Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013173.1 Kokia drynarioides strain JFW-HI SEQ_128192, 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: 49791
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:574 original size:23 final size:23
Alignment explanation
Indices: 499--672 Score: 172
Period size: 23 Copynumber: 7.3 Consensus size: 23
489 ACACTAGCGC
* *
499 GCTCTTTGATTAACACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* * *
522 GCTCTCTGTTTAGC-TTGTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
545 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
*
570 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* * *
593 GCTCTCTGACTAGTACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
616 ACTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
639 GCTCTCTG-TTGCCCAGCACTGTGTGT
1 GCTCTCTGATT----AGCACTGTGTGT
665 GCTCTCTG
1 GCTCTCTG
673 TTTGTTCCGT
Statistics
Matches: 126, Mismatches: 17, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
22 6 0.05
23 81 0.64
25 15 0.12
26 24 0.19
ACGTcount: A:0.11, C:0.24, G:0.23, T:0.43
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:14399 original size:17 final size:17
Alignment explanation
Indices: 14348--14405 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
14338 AATTACTTTC
*
14348 ATATTAAATTAATA-TA
1 ATATTAAATTAAAATTA
* * *
14364 ATATT-TATTAAGATAA
1 ATATTAAATTAAAATTA
*
14380 ATATTAGATTAAAATTA
1 ATATTAAATTAAAATTA
14397 ATATTAAAT
1 ATATTAAAT
14406 CTTATTAAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
15 6 0.18
16 11 0.33
17 16 0.48
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
ATATTAAATTAAAATTA
Found at i:14823 original size:11 final size:10
Alignment explanation
Indices: 14809--14866 Score: 53
Period size: 10 Copynumber: 5.6 Consensus size: 10
14799 AAATTTTATT
14809 AAAATCAATAA
1 AAAAT-AATAA
*
14820 AAAATATTAA
1 AAAATAATAA
*
14830 AAAATACAGAA
1 AAAATA-ATAA
*
14841 AAAATATTAA
1 AAAATAATAA
* *
14851 AAAATTATAG
1 AAAATAATAA
14861 AAAATA
1 AAAATA
14867 TTTTAAATTT
Statistics
Matches: 37, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
10 24 0.65
11 13 0.35
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.22
Consensus pattern (10 bp):
AAAATAATAA
Found at i:14833 original size:21 final size:20
Alignment explanation
Indices: 14809--14868 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 20
14799 AAATTTTATT
14809 AAAATCAATAAAAAATATTAA
1 AAAAT-AATAAAAAATATTAA
*
14830 AAAATACAGAAAAAATATTAA
1 AAAATA-ATAAAAAATATTAA
* *
14851 AAAATTATAGAAAATATT
1 AAAATAATAAAAAATATT
14869 TTAAATTTGG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 11 0.32
21 23 0.68
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.25
Consensus pattern (20 bp):
AAAATAATAAAAAATATTAA
Found at i:14872 original size:22 final size:21
Alignment explanation
Indices: 14818--14873 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
