Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013985.1 Kokia drynarioides strain JFW-HI SEQ_129016, 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: 121132
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 20 characters in sequence are not A, C, G, or T
Found at i:1686 original size:34 final size:35
Alignment explanation
Indices: 1647--1730 Score: 152
Period size: 34 Copynumber: 2.4 Consensus size: 35
1637 TTTCTATGTG
1647 AAATTGAAGAGAAAGAGAAGAAAC-AAAAGGGACC
1 AAATTGAAGAGAAAGAGAAGAAACAAAAAGGGACC
1681 AAATTGAAGAGAAAGAGAAGAAACAAAAAGGGACC
1 AAATTGAAGAGAAAGAGAAGAAACAAAAAGGGACC
*
1716 AAATTGAAGATAAAG
1 AAATTGAAGAGAAAG
1731 GAAAAGAATA
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
34 24 0.50
35 24 0.50
ACGTcount: A:0.60, C:0.07, G:0.25, T:0.08
Consensus pattern (35 bp):
AAATTGAAGAGAAAGAGAAGAAACAAAAAGGGACC
Found at i:2692 original size:24 final size:26
Alignment explanation
Indices: 2665--2713 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
2655 AGAGAAATGT
2665 AAATG-TGATATATGA-A-ATTATGAG
1 AAATGATGA-ATATGAGAGATTATGAG
2689 AAATGATGAATATGAGAGATTATGA
1 AAATGATGAATATGAGAGATTATGA
2714 CCATGTAGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 11 0.50
25 4 0.18
26 7 0.32
ACGTcount: A:0.47, C:0.00, G:0.22, T:0.31
Consensus pattern (26 bp):
AAATGATGAATATGAGAGATTATGAG
Found at i:2841 original size:47 final size:47
Alignment explanation
Indices: 2784--2899 Score: 214
Period size: 47 Copynumber: 2.5 Consensus size: 47
2774 CGCTTCTGTT
*
2784 CAGCACTGTGTGTGCTTCTGTTCAACACTGTGTGTGCTTCTGTTACC
1 CAGCACTGTGTGTGCTTCTGTTCAACACCGTGTGTGCTTCTGTTACC
*
2831 CAGCACTGTGTGTGCTTCTGTTCAGCACCGTGTGTGCTTCTGTTACC
1 CAGCACTGTGTGTGCTTCTGTTCAACACCGTGTGTGCTTCTGTTACC
2878 CAGCACTGTGTGTGCTTCTGTT
1 CAGCACTGTGTGTGCTTCTGTT
2900 TACCCAGCAC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 67 1.00
ACGTcount: A:0.11, C:0.26, G:0.25, T:0.38
Consensus pattern (47 bp):
CAGCACTGTGTGTGCTTCTGTTCAACACCGTGTGTGCTTCTGTTACC
Found at i:2843 original size:25 final size:25
Alignment explanation
Indices: 2784--2910 Score: 185
Period size: 22 Copynumber: 5.3 Consensus size: 25
2774 CGCTTCTGTT
2784 CAGCACTGTGTGTGCTTCTGTT---
1 CAGCACTGTGTGTGCTTCTGTTACC
*
2806 CAACACTGTGTGTGCTTCTGTTACC
1 CAGCACTGTGTGTGCTTCTGTTACC
2831 CAGCACTGTGTGTGCTTCTGTT---
1 CAGCACTGTGTGTGCTTCTGTTACC
*
2853 CAGCACCGTGTGTGCTTCTGTTACC
1 CAGCACTGTGTGTGCTTCTGTTACC
2878 CAGCACTGTGTGTGCTTCTGTTTACC
1 CAGCACTGTGTGTGCTTCTG-TTACC
2904 CAGCACT
1 CAGCACT
2911 TATGTACCTC
Statistics
Matches: 94, Mismatches: 4, Indels: 10
0.87 0.04 0.09
Matches are distributed among these distances:
22 42 0.45
25 40 0.43
26 12 0.13
ACGTcount: A:0.13, C:0.28, G:0.24, T:0.36
Consensus pattern (25 bp):
CAGCACTGTGTGTGCTTCTGTTACC
Found at i:2922 original size:25 final size:26
Alignment explanation
Indices: 2869--2924 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
2859 CGTGTGTGCT
* * *
2869 TCTG-TTACCCAGCACTGTGTGTGCT
1 TCTGTTTACCCAGCACTGTATGTACC
2894 TCTGTTTACCCAGCACT-TATGTACC
1 TCTGTTTACCCAGCACTGTATGTACC
2919 TCTGTT
1 TCTGTT
2925 AAGTACTTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 15 0.56
26 12 0.44
ACGTcount: A:0.14, C:0.29, G:0.18, T:0.39
Consensus pattern (26 bp):
TCTGTTTACCCAGCACTGTATGTACC
Found at i:3879 original size:16 final size:16
Alignment explanation
Indices: 3834--3881 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
3824 AAAAAATTCA
3834 ATAAA-TAAAAAATAT
1 ATAAATTAAAAAATAT
