Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013036.1 Kokia drynarioides strain JFW-HI SEQ_128054, 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: 76120
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:3884 original size:14 final size:12
Alignment explanation
Indices: 3857--3899 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
3847 CAATGACCCA
3857 TCTTTTTTTCTT
1 TCTTTTTTTCTT
3869 TCTTTTTTTGCTT
1 TCTTTTTTT-CTT
*
3882 T-TCTTTTTCTT
1 TCTTTTTTTCTT
3893 TCTTTTT
1 TCTTTTT
3900 ACTTTATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 4 0.15
12 19 0.70
13 4 0.15
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.81
Consensus pattern (12 bp):
TCTTTTTTTCTT
Found at i:6997 original size:80 final size:80
Alignment explanation
Indices: 6905--7054 Score: 282
Period size: 80 Copynumber: 1.9 Consensus size: 80
6895 ATTTCTATGA
**
6905 TTATTTATTTGTGTTAATTTATAGAATAAAAATTTAAAAATTATATATATTTTGTACATTTGAAA
1 TTATTTATTTGTGTTAATTTATAGAATAAAAATTTAAAAATTATATATATTTCCTACATTTGAAA
6970 TTTAATTCAGATTTG
66 TTTAATTCAGATTTG
6985 TTATTTATTTGTGTTAATTTATAGAATAAAAATTTAAAAATTATATATATTTCCTACATTTGAAA
1 TTATTTATTTGTGTTAATTTATAGAATAAAAATTTAAAAATTATATATATTTCCTACATTTGAAA
7050 TTTAA
66 TTTAA
7055 GAATACATCT
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
80 68 1.00
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.49
Consensus pattern (80 bp):
TTATTTATTTGTGTTAATTTATAGAATAAAAATTTAAAAATTATATATATTTCCTACATTTGAAA
TTTAATTCAGATTTG
Found at i:13548 original size:20 final size:21
Alignment explanation
Indices: 13512--13555 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
13502 GATTAATACA
*
13512 AATTAAAAACATAAAATT-TT
1 AATTAAAAAAATAAAATTATT
13532 AATTAAATAAAAT-AAATTATT
1 AATTAAA-AAAATAAAATTATT
13553 AAT
1 AAT
13556 ATTCATCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (21 bp):
AATTAAAAAAATAAAATTATT
Found at i:15239 original size:105 final size:105
Alignment explanation
Indices: 15018--15232 Score: 358
Period size: 105 Copynumber: 2.0 Consensus size: 105
15008 TGTTTTAGTT
* *
15018 AATGGTCATTGCTTGCAGAACAAAATGGATAAAGCTAGAAGAGTTTTGAAGTTGATGATTGAGAA
1 AATGGTCATTGCTTGCAGAACAAAATGGATAAAGCTAGAAGAGTTTTCAACTTGATGATTGAGAA
* * * *
15083 GGGTTGTGAGCCTGATATGGTTATTTACAACACCATGATT
66 GGGTTGTGAGCCTGATATAGTTACTTACAACACCATAATC
**
15123 AATGGTCATTGCTTGCAGAATGAAATGGATAAAGCTAGAAGAGTTTTCAACTTGATGATTGAGAA
1 AATGGTCATTGCTTGCAGAACAAAATGGATAAAGCTAGAAGAGTTTTCAACTTGATGATTGAGAA
15188 GGGTTGTGAGCCTGATATAGTTACTTACAACACCATAATC
66 GGGTTGTGAGCCTGATATAGTTACTTACAACACCATAATC
15228 AATGG
1 AATGG
15233 ATATTGCAAA
Statistics
Matches: 102, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
105 102 1.00
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.30
Consensus pattern (105 bp):
AATGGTCATTGCTTGCAGAACAAAATGGATAAAGCTAGAAGAGTTTTCAACTTGATGATTGAGAA
GGGTTGTGAGCCTGATATAGTTACTTACAACACCATAATC
Found at i:17295 original size:105 final size:105
Alignment explanation
Indices: 17129--17364 Score: 269
Period size: 105 Copynumber: 2.2 Consensus size: 105
17119 CAATATTTCA
* * * * * * * *
17129 CCTAATATTGTCACTTATACTATATTGATTGATGCACTTTGCAAGGATGGAAGGATTTCTAAAGC
1 CCTAATGTTGTCACCTATAATACATTGATTGATGCACATTGCAAGAAGGGAAGGATCTCTAAAGC
17194 TGTA-GAGACCGTTGACACAATGAGAAAGCAAGGCATTGAG
66 TG-AGGAGACCGTTGACACAATGAGAAAGCAAGGCATTGAG
* * *
