Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014619.1 Kokia drynarioides strain JFW-HI SEQ_129658, 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: 73834
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 22 characters in sequence are not A, C, G, or T
Found at i:688 original size:31 final size:31
Alignment explanation
Indices: 642--703 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
632 GTTTTTCAAT
*
642 TTTTAAGGGTTCAAATTTTATTTTATTTTTAC
1 TTTTAACGGTTCAAATTTT-TTTTATTTTTAC
*
674 TTTTAACGG-TCAAATTTTTTTTTTTTTTAC
1 TTTTAACGGTTCAAATTTTTTTTATTTTTAC
704 GATCTTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 11 0.39
31 9 0.32
32 8 0.29
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.61
Consensus pattern (31 bp):
TTTTAACGGTTCAAATTTTTTTTATTTTTAC
Found at i:756 original size:32 final size:33
Alignment explanation
Indices: 695--756 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
685 AAATTTTTTT
*
695 TTTTTTTACGATCTTTTAAGACACCTAAAAAAG
1 TTTTTTTACGATCTTTTAAGACACATAAAAAAG
*
728 TTTTTTTCCGA-CTTTTAAGGA-ACATAAAA
1 TTTTTTTACGATCTTTTAA-GACACATAAAA
757 TCTCATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 14 0.54
33 12 0.46
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (33 bp):
TTTTTTTACGATCTTTTAAGACACATAAAAAAG
Found at i:8507 original size:19 final size:20
Alignment explanation
Indices: 8459--8507 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
8449 AAACTCACCT
8459 TAAAAGCAAACACCAGAAAAA
1 TAAAAG-AAACACCAGAAAAA
*
8480 TAAATGAAAC-CCA-AAAAA
1 TAAAAGAAACACCAGAAAAA
8498 TCAAAAGAAA
1 T-AAAAGAAA
8508 AACAGATGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 6 0.24
19 10 0.40
20 4 0.16
21 5 0.20
ACGTcount: A:0.67, C:0.16, G:0.08, T:0.08
Consensus pattern (20 bp):
TAAAAGAAACACCAGAAAAA
Found at i:15616 original size:18 final size:18
Alignment explanation
Indices: 15593--15627 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
15583 AAGTAATTTC
*
15593 AACATTGGAAAGTTTCAT
1 AACATTGGAAAGATTCAT
*
15611 AACATTTGAAAGATTCA
1 AACATTGGAAAGATTCA
15628 AAAATTAGTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.31
Consensus pattern (18 bp):
AACATTGGAAAGATTCAT
Found at i:17660 original size:21 final size:21
Alignment explanation
Indices: 17636--17676 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
17626 AAGTGATAGT
*
17636 TCTACTGATAC-AAGAAACTCC
1 TCTACCGATACTAA-AAACTCC
17657 TCTACCGATACTAAAAACTC
1 TCTACCGATACTAAAAACTC
17677 TAGAGAACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.39, C:0.29, G:0.07, T:0.24
Consensus pattern (21 bp):
TCTACCGATACTAAAAACTCC
Found at i:19313 original size:38 final size:38
Alignment explanation
Indices: 19201--19663 Score: 404
Period size: 38 Copynumber: 11.9 Consensus size: 38
19191 AAGGTGGAAG
*
19201 ACTGATTATACTGAATGTTTGCTTAAACGAGCGAATCC
1 ACTGATTATACTGAATGTTTGCTCAAACGAGCGAATCC
