Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009445.1 Kokia drynarioides strain JFW-HI SEQ_124152, 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: 73358
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Found at i:809 original size:60 final size:58
Alignment explanation
Indices: 663--990 Score: 353
Period size: 60 Copynumber: 5.6 Consensus size: 58
653 TTTACCAAAT
* * *
663 AAAAAAGGGGTGTCGGCCATTGCATGGCCAACACCAAAAAAATTTGAATTTTTTATCTA
1 AAAAAAGGGGTGTCGGCCATTGCATGACCAACACC-AAAAAATTTGAATTTTTTTTCTC
*** *
722 AAAAAAGGGGTGTCGATTATTGCATGACCAACACCAAAAATTTTTGAAATTTTTTTTCTC
1 AAAAAAGGGGTGTCGGCCATTGCATGACCAACACCAAAAA-ATTTG-AATTTTTTTTCTC
* * *
782 AAAAAGGGGGTGTCGGCCA-TGCAATGACCAACACCCAAAAA--TGCATTTTTTTTCT-
1 AAAAAAGGGGTGTCGGCCATTGC-ATGACCAACACCAAAAAATTTGAATTTTTTTTCTC
* * *
837 GAAAAAGAGAGTGTCGGTCATTGCATGACCAACACCAAAAAAGTTTGAATTTTTTTTCCTC
1 AAAAAAG-GGGTGTCGGCCATTGCATGACCAACACCAAAAAA-TTTGAATTTTTTTT-CTC
* * * *
898 AAAAATGGGGTGTCGGCCATTGCATGAACAATACCAAAAAATTT-AA-TTTTTATCTGAC
1 AAAAAAGGGGTGTCGGCCATTGCATGACCAACACCAAAAAATTTGAATTTTTTTTCT--C
* * *
956 AAAAAAGGGGTGTCGGCCGTTGTATGGCCAACACC
1 AAAAAAGGGGTGTCGGCCATTGCATGACCAACACC
991 CAAATTTTTT
Statistics
Matches: 224, Mismatches: 33, Indels: 25
0.79 0.12 0.09
Matches are distributed among these distances:
55 5 0.02
56 40 0.18
57 11 0.05
58 37 0.17
59 52 0.23
60 74 0.33
61 5 0.02
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (58 bp):
AAAAAAGGGGTGTCGGCCATTGCATGACCAACACCAAAAAATTTGAATTTTTTTTCTC
Found at i:1006 original size:116 final size:115
Alignment explanation
Indices: 663--1006 Score: 376
Period size: 116 Copynumber: 3.0 Consensus size: 115
653 TTTACCAAAT
*
663 AAAAAAGGGGTGTCGGCCATTGCATGGCCAACACCAAAAAAATTTGAATTTTTTATCT-AAAAAA
1 AAAAAAGGGGTGTCGGCCATTGCATGACCAACACC-AAAAAATTT-AA-TTTTTATCTGAAAAAA
* *
727 AGGGGTGTCGATTATTGCATGACCAACACCAAAAATTTTTGAAATTTTTTTTCTC
63 AGGGGTGTCGGTCATTGCATGACCAACACCAAAAATTTTT--AATTTTTTTTCTC
* * ** * * *
782 AAAAAGGGGGTGTCGGCCA-TGCAATGACCAACACCCAAAAATGCATTTTTTTTCTGAAAAAGA-
1 AAAAAAGGGGTGTCGGCCATTGC-ATGACCAACACCAAAAAATTTAATTTTTATCTGAAAAAAAG
* * *
845 GAGTGTCGGTCATTGCATGACCAACACCAAAAAAGTTTGAATTTTTTTTCCTC
65 GGGTGTCGGTCATTGCATGACCAACACC-AAAAATTTTTAATTTTTTTT-CTC
* * *
898 AAAAATGGGGTGTCGGCCATTGCATGAACAATACCAAAAAATTTAATTTTTATCTGACAAAAAAG
1 AAAAAAGGGGTGTCGGCCATTGCATGACCAACACCAAAAAATTTAATTTTTATCTGA-AAAAAAG
* * * * *
963 GGGTGTCGGCCGTTGTATGGCCAACACC-CAAATTTTT--TTTTTTT
65 GGGTGTCGGTCATTGCATGACCAACACCAAAAATTTTTAATTTTTTT
1007 CAAATTCTCA
Statistics
Matches: 188, Mismatches: 30, Indels: 19
0.79 0.13 0.08
Matches are distributed among these distances:
114 7 0.04
115 10 0.05
116 87 0.46
117 23 0.12
118 32 0.17
119 29 0.15
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.30
Consensus pattern (115 bp):
