Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013011.1 Kokia drynarioides strain JFW-HI SEQ_128029, 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: 152232
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 201 characters in sequence are not A, C, G, or T
Found at i:5143 original size:33 final size:33
Alignment explanation
Indices: 5075--5147 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
5065 TGGAAAAGCT
* * *
5075 AATATTTTCTGTTGTTTTGATGAATCTGTGTAA
1 AATATTTTCTGTTGTTTGGATGAATCTCTGAAA
* *
5108 AATATTTTCTGTTGTTTGGCTG-ATTTCCTGAAA
1 AATATTTTCTGTTGTTTGGATGAATCT-CTGAAA
5141 AATATTT
1 AATATTT
5148 CATAAAAGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
32 3 0.09
33 31 0.91
ACGTcount: A:0.25, C:0.08, G:0.16, T:0.51
Consensus pattern (33 bp):
AATATTTTCTGTTGTTTGGATGAATCTCTGAAA
Found at i:5281 original size:15 final size:16
Alignment explanation
Indices: 5258--5305 Score: 51
Period size: 19 Copynumber: 2.8 Consensus size: 16
5248 TAATCATGTT
5258 TTAATTTTAATTAATC
1 TTAATTTTAATTAATC
*
5274 TTAATTTACTTAATTAAGC
1 TTAA-TT--TTAATTAATC
5293 TTAATTGTTAATT
1 TTAATT-TTAATT
5306 TTGTACATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 4 0.15
17 8 0.30
18 2 0.07
19 13 0.48
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.54
Consensus pattern (16 bp):
TTAATTTTAATTAATC
Found at i:5281 original size:21 final size:21
Alignment explanation
Indices: 5234--5307 Score: 62
Period size: 21 Copynumber: 3.5 Consensus size: 21
5224 GATAAAGCTT
* *
5234 ATTTATATTTTAATTAATCATG
1 ATTTA-ATTTTAATTAATCTTA
*
5256 TTTTAATTTTAATTAATCTTA
1 ATTTAATTTTAATTAATCTTA
* *
5277 ATTT-A-CTTAATTAAGCTTA
1 ATTTAATTTTAATTAATCTTA
5296 ATTGTTAATTTT
1 A-T-TTAATTTT
5308 GTACATTAGG
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
19 13 0.32
20 2 0.05
21 19 0.46
22 5 0.12
23 2 0.05
ACGTcount: A:0.34, C:0.05, G:0.04, T:0.57
Consensus pattern (21 bp):
ATTTAATTTTAATTAATCTTA
Found at i:8523 original size:9 final size:9
Alignment explanation
Indices: 8509--8611 Score: 54
Period size: 9 Copynumber: 11.6 Consensus size: 9
8499 CTACTTTTAT
8509 TAAAAATTA
1 TAAAAATTA
8518 TAAAAA-TA
1 TAAAAATTA
*
8526 T-AAAATCAA
1 TAAAAAT-TA
**
8535 TAAAAGCTA
1 TAAAAATTA
8544 TAAAAAATTAA
1 T-AAAAATT-A
8555 TAGAAAATT-
1 TA-AAAATTA
*
8564 TAAATA-T-
1 TAAAAATTA
8571 TAAAAATTA
1 TAAAAATTA
* *
8580 GAAAAAATA
1 TAAAAATTA
**
8589 TAAAAATCG
1 TAAAAATTA
*
8598 TAAAAAATA
1 TAAAAATTA
8607 TAAAA
1 TAAAA
8612 TTTTATAAAT
Statistics
Matches: 69, Mismatches: 17, Indels: 16
0.68 0.17 0.16
Matches are distributed among these distances:
7 10 0.14
8 7 0.10
9 35 0.51
10 9 0.13
11 8 0.12
ACGTcount: A:0.67, C:0.03, G:0.04, T:0.26
Consensus pattern (9 bp):
TAAAAATTA
Found at i:8594 original size:18 final size:18
Alignment explanation
Indices: 8565--8611 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
8555 TAGAAAATTT
8565 AAATATTAAAAATTAG-AAA
1 AAATA-TAAAAA-TAGTAAA
*
8584 AAATATAAAAATCGTAAA
1 AAATATAAAAATAGTAAA
8602 AAATATAAAA
1 AAATATAAAA
8612 TTTTATAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 2 0.08
18 19 0.73
19 5 0.19
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.23
Consensus pattern (18 bp):
AAATATAAAAATAGTAAA
Found at i:12734 original size:12 final size:12
Alignment explanation
Indices: 12711--12827 Score: 91
Period size: 12 Copynumber: 10.2 Consensus size: 12
12701 ATAACTAAAG
*
12711 TAACAACCAAAA
1 TAACAACAAAAA
*
12723 TAGCAACAAAAA
1 TAACAACAAAAA
*
12735 TAACAGC-AAAA
1 TAACAACAAAAA
12746 T---AACAAAAA
1 TAACAACAAAAA
*
12755 TAACAA-TAAAA
1 TAACAACAAAAA
* *
12766 CAGCAACAAAAA
1 TAACAACAAAAA
* **
12778 TAATAGTAAAAA
1 TAACAACAAAAA
12790 TAACAACAAAAA
1 TAACAACAAAAA
* *
12802 CAACAATAAAAA
1 TAACAACAAAAA
*
12814 TAACAATAAAAA
1 TAACAACAAAAA
12826 TA
1 TA
12828 GCATTAAAAT
Statistics
Matches: 80, Mismatches: 20, Indels: 10
0.73 0.18 0.09
Matches are distributed among these distances:
8 2 0.03
9 5 0.06
11 13 0.16
12 60 0.75
ACGTcount: A:0.70, C:0.15, G:0.03, T:0.12
Consensus pattern (12 bp):
TAACAACAAAAA
Found at i:12738 original size:44 final size:43
Alignment explanation
Indices: 12686--12807 Score: 138
Period size: 44 Copynumber: 2.8 Consensus size: 43
12676 AAAAACGTAT
* * * * *
12686 AAAAATAACATCCAAATAACTAAAGTAACAACCAAAATAGCAAC
1 AAAAATAACAGCAAAATAACAAAAATAACAA-CAAAACAGCAAC
*
12730 AAAAATAACAGCAAAATAACAAAAATAACAATAAAACAGCAAC
1 AAAAATAACAGCAAAATAACAAAAATAACAACAAAACAGCAAC
* *
12773 AAAAATAATAGTAAAAATAACAACAAA-AACAACAA
1 AAAAATAACAG-CAAAATAACAA-AAATAACAACAA
12808 TAAAAATAAC
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
43 20 0.30
44 44 0.66
45 3 0.04
ACGTcount: A:0.68, C:0.16, G:0.04, T:0.11
Consensus pattern (43 bp):
AAAAATAACAGCAAAATAACAAAAATAACAACAAAACAGCAAC
Found at i:12745 original size:11 final size:9
Alignment explanation
Indices: 12727--12842 Score: 51
Period size: 9 Copynumber: 12.6 Consensus size: 9
12717 CCAAAATAGC
12727 AACAAAAAT
1 AACAAAAAT
12736 AACAGCAAAAT
1 AACA--AAAAT
12747 AACAAAAAT