* * * ** * **
19239 ATTTATTGTACTGAATGACTACTCAATTGAGCGAATCC
1 ACTGATTATACTGAATGTTTGCTCAAACGAGCGAATCC
* * * * *
19277 ATTGAATATACTGAATGTTTGCTAAAATGAGTGAATCC
1 ACTGATTATACTGAATGTTTGCTCAAACGAGCGAATCC
* * * *
19315 ACTCATTATACTGAATGTTTGATCAAATGAGTGAATCC
1 ACTGATTATACTGAATGTTTGCTCAAACGAGCGAATCC
* * * *
19353 ACTCATTATACTGAATGTTTGATCAAATGAGAGAATCC
1 ACTGATTATACTGAATGTTTGCTCAAACGAGCGAATCC
* * * * * * * *
19391 ACTAACTATATTGAGTGATTACTCAAATGAACGAATCC
1 ACTGATTATACTGAATGTTTGCTCAAACGAGCGAATCC
* *
19429 AATGATTATATTGAATGTTTGCTCAAACGAGCGAATCC
1 ACTGATTATACTGAATGTTTGCTCAAACGAGCGAATCC
* *
19467 ACTGATTTTACTAAATGTTTGCTCAAACGTTGCTCAAACGAGCGAATCC
1 ACTGATTATACTGAA----TG-T------TTGCTCAAACGAGCGAATCC
* *
19516 ACTGATTTTACTAAATGTTTGCTCAAACGAGCGAATCC
1 ACTGATTATACTGAATGTTTGCTCAAACGAGCGAATCC
* * *
19554 ATTAATTATACTGAATGATTGCTCAAACGAGCGAATCC
1 ACTGATTATACTGAATGTTTGCTCAAACGAGCGAATCC
* * * *
19592 ATTGATTTTACTGAATGTTTGCTCAAACAAACGAATCC
1 ACTGATTATACTGAATGTTTGCTCAAACGAGCGAATCC
* * * *
19630 ACTGATTTTACTAAATGCTTGCTCAAACAAGCGA
1 ACTGATTATACTGAATGTTTGCTCAAACGAGCGA
19664 TAACTAATAG
Statistics
Matches: 355, Mismatches: 59, Indels: 22
0.81 0.14 0.05
Matches are distributed among these distances:
38 314 0.88
42 2 0.01
43 1 0.00
44 1 0.00
45 2 0.01
49 35 0.10
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (38 bp):
ACTGATTATACTGAATGTTTGCTCAAACGAGCGAATCC
Found at i:19519 original size:49 final size:49
Alignment explanation
Indices: 19447--19544 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
19437 TATTGAATGT
19447 TTGCTCAAACGAGCGAATCCACTGATTTTACTAAATGTTTGCTCAAACG
1 TTGCTCAAACGAGCGAATCCACTGATTTTACTAAATGTTTGCTCAAACG
19496 TTGCTCAAACGAGCGAATCCACTGATTTTACTAAATGTTTGCTCAAACG
1 TTGCTCAAACGAGCGAATCCACTGATTTTACTAAATGTTTGCTCAAACG
19545 AGCGAATCCA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (49 bp):
TTGCTCAAACGAGCGAATCCACTGATTTTACTAAATGTTTGCTCAAACG
Found at i:19576 original size:87 final size:87
Alignment explanation
Indices: 19412--19657 Score: 244
Period size: 87 Copynumber: 3.0 Consensus size: 87
19402 TGAGTGATTA
* * * * *
19412 CTCAAATGAACGAATCCAATGATTATATTGAATGTTTGCTCAAACGAGCGAATCCACTGATTTTA
1 CTCAAACGAACGAATCCAATGATTATACTAAATGTTTGCTCAAACGAGCGAATCCACTAATTATA
*
19477 CTAAATGTTTGCTCAAACGTTG
66 CTAAATGATTGCTCAAACGTTG
* * * *
19499 CTCAAACGAGCGAATCCACTGATTTTACTAAATGTTTGCTCAAACGAGCGAATCCATTAATTATA
1 CTCAAACGAACGAATCCAATGATTATACTAAATGTTTGCTCAAACGAGCGAATCCACTAATTATA
*
19564 CTGAATGATTGCTCAAAC---G
66 CTAAATGATTGCTCAAACGTTG
* * * * * * *
19583 -----A-G--CGAATCCATTGATTTTACTGAATGTTTGCTCAAACAAACGAATCCACTGATTTTA
1 CTCAAACGAACGAATCCAATGATTATACTAAATGTTTGCTCAAACGAGCGAATCCACTAATTATA
*
19640 CTAAATGCTTGCTCAAAC
66 CTAAATGATTGCTCAAAC
19658 AAGCGATAAC
Statistics
Matches: 139, Mismatches: 20, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
76 64 0.46