17234 CCTAATGTTGTCACGTATAATACATTGGTTGATGCACATTGCCAAGAAGGGATGG-TCTCTAAAG
1 CCTAATGTTGTCACCTATAATACATTGATTGATGCACATTG-CAAGAAGGGAAGGATCTCTAAAG
* ** * * *
17298 CTGAGGATATTGTTGACGCAATGATAAAGCGAGGCATTGAG
65 CTGAGGAGACCGTTGACACAATGAGAAAGCAAGGCATTGAG
* *
17339 CCTAATGTTGTTACCTATAATGCATT
1 CCTAATGTTGTCACCTATAATACATT
17365 AATCAGCGGT
Statistics
Matches: 110, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
104 1 0.01
105 99 0.90
106 10 0.09
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (105 bp):
CCTAATGTTGTCACCTATAATACATTGATTGATGCACATTGCAAGAAGGGAAGGATCTCTAAAGC
TGAGGAGACCGTTGACACAATGAGAAAGCAAGGCATTGAG
Found at i:19153 original size:31 final size:31
Alignment explanation
Indices: 19081--19179 Score: 98
Period size: 31 Copynumber: 3.3 Consensus size: 31
19071 ATTAATCTCA
* *
19081 TAAA-TTTTTAAAAATTTTAATCAAACCCCC
1 TAAATTTTTTAAAAATTATAATTAAACCCCC
* * *
19111 --AGTTCTTTTAAAAGATTATCATTAAA-CTCC
1 TAAATT-TTTTAAAA-ATTATAATTAAACCCCC
*
19141 TAAATTTTTTAAAAATTGTAATTAAACCCCC
1 TAAATTTTTTAAAAATTATAATTAAACCCCC
19172 TAAATTTT
1 TAAATTTT
19180 AGTCCCAAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
28 1 0.02
29 1 0.02
30 21 0.39
31 28 0.52
32 3 0.06
ACGTcount: A:0.40, C:0.16, G:0.03, T:0.40
Consensus pattern (31 bp):
TAAATTTTTTAAAAATTATAATTAAACCCCC
Found at i:19167 original size:30 final size:30
Alignment explanation
Indices: 19055--19179 Score: 92
Period size: 31 Copynumber: 4.1 Consensus size: 30
19045 TTTTTATTTT
* * * * *
19055 TTTTTTGAAAATTCTGATTAATCTCATAAA
1 TTTTTTAAAAATTATAATTAAACTCCTAAA
* * ** *
19085 -TTTTTAAAAATTTTAATCAAAC-CCCCAG
1 TTTTTTAAAAATTATAATTAAACTCCTAAA
*
19113 TTCTTTTAAAAGATTATCATTAAACTCCTAAA
1 TT-TTTTAAAA-ATTATAATTAAACTCCTAAA
* *
19145 TTTTTTAAAAATTGTAATTAAACCCCCTAAA
1 TTTTTTAAAAATTATAATTAAA-CTCCTAAA
19176 TTTT
1 TTTT
19180 AGTCCCAAAA
Statistics
Matches: 72, Mismatches: 18, Indels: 9
0.73 0.18 0.09
Matches are distributed among these distances:
28 2 0.03
29 18 0.25
30 18 0.25
31 29 0.40
32 5 0.07
ACGTcount: A:0.38, C:0.15, G:0.04, T:0.42
Consensus pattern (30 bp):
TTTTTTAAAAATTATAATTAAACTCCTAAA
Found at i:24846 original size:20 final size:19
Alignment explanation
Indices: 24788--24854 Score: 57
Period size: 19 Copynumber: 3.4 Consensus size: 19
24778 TTTTGAAAAA
24788 TTTAAAA-TTTT-GAACTTT
1 TTTAAAATTTTTAGAA-TTT
*
24806 CTTTATATATTCTTTAGAATTTT
1 -TTTA-AAATT-TTTAGAA-TTT
*
24829 TTTAAAATTTTTATAATTT
1 TTTAAAATTTTTAGAATTT
24848 TTTAAAA
1 TTTAAAA
24855 AATATAAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
19 14 0.35
20 8 0.20
21 5 0.12
22 7 0.17
23 6 0.15
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.58
Consensus pattern (19 bp):
TTTAAAATTTTTAGAATTT
Found at i:24855 original size:20 final size:20
Alignment explanation
Indices: 24818--24855 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
24808 TTATATATTC
*
24818 TTTAGAATTTTTTTAAAATT
1 TTTAGAATTTTTTAAAAATT
*
24838 TTTATAATTTTTTAAAAA
1 TTTAGAATTTTTTAAAAA
24856 ATATAAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (20 bp):
TTTAGAATTTTTTAAAAATT
Found at i:24878 original size:18 final size:18
Alignment explanation
Indices: 24857--24891 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
24847 TTTTAAAAAA
24857 TATAA-ATTTTAGAATTTT
1 TATAATATTTTA-AATTTT
24875 TATAATATTTTAAATTT
1 TATAATATTTTAAATTT