AAAAAAGGGGTGTCGGCCATTGCATGACCAACACCAAAAAATTTAATTTTTATCTGAAAAAAAGG
GGTGTCGGTCATTGCATGACCAACACCAAAAATTTTTAATTTTTTTTCTC
Found at i:2205 original size:22 final size:21
Alignment explanation
Indices: 2158--2207 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
2148 ATATGAATAG
*
2158 TTTAGAATTCATTACGAAAAAT
1 TTTAAAATTCATTAC-AAAAAT
2180 TTTAAAATTCATTA-AAAATAT
1 TTTAAAATTCATTACAAAA-AT
2201 ATTTAAA
1 -TTTAAA
2208 TAAAAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 4 0.16
21 2 0.08
22 19 0.76
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (21 bp):
TTTAAAATTCATTACAAAAAT
Found at i:2262 original size:3 final size:3
Alignment explanation
Indices: 2254--2285 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2244 TTAAAAGGAG
2254 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2286 TGCTTTTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:4652 original size:14 final size:14
Alignment explanation
Indices: 4635--4666 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
4625 GATATTATAC
*
4635 ATATTTTATTCATA
1 ATATTTTATTCACA
4649 ATATTTTATTCACA
1 ATATTTTATTCACA
4663 ATAT
1 ATAT
4667 ATCTTAAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (14 bp):
ATATTTTATTCACA
Found at i:12423 original size:20 final size:21
Alignment explanation
Indices: 12386--12424 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
12376 TTATGGTTAA
*
12386 AAAATATTTATTATATTTATT
1 AAAATATTTATAATATTTATT
12407 AAAATATTT-TAATATTTA
1 AAAATATTTATAATATTTA
12425 AAACGTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
AAAATATTTATAATATTTATT
Found at i:21718 original size:20 final size:20
Alignment explanation
Indices: 21689--21726 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
21679 TTGTTAAGTA
*
21689 TTTTTTTTTTTCTCTCTCTG
1 TTTTTGTTTTTCTCTCTCTG
*
21709 TTTTTGTTTTTTTCTCTC
1 TTTTTGTTTTTCTCTCTC
21727 AACTTCTCAA
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:0.00, C:0.18, G:0.05, T:0.76
Consensus pattern (20 bp):
TTTTTGTTTTTCTCTCTCTG
Found at i:32739 original size:2 final size:2
Alignment explanation
Indices: 32732--32757 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
32722 AGAACACAAA
32732 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
32758 TTTTGAGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:33483 original size:18 final size:18
Alignment explanation
Indices: 33460--33496 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
33450 ACTTATCTTT
33460 CATGTATTTATCATTTCA
1 CATGTATTTATCATTTCA
33478 CATGTATTTATCATTTCA
1 CATGTATTTATCATTTCA
33496 C
1 C
33497 TTACCTCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.19, G:0.05, T:0.49
Consensus pattern (18 bp):
CATGTATTTATCATTTCA
Found at i:33717 original size:23 final size:23
Alignment explanation
Indices: 33687--33815 Score: 120
Period size: 23 Copynumber: 5.6 Consensus size: 23