1 AACAAAAAT
*
12756 AACAATAA-
1 AACAAAAAT
** *
12764 AACAGCAAC
1 AACAAAAAT
12773 AA-AAATAAT
1 AACAAA-AAT
**
12782 AGTAAAAAT
1 AACAAAAAT
12791 AACAACAAA-
1 AACAA-AAAT
*
12800 AACAACAAT
1 AACAAAAAT
*
12809 AA-AAATAAC
1 AACAAA-AAT
*
12818 AATAAAAAT
1 AACAAAAAT
*
12827 AGCATTAAAAT
1 AACA--AAAAT
12838 AACAA
1 AACAA
12843 TCAAAACAGT
Statistics
Matches: 80, Mismatches: 16, Indels: 22
0.68 0.14 0.19
Matches are distributed among these distances:
8 11 0.14
9 43 0.54
10 9 0.11
11 17 0.21
ACGTcount: A:0.71, C:0.13, G:0.03, T:0.13
Consensus pattern (9 bp):
AACAAAAAT
Found at i:12745 original size:23 final size:23
Alignment explanation
Indices: 12718--12806 Score: 85
Period size: 23 Copynumber: 4.0 Consensus size: 23
12708 AAGTAACAAC
12718 CAAAATAGCAACAAAAATAACAG
1 CAAAATAGCAACAAAAATAACAG
*
12741 CAAAAT---AACAAAAATAACAA
1 CAAAATAGCAACAAAAATAACAG
* * *
12761 TAAAACAGCAACAAAAATAATAG
1 CAAAATAGCAACAAAAATAACAG
* * *
12784 TAAAAATAACAACAAAAACAACA
1 -CAAAATAGCAACAAAAATAACA
12807 ATAAAAATAA
Statistics
Matches: 52, Mismatches: 10, Indels: 7
0.75 0.14 0.10
Matches are distributed among these distances:
20 17 0.33
23 18 0.35
24 17 0.33
ACGTcount: A:0.70, C:0.16, G:0.04, T:0.10
Consensus pattern (23 bp):
CAAAATAGCAACAAAAATAACAG
Found at i:12752 original size:20 final size:20
Alignment explanation
Indices: 12686--12759 Score: 69
Period size: 20 Copynumber: 3.5 Consensus size: 20
12676 AAAAACGTAT
12686 AAAAATAACATCC-AAATAAC
1 AAAAATAACA-CCAAAATAAC
* *
12706 TAAAGTAACAACCAAAATAGCAAC
1 AAAAATAAC-ACCAAAAT---AAC
*
12730 AAAAATAACAGCAAAATAAC
1 AAAAATAACACCAAAATAAC
12750 AAAAATAACA
1 AAAAATAACA
12760 ATAAAACAGC
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
20 22 0.50
21 5 0.11
23 7 0.16
24 10 0.23
ACGTcount: A:0.66, C:0.18, G:0.04, T:0.12
Consensus pattern (20 bp):
AAAAATAACACCAAAATAAC
Found at i:12812 original size:23 final size:24
Alignment explanation
Indices: 12719--12848 Score: 110
Period size: 24 Copynumber: 5.6 Consensus size: 24
12709 AGTAACAACC
* **
12719 AAAATAGCAACAAAAATAAC-AGC
1 AAAATAACAACAAAAATAACAATA
12742 AAAAT---AACAAAAATAACAAT-
1 AAAATAACAACAAAAATAACAATA
* * * *
12762 AAAACAGCAACAAAAATAATAGTA
1 AAAATAACAACAAAAATAACAATA
*
12786 AAAATAACAACAAAAACAACAATA
1 AAAATAACAACAAAAATAACAATA
* * *
12810 AAAATAACAATAAAAATAGC-ATT
1 AAAATAACAACAAAAATAACAATA
12833 AAAATAACAATCAAAA
1 AAAATAACAA-CAAAA
12849 CAGTAAAAAA
Statistics
Matches: 87, Mismatches: 14, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
20 16 0.18
21 1 0.01
23 30 0.34
24 40 0.46
ACGTcount: A:0.70, C:0.13, G:0.04, T:0.13
Consensus pattern (24 bp):
AAAATAACAACAAAAATAACAATA
Found at i:12835 original size:12 final size:12
Alignment explanation
Indices: 12750--12848 Score: 94
Period size: 12 Copynumber: 8.3 Consensus size: 12
12740 GCAAAATAAC
12750 AAAAATAACAAT
1 AAAAATAACAAT
* * *
12762 -AAAACAGCAAC
1 AAAAATAACAAT
* *
12773 AAAAATAATAGT
1 AAAAATAACAAT
*
12785 AAAAATAACAAC
1 AAAAATAACAAT
*
12797 AAAAACAACAAT
1 AAAAATAACAAT
12809 AAAAATAACAAT
1 AAAAATAACAAT
*
12821 AAAAATAGC-AT
1 AAAAATAACAAT
*
12832 TAAAATAACAAT
1 AAAAATAACAAT
12844 CAAAA
1 -AAAA
12849 CAGTAAAAAA
Statistics
Matches: 66, Mismatches: 18, Indels: 5
0.74 0.20 0.06
Matches are distributed among these distances:
11 17 0.26
12 46 0.70
13 3 0.05
ACGTcount: A:0.71, C:0.12, G:0.03, T:0.14
Consensus pattern (12 bp):
AAAAATAACAAT
Found at i:12859 original size:23 final size:23
Alignment explanation
Indices: 12785--12859 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 23
12775 AAATAATAGT
*
12785 AAAAATAACAA-CAAAAACAACAA
1 AAAAATAACAATC-AAAACAGCAA
* * *
12808 TAAAAATAACAATAAAAATAGCAT
1 -AAAAATAACAATCAAAACAGCAA
* *
12832 TAAAATAACAATCAAAACAGTAA
1 AAAAATAACAATCAAAACAGCAA
12855 AAAAA
1 AAAAA
12860 GCACCAAAAT
Statistics
Matches: 40, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
23 22 0.55
24 18 0.45
ACGTcount: A:0.72, C:0.12, G:0.03, T:0.13
Consensus pattern (23 bp):
AAAAATAACAATCAAAACAGCAA
Found at i:12867 original size:20 final size:19
Alignment explanation
Indices: 12844--12930 Score: 66
Period size: 21 Copynumber: 4.3 Consensus size: 19
12834 AAATAACAAT
*
12844 CAAAACAGTAAAAAAAGCAC
1 CAAAATAGTAAAAAAA-CAC
*
12864 CAAAATAATAAAAAGCAACAC
1 CAAAATAGTAAAAA--AACAC
* * *
12885 TAAAATAGCAAAAAAATAAC
1 CAAAATAGTAAAAAAA-CAC
*
12905 CAAAATAGGAAAAAAAAACAC
1 CAAAATA-G-TAAAAAAACAC
12926 CAAAA
1 CAAAA
12931 CAACAATATA
Statistics
Matches: 53, Mismatches: 9, Indels: 9
0.75 0.13 0.13
Matches are distributed among these distances:
19 2 0.04
20 20 0.38
21 22 0.42
22 9 0.17
ACGTcount: A:0.69, C:0.16, G:0.07, T:0.08
Consensus pattern (19 bp):
CAAAATAGTAAAAAAACAC
Found at i:12877 original size:21 final size:20
Alignment explanation
Indices: 12853--12930 Score: 68
Period size: 21 Copynumber: 3.8 Consensus size: 20
12843 TCAAAACAGT
* **
12853 AAAAAAAGCACCAAAATAAT
1 AAAAAAAACACCAAAATAGC
* *
12873 AAAAAGCAACACTAAAATAGC
1 AAAAA-AAACACCAAAATAGC
*
12894 AAAAAAATA-ACCAAAATAGGA
