Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014571.1 Kokia drynarioides strain JFW-HI SEQ_129610, 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: 58196
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:1585 original size:51 final size:51
Alignment explanation
Indices: 1530--1626 Score: 126
Period size: 51 Copynumber: 1.9 Consensus size: 51
1520 AGTATTACTC
**
1530 AAAAAAACA-AGTATAATTAAAACATGTAATGAA-ATTATTAAAAAAAACTTA
1 AAAAAAACAGA-TATAATTAAAACATACAAT-AATATTATTAAAAAAAACTTA
* *
1581 AAAAAATCAGATATAATTAAAACCTACAATAATATTATTAAAAAAA
1 AAAAAAACAGATATAATTAAAACATACAATAATATTATTAAAAAAA
1627 TTATCTTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
50 2 0.05
51 37 0.93
52 1 0.03
ACGTcount: A:0.63, C:0.07, G:0.04, T:0.26
Consensus pattern (51 bp):
AAAAAAACAGATATAATTAAAACATACAATAATATTATTAAAAAAAACTTA
Found at i:3145 original size:24 final size:26
Alignment explanation
Indices: 3099--3147 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
3089 ACAAAAAATT
* *
3099 ATATAAATTTATTAAATATTAATATA
1 ATATAAATATATTAAATAATAATATA
3125 ATATAAATAT-TTAAA-AATAATAT
1 ATATAAATATATTAAATAATAATAT
3148 GGGTAGATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.33
25 5 0.24
26 9 0.43
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
ATATAAATATATTAAATAATAATATA
Found at i:5461 original size:20 final size:20
Alignment explanation
Indices: 5436--5490 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
5426 TTTTTTTTTA
5436 ATTTTATAA-TTTATTAGAAT
1 ATTTTATAAGTTT-TTAGAAT
*
5456 ATTTTATAAGTTTTTATAAT
1 ATTTTATAAGTTTTTAGAAT
*
5476 A-TTTATAAATTTTTA
1 ATTTTATAAGTTTTTA
5491 TGAAAGTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
19 13 0.41
20 16 0.50
21 3 0.09
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (20 bp):
ATTTTATAAGTTTTTAGAAT
Found at i:10452 original size:11 final size:11
Alignment explanation
Indices: 10436--10461 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
10426 ATTTATATAT
10436 ATTTAGTTTTA
1 ATTTAGTTTTA
10447 ATTTAGTTTTA
1 ATTTAGTTTTA
10458 ATTT
1 ATTT
10462 TTTAATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (11 bp):
ATTTAGTTTTA
Found at i:10498 original size:26 final size:24
Alignment explanation
Indices: 10453--10513 Score: 77
Period size: 26 Copynumber: 2.5 Consensus size: 24
10443 TTTAATTTAG
* **
10453 TTTTAATTTTTTAATTTTATATAT
1 TTTTTATTTTTTAAAATTATATAT
10477 ATATTTTATTTTTTAAAATTATATAT
1 -T-TTTTATTTTTTAAAATTATATAT
10503 TTTTTATTTTT
1 TTTTTATTTTT
10514 ATGTAATTCC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 10 0.31
25 2 0.06
26 20 0.62
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (24 bp):
TTTTTATTTTTTAAAATTATATAT
Found at i:21059 original size:102 final size:105
Alignment explanation
Indices: 20874--21082 Score: 354
Period size: 102 Copynumber: 2.0 Consensus size: 105
20864 TAGGTTTTGC
20874 ATTTAGATATTAGGTTTTTTTGGTAAATATTATTGGGTGCTGTCATTTTCATTGTAGGTAGCTTC
1 ATTTAGATATTAGGTTTTTTTGGTAAATATTATT-GGTGCTGTCATTTTCATTGTAGGTAGCTTC
* *
20939 TGTGAATTATTTGTTCATTAAGTTGGAGTTGTAAAGTTTGTT
65 TGTGAATTATTAGGTCATTAAGTTGGAGTT-TAAAGTTTGTT
