Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013858.1 Kokia drynarioides strain JFW-HI SEQ_128886, 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: 95422
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 135 characters in sequence are not A, C, G, or T
Found at i:4111 original size:3 final size:3
Alignment explanation
Indices: 4103--4159 Score: 60
Period size: 3 Copynumber: 19.0 Consensus size: 3
4093 TTAAATGAAT
* * * * **
4103 TAA TAA TAA TAA TAA TAG TAA TAT TAA TAA TAC TAA TAC TAA TTT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4151 TAA TAA TAA
1 TAA TAA TAA
4160 AAAAGAATAC
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:4132 original size:21 final size:21
Alignment explanation
Indices: 4106--4159 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
4096 AATGAATTAA
*
4106 TAATAATAATAATAGTAATAT
1 TAATAATAATAATACTAATAT
* *
4127 TAATAATACTAATACTAATTT
1 TAATAATAATAATACTAATAT
4148 TAATAATAATAA
1 TAATAATAATAA
4160 AAAAGAATAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.39
Consensus pattern (21 bp):
TAATAATAATAATACTAATAT
Found at i:5271 original size:29 final size:30
Alignment explanation
Indices: 5220--5450 Score: 154
Period size: 30 Copynumber: 7.8 Consensus size: 30
5210 GAAAGTCCCC
*
5220 AAACTTTCC-AAAATTTCATTTTTAACCTT
1 AAACTTTCCAAAAATTACATTTTTAACCTT
* **
5249 AAATTTTCCAAAAATTACATTTTT-ACCCC
1 AAACTTTCCAAAAATTACATTTTTAACCTT
* * * *
5278 AAACTTT-CTAAAATT-CTATTTTTTACATC
1 AAACTTTCCAAAAATTAC-ATTTTTAACCTT
* * * *
5307 GAATTTTCCAAAAATTACATTTTCACCCTCT
1 AAACTTTCCAAAAATTACATTTTTAACCT-T
* * *
5338 -AACTTTCC-AAAATTCCATTTTTGACCCT
1 AAACTTTCCAAAAATTACATTTTTAACCTT
* * * *
5366 AAAATTTCAAAAAAATACATTTTTACCCTT
1 AAACTTTCCAAAAATTACATTTTTAACCTT
* * * *
5396 GAACTTTCC-AAAA-TACTTTTTTTGACCCT
1 AAACTTTCCAAAAATTAC-ATTTTTAACCTT
*
5425 AAATTTTTCCAAAAATTACATTTTTA
1 AAA-CTTTCCAAAAATTACATTTTTA
5451 CCCCAAACCT
Statistics
Matches: 150, Mismatches: 40, Indels: 22
0.71 0.19 0.10
Matches are distributed among these distances:
27 1 0.01
28 17 0.11
29 59 0.39
30 60 0.40
31 10 0.07
32 3 0.02
ACGTcount: A:0.35, C:0.21, G:0.02, T:0.42
Consensus pattern (30 bp):
AAACTTTCCAAAAATTACATTTTTAACCTT
Found at i:5483 original size:59 final size:59
Alignment explanation
Indices: 5219--5458 Score: 279
Period size: 59 Copynumber: 4.1 Consensus size: 59
5209 TGAAAGTCCC
* * *
5219 CAAACTTTCCAAAATTTCATTTTTAACCTTAAATTTTCCAAAAATTACATTTTTACCC-
1 CAAACTTTCCAAAATTCCATTTTTGACCCTAAATTTTCCAAAAATTACATTTTTACCCT
* * * * * *
5277 CAAACTTTCTAAAATTCTATTTTTTA-CATCGAATTTTCCAAAAATTACATTTTCACCCT
1 CAAACTTTCCAAAATTCCATTTTTGACCCT-AAATTTTCCAAAAATTACATTTTTACCCT
* * * *
5336 CTAACTTTCCAAAATTCCATTTTTGACCCTAAAATTTCAAAAAAATACATTTTTACCCT
1 CAAACTTTCCAAAATTCCATTTTTGACCCTAAATTTTCCAAAAATTACATTTTTACCCT
** * **
5395 TGAACTTTCCAAAATACTTTTTTTGACCCTAAATTTTTCCAAAAATTACATTTTTACCC-
1 CAAACTTTCCAAAATTCCATTTTTGACCCTAAA-TTTTCCAAAAATTACATTTTTACCCT
5454 CAAAC
1 CAAAC
