Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005005.1 Kokia drynarioides strain JFW-HI SEQ_118764, 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: 125482
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 11 characters in sequence are not A, C, G, or T
Found at i:1645 original size:19 final size:18
Alignment explanation
Indices: 1623--1683 Score: 52
Period size: 19 Copynumber: 3.3 Consensus size: 18
1613 ATTATTTTTT
1623 AAAATCTAAATATATTATA
1 AAAATCTAAAT-TATTATA
* * *
1642 AAAA-GTAAATTATTTTTT
1 AAAATCTAAATTA-TTATA
*
1660 TAAATCTAAATTTATTATA
1 AAAATCTAAA-TTATTATA
1679 AAAAT
1 AAAAT
1684 TATAAATAAA
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
17 2 0.06
18 11 0.35
19 15 0.48
20 3 0.10
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (18 bp):
AAAATCTAAATTATTATA
Found at i:1676 original size:37 final size:37
Alignment explanation
Indices: 1608--1682 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
1598 AAAATAACTT
1608 AGTAAATTATTTTTTAAAATCTAAATATATTATAAAA
1 AGTAAATTATTTTTTAAAATCTAAATATATTATAAAA
* *
1645 AGTAAATTATTTTTTTAAATCTAAATTTATTATAAAA
1 AGTAAATTATTTTTTAAAATCTAAATATATTATAAAA
1682 A
1 A
1683 TTATAAATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (37 bp):
AGTAAATTATTTTTTAAAATCTAAATATATTATAAAA
Found at i:16612 original size:3 final size:3
Alignment explanation
Indices: 16604--16628 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
16594 TCATTATCTT
16604 TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA T
16629 TGGTTTACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (3 bp):
TGA
Found at i:20523 original size:30 final size:33
Alignment explanation
Indices: 20487--20546 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
20477 GAGCTTCTTA
*
20487 ATTTGCACA-TTG-AAA-CAATCATTTGAGCTT
1 ATTTGCACATTTGAAAAGCAAGCATTTGAGCTT
20517 ATTTGCACATTTGAAAAGCAAGCATTTGAG
1 ATTTGCACATTTGAAAAGCAAGCATTTGAG
20547 GGATAACTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 9 0.35
31 3 0.12
32 3 0.12
33 11 0.42
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (33 bp):
ATTTGCACATTTGAAAAGCAAGCATTTGAGCTT
Found at i:26553 original size:18 final size:18
Alignment explanation
Indices: 26518--26554 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
26508 TTTTTCAAAG
26518 TAAAGTGACAAAATGATA
1 TAAAGTGACAAAATGATA
26536 TAAAGATGACAAAA-GATA
1 TAAAG-TGACAAAATGATA
26554 T
1 T
26555 TAGAGGTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.57, C:0.05, G:0.16, T:0.22
Consensus pattern (18 bp):
TAAAGTGACAAAATGATA
Found at i:30873 original size:22 final size:23
Alignment explanation
Indices: 30835--30878 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
30825 ATTTTAATAT
30835 TTTTATAATATTTATAAGTTTTTG
1 TTTTATAATATTTATAA-TTTTTG
30859 TTTT-TAAT-TTTATAATTTTT
1 TTTTATAATATTTATAATTTTT
30879 ATAAGTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 5 0.25
22 7 0.35
23 4 0.20
24 4 0.20
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (23 bp):
TTTTATAATATTTATAATTTTTG
Found at i:30880 original size:9 final size:9
Alignment explanation
Indices: 30793--30882 Score: 50
Period size: 9 Copynumber: 10.7 Consensus size: 9
30783 TTTATTAATC
*
30793 TTATATTTT
1 TTATAATTT
30802 TTATAATTT
1 TTATAATTT
* **
30811 ATTAGAAAAT
1 -TTATAATTT
30821 TTA-AATTT
1 TTATAATTT
*
30829 TAAT-ATTT
1 TTATAATTT
*
30837 TTATAATAT
1 TTATAATTT
*
30846 TTATAAGTT
1 TTATAATTT
*
30855 TT-T--GTT
1 TTATAATTT
30861 TT-TAA-TT
1 TTATAATTT
30868 TTATAATTT
1 TTATAATTT
30877 TTATAA
1 TTATAA
30883 GTTTATGTAA
Statistics
Matches: 63, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
6 6 0.10
7 4 0.06
8 16 0.25
9 31 0.49
10 6 0.10
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (9 bp):
TTATAATTT
Found at i:30965 original size:21 final size:20
Alignment explanation