20981 ATTTAGATATTAGGTTTTTTTGGT-AA-A-TATT-GTGCTGTCATTTTCATTGTAGGTAGCTTCT
1 ATTTAGATATTAGGTTTTTTTGGTAAATATTATTGGTGCTGTCATTTTCATTGTAGGTAGCTTCT
21042 GTGAATTATTAGGTCATTAAGTTGGAGTTTAAAGTTTGTT
66 GTGAATTATTAGGTCATTAAGTTGGAGTTTAAAGTTTGTT
21082 A
1 A
21083 GGTAAGTGGC
Statistics
Matches: 100, Mismatches: 2, Indels: 6
0.93 0.02 0.06
Matches are distributed among these distances:
101 12 0.12
102 57 0.57
104 4 0.04
105 1 0.01
106 2 0.02
107 24 0.24
ACGTcount: A:0.23, C:0.06, G:0.22, T:0.49
Consensus pattern (105 bp):
ATTTAGATATTAGGTTTTTTTGGTAAATATTATTGGTGCTGTCATTTTCATTGTAGGTAGCTTCT
GTGAATTATTAGGTCATTAAGTTGGAGTTTAAAGTTTGTT
Found at i:25986 original size:2 final size:2
Alignment explanation
Indices: 25979--26003 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
25969 ATGGAGAATA
25979 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
26004 CCACCAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:32878 original size:20 final size:20
Alignment explanation
Indices: 32825--32886 Score: 88
Period size: 20 Copynumber: 3.1 Consensus size: 20
32815 AATGTATGAG
*
32825 TAGAAATGAACTTATATAAA
1 TAGAAATGAACTTGTATAAA
*
32845 TAGAAATGAACTTGTATAGA
1 TAGAAATGAACTTGTATAAA
* *
32865 TAGAAGTGAACTTGTATCAA
1 TAGAAATGAACTTGTATAAA
32885 TA
1 TA
32887 TAAGATGCAC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.47, C:0.06, G:0.16, T:0.31
Consensus pattern (20 bp):
TAGAAATGAACTTGTATAAA
Found at i:34431 original size:17 final size:18
Alignment explanation
Indices: 34411--34449 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
34401 AATTATTTAA
34411 AAAATAATATAAT-TTTT
1 AAAATAATATAATCTTTT
**
34428 AAAATTTTATAATCTTTT
1 AAAATAATATAATCTTTT
34446 AAAA
1 AAAA
34450 AATTAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
AAAATAATATAATCTTTT
Found at i:35536 original size:31 final size:31
Alignment explanation
Indices: 35501--35637 Score: 114
Period size: 31 Copynumber: 4.6 Consensus size: 31
35491 CTTAATATAA
35501 AATTTGGTACCTAAACTTGACA-TATTTTCTT
1 AATTTGGTACCTAAACTTGACACT-TTTTCTT
* * *
35532 AATTTGGTATCTAAA-TT-----TTTTTGATCC
1 AATTTGGTACCTAAACTTGACACTTTTT-CT-T
35559 AATTTGGTA-CTCAAACTTGACACTTTTTCTT
1 AATTTGGTACCT-AAACTTGACACTTTTTCTT
*
35590 AATTTGGTACCTAAACTTGACACTATTT-TT
1 AATTTGGTACCTAAACTTGACACTTTTTCTT
*
35620 AAGTTT-GTACTTAAACTT
1 AA-TTTGGTACCTAAACTT
35638 TTTGGGTCCA
Statistics
Matches: 88, Mismatches: 7, Indels: 23
0.75 0.06 0.19
Matches are distributed among these distances:
25 4 0.05
26 4 0.05
27 12 0.14
28 2 0.02
30 17 0.19
31 41 0.47
32 3 0.03
33 5 0.06
ACGTcount: A:0.28, C:0.15, G:0.10, T:0.46
Consensus pattern (31 bp):
AATTTGGTACCTAAACTTGACACTTTTTCTT
Found at i:35673 original size:88 final size:89
Alignment explanation
Indices: 35501--35687 Score: 240
Period size: 88 Copynumber: 2.1 Consensus size: 89
35491 CTTAATATAA
* * *
35501 AATTTGGTACCTAAACTTGACATATTTTCTTAATTTGGTATCTAAATTTTTTTGATCCAATTTGG
1 AATTTGGTACCTAAACTTGACATATTTTCTTAATTTGGTATCTAAACTTTTTGGATCCAATTTGA
*
35566 TACTCAAACTTGACACTTTTTCTT
66 TACTCAAACTTGACACTTTTCCTT
*
35590 AATTTGGTACCTAAACTTGACACTA-TTT-TTAAGTTT-GTA-CTTAAACTTTTTGGGTCCAATT
1 AATTTGGTACCTAAACTTGACA-TATTTTCTTAA-TTTGGTATC-TAAACTTTTTGGATCCAATT
