Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011217.1 Kokia drynarioides strain JFW-HI SEQ_126195, 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: 128568
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:617 original size:30 final size:30
Alignment explanation
Indices: 583--749 Score: 114
Period size: 29 Copynumber: 5.7 Consensus size: 30
573 TATTTTATTT
* *
583 AAAAATTACATTTTGATCCTTAAACTTCTC
1 AAAAATTACATTTTGACCCTCAAACTTCTC
*
613 AAAAATTACATTTTGACCCTCAAACTTTTTC
1 AAAAATTACATTTTGACCCTCAAAC-TTCTC
* * * * *
644 -GAAATCATATTTTAACCCT-AAACTTTTC
1 AAAAATTACATTTTGACCCTCAAACTTCTC
* * * * *
672 CAAAATTACATTTTTA-CATCTAACATC-C
1 AAAAATTACATTTTGACCCTCAAACTTCTC
* * *
700 AAAAATTACCATTTTGAACC-CGAACATCT-
1 AAAAATTA-CATTTTGACCCTCAAACTTCTC
729 AAAAATTACCATTTT-ACCCTC
1 AAAAATTA-CATTTTGACCCTC
750 GAGCATAAAA
Statistics
Matches: 110, Mismatches: 20, Indels: 15
0.76 0.14 0.10
Matches are distributed among these distances:
28 18 0.16
29 49 0.45
30 39 0.35
31 4 0.04
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.36
Consensus pattern (30 bp):
AAAAATTACATTTTGACCCTCAAACTTCTC
Found at i:677 original size:29 final size:29
Alignment explanation
Indices: 584--685 Score: 87
Period size: 30 Copynumber: 3.4 Consensus size: 29
574 ATTTTATTTA
* * * * *
584 AAAATTACATTTTGATCCTTAAACTTCTCA
1 AAAATCACATTTT-AACCCTAAACTTTTCC
* * *
614 AAAATTACATTTTGACCCTCAAACTTTTTC
1 AAAATCACATTTTAACCCT-AAACTTTTCC
* *
644 GAAATCATATTTTAACCCTAAACTTTTCC
1 AAAATCACATTTTAACCCTAAACTTTTCC
*
673 AAAATTACATTTT
1 AAAATCACATTTT
686 TACATCTAAC
Statistics
Matches: 57, Mismatches: 14, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
29 22 0.39
30 35 0.61
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.40
Consensus pattern (29 bp):
AAAATCACATTTTAACCCTAAACTTTTCC
Found at i:712 original size:29 final size:29
Alignment explanation
Indices: 673--856 Score: 135
Period size: 29 Copynumber: 6.3 Consensus size: 29
663 AAACTTTTCC
*
673 AAAATTA-CATTTTTACATCTAACATCCA
1 AAAATTACCATTTTTACATCGAACATCCA
* * *
701 AAAATTACCATTTTGA-ACCCGAACATCTA
1 AAAATTACCATTTTTACA-TCGAACATCCA
* * **
730 AAAATTACCA-TTTTACCCTCGAGCATAAA
1 AAAATTACCATTTTTA-CATCGAACATCCA
* *
759 AAAATTATCATTTTGT-C-TCAGAGCATCCA
1 AAAATTACCATTTT-TACATC-GAACATCCA
* * **
788 AAAATTACTATTTTGACCCCGAACATCCA
1 AAAATTACCATTTTTACATCGAACATCCA
** *
817 AAAATTACCATTTTGCCCATTGAACATCCA
1 AAAATTACCATTTT-TACATCGAACATCCA
847 AAAATTACCA
1 AAAATTACCA
857 GTTTACCCCG
Statistics
Matches: 122, Mismatches: 24, Indels: 18
0.74 0.15 0.11
Matches are distributed among these distances:
28 14 0.11
29 83 0.68
30 24 0.20
31 1 0.01
ACGTcount: A:0.40, C:0.24, G:0.06, T:0.30
Consensus pattern (29 bp):
AAAATTACCATTTTTACATCGAACATCCA
Found at i:874 original size:58 final size:57
Alignment explanation
Indices: 695--881 Score: 216
Period size: 58 Copynumber: 3.2 Consensus size: 57
685 TTACATCTAA
*
695 CATCCAAAAATTACCATTTTGAACCC-GAACATCTAAAAATTACCATTTTACCCTCGAG
1 CATCCAAAAATTACCATTTTG-ACCCAGAACATCCAAAAATTACCATTTTACCC-CGAG