1 AAAAAAA-ACACCAAAATA-GC
12915 AAAAAAAACACCAAAA
1 AAAAAAAACACCAAAA
12931 CAACAATATA
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
20 15 0.33
21 31 0.67
ACGTcount: A:0.71, C:0.15, G:0.06, T:0.08
Consensus pattern (20 bp):
AAAAAAAACACCAAAATAGC
Found at i:12925 original size:41 final size:41
Alignment explanation
Indices: 12844--12930 Score: 93
Period size: 41 Copynumber: 2.1 Consensus size: 41
12834 AAATAACAAT
* * * * **
12844 CAAAACAGTAAAAAAAGCACCAAAATAATAAAAAGCAACAC
1 CAAAATAGCAAAAAAAGAACCAAAATAAGAAAAAAAAACAC
* * *
12885 TAAAATAGCAAAAAAATAACCAAAATAGGAAAAAAAAACAC
1 CAAAATAGCAAAAAAAGAACCAAAATAAGAAAAAAAAACAC
12926 CAAAA
1 CAAAA
12931 CAACAATATA
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.69, C:0.16, G:0.07, T:0.08
Consensus pattern (41 bp):
CAAAATAGCAAAAAAAGAACCAAAATAAGAAAAAAAAACAC
Found at i:15089 original size:23 final size:23
Alignment explanation
Indices: 15061--15105 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
15051 ATTATTTTAT
*
15061 AACTCTCCTGCCATTTTGTTTGC
1 AACTCTCCTGCCATTATGTTTGC
15084 AACTCTCCTGCCATTATGTTTG
1 AACTCTCCTGCCATTATGTTTG
15106 TTTTAATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.16, C:0.29, G:0.13, T:0.42
Consensus pattern (23 bp):
AACTCTCCTGCCATTATGTTTGC
Found at i:15833 original size:18 final size:18
Alignment explanation
Indices: 15805--15846 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
15795 TTTTAGTTTC
*
15805 TAACTAAATTCCTGAAATT
1 TAACTAAATTCAT-AAATT
15824 TAAC-AAATTCATAAATT
1 TAACTAAATTCATAAATT
15841 T-ACTAA
1 TAACTAA
15847 TATTGGTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 2 0.10
17 8 0.38
18 7 0.33
19 4 0.19
ACGTcount: A:0.48, C:0.14, G:0.02, T:0.36
Consensus pattern (18 bp):
TAACTAAATTCATAAATT
Found at i:22522 original size:23 final size:23
Alignment explanation
Indices: 22492--22536 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
22482 TATATGAGGA
*
22492 GACATCGAAAACAAATTACATAT
1 GACATCGAAAACAAAGTACATAT
22515 GACATCGAAAACAAAGTACATA
1 GACATCGAAAACAAAGTACATA
22537 CTTCCCATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.53, C:0.18, G:0.11, T:0.18
Consensus pattern (23 bp):
GACATCGAAAACAAAGTACATAT
Found at i:24978 original size:20 final size:20
Alignment explanation
Indices: 24950--25024 Score: 66
Period size: 20 Copynumber: 3.9 Consensus size: 20
24940 ACTTTTGGCA
24950 ATTTC-TCATATATTTTAAT
1 ATTTCTTCATATATTTTAAT
* *
24969 ATTTCTTCATAAATTTTGAT
1 ATTTCTTCATATATTTTAAT
* *
24989 ATTT-TATAAAATATTTTAAT
1 ATTTCT-TCATATATTTTAAT
* *
25009 ATTCCCTCATA-ATTTT
1 ATTTCTTCATATATTTT
25025 CAAAATTAGG
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
19 11 0.26
20 32 0.74
ACGTcount: A:0.33, C:0.11, G:0.01, T:0.55
Consensus pattern (20 bp):
ATTTCTTCATATATTTTAAT
Found at i:37592 original size:17 final size:19
Alignment explanation
Indices: 37562--37603 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
37552 TTGTTAATCA
*
37562 TATTATTTATTTAAATATT
1 TATTATTTATTTAAATAAT
37581 TATT-TTTA-TTAAATAAT
1 TATTATTTATTTAAATAAT
37598 TATTAT
1 TATTAT
37604 ATTTAATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 12 0.57
18 5 0.24
19 4 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTATTTATTTAAATAAT
Found at i:37609 original size:17 final size:16
Alignment explanation
Indices: 37563--37609 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
37553 TGTTAATCAT
37563 ATTATTTATTTAAATA
1 ATTATTTATTTAAATA
* *
37579 TTTATTTTTATTAAATA
1 ATTATTTAT-TTAAATA
37596 ATTATTATATTTAA
1 ATTATT-TATTTAA
37610 TACAATTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
16 7 0.28
17 16 0.64
18 2 0.08
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATTATTTATTTAAATA
Found at i:38375 original size:27 final size:31
Alignment explanation
Indices: 38312--38383 Score: 75
Period size: 31 Copynumber: 2.5 Consensus size: 31
38302 AAACTTGAAT
* *
38312 AATATATATATATTTATTTTATATATTATAA
1 AATATAAATATATTTATTTAATATATTATAA
*
38343 ATTATAAATATA-TT-TTTAATA-ATTA-AA
1 AATATAAATATATTTATTTAATATATTATAA
38370 AATAT-AATA-ATTTA
1 AATATAAATATATTTA
38384 ATTTTTTCGA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
25 1 0.03
26 6 0.17
27 6 0.17
28 4 0.11
29 6 0.17
30 2 0.06
31 10 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (31 bp):
AATATAAATATATTTATTTAATATATTATAA
Found at i:38601 original size:3 final size:3
Alignment explanation
Indices: 38595--38624 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
38585 ACTTTTCTTC
38595 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
38625 ATTTACTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:38680 original size:18 final size:18
Alignment explanation
Indices: 38598--38682 Score: 54
Period size: 18 Copynumber: 4.8 Consensus size: 18
38588 TTTCTTCTAT
38598 TATTATTATTATTATTAT-
1 TATTATTATT-TTATTATA
*
38616 TATTATTATATTTACTATA
1 TATTATTAT-TTTATTATA
* *
38635 TAAATATTA-TTCA--ATA
1 T-ATTATTATTTTATTATA
**
38651 TAGCA-TAGTTTTATTATA
1 TATTATTA-TTTTATTATA