* *
35651 TGATAC-CTGAACTTGACTCTTTTCCTT
63 TGATACTC-AAACTTGACACTTTTCCTT
35678 AATTTGGTAC
1 AATTTGGTAC
35688 TTAATTTTTT
Statistics
Matches: 87, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
87 2 0.02
88 55 0.63
89 28 0.32
90 2 0.02
ACGTcount: A:0.26, C:0.17, G:0.12, T:0.45
Consensus pattern (89 bp):
AATTTGGTACCTAAACTTGACATATTTTCTTAATTTGGTATCTAAACTTTTTGGATCCAATTTGA
TACTCAAACTTGACACTTTTCCTT
Found at i:35899 original size:27 final size:27
Alignment explanation
Indices: 35776--35903 Score: 66
Period size: 27 Copynumber: 4.5 Consensus size: 27
35766 TTTAATAAAT
*
35776 TTAGGTACCAAATTGAATCTAAAAAA-AAC
1 TTAGGTACCAAATTG--GC-AAAAAAGAAC
* *
35805 TTAGGTACCAAATTAGGAAAAAAATGTCAAG
1 TTAGGTACCAAATT-GGCAAAAAA-G--AAC
* **
35836 TTCAGGTACCAAATTGGGAAAAAAG-TG
1 TT-AGGTACCAAATTGGCAAAAAAGAAC
*
35863 TTAAGATACCAAATTAGGTCAAAAAA-AA-
1 TT-AGGTACCAAATT-GG-CAAAAAAGAAC
35891 TTAGGTACCAAAT
1 TTAGGTACCAAAT
35904 ATTATATGAA
Statistics
Matches: 80, Mismatches: 10, Indels: 20
0.73 0.09 0.18
Matches are distributed among these distances:
27 30 0.38
28 4 0.05
29 20 0.25
30 2 0.03
31 12 0.15
32 12 0.15
ACGTcount: A:0.48, C:0.12, G:0.16, T:0.23
Consensus pattern (27 bp):
TTAGGTACCAAATTGGCAAAAAAGAAC
Found at i:36633 original size:7 final size:7
Alignment explanation
Indices: 36623--36655 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
36613 TGTCAAATTA
36623 TTAAATC
1 TTAAATC
36630 TTAAATC
1 TTAAATC
36637 TTAAATC
1 TTAAATC
*
36644 TTAAATT
1 TTAAATC
36651 TTAAA
1 TTAAA
36656 GTTTTTCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (7 bp):
TTAAATC
Found at i:44415 original size:4 final size:4
Alignment explanation
Indices: 44406--44430 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
44396 AACTTAAACC
44406 ATTA ATTA ATTA ATTA ATTA ATTA A
1 ATTA ATTA ATTA ATTA ATTA ATTA A
44431 AAGTTCCTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
ATTA
Found at i:46530 original size:3 final size:3
Alignment explanation
Indices: 46522--46547 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
46512 TTGGTTGGGC
46522 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
46548 AGAAAGAGAA
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:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:48837 original size:2 final size:2
Alignment explanation
Indices: 48825--48878 Score: 67
Period size: 2 Copynumber: 28.0 Consensus size: 2
48815 AATTTATGTA
* * *
48825 AT AT GT AT AT AT AT A- AT TT AT GT A- AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48865 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
48879 TAAAAACTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
1 2 0.05
2 42 0.95
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48842 original size:24 final size:24
Alignment explanation
Indices: 48815--48863 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
48805 GATTGAAACA
*
48815 AATTTATGTAATATGTATATATAT
1 AATTTATGTAATATATATATATAT
48839 AATTTATGTAATATATATATATAT
1 AATTTATGTAATATATATATATAT
48863 A
1 A
48864 TATATATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (24 bp):
AATTTATGTAATATATATATATAT