14808 TAAAATCAAT
14818 AAAAAATATTAAAAAATACAG
1 AAAAAATATTAAAAAATACAG
*
14839 AAAAAATATTAAAAAATTATAG
1 AAAAAATATTAAAAAA-TACAG
* *
14861 AAAATATTTTAAA
1 AAAAAATATTAAA
14874 TTTGGAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
21 16 0.52
22 15 0.48
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.27
Consensus pattern (21 bp):
AAAAAATATTAAAAAATACAG
Found at i:14923 original size:20 final size:21
Alignment explanation
Indices: 14890--14955 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
14880 AAAAAAATAG
* *
14890 AAAAATGATTAAATTA-ATAA
1 AAAAATTATAAAATTAGATAA
14910 AAAAATTATAAAATATAGA-AA
1 AAAAATTATAAAAT-TAGATAA
14931 AAAAATTATAAAATATAGA-AA
1 AAAAATTATAAAAT-TAGATAA
14952 AAAA
1 AAAA
14956 TTAAATAACA
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
20 12 0.29
21 29 0.69
22 1 0.02
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (21 bp):
AAAAATTATAAAATTAGATAA
Found at i:14958 original size:20 final size:21
Alignment explanation
Indices: 14908--14955 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
14898 TTAAATTAAT
14908 AAAAAAATTATAAAATATAGA
1 AAAAAAATTATAAAATATAGA
14929 AAAAAAATTATAAAATATAGA
1 AAAAAAATTATAAAATATAGA
14950 AAAAAA
1 AAAAAA
14956 TTAAATAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (21 bp):
AAAAAAATTATAAAATATAGA
Found at i:15830 original size:28 final size:27
Alignment explanation
Indices: 15766--15827 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
15756 GTAATTAATT
*
15766 AATATTTAAAAATTAAAAATTCAAAAA
1 AATATTTTAAAATTAAAAATTCAAAAA
*
15793 AATATTTTAAAATTAAAAATAT-ATAAA
1 AATATTTTAAAATTAAAAAT-TCAAAAA
15820 AATATTTT
1 AATATTTT
15828 TAATTTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (27 bp):
AATATTTTAAAATTAAAAATTCAAAAA
Found at i:17786 original size:23 final size:23
Alignment explanation
Indices: 17760--17811 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
17750 TTAATTTAAC
* *
17760 TTAATCGAATATGTTCACGAACA
1 TTAATCAAACATGTTCACGAACA
* *
17783 TTAAACAAACATGTTCATGAACA
1 TTAATCAAACATGTTCACGAACA
17806 TATAAT
1 T-TAAT
17812 TGAACATGAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
23 20 0.87
24 3 0.13
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (23 bp):
TTAATCAAACATGTTCACGAACA
Found at i:17959 original size:23 final size:24
Alignment explanation
Indices: 17929--17975 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
17919 TCATTAATAA
17929 ATAAACGAGCC-ATAAATGAGCTT
1 ATAAACGAGCCAATAAATGAGCTT
17952 ATAAACGAGCCAATAAATGAGCTT
1 ATAAACGAGCCAATAAATGAGCTT
17976 GTTCGTAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.45, C:0.17, G:0.17, T:0.21
Consensus pattern (24 bp):
ATAAACGAGCCAATAAATGAGCTT
Found at i:19694 original size:13 final size:15
Alignment explanation
Indices: 19664--19696 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
19654 AAAAATATAA
19664 AATTATAAAAAATGT
1 AATTATAAAAAATGT
19679 AATT-TAAAAAAT-T
1 AATTATAAAAAATGT
19692 AATTA