** * * * * * *
753 CATAAAAAAATTATCATTTTGTCTCAGAGCATCCAAAAATTACTATTTTGACCCCGAA
1 CATCCAAAAATTACCATTTTGACCCAGAACATCCAAAAATTACCATTTT-ACCCCGAG
*
811 CATCCAAAAATTACCATTTTG-CCCATTGAACATCCAAAAATTACCAGTTTACCCCGAG
1 CATCCAAAAATTACCATTTTGACCCA--GAACATCCAAAAATTACCATTTTACCCCGAG
*
869 TATCCAAAAATTA
1 CATCCAAAAATTA
882 TAGTTTTTCC
Statistics
Matches: 107, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
57 5 0.05
58 78 0.73
59 24 0.22
ACGTcount: A:0.39, C:0.25, G:0.07, T:0.28
Consensus pattern (57 bp):
CATCCAAAAATTACCATTTTGACCCAGAACATCCAAAAATTACCATTTTACCCCGAG
Found at i:874 original size:87 final size:87
Alignment explanation
Indices: 695--881 Score: 232
Period size: 87 Copynumber: 2.1 Consensus size: 87
685 TTACATCTAA
* *
695 CATCCAAAAATTACCATTTTGAACCCGAACATCTAAAAATTACCATTTTACCCTCGAGCATAAAA
1 CATCCAAAAATTACCATTTTGAACCCGAACATCCAAAAATTACCATTTTACCCTCGAACATAAAA
* * * *
760 AAATTATCATTTTGTCTCAGAG
66 AAATTACCAGTTTGACCCAGAG
* * * * **
782 CATCCAAAAATTACTATTTTGACCCCGAACATCCAAAAATTACCATTTTGCCCATTGAACATCCA
1 CATCCAAAAATTACCATTTTGAACCCGAACATCCAAAAATTACCATTTTACCC-TCGAACATAAA
*
847 AAAATTACCAGTTT-ACCCCGAG
65 AAAATTACCAGTTTGACCCAGAG
*
869 TATCCAAAAATTA
1 CATCCAAAAATTA
882 TAGTTTTTCC
Statistics
Matches: 85, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
87 66 0.78
88 19 0.22
ACGTcount: A:0.39, C:0.25, G:0.07, T:0.28
Consensus pattern (87 bp):
CATCCAAAAATTACCATTTTGAACCCGAACATCCAAAAATTACCATTTTACCCTCGAACATAAAA
AAATTACCAGTTTGACCCAGAG
Found at i:1058 original size:29 final size:29
Alignment explanation
Indices: 979--1044 Score: 132
Period size: 29 Copynumber: 2.3 Consensus size: 29
969 TTGATCCCCA
979 AATTCTTCGAAAACTGCATTTTCATCCCG
1 AATTCTTCGAAAACTGCATTTTCATCCCG
1008 AATTCTTCGAAAACTGCATTTTCATCCCG
1 AATTCTTCGAAAACTGCATTTTCATCCCG
1037 AATTCTTC
1 AATTCTTC
1045 AAAGCTCTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.27, C:0.27, G:0.09, T:0.36
Consensus pattern (29 bp):
AATTCTTCGAAAACTGCATTTTCATCCCG
Found at i:7387 original size:6 final size:6
Alignment explanation
Indices: 7362--7400 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
7352 ACAATTCATA
* * *
7362 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
7401 ATTTTGATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (6 bp):
TCACTT
Found at i:21183 original size:14 final size:14
Alignment explanation
Indices: 21147--21202 Score: 50
Period size: 13 Copynumber: 4.3 Consensus size: 14
21137 TTATGTTATA
21147 AAATAATATTATATT
1 AAATAATA-TATATT
* *
21162 AACT-ATATATGTT
1 AAATAATATATATT
21175 AAATAATATATA-T
1 AAATAATATATATT
21188 --AT-ATATATATT
1 AAATAATATATATT
21199 AAAT
1 AAAT
21203 CACTAATCCA
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
10 7 0.21
11 3 0.09
13 11 0.33
14 9 0.27
15 3 0.09
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (14 bp):
AAATAATATATATT
Found at i:22771 original size:20 final size:20
Alignment explanation
Indices: 22739--22782 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
22729 TAATATGTTG
*
22739 TTTTTTTTAGTTTAATTTGA
1 TTTTTTTTAGTTTAATTTAA
*
22759 TTTTTCTTT-GTTTTATTTAA
1 TTTTT-TTTAGTTTAATTTAA
