6 Consensus size: 23
68221 AAGAGTACCG
* *
68231 AAGTACTAAACAGAGAGCACACGA
1 AAGTGCTAAACGGAGAGCACAC-A
*
68255 AA-TGCTAAACGGAGAGTACACA
1 AAGTGCTAAACGGAGAGCACACA
* ** *
68277 AAGTACTAATTGAAGAGCACACA
1 AAGTGCTAAACGGAGAGCACACA
68300 AAGTGCTAAACGGAGAGCACACA
1 AAGTGCTAAACGGAGAGCACACA
** *
68323 CTGTGTTAAACGGA
1 AAGTGCTAAACGGA
68337 AAGCGCGCTA
Statistics
Matches: 66, Mismatches: 15, Indels: 3
0.79 0.18 0.04
Matches are distributed among these distances:
22 3 0.05
23 61 0.92
24 2 0.03
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.14
Consensus pattern (23 bp):
AAGTGCTAAACGGAGAGCACACA
Found at i:68271 original size:45 final size:46
Alignment explanation
Indices: 68216--68322 Score: 130
Period size: 46 Copynumber: 2.3 Consensus size: 46
68206 ATACGAAACA
* *
68216 AAACGAAGAGTAC-CGAAGTACTAAACAG-AGAGCACACGAAA-TGCT
1 AAACGGAGAGTACACAAAGTACT-AACAGAAGAGCACAC-AAAGTGCT
**
68261 AAACGGAGAGTACACAAAGTACTAATTGAAGAGCACACAAAGTGCT
1 AAACGGAGAGTACACAAAGTACTAACAGAAGAGCACACAAAGTGCT
*
68307 AAACGGAGAGCACACA
1 AAACGGAGAGTACACA
68323 CTGTGTTAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
45 18 0.33
46 36 0.67
ACGTcount: A:0.47, C:0.20, G:0.22, T:0.11
Consensus pattern (46 bp):
AAACGGAGAGTACACAAAGTACTAACAGAAGAGCACACAAAGTGCT
Found at i:71745 original size:25 final size:26
Alignment explanation
Indices: 71708--71756 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
71698 TTTTTATGTT
* *
71708 TTTAATCTCAATT-TTTTCTTTTTAA
1 TTTAATATAAATTGTTTTCTTTTTAA
*
71733 TTTAATATAAATTGTTTTTTTTTT
1 TTTAATATAAATTGTTTTCTTTTT
71757 CTTTAAAACT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 11 0.55
26 9 0.45
ACGTcount: A:0.24, C:0.06, G:0.02, T:0.67
Consensus pattern (26 bp):
TTTAATATAAATTGTTTTCTTTTTAA
Found at i:76872 original size:2 final size:2
Alignment explanation
Indices: 76865--76893 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
76855 ATAATAGTAC
76865 AT 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 AT A
76894 CACGCCAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:77158 original size:2 final size:2
Alignment explanation
Indices: 77151--77182 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
77141 ATAAATTGCC
77151 AT AT 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 AT AT
77183 TCACATATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:78272 original size:5 final size:5
Alignment explanation
Indices: 78228--78272 Score: 54
Period size: 5 Copynumber: 9.0 Consensus size: 5
78218 AAAGAGTTTC
* * * *
78228 CCAAC CCAAC CCAAC CCAAC CCAAT CCAAT CCAAT CCAAT CCAAT
1 CCAAT CCAAT CCAAT CCAAT CCAAT CCAAT CCAAT CCAAT CCAAT
78273 ATAAAAGGTG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.40, C:0.49, G:0.00, T:0.11
Consensus pattern (5 bp):
CCAAT
Found at i:78272 original size:15 final size:15
Alignment explanation
Indices: 78228--78272 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
78218 AAAGAGTTTC
* *
78228 CCAACCCAACCCAAC
1 CCAACCCAATCCAAT
78243 CCAACCCAATCCAAT
1 CCAACCCAATCCAAT
*
78258 CCAATCCAATCCAAT
1 CCAACCCAATCCAAT