Found at i:51430 original size:60 final size:59
Alignment explanation
Indices: 51365--51881 Score: 318
Period size: 60 Copynumber: 8.7 Consensus size: 59
51355 CGAGAATTTG
* * * *
51365 AAAAATTAAATTTTTTTTGTGTTGGCCATGCAATGGTCGACACCCCTTTTTTGTCAGATA
1 AAAAATTAAA-TTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCTTTTTTATCTGATA
* ** *
51425 AAAAATTCAATTTTTTGGTGTTGGTTATGCAATGGCCGGCA--CCTTTATTTATCTGATAA
1 AAAAATTAAATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCTTT-TTTATCTGAT-A
* ** * *
51484 AAAAATCAAA-TTTTT-GCATTGG---T-C----GAC-AC-CCCCTATTTATCTA-AT-A-A
1 AAAAATTAAATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCT-TTT-T-TATCTGATA
* ** * *
51531 AAAAATTAAATTTTTTGGTGTTGGCTATGCAATAACCGACACCCCTTTTTTTGTCAGATA
1 AAAAATTAAATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCC-TTTTTTATCTGATA
* * * * * *
51591 AAAAATTCAATTTTCTGGTATTGGCCATGTAATGACCGACACCCC-TATTTATCTGATAAA
1 AAAAATTAAATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCTTTTTTATCTGAT--A
* * * * * *
51651 AAAAATCAAATTTGTGGGTGTTGGTCATGCAATGGTCGACACCCCATTTTTATCTGATAA
1 AAAAATTAAATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCTTTTTTATCTGAT-A
* * * * *
51711 AAAAATTAAAATTTTGGGTGTTGACCATGCAATGGCCGACATCCCC-TTTTTATTTGGTA
1 AAAAATTAAATTTTTTGGTGTTGGCCATGCAATGGCCGACA-CCCCTTTTTTATCTGATA
* *
51770 AAAATTTAAATTTTTTTCGTGTCAACCAGTTGGCCATGCAATGGCCGACACCTCC-TTTTTATTT
1 AAAAATTAAA-TTTTTT-G-GT------GTTGGCCATGCAATGGCCGACACC-CCTTTTTTATCT
*
51834 GGTA
56 GATA
* ** *
51838 AAAAATTAATTTTTTTTGGTGTTGGCCATATAATGGACGACACC
1 AAAAATTAA-ATTTTTTGGTGTTGGCCATGCAATGGCCGACACC
51882 AACTTCCTCT
Statistics
Matches: 359, Mismatches: 60, Indels: 76
0.73 0.12 0.15
Matches are distributed among these distances:
47 10 0.03
48 6 0.02
49 12 0.03
50 4 0.01
51 2 0.01
52 1 0.00
53 2 0.01
54 1 0.00
57 12 0.03
58 25 0.07
59 53 0.15
60 158 0.44
61 16 0.04
62 2 0.01
66 2 0.01
67 3 0.01
68 50 0.14
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (59 bp):
AAAAATTAAATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCTTTTTTATCTGATA
Found at i:51594 original size:106 final size:104
Alignment explanation
Indices: 51393--51604 Score: 248
Period size: 106 Copynumber: 2.0 Consensus size: 104
51383 GTGTTGGCCA
* * * * *
51393 TGCAATGGTCGACACCCCTTTTTTGTCAGATAAAAAATTCAATTTTTTGGTGTTGGTTATGCAAT
1 TGCAATGGTCGACACCCCCTATTTATCAGATAAAAAATTAAATTTTTTGGTGTTGGCTATGCAAT
** * *
51458 GGCCGGCACCTTTATTTATCTGATAAAAAAATCAAATTTT
66 AACCGACACCTTTATTTATCAGAT-AAAAAATCAAATTTT
*
51498 TGCATTGGTCGACACCCCCTATTTATCTA-ATAAAAAAATTAAATTTTTTGGTGTTGGCTATGCA
1 TGCAATGGTCGACACCCCCTATTTATC-AGAT-AAAAAATTAAATTTTTTGGTGTTGGCTATGCA
* *
51562 ATAACCGACACCCCTTTTTTTGTCAGATAAAAAATTC-AATTTT
64 ATAACCGACA--CCTTTATTTATCAGATAAAAAA-TCAAATTTT
51605 CTGGTATTGG
Statistics
Matches: 90, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
105 25 0.28
106 38 0.42
107 12 0.13
108 15 0.17
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (104 bp):
TGCAATGGTCGACACCCCCTATTTATCAGATAAAAAATTAAATTTTTTGGTGTTGGCTATGCAAT
AACCGACACCTTTATTTATCAGATAAAAAATCAAATTTT
Found at i:51852 original size:68 final size:68