**
3849 ATAAATTATTAAATAT
1 ATAAATTAAAAAATAT
3865 -TAAATTAAAATAATAT
1 ATAAATTAAAA-AATAT
3881 A
1 A
3882 ACTATTTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
ATAAATTAAAAAATAT
Found at i:3975 original size:241 final size:240
Alignment explanation
Indices: 3544--4023 Score: 728
Period size: 241 Copynumber: 2.0 Consensus size: 240
3534 TATAATACTA
* * *
3544 CTTTAATGTAAATATTAAAATAATGTTAATATTGCTCTATAAAAAATTCAATAAATAAAAATATA
1 CTTTAATGTAAACATTAAAATAATGTTAAGATTACTCTATAAAAAATTCAATAAATAAAAATATA
*
3609 TAAATGATCAAATATTAAATTAAAATAATATAACTATTTTTAAAACGAGATCGAATTAATTTTTT
66 TAAATGATCAAATATTAAATTAAAATAATATAACTATTTTAAAAACGAGATCGAATTAATTTTTT
* * * * *
3674 ATAAATATAAGTGGATTTGGAGATAATTTTAGACTCATATTTTGGGTTGAGTCAAACTTGAGCAA
131 ATAAATATAAGTGGATTTGGAGATAATTTTAAACTCATATTTTGGATCGAGCCAAACTTGAACAA
3739 ACATAAAATATATTAATATAATACTTAGACCCAACTCATAAACAC
196 ACATAAAATATATTAATATAATACTTAGACCCAACTCATAAACAC
* *
3784 CTTTAATGTAAGCATTAAAATAATGTTAAGCTTACTCTATAAAAAATTCAATAAATAAAAAATAT
1 CTTTAATGTAAACATTAAAATAATGTTAAGATTACTCTATAAAAAATTCAATAAAT-AAAAATAT
* * * * * *
3849 ATAAATTATTAAATATTAAATTAAAATAATATAACTATTTTAAAAATGAGTTTGGATTAATTTTT
65 ATAAATGATCAAATATTAAATTAAAATAATATAACTATTTTAAAAACGAGATCGAATTAATTTTT
* * *
3914 TATAAATATGAGTGGGTTTGGATG-TAATTTTAAACTCATATTTTGGATCGAGCCGAACTTGAAC
130 TATAAATATAAGTGGATTTGGA-GATAATTTTAAACTCATATTTTGGATCGAGCCAAACTTGAAC
* * *
3978 AAATATAAAATATATTAATATAATACTTAGGCCCAACTCATGAACA
194 AAACATAAAATATATTAATATAATACTTAGACCCAACTCATAAACA
4024 TCTCTACAAT
Statistics
Matches: 215, Mismatches: 23, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
240 51 0.24
241 163 0.76
242 1 0.00
ACGTcount: A:0.45, C:0.09, G:0.10, T:0.36
Consensus pattern (240 bp):
CTTTAATGTAAACATTAAAATAATGTTAAGATTACTCTATAAAAAATTCAATAAATAAAAATATA
TAAATGATCAAATATTAAATTAAAATAATATAACTATTTTAAAAACGAGATCGAATTAATTTTTT
ATAAATATAAGTGGATTTGGAGATAATTTTAAACTCATATTTTGGATCGAGCCAAACTTGAACAA
ACATAAAATATATTAATATAATACTTAGACCCAACTCATAAACAC
Found at i:5178 original size:22 final size:21
Alignment explanation
Indices: 5148--5188 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
5138 TCAGGATGTA
*
5148 ATATCACTCTTATACATTAACC
1 ATATCACTCTCAT-CATTAACC
*
5170 ATATTACTCTCATCATTAA
1 ATATCACTCTCATCATTAA
5189 TTTTTTTCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.37, C:0.24, G:0.00, T:0.39
Consensus pattern (21 bp):
ATATCACTCTCATCATTAACC
Found at i:10536 original size:3 final size:3
Alignment explanation
Indices: 10530--10554 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
10520 AGGTACCCTT
10530 TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG T
10555 ATTTCCTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:16197 original size:11 final size:11
Alignment explanation
Indices: 16181--16206 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
16171 AAATTACCAC
16181 AAAAAAAAGAA
1 AAAAAAAAGAA
16192 AAAAAAAAGAA
1 AAAAAAAAGAA
16203 AAAA
1 AAAA
16207 GAAACAGAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:20864 original size:2 final size:2
Alignment explanation
Indices: 20853--20885 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
20843 GTCTATAATC
20853 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20886 GCTCTTGGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:23207 original size:6 final size:6
Alignment explanation
Indices: 23196--23220 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
23186 AATATCATTA
23196 ATATTC ATATTC ATATTC ATATTC A