1 AATTA
19697 ATTGTTACGT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 5 0.29
14 8 0.47
15 4 0.24
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (15 bp):
AATTATAAAAAATGT
Found at i:20079 original size:19 final size:19
Alignment explanation
Indices: 20057--20124 Score: 77
Period size: 19 Copynumber: 3.5 Consensus size: 19
20047 AATTACAAAA
*
20057 AAAAATTTAA-ATAATTTT
1 AAAAATTCAACATAATTTT
20075 CAAAAATTCAACATAATTTT
1 -AAAAATTCAACATAATTTT
*
20095 AAAAATTCAAAAT-ATTTAT
1 AAAAATTCAACATAATTT-T
20114 AAAAAATTCAA
1 -AAAAATTCAA
20125 GTTTTATATC
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
18 4 0.09
19 22 0.50
20 18 0.41
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAAATTCAACATAATTTT
Found at i:20184 original size:21 final size:21
Alignment explanation
Indices: 20138--20194 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
20128 TTATATCTTT
**
20138 TAAAAAATTCTAAAAATTAAA
1 TAAAAAATTCTAAAAACCAAA
* *
20159 AAAAAAATTCTAAAAACCATA
1 TAAAAAATTCTAAAAACCAAA
*
20180 TAAAAAAGT-TAAAAA
1 TAAAAAATTCTAAAAA
20195 ATTTAAAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 6 0.20
21 24 0.80
ACGTcount: A:0.68, C:0.07, G:0.02, T:0.23
Consensus pattern (21 bp):
TAAAAAATTCTAAAAACCAAA
Found at i:23099 original size:16 final size:15
Alignment explanation
Indices: 23070--23109 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
23060 TAGGTAATGG
23070 AAATAT-AATAATTT
1 AAATATAAATAATTT
23084 AAATATAAAGTAATTT
1 AAATATAAA-TAATTT
23100 -AATATAAATA
1 AAATATAAATA
23110 TATATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 8 0.33
15 10 0.42
16 6 0.25
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (15 bp):
AAATATAAATAATTT
Found at i:23142 original size:2 final size:2
Alignment explanation
Indices: 23101--23130 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
23091 AAGTAATTTA
*
23101 AT AT AA 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
23131 TTTTTAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:26491 original size:52 final size:52
Alignment explanation
Indices: 26397--26539 Score: 182
Period size: 52 Copynumber: 2.8 Consensus size: 52
26387 ATTTCACTTC
* * *
26397 ATTCATATACTCATGA-GACACATAGCCACCGGACCT-TATAATCCACAAGGG
1 ATTCATATACTCATGATGACACATAGTCAACGGACCTCT-TAATCCACAAAGG
* * **
26448 ATTCATATACTCATGATGACACAGAGTCATCGGACCTCTTAATCCGTAAAGG
1 ATTCATATACTCATGATGACACATAGTCAACGGACCTCTTAATCCACAAAGG
* *
26500 ATTCATATATTCATGATGACACTTAGTCAACGGACCTCTT
1 ATTCATATACTCATGATGACACATAGTCAACGGACCTCTT
26540 CGTTTATGGC
Statistics
Matches: 80, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
51 16 0.20
52 63 0.79
53 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.27
Consensus pattern (52 bp):
ATTCATATACTCATGATGACACATAGTCAACGGACCTCTTAATCCACAAAGG
Found at i:31919 original size:17 final size:17
Alignment explanation
Indices: 31899--31947 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