Alignment explanation
Indices: 51730--51859 Score: 208
Period size: 68 Copynumber: 1.9 Consensus size: 68
51720 AATTTTGGGT
*
51730 GTTGACCATGCAATGGCCGACATCCCCTTTTTATTTGGTAAAAATTTAAATTTTTTTCGTGTCAA
1 GTTGACCATGCAATGGCCGACATCCCCTTTTTATTTGGTAAAAAATTAAATTTTTTTCGTGTCAA
51795 CCA
66 CCA
* * *
51798 GTTGGCCATGCAATGGCCGACA-CCTCCTTTTTATTTGGTAAAAAATTAATTTTTTTTGGTGT
1 GTTGACCATGCAATGGCCGACATCC-CCTTTTTATTTGGTAAAAAATTAAATTTTTTTCGTGT
51860 TGGCCATATA
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
67 2 0.04
68 55 0.96
ACGTcount: A:0.25, C:0.18, G:0.17, T:0.40
Consensus pattern (68 bp):
GTTGACCATGCAATGGCCGACATCCCCTTTTTATTTGGTAAAAAATTAAATTTTTTTCGTGTCAA
CCA
Found at i:55647 original size:11 final size:12
Alignment explanation
Indices: 55607--55655 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
55597 TATTTGTGTA
55607 AAAATTAATTTG
1 AAAATTAATTTG
55619 AAAATTAATTTAAG
1 AAAATTAATTT--G
*
55633 TTGAAATTAATTTG
1 --AAAATTAATTTG
55647 AAAATTAAT
1 AAAATTAAT
55656 GAACATGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
12 19 0.61
14 2 0.06
16 10 0.32
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (12 bp):
AAAATTAATTTG
Found at i:55760 original size:12 final size:11
Alignment explanation
Indices: 55738--55778 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
55728 TTGAAGTTGA
55738 AATTT-AAATT
1 AATTTAAAATT
55748 ACATTTAAAATT
1 A-ATTTAAAATT
55760 AATTTAACAATT
1 AATTTAA-AATT
55772 -ATTTAAA
1 AATTTAAA
55779 TAAAAAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 2 0.07
11 16 0.57
12 10 0.36
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (11 bp):
AATTTAAAATT
Found at i:55826 original size:89 final size:87
Alignment explanation
Indices: 55771--56479 Score: 627
Period size: 84 Copynumber: 8.5 Consensus size: 87
55761 ATTTAACAAT
55771 TATTTAAATAAAAAATATTATTATTATATTACAATTTTTATCAAATAATGTGTTG-ATTTGATAA
1 TATTTAAATAAAAAATATTATTATTATATTACAATTTTTATCAAATAATGTGTTGAATTTGATAA
** *
55835 TACATTATTTATCAAATTTTCA
66 TACATTATAAATCAAATTTACA
55857 TATTTAAATAAAAAATATTATTATTATATTACAATTTTTATCAAATAATGTGTTG-A--T-AT--
1 TATTTAAATAAAAAATATTATTATTATATTACAATTTTTATCAAATAATGTGTTGAATTTGATAA
* * *
55916 T--ATT-T-ACT-AATTTTAAA
66 TACATTATAAATCAAATTTACA
*
55933 TATTTAAATAAAAATTATTA---TTATATTACAATTTTTATCAAATAATGTGTTG-ATTTGATAA
1 TATTTAAATAAAAAATATTATTATTATATTACAATTTTTATCAAATAATGTGTTGAATTTGATAA
* ** * *
55994 TAAATTATTTA-CTAATTTTAAA
66 TACATTATAAATC-AAATTTACA
*
56016 TATTTAAAT-AAAAA-ATTATTATTATATTACAATTTTTATCAAATAATGTGTTG-ATTTAATAA
1 TATTTAAATAAAAAATATTATTATTATATTACAATTTTTATCAAATAATGTGTTGAATTTGATAA
** *
56078 TACATTATTTA-CTAATTTTA-A
66 TACATTATAAATC-AAATTTACA
* *
56099 GTATTTAAAT-AAAAA-ATTATTATTATATTACAATTTTTATCAAATAACGTGTTG-ATTTGACA
1 -TATTTAAATAAAAAATATTATTATTATATTACAATTTTTATCAAATAATGTGTTGAATTTGATA
** * *
56161 ATACATTATTTA-CTAATTTTAAA
65 ATACATTATAAATC-AAATTTACA
* ** * * * *
56184 TATATAAAT-CTAAA-CTTATTATTGTATTACAATTTTTATCAAATAATGTGTTG-ATTTAACAA
1 TATTTAAATAAAAAATATTATTATTATATTACAATTTTTATCAAATAATGTGTTGAATTTGATAA
** * *
56246 TACATTATTTA-CTAATTTTAAA
66 TACATTATAAATC-AAATTTACA
* *
56268 TATTTAAAT-AAAAA-ATTATTATTATATTATAATTTTTTATCAAATAATGTGTTG-ATTTGACA