33677 TGTTGGATAA
33687 CAGAGGGCACACAAAGTGCTAAT
1 CAGAGGGCACACAAAGTGCTAAT
33710 CAGAGGGCACACGAAA-TGCTAAT
1 CAGAGGGCACAC-AAAGTGCTAAT
* *
33733 AACAGAGGGCACACAAAGTGTTGAT
1 --CAGAGGGCACACAAAGTGCTAAT
* *
33758 CAGAGGGCACGA-AACGTGCTAAA
1 CAGAGGGCAC-ACAAAGTGCTAAT
* * * *
33781 CAGAGAGCACACACATTGCTGAT
1 CAGAGGGCACACAAAGTGCTAAT
*
33804 CAGA-AGCACACA
1 CAGAGGGCACACA
33816 TAGTACTGAA
Statistics
Matches: 88, Mismatches: 12, Indels: 13
0.78 0.11 0.12
Matches are distributed among these distances:
22 9 0.10
23 55 0.62
24 7 0.08
25 17 0.19
ACGTcount: A:0.40, C:0.22, G:0.26, T:0.12
Consensus pattern (23 bp):
CAGAGGGCACACAAAGTGCTAAT
Found at i:33744 original size:25 final size:25
Alignment explanation
Indices: 33659--33793 Score: 117
Period size: 23 Copynumber: 5.6 Consensus size: 25
33649 CTGAAGTACT
* * *
33659 TAACAGAGGGCACA-TAAGTGTTGGA
1 TAACAGAGGGCACACAAAGTGCT-AA
33684 TAACAGAGGGCACACAAAGTGCTAA
1 TAACAGAGGGCACACAAAGTGCTAA
33709 T--CAGAGGGCACACGAAA-TGCTAA
1 TAACAGAGGGCACAC-AAAGTGCTAA
* *
33732 TAACAGAGGGCACACAAAGTGTTGA
1 TAACAGAGGGCACACAAAGTGCTAA
*
33757 T--CAGAGGGCACGA-AACGTGCT-A
1 TAACAGAGGGCAC-ACAAAGTGCTAA
*
33779 -AACAGAGAGCACACA
1 TAACAGAGGGCACACA
33794 CATTGCTGAT
Statistics
Matches: 93, Mismatches: 8, Indels: 20
0.77 0.07 0.17
Matches are distributed among these distances:
22 2 0.02
23 45 0.48
24 7 0.08
25 33 0.35
26 6 0.06
ACGTcount: A:0.40, C:0.19, G:0.27, T:0.13
Consensus pattern (25 bp):
TAACAGAGGGCACACAAAGTGCTAA
Found at i:33791 original size:46 final size:47
Alignment explanation
Indices: 33683--33807 Score: 157
Period size: 48 Copynumber: 2.7 Consensus size: 47
33673 TAAGTGTTGG
*
33683 ATAACAGAGGGCACACAAAGTGCTAATCAGAGGGCACACGAAATGCTA
1 ATAACAGAGGGCACACAAAGTGCTGATCAGAGGG-ACACGAAATGCTA
*
33731 ATAACAGAGGGCACACAAAGTGTTGATCAGAGGG-CACGAAACGTGCT-
1 ATAACAGAGGGCACACAAAGTGCTGATCAGAGGGACACGAAA--TGCTA
* * *
33778 A-AACAGAGAGCACACACATTGCTGATCAGA
1 ATAACAGAGGGCACACAAAGTGCTGATCAGA
33808 AGCACACATA
Statistics
Matches: 69, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
46 32 0.46
47 1 0.01
48 36 0.52
ACGTcount: A:0.40, C:0.21, G:0.26, T:0.14
Consensus pattern (47 bp):
ATAACAGAGGGCACACAAAGTGCTGATCAGAGGGACACGAAATGCTA
Found at i:33814 original size:22 final size:22
Alignment explanation
Indices: 33781--33847 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
33771 ACGTGCTAAA
*
33781 CAGAGAGCACACACATTGCTGAT
1 CAGA-AGCACACACAATGCTGAT
* * * *
33804 CAGAAGCACACATAGTACTGAA
1 CAGAAGCACACACAATGCTGAT
33826 CAGAAGCACACACAATGCTGAT
1 CAGAAGCACACACAATGCTGAT
33848 TAGTAAGCGC
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
22 32 0.89
23 4 0.11
ACGTcount: A:0.40, C:0.25, G:0.19, T:0.15
Consensus pattern (22 bp):
CAGAAGCACACACAATGCTGAT
Found at i:40510 original size:15 final size:16
Alignment explanation