38669 TATTATTATTTTAT
1 TATTATTATTTTAT
38683 ATAAATCTAA
Statistics
Matches: 51, Mismatches: 8, Indels: 16
0.68 0.11 0.21
Matches are distributed among these distances:
14 2 0.04
15 2 0.04
16 7 0.14
18 30 0.59
19 4 0.08
20 6 0.12
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (18 bp):
TATTATTATTTTATTATA
Found at i:39949 original size:27 final size:28
Alignment explanation
Indices: 39892--39950 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
39882 TTTTTTATAA
** *
39892 AAATAATTATATTTTTTATTAATTACGT
1 AAATAATTATATTTTTTATTAAACACAT
*
39920 AAATAA-TCTATTTTTTATTAAACACAT
1 AAATAATTATATTTTTTATTAAACACAT
39947 AAAT
1 AAAT
39951 GACCTAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 21 0.78
28 6 0.22
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (28 bp):
AAATAATTATATTTTTTATTAAACACAT
Found at i:40627 original size:13 final size:13
Alignment explanation
Indices: 40609--40634 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40599 TTGGCATCCG
40609 AAAAAAAAAAAGA
1 AAAAAAAAAAAGA
40622 AAAAAAAAAAAGA
1 AAAAAAAAAAAGA
40635 CAAATGATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAGA
Found at i:42948 original size:23 final size:22
Alignment explanation
Indices: 42922--42966 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
42912 ATGATTCGAT
*
42922 TAAATAAATCATTAAAAAAATTA
1 TAAAAAAAT-ATTAAAAAAATTA
* *
42945 TAAAAAAATATTTAAAAGATTA
1 TAAAAAAATATTAAAAAAATTA
42967 GTTCAATTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (22 bp):
TAAAAAAATATTAAAAAAATTA
Found at i:43448 original size:34 final size:36
Alignment explanation
Indices: 43405--43493 Score: 110
Period size: 34 Copynumber: 2.5 Consensus size: 36
43395 AAAATGTTTA
* *
43405 TTCTGTTGAATCGATTGTCATGTTGGAATACTG-T-
1 TTCTTTTGAATCGATTGTCATGGTGGAATACTGCTC
** *
43439 TTCTTTTGAATCGATTGTTGTGGTGGAATATTGCTTC
1 TTCTTTTGAATCGATTGTCATGGTGGAATACTGC-TC
43476 TTCTTTTGAATCGATTGT
1 TTCTTTTGAATCGATTGT
43494 TTATATGTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
34 28 0.60
36 1 0.02
37 18 0.38
ACGTcount: A:0.18, C:0.11, G:0.22, T:0.48
Consensus pattern (36 bp):
TTCTTTTGAATCGATTGTCATGGTGGAATACTGCTC
Found at i:51446 original size:4 final size:4
Alignment explanation
Indices: 51437--51468 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
51427 CAATTACTAG
51437 GAAC GAAC GAAC GAAC GAAC GAAC GAAC GAAC
1 GAAC GAAC GAAC GAAC GAAC GAAC GAAC GAAC
51469 TGTTTCGTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.50, C:0.25, G:0.25, T:0.00
Consensus pattern (4 bp):
GAAC
Found at i:54750 original size:1 final size:1
Alignment explanation
Indices: 54744--54784 Score: 55
Period size: 1 Copynumber: 41.0 Consensus size: 1
54734 TAAAATCTAC
** *
54744 TTTTTTTTTTTTTTTTAATTTTNTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
54785 AATTTTGCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.05, C:0.00, G:0.00, T:0.93
Consensus pattern (1 bp):
T
Found at i:54761 original size:25 final size:24
Alignment explanation
Indices: 54736--54783 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
54726 GTTACTATTA
54736 AAATCTACTTTTTTTTTTTTTTTT
1 AAATCTACTTTTTTTTTTTTTTTT
* * **
54760 AATTTTNTTTTTTTTTTTTTTTTT
1 AAATCTACTTTTTTTTTTTTTTTT
54784 TAATTTTGCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.12, C:0.04, G:0.00, T:0.81
Consensus pattern (24 bp):
AAATCTACTTTTTTTTTTTTTTTT
Found at i:54974 original size:11 final size:11
Alignment explanation
Indices: 54958--55005 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
54948 TTTTTCACTG
54958 TTTTGTTATTA
1 TTTTGTTATTA
* *
54969 TTTTGTTGTCA
1 TTTTGTTATTA
*
54980 TTTTATTATTA
1 TTTTGTTATTA
* *
54991 TGTTGTTATTG
1 TTTTGTTATTA
55002 TTTT
1 TTTT
55006 ATTGTTATCG
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.15, C:0.02, G:0.12, T:0.71
Consensus pattern (11 bp):
TTTTGTTATTA
Found at i:55005 original size:22 final size:22
Alignment explanation
Indices: 54956--55013 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
54946 TATTTTTCAC
* * *
54956 TGTTTTGTTATTATTTTGTTGT
1 TGTTTTATTATTATGTTGTTAT
**
54978 CATTTTATTATTATGTTGTTAT
1 TGTTTTATTATTATGTTGTTAT
*
55000 TGTTTTATTGTTAT
1 TGTTTTATTATTAT
55014 CGTTTGGATA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.16, C:0.02, G:0.14, T:0.69
Consensus pattern (22 bp):
TGTTTTATTATTATGTTGTTAT
Found at i:55007 original size:19 final size:20
Alignment explanation
Indices: 54956--55008 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
54946 TATTTTTCAC
*
54956 TGTT-TTGTTATTATTTTGT
1 TGTTATTGTTATTATTATGT
*
54975 TGTCATT-TTATTATTATGT
1 TGTTATTGTTATTATTATGT
54994 TGTTATTGTT-TTATT
1 TGTTATTGTTATTATT
55009 GTTATCGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 25 0.86
20 4 0.14
ACGTcount: A:0.15, C:0.02, G:0.13, T:0.70
Consensus pattern (20 bp):
TGTTATTGTTATTATTATGT
Found at i:56256 original size:3 final size:3
Alignment explanation
Indices: 56250--56275 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
56240 ATCGTCATCA