Indices: 30922--30965 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 20
30912 ACTTTTTAAA
30922 TTTTATAATTTTACTATGATT
1 TTTTATAATTTTAC-ATGATT
30943 TTTTATAATTTTTA-ATGATT
1 TTTTATAA-TTTTACATGATT
30963 TTT
1 TTT
30966 GCTGAGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 9 0.41
21 8 0.36
22 5 0.23
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (20 bp):
TTTTATAATTTTACATGATT
Found at i:35053 original size:20 final size:20
Alignment explanation
Indices: 34985--35055 Score: 54
Period size: 21 Copynumber: 3.3 Consensus size: 20
34975 TAATTAATAA
*
34985 TAAATTCTATGTAATTTAGT
1 TAAATACTATGTAATTTAGT
* *
35005 TAAAATTAATATAAATAATTTA-T
1 T-AAA-TACTAT--GTAATTTAGT
35028 AATAAATACTATGTAATTTAGT
1 --TAAATACTATGTAATTTAGT
35050 TAAATA
1 TAAATA
35056 TTTAGTATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 14
0.67 0.09 0.24
Matches are distributed among these distances:
20 7 0.18
21 10 0.26
22 5 0.13
23 6 0.15
24 10 0.26
25 1 0.03
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.44
Consensus pattern (20 bp):
TAAATACTATGTAATTTAGT
Found at i:35055 original size:24 final size:24
Alignment explanation
Indices: 34983--35055 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
34973 AATAATTAAT
*
34983 AATAAATTCTATGTAATTTAGTTAA
1 AATAAATACTATGTAATTTAGTT-A
* **
35008 AATTAATA-TAAATAATTTA--T-
1 AATAAATACTATGTAATTTAGTTA
35028 AATAAATACTATGTAATTTAGTTA
1 AATAAATACTATGTAATTTAGTTA
35052 AATA
1 AATA
35056 TTTAGTATAT
Statistics
Matches: 37, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
20 7 0.19
21 9 0.24
22 1 0.03
23 1 0.03
24 13 0.35
25 6 0.16
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.42
Consensus pattern (24 bp):
AATAAATACTATGTAATTTAGTTA
Found at i:40775 original size:10 final size:10
Alignment explanation
Indices: 40760--40874 Score: 59
Period size: 9 Copynumber: 11.9 Consensus size: 10
40750 GTTGGATCTT
40760 TAATTTTTTA
1 TAATTTTTTA
40770 TAA-TTTTTA
1 TAATTTTTTA
40779 -AATTTTTT-
1 TAATTTTTTA
* * *
40787 CAGTTATTTA
1 TAATTTTTTA
40797 -AATTTTTTA
1 TAATTTTTTA
40806 TAA--TTTTA
1 TAATTTTTTA
40814 -AATGTTTTTA
1 TAAT-TTTTTA
*
40824 CAA-TTTTTA
1 TAATTTTTTA
*
40833 TAGATATTTT-
1 TA-ATTTTTTA
*
40843 TAATTATATTTT
1 TAATT-T-TTTA
40855 TAATATTTTTA
1 TAAT-TTTTTA
*
40866 AAATTTTTT
1 TAATTTTTT
40875 TGGTCCGTGG
Statistics
Matches: 82, Mismatches: 9, Indels: 28
0.69 0.08 0.24
Matches are distributed among these distances:
7 2 0.02
8 7 0.09
9 33 0.40
10 19 0.23
11 15 0.18
12 5 0.06
13 1 0.01
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (10 bp):
TAATTTTTTA
Found at i:40784 original size:18 final size:19
Alignment explanation
Indices: 40764--40873 Score: 86
Period size: 18 Copynumber: 5.7 Consensus size: 19
40754 GATCTTTAAT
40764 TTTTTATAATTTTTAAAT-
1 TTTTTATAATTTTTAAATA
* *
40782 TTTTT-CAGTTATTTAAAT-
1 TTTTTATAATT-TTTAAATA
*
40800 TTTTTATAA-TTTTAAATG
1 TTTTTATAATTTTTAAATA
*
40818 TTTTTACAATTTTTATAGATA
1 TTTTTATAATTTTTA-A-ATA
40839 TTTTTAATTATATTTTT-AATA
1 TTTTT-A-TA-ATTTTTAAATA
*
40860 TTTTTAAAATTTTT
1 TTTTTATAATTTTT
40874 TTGGTCCGTG
Statistics
Matches: 75, Mismatches: 8, Indels: 18
0.74 0.08 0.18
Matches are distributed among these distances:
17 10 0.13
18 32 0.43
19 7 0.09
20 2 0.03
21 15 0.20
22 2 0.03
23 1 0.01
24 6 0.08
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.64
Consensus pattern (19 bp):
TTTTTATAATTTTTAAATA
Found at i:42450 original size:18 final size:19
Alignment explanation
Indices: 42429--42464 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
42419 AAAATCTATA
42429 AAAATATT-ATTTTTAAAT
1 AAAATATTAATTTTTAAAT
*
42447 AAAATTTTAATTTTTAAA
1 AAAATATTAATTTTTAAA
42465 AATTAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AAAATATTAATTTTTAAAT
Found at i:51756 original size:26 final size:26
Alignment explanation