5459 CTCCTAAAAA
Statistics
Matches: 151, Mismatches: 27, Indels: 7
0.82 0.15 0.04
Matches are distributed among these distances:
57 2 0.01
58 48 0.32
59 77 0.51
60 24 0.16
ACGTcount: A:0.35, C:0.23, G:0.02, T:0.40
Consensus pattern (59 bp):
CAAACTTTCCAAAATTCCATTTTTGACCCTAAATTTTCCAAAAATTACATTTTTACCCT
Found at i:5554 original size:58 final size:58
Alignment explanation
Indices: 5443--5596 Score: 172
Period size: 60 Copynumber: 2.7 Consensus size: 58
5433 CCAAAAATTA
* *
5443 CATTTTT-ACCCCAAACC-TCCTAAAAATTACCATTTTACCCTCGAATGTCTAAAAACAC
1 CATTTTTAACCCCGAACCTTCC-AAAAATTACCATTTTACCCTCCAATG-CTAAAAACAC
* **
5501 CATTTTTAACCCCCGAACCTTCCAAAAAGTACCATTTTA-CCTCCAGATG-TAAAAATTC
1 CATTTTTAA-CCCCGAACCTTCCAAAAATTACCATTTTACCCTCCA-ATGCTAAAAACAC
* * *
5559 CATTTTTAACCTCGAACCTTCTAAAAATTATCATTTTA
1 CATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTA
5597 TTCCCGAAGC
Statistics
Matches: 83, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
57 25 0.30
58 23 0.28
59 6 0.07
60 26 0.31
61 3 0.04
ACGTcount: A:0.35, C:0.28, G:0.05, T:0.32
Consensus pattern (58 bp):
CATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCTCCAATGCTAAAAACAC
Found at i:5584 original size:30 final size:30
Alignment explanation
Indices: 5435--5587 Score: 90
Period size: 29 Copynumber: 5.2 Consensus size: 30
5425 AAATTTTTCC
* * * *
5435 AAAAATTACATTTTT-ACCCCAAACCTCCT
1 AAAAATTCCATTTTTAACCTCGAACCTTCT
*
5464 AAAAATTACCA-TTTTACCCTCGAA--TGTCT
1 AAAAATT-CCATTTTTAACCTCGAACCT-TCT
** * *
5493 AAAAACACCATTTTTAACCCCCGAACCTTCC
1 AAAAATTCCATTTTTAA-CCTCGAACCTTCT
* * *
5524 AAAAAGTACCA-TTTT-ACCTCCAGA---TGT
1 AAAAA-TTCCATTTTTAACCTCGA-ACCTTCT
5551 AAAAATTCCATTTTTAACCTCGAACCTTCT
1 AAAAATTCCATTTTTAACCTCGAACCTTCT
5581 AAAAATT
1 AAAAATT
5588 ATCATTTTAT
Statistics
Matches: 92, Mismatches: 18, Indels: 27
0.67 0.13 0.20
Matches are distributed among these distances:
26 4 0.04
27 11 0.12
28 10 0.11
29 27 0.29
30 24 0.26
31 11 0.12
32 5 0.05
ACGTcount: A:0.37, C:0.27, G:0.05, T:0.31
Consensus pattern (30 bp):
AAAAATTCCATTTTTAACCTCGAACCTTCT
Found at i:5594 original size:57 final size:58
Alignment explanation
Indices: 5435--5596 Score: 186
Period size: 58 Copynumber: 2.8 Consensus size: 58
5425 AAATTTTTCC
* * * *
5435 AAAAATTACATTTTT-ACCCCAAACCTCCTAAAAATTACCATTTTACCCTCGAATGTCT
1 AAAAATTCCATTTTTAACCCCGAACCTTCTAAAAATTACCATTTTACCCTCCAATG-CT
** * *
5493 AAAAACACCATTTTTAACCCCCGAACCTTCCAAAAAGTACCATTTTA-CCTCCAGATG-T
1 AAAAATTCCATTTTTAA-CCCCGAACCTTCTAAAAATTACCATTTTACCCTCCA-ATGCT
* *
5551 AAAAATTCCATTTTTAACCTCGAACCTTCTAAAAATTATCATTTTA
1 AAAAATTCCATTTTTAACCCCGAACCTTCTAAAAATTACCATTTTA
5597 TTCCCGAAGC
Statistics
Matches: 87, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
57 25 0.29
58 28 0.32
59 6 0.07
60 28 0.32
ACGTcount: A:0.37, C:0.27, G:0.04, T:0.32
Consensus pattern (58 bp):
AAAAATTCCATTTTTAACCCCGAACCTTCTAAAAATTACCATTTTACCCTCCAATGCT
Found at i:5596 original size:30 final size:30
Alignment explanation