1 TATTTAAATAAAAAATATTATTATTATATTACAA-TTTTTATCAAATAATGTGTTGAATTTGATA
** * *
56330 ATACATTATTTA-CTAATTTTAAA
65 ATACATTATAAATC-AAATTTACA
* * *
56353 TATTTAAAT-AAAAA-ATTATTATTATATTATAATTTTTATCAAATAATATGTT--ATTTGACAA
1 TATTTAAATAAAAAATATTATTATTATATTACAATTTTTATCAAATAATGTGTTGAATTTGATAA
** * *
56414 TACATTATTTA-CTAATTTTAAA
66 TACATTATAAATC-AAATTTACA
* *
56436 TATTTAAAT-AAAAA-ATTATTATTGTATTACAATTTTTATTAAAT
1 TATTTAAATAAAAAATATTATTATTATATTACAATTTTTATCAAAT
56480 TTTAAATTTA
Statistics
Matches: 574, Mismatches: 32, Indels: 37
0.89 0.05 0.06
Matches are distributed among these distances:
73 33 0.06
75 1 0.00
76 27 0.05
77 1 0.00
78 2 0.00
79 3 0.01
80 3 0.01
81 6 0.01
82 4 0.01
83 93 0.16
84 261 0.45
85 84 0.15
86 56 0.10
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.48
Consensus pattern (87 bp):
TATTTAAATAAAAAATATTATTATTATATTACAATTTTTATCAAATAATGTGTTGAATTTGATAA
TACATTATAAATCAAATTTACA
Found at i:55917 original size:38 final size:38
Alignment explanation
Indices: 55875--55986 Score: 94
Period size: 38 Copynumber: 3.0 Consensus size: 38
55865 TAAAAAATAT
55875 TATTATTATATTACAATTTTTATCAAATAATGTGTTGA
1 TATTATTATATTACAATTTTTATCAAATAATGTGTTGA
* * ***
55913 TATTATT-TACT--AATTTTAAATATTTAAATAA--AAAT--
1 TATTATTATATTACAATTTT---TA-TCAAATAATGTGTTGA
55948 TATTATTATATTACAATTTTTATCAAATAATGTGTTGA
1 TATTATTATATTACAATTTTTATCAAATAATGTGTTGA
55986 T
1 T
55987 TTGATAATAA
Statistics
Matches: 53, Mismatches: 10, Indels: 22
0.62 0.12 0.26
Matches are distributed among these distances:
34 7 0.13
35 15 0.28
36 4 0.08
37 4 0.08
38 16 0.30
39 7 0.13
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.50
Consensus pattern (38 bp):
TATTATTATATTACAATTTTTATCAAATAATGTGTTGA
Found at i:55928 original size:35 final size:35
Alignment explanation
Indices: 55878--55986 Score: 107
Period size: 35 Copynumber: 3.0 Consensus size: 35
55868 AAAATATTAT
55878 TATTATATTACAATTTTTATCAAATAATGTGTTGA
1 TATTATATTACAATTTTTATCAAATAATGTGTTGA
* ***
55913 TATTAT-TTACTAATTTTAAATATTTAAATAA-AAATT-A
1 TATTATATTAC-AATTTT---TA-TCAAATAATGTGTTGA
55950 TTATTATATTACAATTTTTATCAAATAATGTGTTGA
1 -TATTATATTACAATTTTTATCAAATAATGTGTTGA
55986 T
1 T
55987 TTGATAATAA
Statistics
Matches: 57, Mismatches: 8, Indels: 18
0.69 0.10 0.22
Matches are distributed among these distances:
34 11 0.19
35 17 0.30
36 1 0.02
37 1 0.02
38 16 0.28
39 11 0.19
ACGTcount: A:0.40, C:0.05, G:0.06, T:0.50
Consensus pattern (35 bp):
TATTATATTACAATTTTTATCAAATAATGTGTTGA
Found at i:56058 original size:84 final size:84
Alignment explanation
Indices: 55914--56479 Score: 956
Period size: 84 Copynumber: 6.8 Consensus size: 84
55904 ATGTGTTGAT
55914 ATTATTTACTAATTTTAAATATTTAAAT-AAAAATTATTATTATATTACAATTTTTATCAAATAA
1 ATTATTTACTAATTTTAAATATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAA
* *
55978 TGTGTTGATTTGATAATAA
66 TGTGTTGATTTGACAATAC
55997 ATTATTTACTAATTTTAAATATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAA
1 ATTATTTACTAATTTTAAATATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAA
* *
56062 TGTGTTGATTTAATAATAC
66 TGTGTTGATTTGACAATAC
*
56081 ATTATTTACTAATTTTAAGTATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAA
1 ATTATTTACTAATTTTAAATATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAA
*
56146 CGTGTTGATTTGACAATAC
66 TGTGTTGATTTGACAATAC
* ** * *
56165 ATTATTTACTAATTTTAAATATATAAATCTAAACTTATTATTGTATTACAATTTTTATCAAATAA
1 ATTATTTACTAATTTTAAATATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAA
*
56230 TGTGTTGATTTAACAATAC
66 TGTGTTGATTTGACAATAC
*
56249 ATTATTTACTAATTTTAAATATTTAAATAAAAAATTATTATTATATTATAATTTTTTATCAAATA
1 ATTATTTACTAATTTTAAATATTTAAATAAAAAATTATTATTATATTACAA-TTTTTATCAAATA
56314 ATGTGTTGATTTGACAATAC
65 ATGTGTTGATTTGACAATAC
*
56334 ATTATTTACTAATTTTAAATATTTAAATAAAAAATTATTATTATATTATAATTTTTATCAAATAA
1 ATTATTTACTAATTTTAAATATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAA
*
56399 TATGTT-ATTTGACAATAC
66 TGTGTTGATTTGACAATAC
* *
56417 ATTATTTACTAATTTTAAATATTTAAATAAAAAATTATTATTGTATTACAATTTTTATTAAAT
1 ATTATTTACTAATTTTAAATATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAAT
56480 TTTAAATTTA
Statistics
Matches: 456, Mismatches: 25, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
83 100 0.22
84 273 0.60
85 83 0.18
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.48
Consensus pattern (84 bp):
ATTATTTACTAATTTTAAATATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAA
TGTGTTGATTTGACAATAC
Found at i:56154 original size:168 final size:168
Alignment explanation
Indices: 55771--56479 Score: 1102
Period size: 168 Copynumber: 4.3 Consensus size: 168
55761 ATTTAACAAT
*
55771 TATTTAAATAAAAAATATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGATAAT
1 TATTTAAAT-AAAAA-ATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAAT
* *
55836 ACATTATTTATCAAATTTT-CATATTTAAATAAAAAATATTATTATTATATTACAATTTTTATCA
64 ACATTATTTA-CTAATTTTAAATATTTAAAT-AAAAA-ATTATTATTATATTACAATTTTTATCA
55900 AATAATGTGTTG--------AT--ATTATTTACTAATTTTAAA
126 AATAATGTGTTGATTTAACAATACATTATTTACTAATTTTAAA
* *
55933 TATTTAAAT-AAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGATAATAA
1 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
55997 ATTATTTACTAATTTTAAATATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAA
66 ATTATTTACTAATTTTAAATATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAA
* *
56062 TGTGTTGATTTAATAATACATTATTTACTAATTTTAAG
131 TGTGTTGATTTAACAATACATTATTTACTAATTTTAAA
*
56100 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAACGTGTTGATTTGACAATAC
1 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
* ** * *
56165 ATTATTTACTAATTTTAAATATATAAATCTAAACTTATTATTGTATTACAATTTTTATCAAATAA
66 ATTATTTACTAATTTTAAATATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAA
56230 TGTGTTGATTTAACAATACATTATTTACTAATTTTAAA
131 TGTGTTGATTTAACAATACATTATTTACTAATTTTAAA
*
56268 TATTTAAATAAAAAATTATTATTATATTATAATTTTTTATCAAATAATGTGTTGATTTGACAATA
1 TATTTAAATAAAAAATTATTATTATATTACAA-TTTTTATCAAATAATGTGTTGATTTGACAATA
*
56333 CATTATTTACTAATTTTAAATATTTAAATAAAAAATTATTATTATATTATAATTTTTATCAAATA
65 CATTATTTACTAATTTTAAATATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATA
* *
56398 ATATGTT-ATTTGACAATACATTATTTACTAATTTTAAA
130 ATGTGTTGATTTAACAATACATTATTTACTAATTTTAAA
* *