78 1 0.01
79 1 0.01
84 1 0.01
87 72 0.52
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (87 bp):
CTCAAACGAACGAATCCAATGATTATACTAAATGTTTGCTCAAACGAGCGAATCCACTAATTATA
CTAAATGATTGCTCAAACGTTG
Found at i:19617 original size:163 final size:163
Alignment explanation
Indices: 19337--19657 Score: 453
Period size: 163 Copynumber: 2.0 Consensus size: 163
19327 GAATGTTTGA
* * * * *
19337 TCAAATGAGTGAATCCACTCATTATACTGAATGTTTGATCAAATGAGAGAATCCACTAACTATAT
1 TCAAACGAGCGAATCCACTCATTATACTAAATGTTTGATCAAACGAGAGAATCCACTAACTATAC
* * * * *
19402 TGAGTGATTACTCAAATGAACGAATCCAATGATTATATTGAATGTTTGCTCAAACGAGCGAATCC
66 TGAATGATTACTCAAACGAACGAATCCAATGATTATACTGAATGTTTGCTCAAACAAACGAATCC
*
19467 ACTGATTTTACTAAATGTTTGCTCAAACGTTGC
131 ACTGATTTTACTAAATGCTTGCTCAAACGTTGC
* * * * * *
19500 TCAAACGAGCGAATCCACTGATTTTACTAAATGTTTGCTCAAACGAGCGAATCCATTAATTATAC
1 TCAAACGAGCGAATCCACTCATTATACTAAATGTTTGATCAAACGAGAGAATCCACTAACTATAC
* * * *
19565 TGAATGATTGCTCAAACGAGCGAATCCATTGATTTTACTGAATGTTTGCTCAAACAAACGAATCC
66 TGAATGATTACTCAAACGAACGAATCCAATGATTATACTGAATGTTTGCTCAAACAAACGAATCC
19630 ACTGATTTTACTAAATGCTTGCTCAAAC
131 ACTGATTTTACTAAATGCTTGCTCAAAC
19658 AAGCGATAAC
Statistics
Matches: 137, Mismatches: 21, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
163 137 1.00
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (163 bp):
TCAAACGAGCGAATCCACTCATTATACTAAATGTTTGATCAAACGAGAGAATCCACTAACTATAC
TGAATGATTACTCAAACGAACGAATCCAATGATTATACTGAATGTTTGCTCAAACAAACGAATCC
ACTGATTTTACTAAATGCTTGCTCAAACGTTGC
Found at i:23104 original size:26 final size:26
Alignment explanation
Indices: 23079--23171 Score: 80
Period size: 26 Copynumber: 3.6 Consensus size: 26
23069 GATGAACTTT
* *
23079 CACATTAGATCATCCTGACAGGCTTT
1 CACATTAGATCGTCCTGACAGGCTTC
** * *
23105 TGCATTAGATCGTGCTG-GAGGACTTC
1 CACATTAGATCGTCCTGACAGG-CTTC
* * *
23131 CACATTAGATTGTCTTGACAGACTTC
1 CACATTAGATCGTCCTGACAGGCTTC
*
23157 CACATTAGATTGTCC
1 CACATTAGATCGTCC
23172 AAAAAAATTT
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
25 3 0.06
26 46 0.90
27 2 0.04
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (26 bp):
CACATTAGATCGTCCTGACAGGCTTC
Found at i:36181 original size:41 final size:41
Alignment explanation
Indices: 36136--36258 Score: 165
Period size: 41 Copynumber: 3.0 Consensus size: 41
36126 ATGTATTGAG
*
36136 ATGAGAATGAGATTATGAATAAGGAAGACTCATGTCTCGAA
1 ATGAGAATGAGATTATGATTAAGGAAGACTCATGTCTCGAA
* * *
36177 ATGAGAATGAGATTTTGATTAAGGAAGAATCATGTCTCGAG
1 ATGAGAATGAGATTATGATTAAGGAAGACTCATGTCTCGAA
* * * *
36218 ATGAGAATGAGAATATGGTTAAAGGAAGACTTATGACTCGA
1 ATGAGAATGAGATTATGATT-AAGGAAGACTCATGTCTCGA
36259 TAGAGCATAA
Statistics
Matches: 71, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
41 54 0.76
42 17 0.24
ACGTcount: A:0.40, C:0.08, G:0.26, T:0.26
Consensus pattern (41 bp):
ATGAGAATGAGATTATGATTAAGGAAGACTCATGTCTCGAA