Indices: 5435--5596 Score: 108
Period size: 30 Copynumber: 5.5 Consensus size: 30
5425 AAATTTTTCC
* * * *
5435 AAAAATTA-CATTTTTACCCCAAACCTCCT
1 AAAAATTACCATTTTAACCTCGAACCTTCT
*
5464 AAAAATTACCATTTTACCCTCGAA--TGTCT
1 AAAAATTACCATTTTAACCTCGAACCT-TCT
* * *
5493 AAAAA-CACCATTTTTAACCCCCGAACCTTCC
1 AAAAATTACCA-TTTTAA-CCTCGAACCTTCT
* * *
5524 AAAAAGTACCATTTT-ACCTCCAGA---TGT
1 AAAAATTACCATTTTAACCTCGA-ACCTTCT
5551 AAAAATT-CCATTTTTAACCTCGAACCTTCT
1 AAAAATTACCA-TTTTAACCTCGAACCTTCT
*
5581 AAAAATTATCATTTTA
1 AAAAATTACCATTTTA
5597 TTCCCGAAGC
Statistics
Matches: 101, Mismatches: 18, Indels: 27
0.69 0.12 0.18
Matches are distributed among these distances:
26 3 0.03
27 12 0.12
28 11 0.11
29 24 0.24
30 33 0.33
31 13 0.13
32 5 0.05
ACGTcount: A:0.37, C:0.27, G:0.04, T:0.32
Consensus pattern (30 bp):
AAAAATTACCATTTTAACCTCGAACCTTCT
Found at i:23452 original size:64 final size:62
Alignment explanation
Indices: 23365--23746 Score: 463
Period size: 64 Copynumber: 6.1 Consensus size: 62
23355 AAATAAAAGA
* * *
23365 TTCAATTTTTTTTTGTGTTGGTCATGCAATGGTCGACACCCCTTGGTCTCGGATAAAAAAAT
1 TTCAAATTTTTTTTGTGTTGGTCATGCAATGGCCGACACCCCTTGTTCTCGGATAAAAAAAT
* *
23427 TTCAAATATTTTTTTGGTGTTGGTCATGCAATGGTCGACACCCCTT-TTTTCGGAT--AAAAAT
1 TTCAAAT-TTTTTTT-GTGTTGGTCATGCAATGGCCGACACCCCTTGTTCTCGGATAAAAAAAT
* *
23488 TTCAAATTTTTTTTGTGTTGGTTATGCAATGGCCGACACCCTCTT-TTCTCAGATAAAAAAAT
1 TTCAAATTTTTTTTGTGTTGGTCATGCAATGGCCGACACCC-CTTGTTCTCGGATAAAAAAAT
* * * *
23550 TTCAAATTTTTTTTTGGTGTTGGTCATGCAATGGCCGACACCCTTTTTTCTCGAATAAAAAATT
1 TTCAAA-TTTTTTTT-GTGTTGGTCATGCAATGGCCGACACCCCTTGTTCTCGGATAAAAAAAT
* * * * *
23614 TTCAAATTTTTTTTGTGTTGG-CTATGCAATGGTCGACACCCCCTTGTTTTTGAATAAAAAAAA
1 TTCAAATTTTTTTTGTGTTGGTC-ATGCAATGGCCGACA-CCCCTTGTTCTCGGATAAAAAAAT
* * * *
23677 TTCAATTTTTTTTTTGTGTTGGCCATGCAATGACCGACACCCCCTGTTCTCGGAT-AAAAAAT
1 TTCAA-ATTTTTTTTGTGTTGGTCATGCAATGGCCGACACCCCTTGTTCTCGGATAAAAAAAT
23739 TT-AAATTT
1 TTCAAATTT
23747 ATGATTTTTT
Statistics
Matches: 280, Mismatches: 28, Indels: 26
0.84 0.08 0.08
Matches are distributed among these distances:
59 25 0.09
60 20 0.07
61 16 0.06
62 47 0.17
63 67 0.24
64 104 0.37
65 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.40
Consensus pattern (62 bp):
TTCAAATTTTTTTTGTGTTGGTCATGCAATGGCCGACACCCCTTGTTCTCGGATAAAAAAAT
Found at i:23508 original size:123 final size:125
Alignment explanation
Indices: 23320--23746 Score: 535
Period size: 123 Copynumber: 3.4 Consensus size: 125
23310 AATTTTAAGG
* * * * * * *
23320 GTTGATCATGTAATGGCCGACACCGCTTTTTTGTCAAATAAAAGA-TTCAATTTTTTTTTGTGTT
1 GTTGGTCATGCAATGGCCGACACC-CCTTTTTCTCGAATAAAAAATTTCAAATTTTTTTTGTGTT
* *
23384 GGTCATGCAATGGTCGACACCCCTTGGTCTCGGATAAAAAAATTTCAAATATTTTTTTGGT
65 GGTCATGCAATGGTCGACACCCCTTGTTCTCGGATAAAAAAATTTCAAATTTTTTTTTGGT
* *
23445 GTTGGTCATGCAATGGTCGACACCCCTTTTT-TCGGAT-AAAAATTTCAAATTTTTTTTGTGTTG
1 GTTGGTCATGCAATGGCCGACACCCCTTTTTCTCGAATAAAAAATTTCAAATTTTTTTTGTGTTG
* * *