24892 AAAAAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
TATAATATTTTAAATTTT
Found at i:26109 original size:21 final size:20
Alignment explanation
Indices: 26064--26116 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
26054 CGGTCAAGGG
*
26064 CACGGGCGTGTATATGACAA
1 CACGGGCGTGTGTATGACAA
* *
26084 CACGGGCGTGTGTTTGAGACA
1 CACGGGCGTGTGTATGACA-A
*
26105 CACGGCCGTGTG
1 CACGGGCGTGTG
26117 CCCTGTTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.21, C:0.23, G:0.36, T:0.21
Consensus pattern (20 bp):
CACGGGCGTGTGTATGACAA
Found at i:29879 original size:5 final size:5
Alignment explanation
Indices: 29869--29893 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
29859 CATTCAATCC
29869 TTATT TTATT TTATT TTATT TTATT
1 TTATT TTATT TTATT TTATT TTATT
29894 AAGATTATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTATT
Found at i:39895 original size:26 final size:26
Alignment explanation
Indices: 39866--39920 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
39856 AAAACTTGAA
*
39866 AAATTTCACTCCATTTGACTCAACTC
1 AAATTTCACTCCACTTGACTCAACTC
* * *
39892 AAATTTCATTTCACTTGACTCAATTC
1 AAATTTCACTCCACTTGACTCAACTC
39918 AAA
1 AAA
39921 ATTAGGATGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.36
Consensus pattern (26 bp):
AAATTTCACTCCACTTGACTCAACTC
Found at i:43060 original size:31 final size:31
Alignment explanation
Indices: 43016--43078 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
43006 CGTTATTTGG
* **
43016 AGAACCTTCAAAAAGGTTTGG-CTCTTATTTA
1 AGAACATTCAAAAAAATTTGGCCT-TTATTTA
*
43047 AGAACATTTAAAAAAATTTGGCCTTTATTTA
1 AGAACATTCAAAAAAATTTGGCCTTTATTTA
43078 A
1 A
43079 CTATTTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 25 0.93
32 2 0.07
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.37
Consensus pattern (31 bp):
AGAACATTCAAAAAAATTTGGCCTTTATTTA
Found at i:46644 original size:18 final size:18
Alignment explanation
Indices: 46621--46663 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
46611 GAATAGATTT
46621 TTAATTAAATAATTTT-AA
1 TTAATTAAA-AATTTTAAA
46639 TTAATTAAAAATTTTAAA
1 TTAATTAAAAATTTTAAA
46657 TTAATTA
1 TTAATTA
46664 CACATTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 6 0.25
18 18 0.75
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTAATTAAAAATTTTAAA
Found at i:51927 original size:22 final size:21
Alignment explanation
Indices: 51867--51929 Score: 72
Period size: 23 Copynumber: 2.9 Consensus size: 21
51857 TTAAGAGTCG
51867 AAATTAAATTATAATTTTTAA
1 AAATTAAATTATAATTTTTAA
* *
51888 AATAGTAAAAATATAATTTTTAA
1 AA-A-TTAAATTATAATTTTTAA
*
51911 AGAATTAAATTAAAATTTT
1 A-AATTAAATTATAATTTT
51930 ATTTTTTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
21 2 0.06
22 13 0.38
23 18 0.53
24 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (21 bp):
AAATTAAATTATAATTTTTAA
Found at i:51935 original size:28 final size:29
Alignment explanation
Indices: 51904--51964 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
51894 AAAAATATAA
*
51904 TTTTT-AAAGA-ATTAAATTAAAATTTTAT
1 TTTTTAAAAGAGA-TAAAATAAAATTTTAT
*
51932 TTTTTAAAAGAGATAAAATATAATTTTAT
1 TTTTTAAAAGAGATAAAATAAAATTTTAT
51961 TTTT
1 TTTT
51965 ATTAATTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 5 0.17
29 23 0.79
30 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (29 bp):
TTTTTAAAAGAGATAAAATAAAATTTTAT