22779 TTTT
1 TTTT
22783 CACATTATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.16, C:0.02, G:0.07, T:0.75
Consensus pattern (20 bp):
TTTTTTTTAGTTTAATTTAA
Found at i:31208 original size:19 final size:18
Alignment explanation
Indices: 31173--31211 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
31163 TTTAGCCCCT
*
31173 ATTTTTTTGTCACTTTGA
1 ATTTTTTTATCACTTTGA
*
31191 ATTTTTTTAATCATTTTGA
1 ATTTTTTT-ATCACTTTGA
31210 AT
1 AT
31212 CTCAACCATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.62
Consensus pattern (18 bp):
ATTTTTTTATCACTTTGA
Found at i:34214 original size:27 final size:23
Alignment explanation
Indices: 34151--34201 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
34141 AATTGAACAT
*
34151 AAATT-TTAAAAGTAAAAAAAAA
1 AAATTCTTAAAAATAAAAAAAAA
34173 AAATTCTTAAAAATAAAAATAAAA
1 AAATTCTTAAAAATAAAAA-AAAA
34197 AAATT
1 AAATT
34202 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 5 0.19
23 12 0.46
24 9 0.35
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (23 bp):
AAATTCTTAAAAATAAAAAAAAA
Found at i:47000 original size:6 final size:6
Alignment explanation
Indices: 46991--47060 Score: 50
Period size: 6 Copynumber: 11.3 Consensus size: 6
46981 AAATAATCCT
* * * *
46991 AAATCG AAATCAA AAATCA GAATCC AAATCA AAATCGA AAATCA CAATCA
1 AAATCA AAATC-A AAATCA AAATCA AAATCA AAATC-A AAATCA AAATCA
* * * *
47041 ATATCG ACATCA AATTCA AA
1 AAATCA AAATCA AAATCA AA
47061 TAAACACAAA
Statistics
Matches: 49, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
6 38 0.78
7 11 0.22
ACGTcount: A:0.56, C:0.20, G:0.06, T:0.19
Consensus pattern (6 bp):
AAATCA
Found at i:47020 original size:25 final size:25
Alignment explanation
Indices: 46985--47054 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 25
46975 AAATCGAAAT
*
46985 AATCCTAAATCGAAATCAAAAATCAG
1 AATCC-AAATCGAAATCAAAAATCAC
* *
47011 AATCCAAATCAAAATCGAAAATCAC
1 AATCCAAATCGAAATCAAAAATCAC
*
47036 AAT-CAATATCGACATCAAA
1 AATCCAA-ATCGAAATCAAA
47055 TTCAAATAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
24 3 0.08
25 29 0.78
26 5 0.14
ACGTcount: A:0.54, C:0.21, G:0.06, T:0.19
Consensus pattern (25 bp):
AATCCAAATCGAAATCAAAAATCAC
Found at i:47033 original size:19 final size:19
Alignment explanation
Indices: 46991--47047 Score: 55
Period size: 19 Copynumber: 3.0 Consensus size: 19
46981 AAATAATCCT
*
46991 AAATCGAAATCAAAAATC-A
1 AAATCCAAATC-AAAATCGA
*
47010 GAATCCAAATCAAAATCGA
1 AAATCCAAATCAAAATCGA
*
47029 AAAT-CACAATCAATATCGA
1 AAATCCA-AATCAAAATCGA
47048 CATCAAATTC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 8 0.25
19 24 0.75
ACGTcount: A:0.56, C:0.19, G:0.07, T:0.18
Consensus pattern (19 bp):
AAATCCAAATCAAAATCGA
Found at i:47473 original size:46 final size:47
Alignment explanation
Indices: 47380--47502 Score: 142
Period size: 47 Copynumber: 2.6 Consensus size: 47
47370 CATGTCGATA
* * * *
47380 TTGATTGTGATTTTTAATTTAAGGTTTATTCGATTTTGATTTGGATT
1 TTGATTGTTATTTTTGATTTAGGGTTTATTCGATTTCGATTTGGATT
* *
47427 TTTATTTTTATTTTTGATTTAGGG-TTATTTCGATTTCGA-TTGGATT