23508 GTTATGCAATGGCCGACACCCTCTT-TTCTCAGATAAAAAAATTTCAAATTTTTTTTTGGT
66 GTCATGCAATGGTCGACACCC-CTTGTTCTCGGATAAAAAAATTTCAAATTTTTTTTTGGT
*
23568 GTTGGTCATGCAATGGCCGACACCCTTTTTTCTCGAATAAAAAATTTTCAAATTTTTTTTGTGTT
1 GTTGGTCATGCAATGGCCGACACCCCTTTTTCTCGAATAAAAAA-TTTCAAATTTTTTTTGTGTT
* * * * *
23633 GG-CTATGCAATGGTCGACACCCCCTTGTTTTTGAATAAAAAAAATTC-AATTTTTTTTTTGT
65 GGTC-ATGCAATGGTCGACA-CCCCTTGTTCTCGGATAAAAAAATTTCAAATTTTTTTTTGGT
* * * * *
23694 GTTGGCCATGCAATGACCGACACCCCCTGTTCTCGGATAAAAAATTT-AAATTT
1 GTTGGTCATGCAATGGCCGACACCCCTTTTTCTCGAATAAAAAATTTCAAATTT
23747 ATGATTTTTT
Statistics
Matches: 264, Mismatches: 30, Indels: 17
0.85 0.10 0.05
Matches are distributed among these distances:
122 4 0.02
123 103 0.39
124 20 0.08
125 29 0.11
126 90 0.34
127 18 0.07
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Consensus pattern (125 bp):
GTTGGTCATGCAATGGCCGACACCCCTTTTTCTCGAATAAAAAATTTCAAATTTTTTTTGTGTTG
GTCATGCAATGGTCGACACCCCTTGTTCTCGGATAAAAAAATTTCAAATTTTTTTTTGGT
Found at i:27525 original size:3 final size:3
Alignment explanation
Indices: 27517--27551 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
27507 CATTGTAACT
27517 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC ATTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC T
27552 GAGTGAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.03, C:0.31, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:28114 original size:64 final size:64
Alignment explanation
Indices: 28035--28158 Score: 239
Period size: 64 Copynumber: 1.9 Consensus size: 64
28025 ATGCACATGG
28035 GAACTGATTAAGGAGTTCAAAACCATTTCCTATGTTTGCAAGGCTTTACCAATGGAGTATATGA
1 GAACTGATTAAGGAGTTCAAAACCATTTCCTATGTTTGCAAGGCTTTACCAATGGAGTATATGA
*
28099 GAACTGATTAAGGAGTTCAAAACCATTTCCTATGTTTGCAAGGCTTTGCCAATGGAGTAT
1 GAACTGATTAAGGAGTTCAAAACCATTTCCTATGTTTGCAAGGCTTTACCAATGGAGTAT
28159 TCCACTATGA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 59 1.00
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.31
Consensus pattern (64 bp):
GAACTGATTAAGGAGTTCAAAACCATTTCCTATGTTTGCAAGGCTTTACCAATGGAGTATATGA
Found at i:46357 original size:31 final size:31
Alignment explanation
Indices: 46319--46383 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
46309 AGTAAATCTC
46319 AAAAAAAAAAACCTCCACAATGAATCTAAAA
1 AAAAAAAAAAACCTCCACAATGAATCTAAAA
* * * *
46350 AAAAAAAAAAAGCTCCGCTATGAATCTACAA
1 AAAAAAAAAAACCTCCACAATGAATCTAAAA
46381 AAA
1 AAA
46384 TCAATATTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.62, C:0.18, G:0.06, T:0.14
Consensus pattern (31 bp):
AAAAAAAAAAACCTCCACAATGAATCTAAAA
Found at i:46806 original size:15 final size:18
Alignment explanation
Indices: 46772--46808 Score: 53
Period size: 15 Copynumber: 2.2 Consensus size: 18
46762 ATATATATAC
46772 TAAAGTATTATAAACTAA
1 TAAAGTATTATAAACTAA
46790 TAAA-TATT-TAAAC-AA
1 TAAAGTATTATAAACTAA
46805 TAAA
1 TAAA
46809 ACGTATCATG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.32
16 5 0.26