56250 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
56276 CCTTTTGTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:64383 original size:27 final size:27
Alignment explanation
Indices: 64353--64410 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
64343 TTTCGAAGTG
* *
64353 GTCA-GACGATAGATATCATACTGGTTA
1 GTCAGGAC-ATAGATATAATACAGGTTA
*
64380 GTCAGGACATGGATATAATACAGGTTA
1 GTCAGGACATAGATATAATACAGGTTA
64407 GTCA
1 GTCA
64411 AGTTAGGAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 24 0.89
28 3 0.11
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (27 bp):
GTCAGGACATAGATATAATACAGGTTA
Found at i:67105 original size:27 final size:27
Alignment explanation
Indices: 67075--67136 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
67065 CTACCTGTAT
67075 GGCACCACTAGTGCCACCTACCCAATA
1 GGCACCACTAGTGCCACCTACCCAATA
* * * * *
67102 GGCATCATTAGTGTCGCCTACCCCATA
1 GGCACCACTAGTGCCACCTACCCAATA
67129 GGCACCAC
1 GGCACCAC
67137 CCAGAATTTT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.26, C:0.39, G:0.18, T:0.18
Consensus pattern (27 bp):
GGCACCACTAGTGCCACCTACCCAATA
Found at i:67663 original size:6 final size:6
Alignment explanation
Indices: 67625--67662 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
67615 ACCAAACTTT
* *
67625 ATCTTG ATCTTG ATCTTG AGCTTG ATCTTG ATGTTG AT
1 ATCTTG ATCTTG ATCTTG ATCTTG ATCTTG ATCTTG AT
67663 GGACATCCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.18, C:0.13, G:0.21, T:0.47
Consensus pattern (6 bp):
ATCTTG
Found at i:71606 original size:60 final size:58
Alignment explanation
Indices: 71500--71615 Score: 144
Period size: 59 Copynumber: 2.0 Consensus size: 58
71490 TTTTTTATGC
* *
71500 ACAAAAAAATAAACATACTTAAAATAACAAAAAAAACTTAAATAACATCAACTTTTAT
1 ACAAAAAAATAAACATACTTAAAACAACAAAAAAAACTTAAATAACACCAACTTTTAT
* * **
71558 ACAAGAAAATGAAACATACTTAAAAGCAAC-ATAAAATGTTGAAATAACACCAACTTTT
1 ACAAAAAAAT-AAACATACTTAAAA-CAACAAAAAAAACTT-AAATAACACCAACTTTT
71616 CTAATGATTC
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
58 9 0.18
59 21 0.43
60 19 0.39
ACGTcount: A:0.58, C:0.15, G:0.04, T:0.23
Consensus pattern (58 bp):
ACAAAAAAATAAACATACTTAAAACAACAAAAAAAACTTAAATAACACCAACTTTTAT
Found at i:74610 original size:105 final size:103
Alignment explanation
Indices: 74492--74865 Score: 358
Period size: 113 Copynumber: 3.5 Consensus size: 103
74482 TTGAAGTTCT
*
74492 AGATATCGTTGACACAATGAGAAAGCAAGGCATTGAACCTGATGTTGTCACATATAGTATATTGG
1 AGATATTGTTGACACAATGAGAAAGCAAGGCATTGAACCTGATGTTGTCACATATAGTATATTGG
* *
74557 TTAATGCATATTGCAAGAAGGGTATGATTTCTAAAGCTGA
66 TTGATGCATATTGCAAGAAGGG-ATG-TTTCTAAAGCTAA
** * * **
74597 AGATATTGTTGACAGTATGAGAAAGCTAGGCATTGAGCCTGATGTTGTCACATATAACATATTGG
1 AGATATTGTTGACACAATGAGAAAGCAAGGCATTGAACCTGATGTTGTCACATATAGTATATTGG
* *
74662 TTGATGCGCATTGCAAGGTTGCAAGGAGGGAATTGTTTCTAAAGTTAA
66 TTGAT--GCA-T---A--TTGCAAGAAGGG-A-TGTTTCTAAAGCTAA
* * ** * * *
74710 AGATATTGTTGACACAATGAGAAAGCAAGGTATTGAGCCTGACATTATCACGTATAGTATATTGA
1 AGATATTGTTGACACAATGAGAAAGCAAGGCATTGAACCTGATGTTGTCACATATAGTATATTGG
* * * *
74775 TTGATGCACATTACAAGAAGGAGATGGTTT-TGAAGC-ACT
66 TTGATGCATATTGCAAGAAGG-GAT-GTTTCTAAAGCTA-A
* * *
74814 AGATATTGTTGACACAATGAGAAAGCAAAGCATCGAGA-CTAATGTTGTCACA
1 AGATATTGTTGACACAATGAGAAAGCAAGGCATTGA-ACCTGATGTTGTCACA
74866 GACAGCACTC
Statistics
Matches: 218, Mismatches: 38, Indels: 27
0.77 0.13 0.10
Matches are distributed among these distances:
103 1 0.00
104 47 0.22
105 76 0.35
106 1 0.00
107 4 0.02
108 1 0.00
111 4 0.02
113 82 0.38
114 2 0.01
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.29
Consensus pattern (103 bp):
AGATATTGTTGACACAATGAGAAAGCAAGGCATTGAACCTGATGTTGTCACATATAGTATATTGG
TTGATGCATATTGCAAGAAGGGATGTTTCTAAAGCTAA
Found at i:79094 original size:10 final size:10
Alignment explanation
Indices: 79079--79108 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
79069 TGAAGCGATT
79079 ACCTTCAAAC
1 ACCTTCAAAC
79089 ACCTTCAAAC
1 ACCTTCAAAC
79099 ACCTTCAAAC
1 ACCTTCAAAC
79109 CATGACTCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.20
Consensus pattern (10 bp):
ACCTTCAAAC
Found at i:81305 original size:2 final size:2
Alignment explanation
Indices: 81298--81324 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
81288 GTTAAGCATT
81298 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
81325 AACATAACAA
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:81946 original size:30 final size:30
Alignment explanation
Indices: 81912--82022 Score: 195
Period size: 30 Copynumber: 3.7 Consensus size: 30
81902 CATCCAGATG
*
81912 TAAGGTGATATATATATGTAGCATCAAGAC
1 TAAGGTGAAATATATATGTAGCATCAAGAC
*
81942 TAAGGTGAAATATATCTGTAGCATCAAGAC
1 TAAGGTGAAATATATATGTAGCATCAAGAC
81972 TAAGGTGAAATATATATGTAGCATCAAGAC
1 TAAGGTGAAATATATATGTAGCATCAAGAC
*
82002 TAAGGTGATATATATATGTAG
1 TAAGGTGAAATATATATGTAG
82023 GTAGGCAGGT
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 77 1.00
ACGTcount: A:0.41, C:0.09, G:0.21, T:0.30