1 TTGATTGTTATTTTTGATTTAGGGTTTA-TTCGATTTCGATTTGGATT
47473 TTGATTGTTATTGTTTGGGATTTAGGGTTT
1 TTGATTGTTATT-TTT--GATTTAGGGTTT
47503 TTAAAATTTT
Statistics
Matches: 63, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
46 20 0.32
47 32 0.51
49 9 0.14
50 2 0.03
ACGTcount: A:0.18, C:0.02, G:0.21, T:0.59
Consensus pattern (47 bp):
TTGATTGTTATTTTTGATTTAGGGTTTATTCGATTTCGATTTGGATT
Found at i:82769 original size:13 final size:13
Alignment explanation
Indices: 82751--82775 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
82741 AAATGTTGGG
82751 TTTTTATTTTTTA
1 TTTTTATTTTTTA
82764 TTTTTATTTTTT
1 TTTTTATTTTTT
82776 TCTTCTTAAC
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:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:85963 original size:18 final size:18
Alignment explanation
Indices: 85940--85981 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
85930 TCTTTTCAAT
85940 AAAAAA-TAATAAATTAAA
1 AAAAAACTAA-AAATTAAA
*
85958 AAAAAACTGAAAATTAAA
1 AAAAAACTAAAAATTAAA
85976 AAAAAA
1 AAAAAA
85982 AATCTGAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (18 bp):
AAAAAACTAAAAATTAAA
Found at i:85995 original size:19 final size:19
Alignment explanation
Indices: 85955--86003 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
85945 ATAATAAATT
*
85955 AAAAAAAAACTGAAAATTAA
1 AAAAAAAAACTG-AAATGAA
85975 AAAAAAAAATCTG-AATGAA
1 AAAAAAAAA-CTGAAATGAA
85994 AAAAATAAAA
1 AAAAA-AAAA
86004 ATGACACGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 10 0.38
20 13 0.50
21 3 0.12
ACGTcount: A:0.76, C:0.04, G:0.06, T:0.14
Consensus pattern (19 bp):
AAAAAAAAACTGAAATGAA
Found at i:86522 original size:3 final size:3
Alignment explanation
Indices: 86516--86553 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
86506 CCACCACCAC
86516 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
86554 ACCCAATACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:88074 original size:6 final size:7
Alignment explanation
Indices: 88048--88083 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
88038 ATGAGAAAGG
88048 GGGGTTA
1 GGGGTTA
88055 GGGGTTA
1 GGGGTTA
88062 GGGGTTA
1 GGGGTTA
88069 -GGGTTA
1 GGGGTTA
*
88075 GGGGGTA
1 GGGGTTA
88082 GG
1 GG
88084 AGTGTTTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
6 6 0.22
7 21 0.78
ACGTcount: A:0.14, C:0.00, G:0.61, T:0.25
Consensus pattern (7 bp):
GGGGTTA
Found at i:88074 original size:13 final size:13
Alignment explanation
Indices: 88048--88083 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
88038 ATGAGAAAGG
88048 GGGGTTAGGGGTTA
1 GGGGTTA-GGGTTA
88062 GGGGTTAGGGTTA
1 GGGGTTAGGGTTA
*
88075 GGGGGTAGG
1 GGGGTTAGG
88084 AGTGTTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 14 0.67
14 7 0.33
ACGTcount: A:0.14, C:0.00, G:0.61, T:0.25
Consensus pattern (13 bp):
GGGGTTAGGGTTA
Found at i:96323 original size:20 final size:20
Alignment explanation
Indices: 96298--96337 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
96288 TAAAATCGAT
* *
96298 TTTTCCTTGTAAAATTCAAG
1 TTTTCCTTATAAAAATCAAG
96318 TTTTCCTTATAAAAATCAAG