17 4 0.21
18 4 0.21
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.32
Consensus pattern (18 bp):
TAAAGTATTATAAACTAA
Found at i:47980 original size:19 final size:19
Alignment explanation
Indices: 47956--47992 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
47946 AAAGAAATCC
47956 AGAAATGTTGAATGAATTT
1 AGAAATGTTGAATGAATTT
47975 AGAAATGTTGAATGAATT
1 AGAAATGTTGAATGAATT
47993 CAAAAAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (19 bp):
AGAAATGTTGAATGAATTT
Found at i:48201 original size:23 final size:25
Alignment explanation
Indices: 48164--48228 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 25
48154 TGAAAGAATG
*
48164 AAGAAGAAAGGAATAATG-AAAAAAA
1 AAGAA-AAAGAAATAATGAAAAAAAA
48189 AA-AAAAAGAAATAA-GAAAAAAAA
1 AAGAAAAAGAAATAATGAAAAAAAA
48212 AAGAAAAAGAAAATAAT
1 AAGAAAAAG-AAATAAT
48229 TTTTAAAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
22 1 0.03
23 18 0.51
24 8 0.23
25 8 0.23
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (25 bp):
AAGAAAAAGAAATAATGAAAAAAAA
Found at i:48209 original size:18 final size:17
Alignment explanation
Indices: 48182--48224 Score: 70
Period size: 18 Copynumber: 2.5 Consensus size: 17
48172 AGGAATAATG
48182 AAAA-AAAAAAAAAAGA
1 AAAAGAAAAAAAAAAGA
48198 AATAAGAAAAAAAAAAGA
1 AA-AAGAAAAAAAAAAGA
48216 AAAAGAAAA
1 AAAAGAAAA
48225 TAATTTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.08
17 9 0.36
18 14 0.56
ACGTcount: A:0.88, C:0.00, G:0.09, T:0.02
Consensus pattern (17 bp):
AAAAGAAAAAAAAAAGA
Found at i:50619 original size:14 final size:15
Alignment explanation
Indices: 50600--50628 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
50590 AATTTCAAAG
50600 TTAAAAATTA-AAAA
1 TTAAAAATTATAAAA
50614 TTAAAAATTATAAAA
1 TTAAAAATTATAAAA
50629 ACAAAACAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
TTAAAAATTATAAAA
Found at i:59955 original size:41 final size:41
Alignment explanation
Indices: 59898--59978 Score: 162
Period size: 41 Copynumber: 2.0 Consensus size: 41
59888 GTCACTAGGA
59898 ACAAAAAAGAATGAATTGTCAATTCACTACTTTTAGACAAC
1 ACAAAAAAGAATGAATTGTCAATTCACTACTTTTAGACAAC
59939 ACAAAAAAGAATGAATTGTCAATTCACTACTTTTAGACAA
1 ACAAAAAAGAATGAATTGTCAATTCACTACTTTTAGACAA
59979 TATAATCGAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.47, C:0.16, G:0.10, T:0.27
Consensus pattern (41 bp):
ACAAAAAAGAATGAATTGTCAATTCACTACTTTTAGACAAC
Found at i:64609 original size:11 final size:10
Alignment explanation
Indices: 64590--64623 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
64580 TTTGAGTCAA
64590 TTTGAATTTT
1 TTTGAATTTT
64600 TTTCGAATTTT
1 TTT-GAATTTT
*
64611 TTTAAATTTT
1 TTTGAATTTT
64621 TTT
1 TTT
64624 TTTTCAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.21, C:0.03, G:0.06, T:0.71
Consensus pattern (10 bp):
TTTGAATTTT
Found at i:64627 original size:15 final size:15
Alignment explanation
Indices: 64607--64635 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