31889 GAACCCAAAT
*
31899 TTAAATTTTAATTTATC
1 TTAAATTTAAATTTATC
* *
31916 TTAAGTTTAAATTTATT
1 TTAAATTTAAATTTATC
* *
31933 TTGATTTTAAATTTA
1 TTAAATTTAAATTTA
31948 AAAATTAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (17 bp):
TTAAATTTAAATTTATC
Found at i:31942 original size:23 final size:23
Alignment explanation
Indices: 31895--31949 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
31885 AATTGAACCC
31895 AAATTTAAATTTTAATTTATCTT
1 AAATTTAAATTTTAATTTATCTT
* * *
31918 AAGTTTAAA-TTTATTTTGATTTT
1 AAATTTAAATTTTAATTT-ATCTT
31941 AAATTTAAA
1 AAATTTAAA
31950 AATTAATTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 7 0.26
23 20 0.74
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.55
Consensus pattern (23 bp):
AAATTTAAATTTTAATTTATCTT
Found at i:31978 original size:15 final size:15
Alignment explanation
Indices: 31954--31984 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
31944 TTTAAAAATT
31954 AATTAAAAAGTCCAA
1 AATTAAAAAGTCCAA
*
31969 AATTACAAAGTCCAA
1 AATTAAAAAGTCCAA
31984 A
1 A
31985 TCACAAACCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.16, G:0.06, T:0.19
Consensus pattern (15 bp):
AATTAAAAAGTCCAA
Found at i:32563 original size:9 final size:9
Alignment explanation
Indices: 32549--32580 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
32539 TGTTTTAACA
32549 AATAAATAT
1 AATAAATAT
32558 AATAAATAT
1 AATAAATAT
32567 AATAAATAAT
1 AATAAAT-AT
32577 AATA
1 AATA
32581 TTAAGTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 16 0.73
10 6 0.27
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
AATAAATAT
Found at i:32970 original size:21 final size:22
Alignment explanation
Indices: 32941--32986 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
32931 GCAAAACCCT
*
32941 TTTAGATCTAG-GCTAGATCGTG
1 TTTAGATCTAGACCTAGATC-TG
32963 TTTA-ATCTAGACCTAGATCTG
1 TTTAGATCTAGACCTAGATCTG
32984 TTT
1 TTT
32987 TAAAAGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (22 bp):
TTTAGATCTAGACCTAGATCTG
Found at i:32988 original size:22 final size:20
Alignment explanation
Indices: 32940--32989 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 20
32930 AGCAAAACCC
*
32940 TTTTAGATCTAGGCTAGATCG
1 TTTTA-ATCTAGCCTAGATCG
32961 TGTTTAATCTAGACCTAGATCTG
1 T-TTTAATCTAG-CCTAGATC-G
32984 TTTTAA
1 TTTTAA
32990 AAGAAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 7 0.28
22 16 0.64
23 2 0.08
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.42
Consensus pattern (20 bp):
TTTTAATCTAGCCTAGATCG
Found at i:33850 original size:29 final size:30
Alignment explanation
Indices: 33696--34052 Score: 331
Period size: 30 Copynumber: 12.2 Consensus size: 30
33686 TAGAAATCAT
* * *
33696 ATTTTAACCCTCAAACTTTTCCAAAATTGC
1 ATTTTAACCCTTAAACTTTTCAAAAATTAC
* * * *
33726 ATTTTGACCCTTAAACTTTCCAAAAATCAT
1 ATTTTAACCCTTAAACTTTTCAAAAATTAC
* * *
33756 ATTTTTACCATTAAACTTTTCCAAAATTAC
1 ATTTTAACCCTTAAACTTTTCAAAAATTAC
* *