Indices: 40492--40521 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
40482 TTCTTCTTCG
40492 TATTATT-TTTTTATT
1 TATTATTATTTTTATT
40507 TATTATTATTTTTAT
1 TATTATTATTTTTAT
40522 AAATATAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
TATTATTATTTTTATT
Found at i:40576 original size:15 final size:16
Alignment explanation
Indices: 40545--40579 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
40535 TATAAAATAA
*
40545 TATTTTTTTATTTTAT
1 TATTTATTTATTTTAT
40561 TATTTATTTA-TTTAT
1 TATTTATTTATTTTAT
40576 TATT
1 TATT
40580 GTATGAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
TATTTATTTATTTTAT
Found at i:40596 original size:66 final size:66
Alignment explanation
Indices: 40494--40662 Score: 216
Period size: 66 Copynumber: 2.7 Consensus size: 66
40484 CTTCTTCGTA
* *
40494 TTATTTTTTTATTTA-TTA-TTATT-TTTAT-AA-AT--ATAAATAAATATAAAATAATATT-TT
1 TTATTTTATTATTTATTTATTTATTATTTATGAATATAAATAAATAAATATAAAATAATATTAAT
40551 T
66 T
*
40552 TTATTTTATTATTTATTTATTTATTATTGTATGAATATAAATAAATAAATGTAAAATAATATTAA
1 TTATTTTATTATTTATTTATTTATTATT-TATGAATATAAATAAATAAATATAAAATAATATTAA
40617 TT
65 TT
*
40619 TTGTTTTATTATTTATTTA-TTA-T-TTTATGAATATAAATAAATAA
1 TTATTTTATTATTTATTTATTTATTATTTATGAATATAAATAAATAA
40663 CAAACCAAAA
Statistics
Matches: 98, Mismatches: 4, Indels: 13
0.85 0.03 0.11
Matches are distributed among these distances:
58 14 0.14
59 3 0.03
60 5 0.05
61 2 0.02
62 3 0.03
63 21 0.21
64 4 0.04
65 1 0.01
66 25 0.26
67 20 0.20
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (66 bp):
TTATTTTATTATTTATTTATTTATTATTTATGAATATAAATAAATAAATATAAAATAATATTAAT
T
Found at i:44769 original size:10 final size:11
Alignment explanation
Indices: 44754--44782 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
44744 CTTGAAACCT
44754 AAGAAAAAA-A
1 AAGAAAAAAGA
44764 AAGAAAAAAGA
1 AAGAAAAAAGA
44775 AAGAAAAA
1 AAGAAAAA
44783 GTCAAGATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.50
11 9 0.50
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (11 bp):
AAGAAAAAAGA
Found at i:45685 original size:8 final size:8
Alignment explanation
Indices: 45674--45704 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
45664 AAAAAATTAA
*
45674 AAAAAGGG
1 AAAAAGAG
45682 AAAAAGAG
1 AAAAAGAG
45690 AAAAAGAG
1 AAAAAGAG
45698 AAAAAGA
1 AAAAAGA
45705 AAAGGAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (8 bp):
AAAAAGAG
Found at i:45693 original size:26 final size:25
Alignment explanation
Indices: 45656--45736 Score: 81
Period size: 28 Copynumber: 3.0 Consensus size: 25
45646 GAAATTTAAA
* *
45656 AAAAAGATAAAAAATTAAAAAAAGGG
1 AAAAAGAGAAAAAA-AAAAAAAAGGG
*
45682 AAAAAGAGAAAAAGAGAAAAAGAAAAGG
1 AAAAAGAGAAAAA-A-AAAAA-AAAGGG
45710 AAAAAGAAGAAAAGAAAAAAAAAAGGG
1 AAAAAG-AGAAAA-AAAAAAAAAAGGG
45737 GAGGTCGAGG
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