64597 TTTTTTCGAA
64607 TTTTTTT-AAATTTT
1 TTTTTTTCAAATTTT
64621 TTTTTTTCAAATTTT
1 TTTTTTTCAAATTTT
64636 AAGTTCGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTTTCAAATTTT
Found at i:64944 original size:30 final size:31
Alignment explanation
Indices: 64910--64968 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
64900 AAACTCTTTA
64910 TTTTCACTCAAAACTTTTACTC-CCTCTCAC
1 TTTTCACTCAAAACTTTTACTCTCCTCTCAC
* *
64940 TTTTCTCTTAAAACTTTTACTCTCCTCTC
1 TTTTCACTCAAAACTTTTACTCTCCTCTC
64969 CTCCCCTCCC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 20 0.77
31 6 0.23
ACGTcount: A:0.20, C:0.34, G:0.00, T:0.46
Consensus pattern (31 bp):
TTTTCACTCAAAACTTTTACTCTCCTCTCAC
Found at i:65399 original size:18 final size:17
Alignment explanation
Indices: 65361--65399 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
65351 TAAAAAAATT
* *
65361 ATATTTTTTCATTTAAT
1 ATATTTTTTAATTTAAA
65378 ATATTTTTTAATTTCAAA
1 ATATTTTTTAATTT-AAA
65396 ATAT
1 ATAT
65400 ATAACAACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (17 bp):
ATATTTTTTAATTTAAA
Found at i:67660 original size:56 final size:56
Alignment explanation
Indices: 67593--67700 Score: 198
Period size: 56 Copynumber: 1.9 Consensus size: 56
67583 ACACATACCC
* *
67593 TACTTTAAGATTAACACGTGTATATTCGAAGCAGGTTTGCATACACGGTATTCGCA
1 TACTTTAAGATTAACACGTGTATATTCGAAGCAAGTTTGCATACACAGTATTCGCA
67649 TACTTTAAGATTAACACGTGTATATTCGAAGCAAGTTTGCATACACAGTATT
1 TACTTTAAGATTAACACGTGTATATTCGAAGCAAGTTTGCATACACAGTATT
67701 TGCACCATAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 50 1.00
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (56 bp):
TACTTTAAGATTAACACGTGTATATTCGAAGCAAGTTTGCATACACAGTATTCGCA
Found at i:68753 original size:17 final size:17
Alignment explanation
Indices: 68731--68813 Score: 76
Period size: 17 Copynumber: 4.8 Consensus size: 17
68721 GGCTTTATTT
*
68731 ATTTTAAATTTATAATA
1 ATTTTAAATTTAAAATA
68748 ATTTTAAATTTGAAAATA
1 ATTTTAAATTT-AAAATA
* * * * *
68766 AATTTAAACTCACATTA
1 ATTTTAAATTTAAAATA
*
68783 AATTTAAATTTAAAATAA
1 ATTTTAAATTTAAAAT-A
*
68801 ATTTTAATTTTAA
1 ATTTTAAATTTAA
68814 TTTTAAAATA
Statistics
Matches: 52, Mismatches: 12, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
17 27 0.52
18 25 0.48
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (17 bp):
ATTTTAAATTTAAAATA
Found at i:68812 original size:24 final size:24
Alignment explanation
Indices: 68780--68825 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
68770 TAAACTCACA
68780 TTAAATTTAAATTTAAAATAAATT
1 TTAAATTTAAATTTAAAATAAATT
* *
68804 TTAATTTTAATTTTAAAATAAA
1 TTAAATTTAAATTTAAAATAAA
68826 CTTAATCTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TTAAATTTAAATTTAAAATAAATT
Found at i:68830 original size:23 final size:24
Alignment explanation
Indices: 68780--68837 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
68770 TAAACTCACA
* *
68780 TTAAATTTAAATTTAAAATAAATT
1 TTAATTTTAAATTTAAAATAAATC
*