Consensus pattern (30 bp):
TAAGGTGAAATATATATGTAGCATCAAGAC
Found at i:86175 original size:18 final size:19
Alignment explanation
Indices: 86154--86191 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
86144 TTAAATATAT
* *
86154 AAAAA-TAAATTTTTTTTA
1 AAAAATTAAAATTTTATTA
86172 AAAAATTAAAATTTTATTA
1 AAAAATTAAAATTTTATTA
86191 A
1 A
86192 GTCCTAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AAAAATTAAAATTTTATTA
Found at i:86465 original size:39 final size:38
Alignment explanation
Indices: 86416--86491 Score: 107
Period size: 39 Copynumber: 2.0 Consensus size: 38
86406 GCATTTCATA
86416 ATTTTTTTTATGAATTCTATAAAATTTTATAATTTTTT
1 ATTTTTTTTATGAATTCTATAAAATTTTATAATTTTTT
* * * *
86454 ATTTTATTTTATGATTTTTGTAAAATTTTCTAATTTTT
1 ATTTT-TTTTATGAATTCTATAAAATTTTATAATTTTT
86492 AATAAATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
38 5 0.15
39 28 0.85
ACGTcount: A:0.29, C:0.03, G:0.04, T:0.64
Consensus pattern (38 bp):
ATTTTTTTTATGAATTCTATAAAATTTTATAATTTTTT
Found at i:86497 original size:20 final size:19
Alignment explanation
Indices: 86433--86512 Score: 65
Period size: 19 Copynumber: 4.2 Consensus size: 19
86423 TTATGAATTC
86433 TATAAAATTTTATAATTTTT
1 TATAAAATTTTATAA-TTTT
*** *
86453 TATTTTATTTTATGATTTT
1 TATAAAATTTTATAATTTT
* *
86472 TGTAAAATTTTCTAATTTT
1 TATAAAATTTTATAATTTT
*
86491 TA-ATAAATTTTA-ATTTTT
1 TATA-AAATTTTATAATTTT
86509 TATA
1 TATA
86513 TTTTAATTAA
Statistics
Matches: 45, Mismatches: 13, Indels: 5
0.71 0.21 0.08
Matches are distributed among these distances:
18 8 0.18
19 26 0.58
20 11 0.24
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (19 bp):
TATAAAATTTTATAATTTT
Found at i:86733 original size:87 final size:85
Alignment explanation
Indices: 86632--86794 Score: 231
Period size: 87 Copynumber: 1.9 Consensus size: 85
86622 TTGAGGGTGT
* *
86632 TTTTTTATGCATTTTGAAAGTTCAAGTACTTAATTG-A-GTAAAAAAAAAAACAAGGGCTTAATT
1 TTTTTGATACATTTTGAAAGTTCAAGTACTTAATTGAATGTAAAAAAAAAAA-AA---CTTAATT
*
86695 GCTCTTTTTGAAAAAGTTTAGGAC
62 ACTCTTTTTGAAAAAGTTTAGGAC
* *
86719 TTTTTGATACATTTTGAAAGTTCAAGTGCTTAATTGAATGTAAAAAAAAAAAAACTTAATTACTT
1 TTTTTGATACATTTTGAAAGTTCAAGTACTTAATTGAATGTAAAAAAAAAAAAACTTAATTACTC
86784 TTTTTGAAAAA
66 TTTTTGAAAAA
86795 AATTGAGGGC
Statistics
Matches: 69, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
85 20 0.29
87 33 0.48
88 3 0.04
89 13 0.19
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.38
Consensus pattern (85 bp):
TTTTTGATACATTTTGAAAGTTCAAGTACTTAATTGAATGTAAAAAAAAAAAAACTTAATTACTC
TTTTTGAAAAAGTTTAGGAC
Found at i:87339 original size:21 final size:22
Alignment explanation
Indices: 87293--87333 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
87283 AATAAAAATG
87293 AAAAAGATTAAAAATGTTATTA
1 AAAAAGATTAAAAATGTTATTA
*
87315 AAAAAGTTTAAAAAT-TTAT
1 AAAAAGATTAAAAATGTTAT
87334 ACAAAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (22 bp):
AAAAAGATTAAAAATGTTATTA
Found at i:87339 original size:22 final size:22
Alignment explanation
Indices: 87293--87339 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
87283 AATAAAAATG
*
87293 AAAAAGATTAAAAATGTTATTA
1 AAAAAGATTAAAAATGTTATCA
*
87315 AAAAAGTTTAAAAAT-TTATACA
1 AAAAAGATTAAAAATGTTAT-CA
87337 AAA
1 AAA
87340 TTTTTAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (22 bp):
AAAAAGATTAAAAATGTTATCA
Found at i:87779 original size:40 final size:40
Alignment explanation
Indices: 87699--87779 Score: 94
Period size: 40 Copynumber: 2.0 Consensus size: 40
87689 GGACTTGAAA
* *
87699 AATATAAAAATAAAATATTGGAAATATTTTAATATAATTT
1 AATATAAAAATAAAATATTGAAAATATATTAATATAATTT
* *
87739 AATATAAAAATAATTATATT-AAAATATGATTAA-ATTATTT
1 AATATAAAAATAA-AATATTGAAAATAT-ATTAATATAATTT
87779 A
1 A
87780 TTATCATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
40 26 0.74
41 9 0.26
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.41
Consensus pattern (40 bp):
AATATAAAAATAAAATATTGAAAATATATTAATATAATTT
Found at i:90024 original size:50 final size:50
Alignment explanation
Indices: 89949--90049 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 50
89939 TTATTTTAGC
*
89949 GTTCGAGCTAACAAGGAATTCGGATAAAACATTAAACGCAACCCCTGTTT
1 GTTCGAGCTAACAAAGAATTCGGATAAAACATTAAACGCAACCCCTGTTT
89999 GTTCGAGCTAACAAAGAATTCGGATAAAACATTAAACGCAACCCCTGTTT
1 GTTCGAGCTAACAAAGAATTCGGATAAAACATTAAACGCAACCCCTGTTT
90049 G
1 G
90050 ACTAATAACG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.24
Consensus pattern (50 bp):
GTTCGAGCTAACAAAGAATTCGGATAAAACATTAAACGCAACCCCTGTTT
Found at i:94932 original size:18 final size:17
Alignment explanation
Indices: 94902--94949 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 17
94892 TCTTTTTTCA
* *
94902 ATTTTAACAATTTTTAC
1 ATTTTAAAAATTTTAAC
*
94919 ATTTTAAAACATTTTAAT
1 ATTTTAAAA-ATTTTAAC
*
94937 ATTTTAATAATTT
1 ATTTTAAAAATTT
94950 ATCTATATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTAAAAATTTTAAC
Found at i:99335 original size:47 final size:47
Alignment explanation
Indices: 99266--99359 Score: 170