33786 ATTTTAACCCCTAAAACTTTTCCAAAATTAC
1 ATTTTAA-CCCTTAAACTTTTCAAAAATTAC
*
33817 ATTTTAACTCTTAAACTTTTC-AAAATTAC
1 ATTTTAACCCTTAAACTTTTCAAAAATTAC
* * *
33846 ATTTTAACCCCTAAACTTTTCCAAAATCAC
1 ATTTTAACCCTTAAACTTTTCAAAAATTAC
*
33876 ATTTTAACCC-TAAA--TTCCAAAAAATTAC
1 ATTTTAACCCTTAAACTTTTC-AAAAATTAC
* * **
33904 ACTTT-ACCCCTAAACTTTAAAAAAATTAC
1 ATTTTAACCCTTAAACTTTTCAAAAATTAC
* * *
33933 ATTTTGA-CCTCAAAC-TTCCAAAAATTAC
1 ATTTTAACCCTTAAACTTTTCAAAAATTAC
* *
33961 ATTTT-ACCC-CAAACTTTTCTAAAATTAC
1 ATTTTAACCCTTAAACTTTTCAAAAATTAC
* *
33989 ATTTTTACCCTTAAAC-TTCCAAAAATCT-C
1 ATTTTAACCCTTAAACTTTTCAAAAAT-TAC
* * *
34018 ATTTTTACCCCTAAACTTCTCAAAAATTAC
1 ATTTTAACCCTTAAACTTTTCAAAAATTAC
34048 ATTTT
1 ATTTT
34053 TGCCCTTGAA
Statistics
Matches: 273, Mismatches: 40, Indels: 28
0.80 0.12 0.08
Matches are distributed among these distances:
27 13 0.05
28 49 0.18
29 79 0.29
30 104 0.38
31 28 0.10
ACGTcount: A:0.38, C:0.24, G:0.01, T:0.37
Consensus pattern (30 bp):
ATTTTAACCCTTAAACTTTTCAAAAATTAC
Found at i:34053 original size:59 final size:59
Alignment explanation
Indices: 33696--34072 Score: 369
Period size: 57 Copynumber: 6.4 Consensus size: 59
33686 TAGAAATCAT
* * * * * * * *
33696 ATTTTAACCCTCAAACTTTTCC-AAAATTGCATTTTGACCCTTAAACTTTCCAAAAATCAT
1 ATTTTTACCCTTAAAC--TTCCAAAAATTACATTTTTACCCCTAAACTTTTCAAAAATTAC
* * *
33756 ATTTTTACCATTAAACTTTTCC-AAAATTACATTTTAACCCCTAAAACTTTTCCAAAATTAC
1 ATTTTTACCCTTAAAC--TTCCAAAAATTACATTTTTACCCCT-AAACTTTTCAAAAATTAC
* * * * * *
33817 ATTTTAACTCTTAAACTTTTC-AAAATTACATTTTAACCCCTAAACTTTTCCAAAATCAC
1 ATTTTTACCCTTAAAC-TTCCAAAAATTACATTTTTACCCCTAAACTTTTCAAAAATTAC
* * **
33876 ATTTTAACCC-TAAA-TTCCAAAAAATTACA-CTTTACCCCTAAACTTTAAAAAAATTAC
1 ATTTTTACCCTTAAACTTCC-AAAAATTACATTTTTACCCCTAAACTTTTCAAAAATTAC
* * *
33933 ATTTTGA-CCTCAAACTTCCAAAAATTACA-TTTTACCCC-AAACTTTTCTAAAATTAC
1 ATTTTTACCCTTAAACTTCCAAAAATTACATTTTTACCCCTAAACTTTTCAAAAATTAC
*
33989 ATTTTTACCCTTAAACTTCCAAAAATCT-CATTTTTACCCCTAAACTTCTCAAAAATTAC
1 ATTTTTACCCTTAAACTTCCAAAAAT-TACATTTTTACCCCTAAACTTTTCAAAAATTAC
* *
34048 ATTTTTGCCCTTGAACTTCCAAAAA
1 ATTTTTACCCTTAAACTTCCAAAAA
34073 AAAAAAAATC
Statistics
Matches: 273, Mismatches: 35, Indels: 19
0.83 0.11 0.06
Matches are distributed among these distances:
56 26 0.10
57 68 0.25
58 27 0.10
59 65 0.24
60 60 0.22
61 27 0.10
ACGTcount: A:0.38, C:0.24, G:0.01, T:0.37
Consensus pattern (59 bp):
ATTTTTACCCTTAAACTTCCAAAAATTACATTTTTACCCCTAAACTTTTCAAAAATTAC
Found at i:34089 original size:37 final size:37
Alignment explanation
Indices: 34039--34109 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
34029 TAAACTTCTC
* *
34039 AAAAATTACATTTTTGCCCTTGAACTTCCAAAAAAAA
1 AAAAATCACATTTTGGCCCTTGAACTTCCAAAAAAAA
*
34076 AAAAATCATATTTTGGCCCTTGAACTTCCAAAAA
1 AAAAATCACATTTTGGCCCTTGAACTTCCAAAAA
34110 TCACATTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.44, C:0.20, G:0.07, T:0.30
Consensus pattern (37 bp):
AAAAATCACATTTTGGCCCTTGAACTTCCAAAAAAAA