Found at i:42050 original size:15 final size:15
Alignment explanation
Indices: 42030--42059 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
42020 AAAAGATAAA
*
42030 AAGTTGTTTGTTGAG
1 AAGTTGTCTGTTGAG
42045 AAGTTGTCTGTTGAG
1 AAGTTGTCTGTTGAG
42060 GCGACTGAAA
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:0.20, C:0.03, G:0.33, T:0.43
Consensus pattern (15 bp):
AAGTTGTCTGTTGAG
Found at i:46797 original size:24 final size:26
Alignment explanation
Indices: 46770--46817 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
46760 AGAGAAATGT
46770 AAATG-TGATATATGA-A-ATTATGAG
1 AAATGATGA-ATATGAGAGATTATGAG
46794 AAATGATGAATATGAGAGATTATG
1 AAATGATGAATATGAGAGATTATG
46818 CCCATGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (26 bp):
AAATGATGAATATGAGAGATTATGAG
Found at i:46968 original size:24 final size:22
Alignment explanation
Indices: 46885--46971 Score: 95
Period size: 22 Copynumber: 3.9 Consensus size: 22
46875 AGCGTGCCTA
* *
46885 CTGTTTAGCACAT-TTTGTGCCCT
1 CTGTTTAGCAC-TGTGTGTG-CTT
*
46908 CTGTTCAGCACTGTGTGTGCTT
1 CTGTTTAGCACTGTGTGTGCTT
*
46930 CTGTTTAGTACTGTGTGTGCTT
1 CTGTTTAGCACTGTGTGTGCTT
* *
46952 CTGTTTAGCGCTTTGTGTGC
1 CTGTTTAGCACTGTGTGTGC
46972 CTATTGTTGC
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
22 40 0.73
23 15 0.27
ACGTcount: A:0.09, C:0.21, G:0.25, T:0.45
Consensus pattern (22 bp):
CTGTTTAGCACTGTGTGTGCTT
Found at i:47650 original size:21 final size:19
Alignment explanation
Indices: 47626--47664 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
47616 TTGGAATACT
47626 ATGAACTTATGCAATGAGATG
1 ATGAA-TTATG-AATGAGATG
*
47647 ATGAATTTTGAATGAGAT
1 ATGAATTATGAATGAGAT
47665 TGTGTTTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 4 0.24
21 5 0.29
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.33
Consensus pattern (19 bp):
ATGAATTATGAATGAGATG
Found at i:49542 original size:41 final size:41
Alignment explanation
Indices: 49436--49653 Score: 206
Period size: 41 Copynumber: 5.2 Consensus size: 41
49426 GGTGTATTAA
** * * * *
49436 AAGGAAGACTCATGTCTCGGGTTGAGCATGAGA-AATTGTAT
1 AAGGAAGACTCATGTCTCAAGATGAGAATGAGACTA-TGAAT
* *
49477 AAATGGAAGACTTATGTGTCAAGATGAGAATGAGACTATGAAT
1 -AA-GGAAGACTCATGTCTCAAGATGAGAATGAGACTATGAAT
* *
49520 AAGGAAGACTCATGTCTTAAGATGAGAATGAGACTTTGAAT
1 AAGGAAGACTCATGTCTCAAGATGAGAATGAGACTATGAAT
* * * * *
49561 AAGGACGATTCATGTCTCGAA-ATGAGAATGAGATTTTGATT
1 AAGGAAGACTCATGTCTC-AAGATGAGAATGAGACTATGAAT
* * **
49602 AAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGGTT
1 AAGGAAGACTCATGTCTCAAGATGAGAATGAGACTATGAAT
49643 AAAGGAAGACT
1 -AAGGAAGACT
49654 TATGACTCGA
Statistics
Matches: 148, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
40 1 0.01
41 101 0.68
42 16 0.11
43 29 0.20
44 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.27, T:0.26
Consensus pattern (41 bp):
AAGGAAGACTCATGTCTCAAGATGAGAATGAGACTATGAAT