Period size: 47 Copynumber: 2.0 Consensus size: 47
99256 GAGGTGAACA
99266 AGGCAGTAGATGCAATGGCGAAGATTAGACCAACAGCACGGGCCTTT
1 AGGCAGTAGATGCAATGGCGAAGATTAGACCAACAGCACGGGCCTTT
* *
99313 AGGCAGTAGATGCGATGGCGAAGATTAGACCAACAGCATGGGCCTTT
1 AGGCAGTAGATGCAATGGCGAAGATTAGACCAACAGCACGGGCCTTT
99360 TTGGTTTGCA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.31, C:0.20, G:0.31, T:0.18
Consensus pattern (47 bp):
AGGCAGTAGATGCAATGGCGAAGATTAGACCAACAGCACGGGCCTTT
Found at i:106746 original size:29 final size:28
Alignment explanation
Indices: 106679--106742 Score: 119
Period size: 28 Copynumber: 2.3 Consensus size: 28
106669 CGAGAAATTA
106679 ATTTTAAATTTCATAAAAATAAAAATAT
1 ATTTTAAATTTCATAAAAATAAAAATAT
*
106707 ATTTTAAATTTCATAAAATTAAAAATAT
1 ATTTTAAATTTCATAAAAATAAAAATAT
106735 ATTTTAAA
1 ATTTTAAA
106743 ATTTATTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (28 bp):
ATTTTAAATTTCATAAAAATAAAAATAT
Found at i:114284 original size:12 final size:12
Alignment explanation
Indices: 114262--114297 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
114252 TATTCTCCAC
*
114262 TCTATACCAACA
1 TCTAAACCAACA
*
114274 TGTAAACCAACA
1 TCTAAACCAACA
114286 TCTAAACCAACA
1 TCTAAACCAACA
114298 ATATTTTCCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.47, C:0.31, G:0.03, T:0.19
Consensus pattern (12 bp):
TCTAAACCAACA
Found at i:116080 original size:14 final size:15
Alignment explanation
Indices: 116061--116109 Score: 64
Period size: 14 Copynumber: 3.2 Consensus size: 15
116051 GGATTCAAAT
116061 AAAAACCTAAAAC-A
1 AAAAACCTAAAACTA
116075 AAAAACCTAAAACTAA
1 AAAAACCTAAAACT-A
*
116091 AAATAAACTAAAACTA
1 AAA-AACCTAAAACTA
116107 AAA
1 AAA
116110 CTAAATAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 13 0.42
16 8 0.26
17 10 0.32
ACGTcount: A:0.71, C:0.16, G:0.00, T:0.12
Consensus pattern (15 bp):
AAAAACCTAAAACTA
Found at i:116093 original size:7 final size:6
Alignment explanation
Indices: 116062--116141 Score: 58
Period size: 6 Copynumber: 12.8 Consensus size: 6
116052 GATTCAAATA
* *
116062 AAAACCT AAAACAA AAAACCT AAAACT AAAAAT -AAACT AAAACT AAAACT
1 AAAA-CT AAAAC-T AAAA-CT AAAACT AAAACT AAAACT AAAACT AAAACT
*
116112 -AAA-T AAAAACCT AAAACT ACTAACT AAAAC
1 AAAACT -AAAA-CT AAAACT A-AAACT AAAAC
116142 CCTAAAACAC
Statistics
Matches: 59, Mismatches: 6, Indels: 17
0.72 0.07 0.21
Matches are distributed among these distances:
4 1 0.02
5 7 0.12
6 28 0.47
7 21 0.36
8 2 0.03
ACGTcount: A:0.66, C:0.19, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAACT
Found at i:116093 original size:21 final size:21
Alignment explanation
Indices: 116069--116149 Score: 60
Period size: 21 Copynumber: 3.9 Consensus size: 21
116059 ATAAAAACCT
116069 AAAACAAAAAACCTAAAACTA
1 AAAACAAAAAACCTAAAACTA
* *
116090 AAAATAAACTAAAACTAAAACT-
1 AAAACAAA--AAACCTAAAACTA
*
116112 -AAA-TAAAAACCTAAAACTA
1 AAAACAAAAAACCTAAAACTA
** * *
116131 CTAACTAAAACCCTAAAAC
1 AAAACAAAAAACCTAAAAC
116150 ACTTGGCAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
18 11 0.22
20 4 0.08
21 23 0.47
23 11 0.22
ACGTcount: A:0.65, C:0.20, G:0.00, T:0.15
Consensus pattern (21 bp):
AAAACAAAAAACCTAAAACTA
Found at i:116120 original size:17 final size:17
Alignment explanation
Indices: 116081--116141 Score: 70
Period size: 17 Copynumber: 3.4 Consensus size: 17
116071 AACAAAAAAC
*
116081 CTAAAACTAAAAATAAA
1 CTAAAACTAAAACTAAA
116098 CTAAAACTAAAACTAAA
1 CTAAAACTAAAACTAAA
116115 -TAAAAACCTAAAACTACTAA
1 CT-AAAA-CTAAAACTA--AA
116135 CTAAAAC
1 CTAAAAC
116142 CCTAAAACAC
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
16 1 0.03
17 20 0.53
18 9 0.24
19 1 0.03
20 6 0.16
21 1 0.03
ACGTcount: A:0.64, C:0.18, G:0.00, T:0.18
Consensus pattern (17 bp):
CTAAAACTAAAACTAAA
Found at i:131810 original size:21 final size:21
Alignment explanation
Indices: 131772--131826 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
131762 AAAAAGACAT
* **
131772 GTATTGATAGATATCTTAAAG
1 GTATTGATACATGCCTTAAAG
**
131793 GTATTGATACATGCCTTAACT
1 GTATTGATACATGCCTTAAAG
*
131814 ATATTGATACATG
1 GTATTGATACATG
131827 AGTGTCAGAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (21 bp):
GTATTGATACATGCCTTAAAG
Found at i:141663 original size:17 final size:17
Alignment explanation
Indices: 141637--141680 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
141627 ATCTTTATTG
* * *
141637 AATCCTTAAAATTTTGA
1 AATCCCTAAAATGTTAA
*
141654 AATCTCTAAAATGTTAA
1 AATCCCTAAAATGTTAA
141671 AATCCCTAAA
1 AATCCCTAAA
141681 TCATTAGCCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (17 bp):
AATCCCTAAAATGTTAA
Found at i:141734 original size:16 final size:16
Alignment explanation
Indices: 141707--141764 Score: 75
Period size: 16 Copynumber: 3.6 Consensus size: 16
141697 ATATTCTTTG
141707 AATCCCTAAAATATTGA
1 AATCCCT-AAATATTGA
141724 AATCCCTAAATATTGA
1 AATCCCTAAATATTGA
141740 AATCCAC-AAATCATTG-
1 AATCC-CTAAAT-ATTGA
141756 AATCCCTAA
1 AATCCCTAA
141765 CCCAAGAACG
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