Found at i:34118 original size:29 final size:29
Alignment explanation
Indices: 34076--34137 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
34066 CCAAAAAAAA
* * *
34076 AAAAATCATATTTTGGCCCTTGAACTTCC
1 AAAAATCACATTTTGACCCTCGAACTTCC
* *
34105 AAAAATCACATTTTTACCCTCGAATTTCC
1 AAAAATCACATTTTGACCCTCGAACTTCC
34134 AAAA
1 AAAA
34138 TTACCATTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.32
Consensus pattern (29 bp):
AAAAATCACATTTTGACCCTCGAACTTCC
Found at i:34153 original size:29 final size:29
Alignment explanation
Indices: 34116--34245 Score: 76
Period size: 28 Copynumber: 4.5 Consensus size: 29
34106 AAAATCACAT
*
34116 TTTTA-CCCTCGAATTTCCAAAATTACCA
1 TTTTACCCCTCAAATTTCCAAAATTACCA
* *
34144 TTTTACCCCTTGACA--TCCAAAAGTTACCA
1 TTTTACCCC-TCAAATTTCCAAAA-TTACCA
* * *
34173 TTCTTGCTCC-CAAATTTCCAAAAGT-CACA
1 TT-TTACCCCTCAAATTTCCAAAATTAC-CA
*
34202 TTTTCGACCCCTAAAACTTTCCAAAATTA-CA
1 TTTT--ACCCCTCAAA-TTTCCAAAATTACCA
*
34233 TTTTA-ACCTCAAA
1 TTTTACCCCTCAAA
34246 CTCTTCGAAA
Statistics
Matches: 76, Mismatches: 14, Indels: 24
0.67 0.12 0.21
Matches are distributed among these distances:
28 23 0.30
29 17 0.22
30 17 0.22
31 9 0.12
32 10 0.13
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (29 bp):
TTTTACCCCTCAAATTTCCAAAATTACCA
Found at i:36874 original size:52 final size:52
Alignment explanation
Indices: 36794--36922 Score: 186
Period size: 52 Copynumber: 2.5 Consensus size: 52
36784 ATTTCACTTC
** * * * *
36794 ATTCATATACTCACGATGACACAGAGTCATCGGACCTCTTTATCTGTAAGGG
1 ATTCATATACTCACGATGACACTTAGTCATCAGACCTCTTAATCCGTAAAGG
*
36846 ATTCATATACTCACGATGACACTTAGTCATCAGAGCTCTTAATCCGTAAAGG
1 ATTCATATACTCACGATGACACTTAGTCATCAGACCTCTTAATCCGTAAAGG
*
36898 ATTCATATACTTACGATGACACTTA
1 ATTCATATACTCACGATGACACTTA
36923 ATAATCGAAC
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (52 bp):
ATTCATATACTCACGATGACACTTAGTCATCAGACCTCTTAATCCGTAAAGG
Found at i:39896 original size:19 final size:19
Alignment explanation
Indices: 39874--39922 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 19
39864 ATCACAAAAT
*
39874 AATTCAAAATAATTTTTAA-
1 AATTCAAAAT-ATTTATAAG
39893 AATTCAAAATATTTATAAG
1 AATTCAAAATATTTATAAG
39912 AATTCCAAAAT
1 AATT-CAAAAT
39923 TTTTTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 7 0.26
19 14 0.52
20 6 0.22
ACGTcount: A:0.53, C:0.08, G:0.02, T:0.37
Consensus pattern (19 bp):
AATTCAAAATATTTATAAG
Found at i:41536 original size:18 final size:16
Alignment explanation
Indices: 41504--41537 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
41494 ATTTAATTCG
41504 ATTAATTAGTTGGTTA
1 ATTAATTAGTTGGTTA
41520 ATTAATCTAGTTTGGTTA
1 ATTAAT-TAG-TTGGTTA
41538 GAGGTCGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 3 0.19
18 7 0.44
ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50
Consensus pattern (16 bp):
ATTAATTAGTTGGTTA
Found at i:43066 original size:24 final size:22
Alignment explanation