56436 TATTTAAATAAAAAATTATTATTGTATTACAATTTTTATTAAAT
1 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAAT
56480 TTTAAATTTA
Statistics
Matches: 507, Mismatches: 27, Indels: 21
0.91 0.05 0.04
Matches are distributed among these distances:
157 39 0.08
158 12 0.02
159 68 0.13
160 4 0.01
162 9 0.02
165 2 0.00
167 38 0.07
168 239 0.47
169 96 0.19
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.48
Consensus pattern (168 bp):
TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
ATTATTTACTAATTTTAAATATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAA
TGTGTTGATTTAACAATACATTATTTACTAATTTTAAA
Found at i:56289 original size:252 final size:248
Alignment explanation
Indices: 55771--56479 Score: 1103
Period size: 252 Copynumber: 2.8 Consensus size: 248
55761 ATTTAACAAT
55771 TATTTAAATAAAAAATATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGATAAT
1 TATTTAAAT-AAAAA-ATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGATAAT
* *
55836 ACATTATTTATCAAATTTTCATATTTAAATAAAAAATATTATTATTATATTACAATTTTTATCAA
64 ACATTATTTA-CTAATTTTAATATTTAAAT-AAAAA-ATTATTATTATATTACAATTTTTATCAA
*
55901 ATAATG-TG--TTG---AT--ATTATTTACTAATTTTAAATATTTAAATAAAAATTATTATTATA
126 ATAATGTTGATTTGACAATACATTATTTACTAATTTTAAATATTTAAATAAAAATTATTATTGTA
* *
55958 TTACAATTTTTATCAAATAATGTGTTGATTTGATAATAAATTATTTACTAATTTTAAA
191 TTACAATTTTTATCAAATAATGTGTTGATTTAACAATAAATTATTTACTAATTTTAAA
*
56016 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTAATAATAC
1 TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGATAATAC
56081 ATTATTTACTAATTTTAAGTATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAA
66 ATTATTTACTAATTTTAA-TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAA
* * *
56146 CGTGTTGATTTGACAATACATTATTTACTAATTTTAAATATATAAATCTAAACTTATTATTGTAT
130 --TGTTGATTTGACAATACATTATTTACTAATTTTAAATATTTAAAT-AAAAATTATTATTGTAT
*
56211 TACAATTTTTATCAAATAATGTGTTGATTTAACAATACATTATTTACTAATTTTAAA
192 TACAATTTTTATCAAATAATGTGTTGATTTAACAATAAATTATTTACTAATTTTAAA
* *
56268 TATTTAAATAAAAAATTATTATTATATTATAATTTTTTATCAAATAATGTGTTGATTTGACAATA
1 TATTTAAATAAAAAATTATTATTATATTACAA-TTTTTATCAAATAATGTGTTGATTTGATAATA
*
56333 CATTATTTACTAATTTTAAATATTTAAATAAAAAATTATTATTATATTATAATTTTTATCAAATA
65 CATTATTTACTAATTTT-AATATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAAT-
56398 ATATGTT-ATTTGACAATACATTATTTACTAATTTTAAATATTTAAATAAAAAATTATTATTGTA
128 A-ATGTTGATTTGACAATACATTATTTACTAATTTTAAATATTTAAAT-AAAAATTATTATTGTA
*
56462 TTACAATTTTTATTAAAT
191 TTACAATTTTTATCAAAT
56480 TTTAAATTTA
Statistics
Matches: 429, Mismatches: 19, Indels: 25
0.91 0.04 0.05
Matches are distributed among these distances:
241 32 0.07
242 13 0.03
243 69 0.16
244 7 0.02
245 9 0.02
246 3 0.01
249 2 0.00
251 27 0.06
252 169 0.39
253 94 0.22
254 3 0.01
255 1 0.00
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.48
Consensus pattern (248 bp):
TATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGATAATAC
ATTATTTACTAATTTTAATATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAAT
GTTGATTTGACAATACATTATTTACTAATTTTAAATATTTAAATAAAAATTATTATTGTATTACA
ATTTTTATCAAATAATGTGTTGATTTAACAATAAATTATTTACTAATTTTAAA
Done.