78273 ATAAAAGGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.40, C:0.49, G:0.00, T:0.11
Consensus pattern (15 bp):
CCAACCCAATCCAAT
Found at i:81962 original size:15 final size:14
Alignment explanation
Indices: 81935--81961 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
81925 ACGAATAATA
81935 AAATATTAAAAAAT
1 AAATATTAAAAAAT
81949 AAATATTAAAAAA
1 AAATATTAAAAAA
81962 ACATAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AAATATTAAAAAAT
Found at i:82210 original size:22 final size:23
Alignment explanation
Indices: 82151--82211 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
82141 GGAGAGCCGA
** *
82151 AATTAAATCGAAATTTTTATAAT
1 AATTAAATTAAAATTTTTAAAAT
* * *
82174 AATAAAAATATAATTTTTAAAAT
1 AATTAAATTAAAATTTTTAAAAT
82197 -ATTAAATTAAAATTT
1 AATTAAATTAAAATTT
82212 ATCATTTTAA
Statistics
Matches: 29, Mismatches: 9, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
22 12 0.41
23 17 0.59
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
AATTAAATTAAAATTTTTAAAAT
Found at i:84123 original size:327 final size:327
Alignment explanation
Indices: 83529--84179 Score: 1259
Period size: 328 Copynumber: 2.0 Consensus size: 327
83519 AAATTAAGGG
83529 TATGGCTTCTGGAAACTACATTTTTGTAATTTATAGAATTTTAAATTAATAATAATAAAATTATA
1 TATGGCTTCTGGAAACTACATTTTTGTAATTTATAGAATTTTAAATTAATAATAATAAAATTATA
83594 TTTTGATTTTTTAAAATGATAAAAATTTGATTCAATCTTTTAAAATTATAAAGATGCAAGTTATT
66 TTTTGATTTTTTAAAATGATAAAAATTTGATTCAATCTTTTAAAATTATAAAGATGCAAGTTATT
83659 ACAATGATGAAATTACATTTTTATTATCGTAAAAATATACGATCTAATTCCACAAAAAAAAAATT
131 ACAATGATGAAATTACATTTTTATTATCGTAAAAATATACGATCTAATTCCACAAAAAAAAAATT
83724 CTGACTTCGCCTCTTAATATAATTATCATTTCTTTATTTTTTTGGATTTCATTTTATGCTTAAAT
196 CTGACTTCGCCTCTTAATATAATTATCATTTCTTTATTTTTTTGGATTTCATTTTATGCTTAAAT
83789 GTTTATTTTTTTAATATTGAAATACTTAGAGTTTAAATTATTTTATTTAAATTTTATGCATATTC
261 GTTTATTTTTTTAATATTGAAATACTTAGAGTTTAAATTATTTTATTTAAATTTTATGCATATTC
83854 GC
326 GC
*
83856 TATGGCTTCTGGAAACTACATTTTTTGTAATTTATAGAATTTTAAATTAATAATAGTAAAATTAT
1 TATGGCTTCTGGAAACTACA-TTTTTGTAATTTATAGAATTTTAAATTAATAATAATAAAATTAT
83921 ATTTTGATTTTTTAAAATGATAAAAATTTGATTCAATCTTTTAAAATTATAAAGATGCAAGTTAT
65 ATTTTGATTTTTTAAAATGATAAAAATTTGATTCAATCTTTTAAAATTATAAAGATGCAAGTTAT
*
83986 TACAATGATGAAATTATATTTTTATTATCGTAAAAATATACGATCTAATTCCAC-AAAAAAAAAT
130 TACAATGATGAAATTACATTTTTATTATCGTAAAAATATACGATCTAATTCCACAAAAAAAAAAT
84050 TCTGACTTCGCCTCTTAATATAATTATCATTTCTTTATTTTTTTGGATTTCATTTTATGCTTAAA
195 TCTGACTTCGCCTCTTAATATAATTATCATTTCTTTATTTTTTTGGATTTCATTTTATGCTTAAA
*
84115 TGTTTATTTTTTTAATATTGAAATATTTAGAGTTTAAATTATTTTATTTAAATTTTATGCATATT
260 TGTTTATTTTTTTAATATTGAAATACTTAGAGTTTAAATTATTTTATTTAAATTTTATGCATATT
84180 AGCTTCTTAG
Statistics
Matches: 320, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
327 159 0.50
328 161 0.50
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (327 bp):
TATGGCTTCTGGAAACTACATTTTTGTAATTTATAGAATTTTAAATTAATAATAATAAAATTATA
TTTTGATTTTTTAAAATGATAAAAATTTGATTCAATCTTTTAAAATTATAAAGATGCAAGTTATT
ACAATGATGAAATTACATTTTTATTATCGTAAAAATATACGATCTAATTCCACAAAAAAAAAATT