15 1 0.03
16 25 0.66
17 12 0.32
ACGTcount: A:0.45, C:0.22, G:0.05, T:0.28
Consensus pattern (16 bp):
AATCCCTAAATATTGA
Found at i:141939 original size:12 final size:12
Alignment explanation
Indices: 141914--141947 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
141904 ATGATTTGGT
141914 TTGATTTGTTTTG
1 TTGATTT-TTTTG
141927 TTGATTTTTTTG
1 TTGATTTTTTTG
*
141939 TCGATTTTT
1 TTGATTTTT
141948 AATGCGACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 13 0.65
13 7 0.35
ACGTcount: A:0.09, C:0.03, G:0.18, T:0.71
Consensus pattern (12 bp):
TTGATTTTTTTG
Found at i:142658 original size:33 final size:33
Alignment explanation
Indices: 142592--142670 Score: 104
Period size: 33 Copynumber: 2.4 Consensus size: 33
142582 TGTTGACCGT
**
142592 TGGGGAGGGTGATGATGAAGTTGTAAAAGTTGA
1 TGGGGAGGGTGATGATGAAGGGGTAAAAGTTGA
* *
142625 TGGGGAGGGTGATGATGAAGGGGTAGAATTTGA
1 TGGGGAGGGTGATGATGAAGGGGTAAAAGTTGA
* *
142658 TGGTGAAGGTGAT
1 TGGGGAGGGTGAT
142671 CTGAAAAGGG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.28, C:0.00, G:0.46, T:0.27
Consensus pattern (33 bp):
TGGGGAGGGTGATGATGAAGGGGTAAAAGTTGA
Found at i:142715 original size:33 final size:33
Alignment explanation
Indices: 142678--142745 Score: 82
Period size: 33 Copynumber: 2.1 Consensus size: 33
142668 GATCTGAAAA
* * *
142678 GGGTAGAAGCTGTTGAGGAATATGATGTAGGAG
1 GGGTACAAGCTGATGAGGAAGATGATGTAGGAG
* * *
142711 GGGTACAAGCTGATGTGGAGGGTGATGTAGGAG
1 GGGTACAAGCTGATGAGGAAGATGATGTAGGAG
142744 GG
1 GG
142746 TCTACTGTTG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.26, C:0.04, G:0.47, T:0.22
Consensus pattern (33 bp):
GGGTACAAGCTGATGAGGAAGATGATGTAGGAG
Found at i:146226 original size:24 final size:24
Alignment explanation
Indices: 146194--146276 Score: 139
Period size: 24 Copynumber: 3.5 Consensus size: 24
146184 TTTAGCCCAC
*
146194 ACGAACCCAGAATGGTTAGCTCTT
1 ACGAGCCCAGAATGGTTAGCTCTT
* *
146218 ATGAGCCCAGAATGGTTAGCACTT
1 ACGAGCCCAGAATGGTTAGCTCTT
146242 ACGAGCCCAGAATGGTTAGCTCTT
1 ACGAGCCCAGAATGGTTAGCTCTT
146266 ACGAGCCCAGA
1 ACGAGCCCAGA
146277 TAGAGTTTAA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 54 1.00
ACGTcount: A:0.29, C:0.25, G:0.24, T:0.22
Consensus pattern (24 bp):
ACGAGCCCAGAATGGTTAGCTCTT
Found at i:149658 original size:15 final size:15
Alignment explanation
Indices: 149640--149670 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
149630 AATTTTCGGA
149640 ATAATTAGGGATTTC
1 ATAATTAGGGATTTC
*
149655 ATAATTTGGGATTTC
1 ATAATTAGGGATTTC
149670 A
1 A
149671 CGATTTTGTT
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:0.32, C:0.06, G:0.19, T:0.42
Consensus pattern (15 bp):
ATAATTAGGGATTTC
Found at i:150413 original size:137 final size:136
Alignment explanation
Indices: 150262--150537 Score: 525
Period size: 137 Copynumber: 2.0 Consensus size: 136
150252 TCTTTAACTA
150262 TTAAGTTAGTTATGACTGTAACTCATTTTTATTTACTTGTTTAGTACGTCAAACTCCTTGTATTT
1 TTAAGTTAGTTATGACTGTAACTCATTTTTATTTACTTGTTTAGTACGTCAAACTCCTTGTATTT
*
150327 TTCTGTTTAATCCTAGTTTTAATGTAATTCACCTTCCTTTTAGTTTTAGCATAAAAAATATGATT
66 TTCAGTTTAATCCTAGTTTTAATGTAATTCACCTTCCTTTTAGTTTTAGCATAAAAAATATGATT
150392 TTTTTT
131 TTTTTT
*
150398 TTNAAGTTAGTTATGACTGTAACTCATTTTTATTTACTTGTTTAGTACTTCAAACTCCTTGTATT
1 TT-AAGTTAGTTATGACTGTAACTCATTTTTATTTACTTGTTTAGTACGTCAAACTCCTTGTATT
150463 TTTCAGTTTAATCCTAGTTTTAATGTAATTCACCTTCCTTTTAGTTTTAGCATAAAAAATATGAT
65 TTTCAGTTTAATCCTAGTTTTAATGTAATTCACCTTCCTTTTAGTTTTAGCATAAAAAATATGAT
150528 TTTTTTT
130 TTTTTTT
150535 TTA
1 TTA
150538 GTGTTCTTCT
Statistics
Matches: 137, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
136 3 0.02
137 134 0.98
ACGTcount: A:0.26, C:0.13, G:0.10, T:0.51
Consensus pattern (136 bp):
TTAAGTTAGTTATGACTGTAACTCATTTTTATTTACTTGTTTAGTACGTCAAACTCCTTGTATTT
TTCAGTTTAATCCTAGTTTTAATGTAATTCACCTTCCTTTTAGTTTTAGCATAAAAAATATGATT
TTTTTT
Found at i:150490 original size:71 final size:71
Alignment explanation
Indices: 150278--150490 Score: 185
Period size: 71 Copynumber: 3.1 Consensus size: 71
150268 TAGTTATGAC
*
150278 TGTAACTCATTTTTATTTACTTGTTTAGTACGTCAAACTCCTTGTATTTTTCTGTTTAATCCTAG
1 TGTAACTCATTTTTATTTACTTGTTTAGTACTTCAAACTCCTTGTATTTTTCTGTTTAATCCTAG
150343 TTTTAA
66 TTTTAA
* ** * * ** * * *
150349 TGTAATTCACCTTCCT-TTTA-GT-TTTAGCA-TAAAAAAT--ATG-ATTTTT-TTTTTNAAGT-
1 TGTAACTCA--TTTTTATTTACTTGTTTAGTACTTCAAACTCCTTGTATTTTTCTGTTT-AA-TC
* *
150405 -TAGTTATGAC
62 CTAGTT-TTAA
*
150415 TGTAACTCATTTTTATTTACTTGTTTAGTACTTCAAACTCCTTGTATTTTTCAGTTTAATCCTAG
1 TGTAACTCATTTTTATTTACTTGTTTAGTACTTCAAACTCCTTGTATTTTTCTGTTTAATCCTAG
150480 TTTTAA
66 TTTTAA
150486 TGTAA
1 TGTAA
150491 TTCACCTTCC
Statistics
Matches: 101, Mismatches: 26, Indels: 30
0.64 0.17 0.19
Matches are distributed among these distances:
64 3 0.03
65 13 0.13
66 19 0.19
67 9 0.09
68 5 0.05
69 4 0.04
70 9 0.09
71 24 0.24
72 12 0.12
73 3 0.03
ACGTcount: A:0.25, C:0.14, G:0.10, T:0.51
Consensus pattern (71 bp):
TGTAACTCATTTTTATTTACTTGTTTAGTACTTCAAACTCCTTGTATTTTTCTGTTTAATCCTAG
TTTTAA
Done.