Found at i:52165 original size:17 final size:17
Alignment explanation
Indices: 52145--52182 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
52135 AAATATAAAA
*
52145 ATAAAAAAAATTAAATT
1 ATAAAAAAAATAAAATT
*
52162 ATAAATAAAATAAAATT
1 ATAAAAAAAATAAAATT
52179 -TAAA
1 ATAAA
52183 CACATAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAAAAAATAAAATT
Found at i:52176 original size:22 final size:22
Alignment explanation
Indices: 52133--52178 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
52123 TACATATGAT
52133 TTAAATATAAAAATAAAAAAAA
1 TTAAATATAAAAATAAAAAAAA
*
52155 TTAAAT-TATAAATAAAATAAAA
1 TTAAATATAAAAATAAAA-AAAA
52177 TT
1 TT
52179 TAAACACATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (22 bp):
TTAAATATAAAAATAAAAAAAA
Found at i:52181 original size:23 final size:23
Alignment explanation
Indices: 52131--52182 Score: 72
Period size: 21 Copynumber: 2.3 Consensus size: 23
52121 TCTACATATG
52131 ATTTAAATATAAAAATAAAAAAA
1 ATTTAAATATAAAAATAAAAAAA
*
52154 A-TTAAAT-TATAAATAAAATAAA
1 ATTTAAATATAAAAATAAAA-AAA
52176 ATTTAAA
1 ATTTAAA
52183 CACATAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 10 0.38
22 10 0.38
23 6 0.23
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (23 bp):
ATTTAAATATAAAAATAAAAAAA
Found at i:52534 original size:21 final size:22
Alignment explanation
Indices: 52510--52551 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
52500 AAAGGAATGG
* *
52510 AATAAAT-GTAAAAAATTGAAA
1 AATAAATAATAAAAAAATGAAA
52531 AATAAATAATAAAAAAATGAA
1 AATAAATAATAAAAAAATGAA
52552 TTTTTTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.21
Consensus pattern (22 bp):
AATAAATAATAAAAAAATGAAA
Found at i:58636 original size:24 final size:23
Alignment explanation
Indices: 58589--58636 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
58579 TCAACTAAAG
*
58589 ACATATTTTTTATTATATATATA
1 ACATATTTTTTATTATATAGATA
* *
58612 ACATAATTTTTTTTTATTTAGATA
1 ACAT-ATTTTTTATTATATAGATA
58636 A
1 A
58637 TGATTGTGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (23 bp):
ACATATTTTTTATTATATAGATA
Found at i:64224 original size:41 final size:40
Alignment explanation
Indices: 64177--64348 Score: 154
Period size: 41 Copynumber: 4.2 Consensus size: 40
64167 AGGCTTTAAA
64177 CCTAGCAAGGTTTGTGCCAGTGTACATT-ATT-AGGCTTTGTG
1 CCTAGC-AGGTTTGTGCCAGTGT--ATTGATTCAGGCTTTGTG
* *
64218 CCTAGCAGGCTTTATGCCAGTGTATTGATTCAGGCTTTGTT
1 CCTAGCAGG-TTTGTGCCAGTGTATTGATTCAGGCTTTGTG
* *
64259 CCTAGCAGACTTCGTGCC-GATGTATTGATTCAGGCTTTGTG
1 CCTAGCAG-GTTTGTGCCAG-TGTATTGATTCAGGCTTTGTG
* * * * * **
64300 CCTAGCA-GTTTCGAGCCGGTATATTGAATCAGGCCTTAAG
1 CCTAGCAGGTTT-GTGCCAGTGTATTGATTCAGGCTTTGTG
64340 CCTAGCAGG
1 CCTAGCAGG
64349 CGTCGCGCCG
Statistics
Matches: 109, Mismatches: 14, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
39 5 0.05
40 34 0.31
41 70 0.64
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.33
Consensus pattern (40 bp):
CCTAGCAGGTTTGTGCCAGTGTATTGATTCAGGCTTTGTG
Found at i:64370 original size:41 final size:41
Alignment explanation
Indices: 64217--64371 Score: 125
Period size: 41 Copynumber: 3.8 Consensus size: 41
64207 TAGGCTTTGT
* * * * **
64217 GCCTAGCAGGCTT-TATGCCAGTGTATTGATTCAGGCTTTGT
1 GCCTAGCAGGCTTCGA-GCCGGTGTATTGAATCAGGCCTTAA
* * * * * * **
64258 TCCTAGCAGACTTCGTGCCGATGTATTGATTCAGGCTTTGT
1 GCCTAGCAGGCTTCGAGCCGGTGTATTGAATCAGGCCTTAA