1 TTTTCCTTATAAAAATCAAG
96338 GTAATTTCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.42
Consensus pattern (20 bp):
TTTTCCTTATAAAAATCAAG
Found at i:96332 original size:21 final size:19
Alignment explanation
Indices: 96287--96337 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
96277 AATTAAAAAG
* *
96287 ATAAAATCGATTTTTCCTT
1 ATAAAATCAAGTTTTCCTT
*
96306 GTAAAATTCAAGTTTTCCTT
1 ATAAAA-TCAAGTTTTCCTT
96326 ATAAAAATCAAG
1 AT-AAAATCAAG
96338 GTAATTTCCT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 5 0.19
20 17 0.65
21 4 0.15
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39
Consensus pattern (19 bp):
ATAAAATCAAGTTTTCCTT
Found at i:98348 original size:30 final size:30
Alignment explanation
Indices: 98230--98356 Score: 82
Period size: 30 Copynumber: 4.2 Consensus size: 30
98220 ATTTAAAATT
* * *
98230 TTTTTAAGA-GTTTAAATTAAATTATA-TA
1 TTTTTAAGAGGTTAAAATAAAATTTTATTA
* * *
98258 TTTTTATA-ATAGTAAAAATATAATTTTATTA
1 TTTTTA-AGA-GGTTAAAATAAAATTTTATTA
* * * *
98289 -TTTTAATAGTTTATATATCAAATTTTTATTA
1 TTTTTAAGAGGTTA-AAAT-AAAATTTTATTA
*
98320 TTTTTGAGAGGTTAAAATAAAATTTTATTA
1 TTTTTAAGAGGTTAAAATAAAATTTTATTA
*
98350 TTATTAA
1 TTTTTAA
98357 TTTAAAATTT
Statistics
Matches: 73, Mismatches: 18, Indels: 14
0.70 0.17 0.13
Matches are distributed among these distances:
28 7 0.10
29 4 0.05
30 37 0.51
31 15 0.21
32 10 0.14
ACGTcount: A:0.41, C:0.01, G:0.06, T:0.52
Consensus pattern (30 bp):
TTTTTAAGAGGTTAAAATAAAATTTTATTA
Found at i:98356 original size:22 final size:23
Alignment explanation
Indices: 98331--98381 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
98321 TTTTGAGAGG
98331 TTAAAATAAAATTTTAT-TATTA
1 TTAAAATAAAATTTTATATATTA
**
98353 TTAATTTAAAATTTTATATATTA
1 TTAAAATAAAATTTTATATATTA
*
98376 TAAAAA
1 TTAAAA
98382 ACTTAAATTA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TTAAAATAAAATTTTATATATTA
Found at i:106952 original size:2 final size:2
Alignment explanation
Indices: 106945--106986 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
106935 TTCATCCATA
106945 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
106987 AAACAAAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:110758 original size:16 final size:17
Alignment explanation
Indices: 110728--110762 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
110718 TCTCTTTGTT
*
110728 TTTTTTTCACCAAATTG
1 TTTTTTTCACAAAATTG
110745 TTTTTTTC-CAAAATTG
1 TTTTTTTCACAAAATTG
110761 TT
1 TT
110763 GCTGCCATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.23, C:0.14, G:0.06, T:0.57
Consensus pattern (17 bp):
TTTTTTTCACAAAATTG
Found at i:113717 original size:18 final size:18
Alignment explanation
Indices: 113696--113730 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
113686 AATGATATAT
*
113696 TAATTAATAATAATATTA
1 TAATAAATAATAATATTA
113714 TAATAAATAATAATATT
1 TAATAAATAATAATATT
113731 TTATTATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATAAATAATAATATTA
Found at i:115300 original size:42 final size:42
Alignment explanation
Indices: 115213--115408 Score: 254