CTGACTTCGCCTCTTAATATAATTATCATTTCTTTATTTTTTTGGATTTCATTTTATGCTTAAAT
GTTTATTTTTTTAATATTGAAATACTTAGAGTTTAAATTATTTTATTTAAATTTTATGCATATTC
GC
Found at i:87780 original size:18 final size:18
Alignment explanation
Indices: 87756--87822 Score: 89
Period size: 18 Copynumber: 3.7 Consensus size: 18
87746 AAGACTTTGA
*
87756 GAGCATACTGGCTCGTTT
1 GAGCATACTGGCTCTTTT
* **
87774 AAGCATACTAACTCTTTT
1 GAGCATACTGGCTCTTTT
*
87792 GAGCATATTGGCTCTTTT
1 GAGCATACTGGCTCTTTT
87810 GAGCATACTGGCT
1 GAGCATACTGGCT
87823 TGTAAGGGCA
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (18 bp):
GAGCATACTGGCTCTTTT
Found at i:88774 original size:12 final size:12
Alignment explanation
Indices: 88743--88778 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
88733 ACTTAATGCA
88743 TGTATATTCTTG
1 TGTATATTCTTG
88755 TG-ATATTCTTG
1 TGTATATTCTTG
88766 TGTATATTCTTG
1 TGTATATTCTTG
88778 T
1 T
88779 TTTGGGTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.48
12 12 0.52
ACGTcount: A:0.17, C:0.08, G:0.17, T:0.58
Consensus pattern (12 bp):
TGTATATTCTTG
Found at i:91029 original size:24 final size:24
Alignment explanation
Indices: 90999--91045 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
90989 CAGTTGCAGT
* *
90999 TCAAATACAGAACCAAATGCATAC
1 TCAAATACAAAAACAAATGCATAC
91023 TCAAATACAAAAACAAATGCATA
1 TCAAATACAAAAACAAATGCATA
91046 ATCATATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.55, C:0.21, G:0.06, T:0.17
Consensus pattern (24 bp):
TCAAATACAAAAACAAATGCATAC
Found at i:92528 original size:17 final size:17
Alignment explanation
Indices: 92504--92579 Score: 82
Period size: 17 Copynumber: 4.5 Consensus size: 17
92494 CCCAACGAAT
*
92504 ATTTAAATTTATTTTAA
1 ATTTAAATTTATTATAA
* *
92521 AATTAAATTTATCATAA
1 ATTTAAATTTATTATAA
*
92538 GTTTAAATTTATTATAA
1 ATTTAAATTTATTATAA
* *
92555 ATTTAAAATTTA-AATAT
1 ATTT-AAATTTATTATAA
92572 ATTTAAAT
1 ATTTAAAT
92580 CAAGTCCAAT
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
16 4 0.08
17 38 0.78
18 7 0.14
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (17 bp):
ATTTAAATTTATTATAA
Found at i:92577 original size:34 final size:34
Alignment explanation
Indices: 92502--92579 Score: 97
Period size: 34 Copynumber: 2.3 Consensus size: 34
92492 GGCCCAACGA
* *
92502 ATATTTAAATTTATTTTAAAATTAAATTTATCAT
1 ATATTTAAATTTATTATAAAATTAAATTTATAAT
*
92536 A-AGTTTAAATTTATTATAAATTTAAAATTTA-AAT
1 ATA-TTTAAATTTATTATAAAATT-AAATTTATAAT
92570 ATATTTAAAT
1 ATATTTAAAT
92580 CAAGTCCAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
33 1 0.03
34 29 0.76
35 8 0.21
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (34 bp):
ATATTTAAATTTATTATAAAATTAAATTTATAAT
Found at i:94435 original size:30 final size:30
Alignment explanation
Indices: 94287--94418 Score: 209
Period size: 29 Copynumber: 4.5 Consensus size: 30
94277 CAAGAGGTCT
94287 CGAAACTTCCAAAAATTCCA-TTTTGACCC
1 CGAAACTTCCAAAAATTCCATTTTTGACCC
94316 CTG-AACTTCCAAAAATTCCATTTTTGACCC
1 C-GAAACTTCCAAAAATTCCATTTTTGACCC
*
94346 CG-AGCTTCCAAAAATTCCATTTTTGACCC
1 CGAAACTTCCAAAAATTCCATTTTTGACCC