Found at i:50869 original size:73 final size:73
Alignment explanation
Indices: 50759--50904 Score: 283
Period size: 73 Copynumber: 2.0 Consensus size: 73
50749 AGATCCAAGA
*
50759 AAACTAAAGATTATTGATACTAAAGTTAAGTCAAGTCCGTGGAGAAGTTCAGATCCCCGATCAAC
1 AAACTAAAGATTATTGATACTAAAGTTAAGTCAAGTCCATGGAGAAGTTCAGATCCCCGATCAAC
50824 ATGATGAT
66 ATGATGAT
50832 AAACTAAAGATTATTGATACTAAAGTTAAGTCAAGTCCATGGAGAAGTTCAGATCCCCGATCAAC
1 AAACTAAAGATTATTGATACTAAAGTTAAGTCAAGTCCATGGAGAAGTTCAGATCCCCGATCAAC
50897 ATGATGAT
66 ATGATGAT
50905 CTATCTTTCA
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.26
Consensus pattern (73 bp):
AAACTAAAGATTATTGATACTAAAGTTAAGTCAAGTCCATGGAGAAGTTCAGATCCCCGATCAAC
ATGATGAT
Found at i:51507 original size:20 final size:20
Alignment explanation
Indices: 51482--51523 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
51472 CCAAAAGGCT
51482 GTCGCAACATCAATACATAG
1 GTCGCAACATCAATACATAG
51502 GTCGCAACATCAATACATAG
1 GTCGCAACATCAATACATAG
51522 GT
1 GT
51524 ATTTAGTAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (20 bp):
GTCGCAACATCAATACATAG
Found at i:58075 original size:2 final size:2
Alignment explanation
Indices: 58068--58097 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
58058 GTAAATGTAT
58068 TA TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
58098 TCTAAAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:58927 original size:29 final size:29
Alignment explanation
Indices: 58895--59044 Score: 149
Period size: 29 Copynumber: 5.0 Consensus size: 29
58885 TTTCTCTAAA
* *
58895 ATTTATGAAAAGGTCATATCCGAATGGAT
1 ATTTTTGAAAAGGTTATATCCGAATGGAT
* *
58924 ATTTTTTTAAAAAGGGTTATATCCGAAAGGAT
1 A--TTTTTGAAAA-GGTTATATCCGAATGGAT
* *
58956 ATTTTTAAAAAGGTTATATCCGAATGAAT
1 ATTTTTGAAAAGGTTATATCCGAATGGAT
* * * *
58985 GTTTTTGGAAAGGTTATATCCAAATGGGT
1 ATTTTTGAAAAGGTTATATCCGAATGGAT
*
59014 ATTTTTGAAAAGGATATTATCCGGAA-GGAT
1 ATTTTTGAAAAGGTTA-TATCC-GAATGGAT
59044 A
1 A
59045 ATAAATGAAA
Statistics
Matches: 99, Mismatches: 17, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
29 53 0.54
30 19 0.19
31 10 0.10
32 17 0.17
ACGTcount: A:0.37, C:0.07, G:0.21, T:0.35
Consensus pattern (29 bp):
ATTTTTGAAAAGGTTATATCCGAATGGAT
Found at i:59062 original size:40 final size:40
Alignment explanation
Indices: 59018--59106 Score: 133
Period size: 40 Copynumber: 2.2 Consensus size: 40
59008 ATGGGTATTT
** *
59018 TTGAAAAGGATATTATCCGGAAGGATAATAAATGAAAAGG
1 TTGAAAAGGATATTATCCAAAAAGATAATAAATGAAAAGG
*
59058 TTGAAAAGGATGTTATCCAAAAAGATAATAAATGAAAAGG
1 TTGAAAAGGATATTATCCAAAAAGATAATAAATGAAAAGG
*
59098 TCGAAAAGG
1 TTGAAAAGG
59107 TAAATTTATT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.49, C:0.06, G:0.24, T:0.21
Consensus pattern (40 bp):
TTGAAAAGGATATTATCCAAAAAGATAATAAATGAAAAGG
Found at i:60888 original size:13 final size:15
Alignment explanation