26 12 0.26
27 10 0.22
28 16 0.35
29 7 0.15
30 1 0.02
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.04
Consensus pattern (25 bp):
AAAAAGAGAAAAAAAAAAAAAAGGG
Found at i:45711 original size:28 final size:26
Alignment explanation
Indices: 45683--45735 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
45673 AAAAAAGGGA
*
45683 AAAAGAGAA-AAAGAGAAAAAGAAAAGG
1 AAAA-AGAAGAAA-AGAAAAAAAAAAGG
45710 AAAAAGAAGAAAAGAAAAAAAAAAGG
1 AAAAAGAAGAAAAGAAAAAAAAAAGG
45736 GGAGGTCGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 17 0.71
27 7 0.29
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (26 bp):
AAAAAGAAGAAAAGAAAAAAAAAAGG
Found at i:45714 original size:12 final size:13
Alignment explanation
Indices: 45691--45734 Score: 54
Period size: 12 Copynumber: 3.4 Consensus size: 13
45681 GAAAAAGAGA
45691 AAAAGAGAAAAAG
1 AAAAGAGAAAAAG
45704 AAAAG-GAAAAAG
1 AAAAGAGAAAAAG
* *
45716 AAGAAAAGAAAAAA
1 AA-AAGAGAAAAAG
45730 AAAAG
1 AAAAG
45735 GGGAGGTCGA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 9 0.35
13 9 0.35
14 8 0.31
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAAGAGAAAAAG
Found at i:45714 original size:20 final size:21
Alignment explanation
Indices: 45683--45734 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
45673 AAAAAAGGGA
45683 AAAAGAGAAAAAG-AGAAAAAG
1 AAAAGAGAAAAAGAAG-AAAAG
45704 AAAAG-GAAAAAGAAGAAAAG
1 AAAAGAGAAAAAGAAGAAAAG
45724 AAAA-A-AAAAAG
1 AAAAGAGAAAAAG
45735 GGGAGGTCGA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
19 6 0.21
20 16 0.55
21 7 0.24
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (21 bp):
AAAAGAGAAAAAGAAGAAAAG
Found at i:46831 original size:50 final size:50
Alignment explanation
Indices: 46654--46830 Score: 210
Period size: 50 Copynumber: 3.5 Consensus size: 50
46644 ATCTTTTACC
* *
46654 CCTAAAGCTGTGGAGGTGTAGATTGAAATTGTAATGGCAAATCTCATACA
1 CCTAAAGCTGTAGAGGTGTAGATTGAAACTGTAATGGCAAATCTCATACA
* * * * * * *
46704 CCTAAAGTTGTGGAGGTGCAGATTGAAACCGCAACGGCAAATATCATACA
1 CCTAAAGCTGTAGAGGTGTAGATTGAAACTGTAATGGCAAATCTCATACA
* * * *
46754 CCTAAAGCTGTAGAGGGGTAGAATGAAGCTGTAATGGCAAATCTCATTCA
1 CCTAAAGCTGTAGAGGTGTAGATTGAAACTGTAATGGCAAATCTCATACA
* * *
46804 CTTAAAGCTGTAGAGGAGAAGATTGAA
1 CCTAAAGCTGTAGAGGTGTAGATTGAA
46831 GTCATAAGGA
Statistics
Matches: 105, Mismatches: 22, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 105 1.00
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.24
Consensus pattern (50 bp):
CCTAAAGCTGTAGAGGTGTAGATTGAAACTGTAATGGCAAATCTCATACA
Found at i:46992 original size:39 final size:40
Alignment explanation
Indices: 46885--48001 Score: 463
Period size: 39 Copynumber: 27.9 Consensus size: 40
46875 AGTTACAACC
* *
46885 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAA-AATCA
1 TCCAATCTTTTATCCTAACCAAAGGGCAAGATTGAAGAA--A