Indices: 43033--43091 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 22
43023 TAATCTTTTA
*
43033 AAAATTATAAAGATATAAATTATT
1 AAAATAATAAA-AT-TAAATTATT
* *
43057 AAAATAATAAAATTACATTTTT
1 AAAATAATAAAATTAAATTATT
*
43079 AAAAT-TTAAAATT
1 AAAATAATAAAATT
43092 TATGTTATAG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 7 0.23
22 12 0.39
23 2 0.06
24 10 0.32
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (22 bp):
AAAATAATAAAATTAAATTATT
Found at i:43806 original size:60 final size:60
Alignment explanation
Indices: 43645--43816 Score: 199
Period size: 59 Copynumber: 2.9 Consensus size: 60
43635 TTAATATAAT
* *
43645 ATTTGGTATCTAAACTTGATACTT-TTTCTTAATTTGGTACTTAAAATTTTTTT-GACCCA
1 ATTTGGTACCTAAACTTGATACTTATTTCTTAATTTGGTACCT-AAATTTTTTTAGACCCA
* * * * *
43704 ATTTGGTTCTTAAACTTGACACTTA-TTCCTAATTTGGTACCTAAATTTTTTTAGATCCA
1 ATTTGGTACCTAAACTTGATACTTATTTCTTAATTTGGTACCTAAATTTTTTTAGACCCA
* * **
43763 ATTTGGTACCTGAACTTGATA-TATATTTTTTAATTTGGTACCTAAGCTTTTTTA
1 ATTTGGTACCTAAACTTGATACT-TATTTCTTAATTTGGTACCTAAATTTTTTTA
43817 AGGCTCAATT
Statistics
Matches: 94, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
58 11 0.12
59 59 0.63
60 24 0.26
ACGTcount: A:0.27, C:0.14, G:0.11, T:0.48
Consensus pattern (60 bp):
ATTTGGTACCTAAACTTGATACTTATTTCTTAATTTGGTACCTAAATTTTTTTAGACCCA
Found at i:49123 original size:58 final size:59
Alignment explanation
Indices: 49022--49299 Score: 206
Period size: 58 Copynumber: 4.8 Consensus size: 59
49012 GTTTAGGGTT
* * *
49022 AAAATTGGAATTTTTAGACATTCG-GGGCT-AAAAGGGTAA-TTTTGAGAGTTTCGAGGTC
1 AAAA-TGGAATTTTTGGACATCCGAGGG-TAAAAATGGTAATTTTTGAGAGTTTCGAGGTC
* * *
49080 GAAAATGGAGTTTTTGGACATCCGA-GG-AAAAATGGTAATTTTTGAAAGTTTCGGGGTC
1 -AAAATGGAATTTTTGGACATCCGAGGGTAAAAATGGTAATTTTTGAGAGTTTCGAGGTC
* ** * *
49138 AAAAATGGAAATTTTGGAGGTTCGAGGGTAAAAATGG-AATTTTTG-GAAGTTTCAAGGTC
1 -AAAATGGAATTTTTGGACATCCGAGGGTAAAAATGGTAATTTTTGAG-AGTTTCGAGGTC
** * * *
49197 AAAATGGAATTTTTGGA-AGT-TTAGGGGT-AAAATTGAAATTTTT-AGAAGTTT-TATGGTC
1 AAAATGGAATTTTTGGACA-TCCGA-GGGTAAAAATGGTAATTTTTGAG-AGTTTCGA-GGTC
*
49255 AAAAATGGAATTTTTGGA-AGTTCGAGGGTAAAAAT-GTAATTTTTG
1 -AAAATGGAATTTTTGGACA-TCCGAGGGTAAAAATGGTAATTTTTG
49300 GATAGTTTAG
Statistics
Matches: 180, Mismatches: 24, Indels: 29
0.77 0.10 0.12
Matches are distributed among these distances:
57 17 0.09
58 93 0.52
59 56 0.31
60 14 0.08
ACGTcount: A:0.34, C:0.05, G:0.27, T:0.34
Consensus pattern (59 bp):
AAAATGGAATTTTTGGACATCCGAGGGTAAAAATGGTAATTTTTGAGAGTTTCGAGGTC
Found at i:49171 original size:29 final size:29
Alignment explanation
Indices: 49081--49306 Score: 203
Period size: 29 Copynumber: 7.7 Consensus size: 29
49071 TTCGAGGTCG
* *
49081 AAAATGGAGTTTTTGGACA-TCCGA-GG-A
1 AAAATGGAATTTTTGGA-AGTTCGAGGGTA
*
49108 AAAATGGTAATTTTTGAAAGTTTCG-GGGTCA
1 AAAATGG-AATTTTTGGAAG-TTCGAGGGT-A
* *
49139 AAAATGGAAATTTTGGAGGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
* *
49168 AAAATGGAATTTTTGGAAGTTTC-AAGGTC
1 AAAATGGAATTTTTGGAAG-TTCGAGGGTA