1 ATATTC ATATTC ATATTC ATATTC A
23221 ATTTAACACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (6 bp):
ATATTC
Found at i:36599 original size:28 final size:27
Alignment explanation
Indices: 36554--36608 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
36544 AATTTTTAAT
* * *
36554 TAATAATTTTTTATTTATATAAATAAAA
1 TAATAATTATGTAATTATAT-AATAAAA
*
36582 TAATAATTATGTAATTATGTAATAAAA
1 TAATAATTATGTAATTATATAATAAAA
36609 AAACATTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (27 bp):
TAATAATTATGTAATTATATAATAAAA
Found at i:37797 original size:11 final size:11
Alignment explanation
Indices: 37770--37812 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
37760 ATGGTAGCAA
*
37770 AACAACAATA-
1 AACAACAACAT
37780 AAGCAACAACAT
1 AA-CAACAACAT
37792 AACAACAACAT
1 AACAACAACAT
37803 AACAACAACA
1 AACAACAACA
37813 AAATAGCAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 2 0.07
11 26 0.87
12 2 0.07
ACGTcount: A:0.65, C:0.26, G:0.02, T:0.07
Consensus pattern (11 bp):
AACAACAACAT
Found at i:38214 original size:2 final size:2
Alignment explanation
Indices: 38207--38233 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
38197 GATAAAAATA
38207 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
38234 AGAGTTATCA
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:38404 original size:8 final size:8
Alignment explanation
Indices: 38391--38426 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
38381 TTTATTAATT
38391 AAAAAATA
1 AAAAAATA
*
38399 AAAAAATT
1 AAAAAATA
*
38407 GAAAAATA
1 AAAAAATA
38415 AAAAAATA
1 AAAAAATA
38423 AAAA
1 AAAA
38427 TGCTTGAGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (8 bp):
AAAAAATA
Found at i:38411 original size:16 final size:16
Alignment explanation
Indices: 38387--38426 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
38377 TATATTTATT
38387 AATTAAAAAATAAAAA
1 AATTAAAAAATAAAAA
*
38403 AATTGAAAAATAAAAA
1 AATTAAAAAATAAAAA
38419 AA-TAAAAA
1 AATTAAAAA
38427 TGCTTGAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 5 0.23
16 17 0.77
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (16 bp):
AATTAAAAAATAAAAA
Found at i:39164 original size:29 final size:27
Alignment explanation
Indices: 39108--39169 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
39098 AAAAGACTTA
*
39108 TATTATATAAGTAAATCTTAATTTAAT
1 TATTATATAAGTAAATATTAATTTAAT
* * *
39135 TTTTATATAATTACAATATTAGTTTAAAT
1 TATTATATAAGTA-AATATTAATTT-AAT
39164 TATTAT
1 TATTAT
39170 TGTTTTGATA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
27 11 0.39
28 9 0.32
29 8 0.29
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (27 bp):
TATTATATAAGTAAATATTAATTTAAT
Found at i:39395 original size:15 final size:15
Alignment explanation
Indices: 39377--39406 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39367 ATAATAAATA
*
39377 ATAAATAATTATATT
1 ATAAATAATCATATT
39392 ATAAATAATCATATT
1 ATAAATAATCATATT
39407 TGTGATAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (15 bp):
ATAAATAATCATATT
Found at i:44745 original size:28 final size:30
Alignment explanation
Indices: 44694--44752 Score: 86
Period size: 28 Copynumber: 2.0 Consensus size: 30
44684 GTATTTGATA
44694 AAAAAATATAAATTTAAAGATTAAAAGAAAT
1 AAAAAATATAAA-TTAAAGATTAAAAGAAAT
*
44725 AAAAAAT-TAAA-TAAAGATTAAAATAAAT
1 AAAAAATATAAATTAAAGATTAAAAGAAAT
44753 TTTTTTTTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 16 0.59
30 4 0.15
31 7 0.26