*
94375 C-AAATTTCCAAAAATTCCATTTTTGACCC
1 CGAAACTTCCAAAAATTCCATTTTTGACCC
94404 CGAAACTTCCAAAAA
1 CGAAACTTCCAAAAA
94419 ATAACATTTT
Statistics
Matches: 95, Mismatches: 4, Indels: 7
0.90 0.04 0.07
Matches are distributed among these distances:
29 72 0.76
30 23 0.24
ACGTcount: A:0.34, C:0.30, G:0.07, T:0.30
Consensus pattern (30 bp):
CGAAACTTCCAAAAATTCCATTTTTGACCC
Found at i:94453 original size:59 final size:58
Alignment explanation
Indices: 94290--94456 Score: 178
Period size: 58 Copynumber: 2.9 Consensus size: 58
94280 GAGGTCTCGA
** *
94290 AACTTCCAAAAATTCCA-TTTTGACCCCTGAACT-TCCAAAAATTCCATTTTTGACCCCG
1 AACTTCCAAAAATAACATTTTTGACCCC--AAATGTCCAAAAATTCCATTTTTGACCCCG
* ** *
94348 AGCTTCCAAAAATTCCATTTTTGACCCCAAATTTCCAAAAATTCCATTTTTGACCCCG
1 AACTTCCAAAAATAACATTTTTGACCCCAAATGTCCAAAAATTCCATTTTTGACCCCG
* ** *
94406 AAACTTCCAAAAAATAACATTTTT-CCCCCGGATGTCCAAAAACTCCATTTT
1 -AACTTCC-AAAAATAACATTTTTGACCCCAAATGTCCAAAAATTCCATTTT
94457 CAACCTTGAA
Statistics
Matches: 95, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
57 3 0.03
58 41 0.43
59 38 0.40
60 13 0.14
ACGTcount: A:0.33, C:0.29, G:0.07, T:0.31
Consensus pattern (58 bp):
AACTTCCAAAAATAACATTTTTGACCCCAAATGTCCAAAAATTCCATTTTTGACCCCG
Found at i:94927 original size:95 final size:96
Alignment explanation
Indices: 94811--95001 Score: 246
Period size: 95 Copynumber: 2.0 Consensus size: 96
94801 AAGACTTTAA
* * *
94811 AATCGAGGTAATATTATTTTAT-TTCGAGTT-TCGAAA-ATTTGTGTCTTAACTTACTAGGTGCA
1 AATCGAGGCAATATTATTTTATCTTCGA-TTCT-GAAATA-TTGCGCCTTAACTTACTAGGTGCA
**
94873 ATTTTTCTTCAAATCAAAATAATCGAATACCCTT
63 ACCTTTCTTCAAATCAAAATAATCGAATACCCTT
*
94907 AATCGAGGCAATGTT-TTTTATCTTCGATTCTGAAATATTGCGCCTTAACTTACTAGGTGCAACC
1 AATCGAGGCAATATTATTTTATCTTCGATTCTGAAATATTGCGCCTTAACTTACTAGGTGCAACC
* * *
94971 TTTCTTCAAATCGAGATAATCGAATATCCTT
66 TTTCTTCAAATCAAAATAATCGAATACCCTT
95002 TTCCCAAATT
Statistics
Matches: 83, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
95 63 0.76
96 20 0.24
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (96 bp):
AATCGAGGCAATATTATTTTATCTTCGATTCTGAAATATTGCGCCTTAACTTACTAGGTGCAACC
TTTCTTCAAATCAAAATAATCGAATACCCTT
Found at i:97286 original size:21 final size:21
Alignment explanation
Indices: 97233--97286 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
97223 TAATAATCTA
* * *
97233 TATGCTAAGTAAAATCTGTAT
1 TATGTTAAGTATAATATGTAT
97254 TATGTTAAGTATAATATGTAT
1 TATGTTAAGTATAATATGTAT
97275 TATGTTAAGTAT
1 TATGTTAAGTAT
97287 GATTTGTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.37, C:0.04, G:0.15, T:0.44
Consensus pattern (21 bp):
TATGTTAAGTATAATATGTAT
Found at i:98538 original size:23 final size:22
Alignment explanation
Indices: 98503--98546 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
98493 ACCGCCACCG
98503 CCACGTCAGCATCCACATCAGCA
1 CCACGTCAGCAT-CACATCAGCA
** *
98526 CCACGTCTTCATCACGTCAGC
1 CCACGTCAGCATCACATCAGC
98547 CACGTGACCT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.25, C:0.43, G:0.14, T:0.18
Consensus pattern (22 bp):
CCACGTCAGCATCACATCAGCA
Done.