* *
64299 GCCTAGCA-GTTTCGAGCCGGTATATTGAATCAGGCCTTAA
1 GCCTAGCAGGCTTCGAGCCGGTGTATTGAATCAGGCCTTAA
* *
64339 GCCTAGCAGGCGTCGCGCCGGTGTATTGAATCA
1 GCCTAGCAGGCTTCGAGCCGGTGTATTGAATCA
64372 AATAAATTAT
Statistics
Matches: 92, Mismatches: 20, Indels: 4
0.79 0.17 0.03
Matches are distributed among these distances:
40 31 0.34
41 61 0.66
ACGTcount: A:0.19, C:0.23, G:0.27, T:0.31
Consensus pattern (41 bp):
GCCTAGCAGGCTTCGAGCCGGTGTATTGAATCAGGCCTTAA
Found at i:65632 original size:54 final size:54
Alignment explanation
Indices: 65571--65707 Score: 186
Period size: 54 Copynumber: 2.5 Consensus size: 54
65561 GCTGAGACAT
* **
65571 AGGCATGTGGCCCAAGTCAATGAGTTACACGTGTGAGCACATGGGCTAAGGCACG
1 AGGCATGTGGCCCAAGTCAATGAGTTACACATGTGAGCACACAGGCTAAGGCA-G
* * * *
65626 A-GCATGTGGCCCAAGTCAGTGAGTTACACATGTGAGCACACAGGTTGAGGCAT
1 AGGCATGTGGCCCAAGTCAATGAGTTACACATGTGAGCACACAGGCTAAGGCAG
*
65679 AGGCGTGTGGCCCAAGTCAATGAGTTACA
1 AGGCATGTGGCCCAAGTCAATGAGTTACA
65708 TGGGCAAATA
Statistics
Matches: 72, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
53 1 0.01
54 70 0.97
55 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.31, T:0.20
Consensus pattern (54 bp):
AGGCATGTGGCCCAAGTCAATGAGTTACACATGTGAGCACACAGGCTAAGGCAG
Found at i:65811 original size:37 final size:37
Alignment explanation
Indices: 65761--65886 Score: 243
Period size: 37 Copynumber: 3.4 Consensus size: 37
65751 CACCATCTTT
*
65761 ATCCACCCCTACACACCATATAGGGTATCAAGTACCC
1 ATCCATCCCTACACACCATATAGGGTATCAAGTACCC
65798 ATCCATCCCTACACACCATATAGGGTATCAAGTACCC
1 ATCCATCCCTACACACCATATAGGGTATCAAGTACCC
65835 ATCCATCCCTACACACCATATAGGGTATCAAGTACCC
1 ATCCATCCCTACACACCATATAGGGTATCAAGTACCC
65872 ATCCATCCCTACACA
1 ATCCATCCCTACACA
65887 TTGCGTAGTG
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
37 88 1.00
ACGTcount: A:0.33, C:0.37, G:0.10, T:0.21
Consensus pattern (37 bp):
ATCCATCCCTACACACCATATAGGGTATCAAGTACCC
Found at i:66716 original size:21 final size:21
Alignment explanation
Indices: 66692--66745 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
66682 CTTGTGCTAG
66692 TTCTACCGATACAAGT-ATAAC
1 TTCTACCGATACAAGTCAT-AC
*
66713 TTCTATCGATACAAGTCATAC
1 TTCTACCGATACAAGTCATAC
*
66734 TTCTACCTATAC
1 TTCTACCGATAC
66746 TAAAAACTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 27 0.93
22 2 0.07
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.33
Consensus pattern (21 bp):
TTCTACCGATACAAGTCATAC
Found at i:68580 original size:15 final size:16
Alignment explanation
Indices: 68553--68593 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
68543 TTTCACCCTA
68553 AGTCC-TTACAAA-TTT
1 AGTCCTTTA-AAATTTT
*
68568 ATTCCTTTAAAATTTT
1 AGTCCTTTAAAATTTT
68584 AGTCCTTTAA
1 AGTCCTTTAA
68594 CATAATTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.32, C:0.17, G:0.05, T:0.46
Consensus pattern (16 bp):
AGTCCTTTAAAATTTT
Found at i:72104 original size:12 final size:12
Alignment explanation
Indices: 72074--72115 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
72064 GTATATAAAA
*
72074 AATAAATATAAT
1 AATAAATTTAAT
*
72086 -TTAAATTTAAT
1 AATAAATTTAAT
*
72097 AATAAATTTAAA
1 AATAAATTTAAT
72109 AATAAAT
1 AATAAAT
72116 AACAATTATA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
11 9 0.36
12 16 0.64
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AATAAATTTAAT
Done.