Indices: 60867--60898 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
60857 TATCCAAAAC
60867 AAATAAAATA-ATAA
1 AAATAAAATATATAA
60881 AAAT-AAATATATAA
1 AAATAAAATATATAA
60895 AAAT
1 AAAT
60899 TAAGAAGGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (15 bp):
AAATAAAATATATAA
Found at i:62195 original size:15 final size:15
Alignment explanation
Indices: 62177--62215 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
62167 TTTAATGGCA
*
62177 TTTATTTTGGTTTTG
1 TTTATTTTGCTTTTG
*
62192 TTTATTTTGCTTTTT
1 TTTATTTTGCTTTTG
*
62207 TTTTTTTTG
1 TTTATTTTG
62216 NNNNNNNNNN
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.05, C:0.03, G:0.13, T:0.79
Consensus pattern (15 bp):
TTTATTTTGCTTTTG
Found at i:72417 original size:23 final size:23
Alignment explanation
Indices: 72343--72432 Score: 76
Period size: 23 Copynumber: 3.9 Consensus size: 23
72333 TAAACAGAAC
* *
72343 AAACAGAGAGTAC-CAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
* *
72365 AAACAGAGAGCACA-TAAGTGTT
1 AAACAGAGAGCACACAAAGTGCT
* *
72387 GGGCAACAGAGAGGACACAAAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
*
72413 AAACAGAGAGTACACAAAGT
1 AAACAGAGAGCACACAAAGT
72433 ACTGAGCACA
Statistics
Matches: 53, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
22 17 0.32
23 18 0.34
25 12 0.23
26 6 0.11
ACGTcount: A:0.47, C:0.17, G:0.24, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:72445 original size:16 final size:16
Alignment explanation
Indices: 72424--72464 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
72414 AACAGAGAGT
72424 ACACAAAGTACTGAGC
1 ACACAAAGTACTGAGC
72440 ACACAAAGTACTGAGC
1 ACACAAAGTACTGAGC
*
72456 ACAGAAAGT
1 ACACAAAGT
72465 GCTAATCAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.12
Consensus pattern (16 bp):
ACACAAAGTACTGAGC
Found at i:72488 original size:23 final size:23
Alignment explanation
Indices: 72452--72663 Score: 245
Period size: 23 Copynumber: 9.2 Consensus size: 23
72442 ACAAAGTACT
* *
72452 GAGCACAGAAAGTGCTAATCAGA
1 GAGCACACACAGTGCTAATCAGA
72475 GAGCACACACAGTGCTGAA-CAGA
1 GAGCACACACAGTGCT-AATCAGA
72498 GAGCACACACAGTGCTGAA-CAGA
1 GAGCACACACAGTGCT-AATCAGA
*
72521 GAGCACACACAGTACTAATCAGA
1 GAGCACACACAGTGCTAATCAGA
* *
72544 GAGCACACACAATGCTAAACAGA
1 GAGCACACACAGTGCTAATCAGA
* *
72567 GAGCAAACATAGTGCTAATCAGA
1 GAGCACACACAGTGCTAATCAGA
*
72590 GAGCACACGA-AGTGCTAATCAAA
1 GAGCACAC-ACAGTGCTAATCAGA
*
72613 GAGCACATGA-AGTGCTAATAACAGA
1 GAGCACA-CACAGTGCTAAT--CAGA
*
72638 GAGCACACATAGTGCT-ATCAGA
1 GAGCACACACAGTGCTAATCAGA
72660 GAGC
1 GAGC
72664 GCGCTAGTGT
Statistics
Matches: 167, Mismatches: 15, Indels: 15
0.85 0.08 0.08
Matches are distributed among these distances:
22 10 0.06
23 135 0.81
24 6 0.04
25 16 0.10
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.13
Consensus pattern (23 bp):
GAGCACACACAGTGCTAATCAGA
Done.