68804 TTAATTTTAATTTTAAAATAAA-C
1 TTAATTTTAAATTTAAAATAAATC
*
68827 TTAATCTTAAA
1 TTAATTTTAAA
68838 ATAAATTTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 9 0.31
24 20 0.69
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (24 bp):
TTAATTTTAAATTTAAAATAAATC
Found at i:68836 original size:17 final size:17
Alignment explanation
Indices: 68810--68847 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
68800 AATTTTAATT
*
68810 TTAATTTTAAAATAAAC
1 TTAATCTTAAAATAAAC
*
68827 TTAATCTTAAAATAAAT
1 TTAATCTTAAAATAAAC
68844 TTAA
1 TTAA
68848 AATGAGTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (17 bp):
TTAATCTTAAAATAAAC
Found at i:71317 original size:3 final size:3
Alignment explanation
Indices: 71309--71360 Score: 86
Period size: 3 Copynumber: 17.3 Consensus size: 3
71299 CTATTTACAC
* *
71309 CAT CAT CAT CAC CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CGT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
71357 CAT C
1 CAT C
71361 GTAACTACAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:81855 original size:2 final size:2
Alignment explanation
Indices: 81848--81875 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
81838 AGAACACAAA
81848 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
81876 TTTTGAGTGA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:89517 original size:223 final size:223
Alignment explanation
Indices: 89129--89581 Score: 879
Period size: 223 Copynumber: 2.0 Consensus size: 223
89119 TCGACTCCCA
* *
89129 CTGTGGTCTGTTTGTTTTTACTTTAGTTGGGCGTGGCTCTCAGTCTTTTCGACGCTTCTTTTTGG
1 CTGTGGTCGGTTTGTTTTTACTTTAGTTGGGCGGGGCTCTCAGTCTTTTCGACGCTTCTTTTTGG
89194 GTTGAATAAATGTTGTGGAGAGAATTGGACTGACCCAATCAAGCGAAACTAAACACTTAATGCGA
66 GTTGAATAAATGTTGTGGAGAGAATTGGACTGACCCAATCAAGCGAAACTAAACACTTAATGCGA
*
89259 CCCAATCCCGAATGAATGTGATGACAATGGGATACTCGAAAGAAATATTAGAGGAAAAGCAATTA
131 CCCAACCCCGAATGAATGTGATGACAATGGGATACTCGAAAGAAATATTAGAGGAAAAGCAATTA
89324 TAAAGATATATTCTAAACCCATAATGAG
196 TAAAGATATATTCTAAACCCATAATGAG
89352 CTGTGGTCGGTTTGTTTTTACTTTAGTTGGGCGGGGCTCTCAGTCTTTTCGACGCTTCTTTTTGG
1 CTGTGGTCGGTTTGTTTTTACTTTAGTTGGGCGGGGCTCTCAGTCTTTTCGACGCTTCTTTTTGG
89417 GTTGAATAAATGTTGTGGAGAGAATTGGACTGACCCAATCAAGCGAAACTAAACACTTAATGCGA
66 GTTGAATAAATGTTGTGGAGAGAATTGGACTGACCCAATCAAGCGAAACTAAACACTTAATGCGA
89482 CCCAACCCCGAATGAATGTGATGACAATGGGATACTCGAAAGAAATATTAGAGGAAAAGCAATTA
131 CCCAACCCCGAATGAATGTGATGACAATGGGATACTCGAAAGAAATATTAGAGGAAAAGCAATTA
89547 TAAAGATATATTCTAAACCCATAATGAG
196 TAAAGATATATTCTAAACCCATAATGAG
89575 CTGTGGT
1 CTGTGGT
89582 ATAATTTTAA
Statistics
Matches: 227, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
223 227 1.00
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (223 bp):
CTGTGGTCGGTTTGTTTTTACTTTAGTTGGGCGGGGCTCTCAGTCTTTTCGACGCTTCTTTTTGG
GTTGAATAAATGTTGTGGAGAGAATTGGACTGACCCAATCAAGCGAAACTAAACACTTAATGCGA
CCCAACCCCGAATGAATGTGATGACAATGGGATACTCGAAAGAAATATTAGAGGAAAAGCAATTA
TAAAGATATATTCTAAACCCATAATGAG
Done.