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.25
Consensus pattern (30 bp):
AAAAAATATAAATTAAAGATTAAAAGAAAT
Found at i:54739 original size:29 final size:30
Alignment explanation
Indices: 54697--54763 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 30
54687 GCTCTTTCAT
* *
54697 GGACACATGGCACATGCATTAA-TTCCTAG
1 GGACATATGGCACATGCATTAATTTCCAAG
* * *
54726 GGACATATTGCACATGCCTTAATTTCGAAG
1 GGACATATGGCACATGCATTAATTTCCAAG
54756 GGACATAT
1 GGACATAT
54764 CTATCCATCA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 19 0.59
30 13 0.41
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (30 bp):
GGACATATGGCACATGCATTAATTTCCAAG
Found at i:60765 original size:6 final size:6
Alignment explanation
Indices: 60754--60784 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
60744 AAATAAAAAA
*
60754 GAAGAT GAAGAT GAAGAT GAAGAT AAAGAT G
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT G
60785 GGAATAAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.32, T:0.16
Consensus pattern (6 bp):
GAAGAT
Found at i:63028 original size:30 final size:31
Alignment explanation
Indices: 62994--63053 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
62984 AAACATATAC
*
62994 ATGTGGTAAAG-GAGTAATTTTTGAACAAGT
1 ATGTGGCAAAGAGAGTAATTTTTGAACAAGT
* *
63024 ATGTGGCAAAGAGAGTATTTTTTTAACAAG
1 ATGTGGCAAAGAGAGTAATTTTTGAACAAG
63054 AACGGTCAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 10 0.38
31 16 0.62
ACGTcount: A:0.37, C:0.05, G:0.25, T:0.33
Consensus pattern (31 bp):
ATGTGGCAAAGAGAGTAATTTTTGAACAAGT
Found at i:69938 original size:2 final size:2
Alignment explanation
Indices: 69931--69966 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
69921 CACGTGTATC
69931 AT AT 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 AT AT
69967 TTTGCGGTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:70628 original size:17 final size:17
Alignment explanation
Indices: 70590--70628 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
70580 AAAATATGTA
*
70590 TTAAAATATAACAAAAT
1 TTAATATATAACAAAAT
*
70607 TTAATATATAACGAAAT
1 TTAATATATAACAAAAT
70624 TTAAT
1 TTAAT
70629 TTTAAATCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (17 bp):
TTAATATATAACAAAAT
Found at i:72085 original size:13 final size:13
Alignment explanation
Indices: 72054--72106 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 13
72044 CTTAAACTAA
* *
72054 ACTTTTCAAGAGT
1 ACTTTTCAAAAGC
* *
72067 AATTTTCAAAATC
1 ACTTTTCAAAAGC
*
72080 ACTTTTCCAAAGC
1 ACTTTTCAAAAGC
*
72093 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
72106 A
1 A
72107 ATACTAAACT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.32
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:76651 original size:10 final size:10
Alignment explanation
Indices: 76623--76694 Score: 58
Period size: 10 Copynumber: 7.1 Consensus size: 10
76613 ATATAAATTT
76623 ATTA-AAAAA
1 ATTATAAAAA
*
76632 ATTTTGAAAAA
1 ATTAT-AAAAA
76643 ATTATAAAAA
1 ATTATAAAAA
**
76653 ATTATTGAAA
1 ATTATAAAAA
76663 ATTAT-AAAA
1 ATTATAAAAA
* *
76672 ATCCAAAAGAAA
1 AT-TATAA-AAA
76684 ATTATAAAAA
1 ATTATAAAAA
76694 A
1 A
76695 ATAGAACCCA
Statistics
Matches: 49, Mismatches: 9, Indels: 9
0.73 0.13 0.13
Matches are distributed among these distances:
9 8 0.16
10 23 0.47
11 13 0.27
12 5 0.10
ACGTcount: A:0.65, C:0.03, G:0.04, T:0.28
Consensus pattern (10 bp):
ATTATAAAAA
Found at i:81285 original size:44 final size:44