* * * * * ** *
46926 TCCGATCTTTCACCCCAATCATGGGGC-AGATTAAAGAAA
1 TCCAATCTTTTATCCTAACCAAAGGGCAAGATTGAAGAAA
**
46965 TTTAATCTTTTATCCTAACCAAAGGGCAAGATTGAAGACAA
1 TCCAATCTTTTATCCTAACCAAAGGGCAAGATTGAAGA-AA
* * ** * **
47006 TCCGATCTTTTACCCCGATCATGGGGC-AGATTGAAGAAA
1 TCCAATCTTTTATCCTAACCAAAGGGCAAGATTGAAGAAA
* *
47045 TCCAATCTTTTATCCTAACCAGAGGGCAAGATTGAAGATCA
1 TCCAATCTTTTATCCTAACCAAAGGGCAAGATTGAAGA-AA
* * ** * ** *
47086 TCCGATCTTTTACCCCGATCATTGGAC-AGATTGAAGAAA
1 TCCAATCTTTTATCCTAACCAAAGGGCAAGATTGAAGAAA
* * *
47125 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCA
1 TCCAATCTTTTATCCTAACCAAAGGGCAAGATTGAAGA-AA
* * * ** * * **
47166 TTCAATATTTTACCCCGATC-ATGGGGTAGATTGAAGAAA
1 TCCAATCTTTTATCCTAACCAAAGGGCAAGATTGAAGAAA
* * *
47205 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCA
1 TCCAATCTTTTATCCTAACCAAAGGGCAAGATTGAAGA-AA
* * **** *
47246 TTCGATCTTTTA-CCCCGTCATAGGGCAA-ATTGAAGAAA
1 TCCAATCTTTTATCCTAACCAAAGGGCAAGATTGAAGAAA
* * * * *
47284 TCCAATCTTTTACCCTAACTAGAGGGCAAGATTAAAGACCA
1 TCCAATCTTTTATCCTAACCAAAGGGCAAGATTGAAGA-AA
* ** * * *
47325 TCCAATCTTTTACCCCGATC-ATGAG-ATAGATTGAAGAAA
1 TCCAATCTTTTATCCTAACCAAAGGGCA-AGATTGAAGAAA
* * * *
47364 TCCAATCTTTTACCCTAACTAGAGGGCAAGATTGAAGACCA
1 TCCAATCTTTTATCCTAACCAAAGGGCAAGATTGAAGA-AA
* * * * **** **
47405 TTCGAT-ATTTAACCCCGTCATGGGGCAA-ATTGAAGAAA
1 TCCAATCTTTTATCCTAACCAAAGGGCAAGATTGAAGAAA
* * * * * *
47443 TTCAACCTTTTA-CCTTAACCAGAGGGTAGGATTGAAGACCA
1 TCCAATCTTTTATCC-TAACCAAAGGGCAAGATTGAAGA-AA
* * * **
47484 TCCAATCTTTTACCCTGATCATGGGGC-AGATTGAAGAAA
1 TCCAATCTTTTATCCTAACCAAAGGGCAAGATTGAAGAAA
* ** *
47523 TCCAATCTTTTA-CTCTAACCAGAGGAAAAAGATTGAAAAGACCA
1 TCCAATCTTTTATC-CTAACCAAAGG-GCAAGATTG--AAGA-AA
** * ** * * *
47567 TCTGATCTTTTACCCCGATC-ATGAGGCAA-ATTGAATAAA
1 TCCAATCTTTTATCCTAACCAAAG-GGCAAGATTGAAGAAA
* * * * *
47606 TCTAATCTTTT-TCCCTAACTAGAGGGCAAGATTAAAGATCA
1 TCCAATCTTTTAT-CCTAACCAAAGGGCAAGATTGAAGA-AA
* * ** * ** *
47647 TCCGATCTTTTACCCCGATCATGGGGC-AGATTAAAGAAA
1 TCCAATCTTTTATCCTAACCAAAGGGCAAGATTGAAGAAA
*
47686 TCCAATCTTTTATCCTAACCAGAGGGCAAGATTGAA-AACCA
1 TCCAATCTTTTATCCTAACCAAAGGGCAAGATTGAAGAA--A
* * * ** *
47727 TCCGATCTTTTA-CCCAGATCATGGGGCAA-ATTAAAGAAA
1 TCCAATCTTTTATCCTA-ACCAAAGGGCAAGATTGAAGAAA
* *
47766 TCCAATCTTTTACCCTAACCAGAA-GGCAAGATTGAAGACCA
1 TCCAATCTTTTATCCTAACCA-AAGGGCAAGATTGAAGA-AA
* * ** * ** *
47807 TCCGATCTTTTACCCCGATCATGGGGC-ATATTGAAGAAA
1 TCCAATCTTTTATCCTAACCAAAGGGCAAGATTGAAGAAA
* * * *
47846 TCTAATCTTCTA-CCTTAACTAAAGGGCAAGATTGAAGACCA
1 TCCAATCTTTTATCC-TAACCAAAGGGCAAGATTGAAGA-AA
* * ** * *
47887 TCCGATCTTTTACCCCGATC-ATGGG-ATAGATTGAAGAAA
1 TCCAATCTTTTATCCTAACCAAAGGGCA-AGATTGAAGAAA
* ** * * ** *
47926 TCCAATCTTTTACCCCGA-CTATGGGGTAGATTGAAGCAA
1 TCCAATCTTTTATCCTAACCAAAGGGCAAGATTGAAGAAA
*
47965 TTCAATCTTTTATCCTAACCAAAGGGC-AGATTGAAGA