Period size: 42 Copynumber: 4.7 Consensus size: 42
115203 GGCAAAGACA
* * * *
115213 TACCACCAAAAATACTACTACCTGTGC-T-T-GTTGCAGATG
1 TACCACCAAAGATACCATTGCCTGTGCTTGTAGTTGCAGATG
* *
115252 TACCACCAAAGATGCCATTGCCTGTGCTTGTAGTAGCAGATG
1 TACCACCAAAGATACCATTGCCTGTGCTTGTAGTTGCAGATG
* * * *
115294 TACCACCAAAAAAACCAGTGCCCGTGCTTGTAGTTGCAGATG
1 TACCACCAAAGATACCATTGCCTGTGCTTGTAGTTGCAGATG
*
115336 TACCACCAAAGATACCATTGCCTGTGCTTGTACTTGCAGATG
1 TACCACCAAAGATACCATTGCCTGTGCTTGTAGTTGCAGATG
* *
115378 TACCACCAAATATACCATTGCTTGTGCTTGT
1 TACCACCAAAGATACCATTGCCTGTGCTTGT
115409 CACTGGGGAA
Statistics
Matches: 135, Mismatches: 19, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
39 22 0.16
40 1 0.01
41 1 0.01
42 111 0.82
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.28
Consensus pattern (42 bp):
TACCACCAAAGATACCATTGCCTGTGCTTGTAGTTGCAGATG
Found at i:120721 original size:48 final size:48
Alignment explanation
Indices: 120662--120761 Score: 182
Period size: 48 Copynumber: 2.1 Consensus size: 48
120652 GAGAAAGAGA
*
120662 TACCCTTTTTACATCCCTTACTGCGATTGTAGTAGGTAAAGATCTTCC
1 TACCCTTTTTACATCCCTTACTGCAATTGTAGTAGGTAAAGATCTTCC
*
120710 TACCCTTTTTACATCCCTTACTGCAATTGTAGTTGGTAAAGATCTTCC
1 TACCCTTTTTACATCCCTTACTGCAATTGTAGTAGGTAAAGATCTTCC
120758 TACC
1 TACC
120762 ATTTCTTTTC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.38
Consensus pattern (48 bp):
TACCCTTTTTACATCCCTTACTGCAATTGTAGTAGGTAAAGATCTTCC
Found at i:124733 original size:2 final size:2
Alignment explanation
Indices: 124726--124754 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
124716 TATCAACAAC
124726 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
124755 ATAAGAGTAA
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:127250 original size:9 final size:10
Alignment explanation
Indices: 127221--127249 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
127211 AATAAAACAA
127221 AGGTTTTTTT
1 AGGTTTTTTT
127231 AGGTTTTTTT
1 AGGTTTTTTT
127241 AGGTTTTTT
1 AGGTTTTTT
127250 ACGTCAAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.10, C:0.00, G:0.21, T:0.69
Consensus pattern (10 bp):
AGGTTTTTTT
Found at i:127629 original size:98 final size:98
Alignment explanation
Indices: 127460--127653 Score: 309
Period size: 98 Copynumber: 2.0 Consensus size: 98
127450 AAATTTTAAA
* *
127460 CTCCATCTTCTCCAATCATTTCCTAAATGAATGATAAATAAAATATTAGTGTAAATAATATAATT
1 CTCCATCTTCTCCAATCATTTCCTAAATGAATGATAAATAAAATATAAGTATAAATAATATAATT
* *
127525 AAGAACATAAATAGCATAATTCAAGGCGAAATG
66 AAGAACATAAATAACATAACTCAAGGCGAAATG
* *
127558 CTCCATTTTCTCCGATCA-TTCCTTAAATGAATGATAAATAAAATATAAGTATAAATAATATAAT
1 CTCCATCTTCTCCAATCATTTCC-TAAATGAATGATAAATAAAATATAAGTATAAATAATATAAT
*
127622 TAAGAACATAAATAACATGACTCAAGGCGAAA
65 TAAGAACATAAATAACATAACTCAAGGCGAAA
127654 AATATCACAA
Statistics
Matches: 88, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
97 4 0.05
98 84 0.95
ACGTcount: A:0.46, C:0.14, G:0.10, T:0.30
Consensus pattern (98 bp):
CTCCATCTTCTCCAATCATTTCCTAAATGAATGATAAATAAAATATAAGTATAAATAATATAATT
AAGAACATAAATAACATAACTCAAGGCGAAATG
Done.