Alignment explanation
Indices: 81222--81309 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
81212 ACTGACAAGG
81222 ACTTTGGAAATGATTTTGTATGCCATGTTAGAAAGGCTAATACA
1 ACTTTGGAAATGATTTTGTATGCCATGTTAGAAAGGCTAATACA
81266 ACTTTGGAAATGATTTTGTATGCCATGTTAGAAAGGCTAATACA
1 ACTTTGGAAATGATTTTGTATGCCATGTTAGAAAGGCTAATACA
81310 CATAATCAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.34
Consensus pattern (44 bp):
ACTTTGGAAATGATTTTGTATGCCATGTTAGAAAGGCTAATACA
Found at i:88374 original size:23 final size:23
Alignment explanation
Indices: 88344--88392 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
88334 CTGACTTCAG
88344 AGAAATGGTAACAAAAATAGATT
1 AGAAATGGTAACAAAAATAGATT
88367 AGAAATGGTAACAAAAATAGATT
1 AGAAATGGTAACAAAAATAGATT
88390 AGA
1 AGA
88393 CTAAAAGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.57, C:0.04, G:0.18, T:0.20
Consensus pattern (23 bp):
AGAAATGGTAACAAAAATAGATT
Found at i:95770 original size:2 final size:2
Alignment explanation
Indices: 95763--95789 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
95753 CTGTCTTTTC
95763 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
95790 TCAAATGGAT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:101320 original size:2 final size:2
Alignment explanation
Indices: 101313--101339 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
101303 AAGTTAATTC
101313 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
101340 ATTTCACATT
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:105478 original size:21 final size:20
Alignment explanation
Indices: 105440--105478 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
105430 AAATAAAAAT
105440 AAAGTAAAGACTCAACAACG
1 AAAGTAAAGACTCAACAACG
105460 AAAG-AAAGAGCTCTAACAA
1 AAAGTAAAGA-CTC-AACAA
105479 TCTTTCAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.29
20 7 0.41
21 5 0.29
ACGTcount: A:0.56, C:0.18, G:0.15, T:0.10
Consensus pattern (20 bp):
AAAGTAAAGACTCAACAACG
Found at i:109453 original size:17 final size:18
Alignment explanation
Indices: 109415--109453 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
109405 CCAATTGCCG
*
109415 CAGTGAGGCGGCTAGCAAC
1 CAGTGAGGCAGCTA-CAAC
109434 CAGTGAGGCAGCTA-AAC
1 CAGTGAGGCAGCTACAAC
109451 CAG
1 CAG
109454 CAACGTACAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
19 13 0.68
ACGTcount: A:0.31, C:0.26, G:0.33, T:0.10
Consensus pattern (18 bp):
CAGTGAGGCAGCTACAAC
Found at i:113085 original size:28 final size:28
Alignment explanation
Indices: 113053--113117 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
113043 GTTCATTTCA
*
113053 AATTATTTAAGTGATT-ATTTTTTAATAG
1 AATTATTTAAGTAATTAATTTTTT-ATAG
* * *
113081 AATTATTTACGTAATTAATTTTTTTTTG
1 AATTATTTAAGTAATTAATTTTTTATAG
113109 AATTATTTA
1 AATTATTTA
113118 GTTAAAATAG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 25 0.78
29 7 0.22
ACGTcount: A:0.34, C:0.02, G:0.08, T:0.57
Consensus pattern (28 bp):
AATTATTTAAGTAATTAATTTTTTATAG
Found at i:114419 original size:14 final size:13
Alignment explanation
Indices: 114400--114446 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
114390 GATTATTTTA
114400 TTTTATTTTAATAT
1 TTTTA-TTTAATAT
114414 TTTTATTTAATAT
1 TTTTATTTAATAT
* *
114427 TATT-TTTAAAAT
1 TTTTATTTAATAT
114439 ATTTTATT
1 -TTTTATT
114447 AGGAGTGTCC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
12 7 0.25
13 14 0.50
14 7 0.25
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTTATTTAATAT
Done.