1 TCCAATCTTTTATCCTAACCAAAGGGCAAGATTGAAGA
48002 CCATCAGATC
Statistics
Matches: 786, Mismatches: 238, Indels: 106
0.70 0.21 0.09
Matches are distributed among these distances:
38 22 0.03
39 288 0.37
40 235 0.30
41 210 0.27
42 8 0.01
43 7 0.01
44 15 0.02
45 1 0.00
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.26
Consensus pattern (40 bp):
TCCAATCTTTTATCCTAACCAAAGGGCAAGATTGAAGAAA
Found at i:47021 original size:80 final size:80
Alignment explanation
Indices: 46885--47940 Score: 1477
Period size: 80 Copynumber: 13.2 Consensus size: 80
46875 AGTTACAACC
* * * *
46885 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAAATCATCCGATCTTTCACCCCAATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
*
46950 GGCAGATTAAAGAAA
66 GGCAGATTGAAGAAA
** * * *
46965 TTTAATCTTTTATCCTAACCAAAGGGCAAGATTGAAGACAATCCGATCTTTTACCCCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
47030 GGCAGATTGAAGAAA
66 GGCAGATTGAAGAAA
* * *
47045 TCCAATCTTTTATCCTAACCAGAGGGCAAGATTGAAGATCATCCGATCTTTTACCCCGATCATTG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
*
47110 GACAGATTGAAGAAA
66 GGCAGATTGAAGAAA
* * *
47125 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATTCAATATTTTACCCCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
*
47190 GGTAGATTGAAGAAA
66 GGCAGATTGAAGAAA
* *
47205 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATTCGATCTTTTACCCCG-TCATAG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
*
47269 GGCAAATTGAAGAAA
66 GGCAGATTGAAGAAA
* * * *
47284 TCCAATCTTTTACCCTAACTAGAGGGCAAGATTAAAGACCATCCAATCTTTTACCCCGATCATGA
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
**
47349 GATAGATTGAAGAAA
66 GGCAGATTGAAGAAA
* * * *
47364 TCCAATCTTTTACCCTAACTAGAGGGCAAGATTGAAGACCATTCGATATTTAACCCCG-TCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
*
47428 GGCAAATTGAAGAAA
66 GGCAGATTGAAGAAA
* * * * * * *
47443 TTCAACCTTTTACCTTAACCAGAGGGTAGGATTGAAGACCATCCAATCTTTTACCCTGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
47508 GGCAGATTGAAGAAA
66 GGCAGATTGAAGAAA
* ** *
47523 TCCAATCTTTTACTCTAACCAGAGGAAAAAGATTGAAAAGACCATCTGATCTTTTACCCCGATCA
1 TCCAATCTTTTACCCTAACCAGAGG-GCAAGATTG--AAGACCATCCGATCTTTTACCCCGATCA
* * *
47588 TGAGGCAAATTGAATAAA
63 TGGGGCAGATTGAAGAAA
* * * * *
47606 TCTAATCTTTTTCCCTAACTAGAGGGCAAGATTAAAGATCATCCGATCTTTTACCCCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
*
47671 GGCAGATTAAAGAAA
66 GGCAGATTGAAGAAA
* * *
47686 TCCAATCTTTTATCCTAACCAGAGGGCAAGATTGAAAACCATCCGATCTTTTACCCAGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
* *
47751 GGCAAATTAAAGAAA
66 GGCAGATTGAAGAAA
*
47766 TCCAATCTTTTACCCTAACCAGAAGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
*
47831 GGCATATTGAAGAAA
66 GGCAGATTGAAGAAA
* * * * *
47846 TCTAATCTTCTACCTTAACTAAAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
**
47911 GATAGATTGAAGAAA