*
49197 AAAATGGAATTTTTGGAAGTT-TAGGGGTA
1 AAAATGGAATTTTTGGAAGTTCGA-GGGTA
* * * ** *
49226 AAATTGAAATTTTTAGAAGTTTTATGGTCA
1 AAAATGGAATTTTTGGAAGTTCGAGGGT-A
49256 AAAATGGAATTTTTGGAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
*
49285 AAAATGTAATTTTTGGATAGTT
1 AAAATGGAATTTTTGGA-AGTT
49307 TAGGGACCTC
Statistics
Matches: 163, Mismatches: 23, Indels: 23
0.78 0.11 0.11
Matches are distributed among these distances:
27 8 0.05
28 11 0.07
29 91 0.56
30 45 0.28
31 8 0.05
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.35
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTCGAGGGTA
Found at i:49182 original size:117 final size:116
Alignment explanation
Indices: 49068--49307 Score: 295
Period size: 117 Copynumber: 2.0 Consensus size: 116
49058 TAATTTTGAG
* * * *
49068 AGTTTCGAGGTCGAAAATGGAGTTTTTGGACA-TCCGAGGAAAAATGGTAATTTTT-GAAAGTTT
1 AGTTTCAAGGTC-AAAATGGAATTTTTGGA-AGTCAGAGGAAAAATGGAAATTTTTAG-AAGTTT
* *
49131 CGGGGTCAAAAATGGAAATTTTGGAGGTTCGAGGGTAAAAATGGAATTTTTGGA
63 CAGGGTCAAAAATGGAAATTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGA
* * * * *
49185 AGTTTCAAGGTCAAAATGGAATTTTTGGAAGTTTAGGGGTAAAATTGAAATTTTTAGAAGTTTTA
1 AGTTTCAAGGTCAAAATGGAATTTTTGGAAG-TCAGAGGAAAAATGGAAATTTTTAGAAGTTTCA
* * *
49250 TGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGGA
65 GGGTCAAAAATGGAAATTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGA
49302 TAGTTT
1 -AGTTT
49308 AGGGACCTCC
Statistics
Matches: 105, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
115 1 0.01
116 16 0.15
117 82 0.78
118 6 0.06
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.35
Consensus pattern (116 bp):
AGTTTCAAGGTCAAAATGGAATTTTTGGAAGTCAGAGGAAAAATGGAAATTTTTAGAAGTTTCAG
GGTCAAAAATGGAAATTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGA
Found at i:49286 original size:59 final size:59
Alignment explanation
Indices: 49068--49307 Score: 256
Period size: 58 Copynumber: 4.1 Consensus size: 59
49058 TAATTTTGAG
* * * * * *
49068 AGTTTCGAGGTCGAAAATGGAGTTTTTGGACA-TCCGA-GG-AAAAATGGTAATTTTTGAA
1 AGTTTCAAGGTCAAAAATGGAATTTTTGGA-AGTTCGAGGGTAAAAAT-GAAATTTTTGGA
** * * *
49126 AGTTTCGGGGTCAAAAATGGAAATTTTGGAGGTTCGAGGGTAAAAATGGAATTTTTGGA
1 AGTTTCAAGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGAAATTTTTGGA
* * *
49185 AGTTTCAAGGTC-AAAATGGAATTTTTGGAAGTT-TAGGGGTAAAATTGAAATTTTTAGA
1 AGTTTCAAGGTCAAAAATGGAATTTTTGGAAGTTCGA-GGGTAAAAATGAAATTTTTGGA
* * *
49243 AGTTTTATGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGGA
1 AGTTTCAAGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGAAATTTTTGGA
49302 TAGTTT
1 -AGTTT
49308 AGGGACCTCC
Statistics
Matches: 153, Mismatches: 22, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
57 1 0.01
58 78 0.51
59 62 0.41
60 12 0.08
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.35
Consensus pattern (59 bp):
AGTTTCAAGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGAAATTTTTGGA
Done.