66 GGCAGATTGAAGAAA
47926 TCCAATCTTTTACCC
1 TCCAATCTTTTACCC
47941 CGACTATGGG
Statistics
Matches: 858, Mismatches: 113, Indels: 10
0.87 0.12 0.01
Matches are distributed among these distances:
79 136 0.16
80 649 0.76
81 6 0.01
82 6 0.01
83 61 0.07
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (80 bp):
TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
GGCAGATTGAAGAAA
Found at i:50318 original size:14 final size:16
Alignment explanation
Indices: 50299--50331 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
50289 TATAAAAACC
50299 AAAAAAAT-AAG-TAA
1 AAAAAAATCAAGCTAA
50313 AAAAAAATCAAGCTAA
1 AAAAAAATCAAGCTAA
50329 AAA
1 AAA
50332 TAGAAGCTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 3 0.18
16 6 0.35
ACGTcount: A:0.76, C:0.06, G:0.06, T:0.12
Consensus pattern (16 bp):
AAAAAAATCAAGCTAA
Found at i:55582 original size:23 final size:23
Alignment explanation
Indices: 55548--55605 Score: 109
Period size: 23 Copynumber: 2.6 Consensus size: 23
55538 AAAGTGTGCT
55548 AGACT-GGTGCAAACAGCAGCAA
1 AGACTGGGTGCAAACAGCAGCAA
55570 AGACTGGGTGCAAACAGCAGCAA
1 AGACTGGGTGCAAACAGCAGCAA
55593 AGACTGGGTGCAA
1 AGACTGGGTGCAA
55606 CAGTTGAAGC
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 5 0.14
23 30 0.86
ACGTcount: A:0.38, C:0.21, G:0.31, T:0.10
Consensus pattern (23 bp):
AGACTGGGTGCAAACAGCAGCAA
Found at i:61187 original size:24 final size:23
Alignment explanation
Indices: 61138--61181 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
61128 GGGTTTTCTA
61138 AATTTTTTAGTGTAAATTATATC
1 AATTTTTTAGTGTAAATTATATC
61161 AATTTTTTA-T-TAAAATTATAT
1 AATTTTTTAGTGT-AAATTATAT
61182 TTCAATCGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 1 0.05
22 10 0.50
23 9 0.45
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (23 bp):
AATTTTTTAGTGTAAATTATATC
Found at i:64908 original size:2 final size:2
Alignment explanation
Indices: 64901--64927 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
64891 ACAACATTAT
64901 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
64928 GATGAAGGTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:66806 original size:17 final size:17
Alignment explanation
Indices: 66784--66816 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
66774 GAAAATTTAA
66784 AATTTTA-AATAAAAATT
1 AATTTTATAA-AAAAATT
66801 AATTTTATAAAAAAAT
1 AATTTTATAAAAAAAT
66817 ATTCTAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AATTTTATAAAAAAATT
Found at i:67427 original size:16 final size:17
Alignment explanation
Indices: 67392--67424 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
67382 AAGAGAATGG
67392 AAAAAAAAAAGAAATTT
1 AAAAAAAAAAGAAATTT
67409 AAAAAATAAAA-AAATT
1 AAAAAA-AAAAGAAATT
67425 AAATTGCTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (17 bp):
AAAAAAAAAAGAAATTT
Done.