Indices: 51726--51786 Score: 122
Period size: 26 Copynumber: 2.3 Consensus size: 26
51716 GAACATTTGG
51726 AAATTTTTAAAAGTTTTCATCTTTTT
1 AAATTTTTAAAAGTTTTCATCTTTTT
51752 AAATTTTTAAAAGTTTTCATCTTTTT
1 AAATTTTTAAAAGTTTTCATCTTTTT
51778 AAATTTTTA
1 AAATTTTTA
51787 GAGTTACTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.33, C:0.07, G:0.03, T:0.57
Consensus pattern (26 bp):
AAATTTTTAAAAGTTTTCATCTTTTT
Found at i:53758 original size:20 final size:19
Alignment explanation
Indices: 53733--53793 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 19
53723 GCTTATAATA
53733 TTAAATTTATTTTTGAATTT
1 TTAAATTT-TTTTTGAATTT
* *
53753 TTAAATTCTTTTATAAATTT
1 TTAAATT-TTTTTTGAATTT
*
53773 TTATAA-ATTTTTTGAATTT
1 TTA-AATTTTTTTTGAATTT
53792 TT
1 TT
53794 TATAATTTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
19 12 0.35
20 19 0.56
21 3 0.09
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (19 bp):
TTAAATTTTTTTTGAATTT
Found at i:53774 original size:10 final size:10
Alignment explanation
Indices: 53748--53820 Score: 57
Period size: 10 Copynumber: 7.5 Consensus size: 10
53738 TTTATTTTTG
53748 AATTTTTA-A
1 AATTTTTATA
*
53757 ATTCTTTTATA
1 AAT-TTTTATA
53768 AATTTTTATA
1 AATTTTTATA
*
53778 AATTTTT-TG
1 AATTTTTATA
53787 AATTTTT-TA
1 AATTTTTATA
53796 TAA-TTTTAT-
1 -AATTTTTATA
*
53805 AATTTATATA
1 AATTTTTATA
53815 TAATTT
1 -AATTT
53821 CGAATATTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
8 2 0.04
9 20 0.38
10 22 0.42
11 8 0.15
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (10 bp):
AATTTTTATA
Found at i:53783 original size:19 final size:19
Alignment explanation
Indices: 53761--53820 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
53751 TTTTAAATTC
53761 TTTTATAAATTTTTATA-AA
1 TTTTAT-AATTTTTATATAA
*
53780 TTTTTTGAATTTTT-TATAA
1 TTTTAT-AATTTTTATATAA
*
53799 TTTTATAATTTATATATAA
1 TTTTATAATTTTTATATAA
53818 TTT
1 TTT
53821 CGAATATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
18 8 0.23
19 27 0.77
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTTATAATTTTTATATAA
Found at i:53784 original size:30 final size:28
Alignment explanation
Indices: 53750--53806 Score: 78
Period size: 31 Copynumber: 1.9 Consensus size: 28
53740 TATTTTTGAA
53750 TTTTTAAATTCTTTTATAAATTTTTATAAAT
1 TTTTTAAATT-TTTTAT-AA-TTTTATAAAT
*
53781 TTTTTGAATTTTTTATAATTTTATAA
1 TTTTTAAATTTTTTATAATTTTATAA
53807 TTTATATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 8 0.32
29 2 0.08
30 6 0.24
31 9 0.36
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (28 bp):
TTTTTAAATTTTTTATAATTTTATAAAT
Found at i:54557 original size:7 final size:7
Alignment explanation
Indices: 54545--54582 Score: 69
Period size: 7 Copynumber: 5.6 Consensus size: 7
54535 TGATTAGATT
54545 AAAAATA
1 AAAAATA
54552 AAAAATA
1 AAAAATA
54559 AAAAATA
1 AAAAATA
54566 AAAAAT-
1 AAAAATA
54572 AAAAATA
1 AAAAATA
54579 AAAA
1 AAAA
54583 TACCCAATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.20
7 24 0.80
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (7 bp):
AAAAATA
Found at i:63448 original size:49 final size:49
Alignment explanation
Indices: 63376--63471 Score: 140
Period size: 49 Copynumber: 2.0 Consensus size: 49
63366 TCTATTTAAA
* * * *
63376 GGTTGAAAAAACCTTATCTAATCAATGTCAAATAGATGAAGTGTAGTAT
1 GGTTGAAAAAACCTTATCTAATCAATATAAAAGAGAAGAAGTGTAGTAT
63425 GGTTG-AAAAACCTTATTCTAATCAATATAAAAGAGAAGAAGTGTAGT
1 GGTTGAAAAAACCTTA-TCTAATCAATATAAAAGAGAAGAAGTGTAGT
63472 TCTGTACGGA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
48 10 0.24
49 32 0.76
ACGTcount: A:0.43, C:0.09, G:0.19, T:0.29
Consensus pattern (49 bp):
GGTTGAAAAAACCTTATCTAATCAATATAAAAGAGAAGAAGTGTAGTAT
Found at i:65791 original size:22 final size:22
Alignment explanation
Indices: 65745--65792 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
65735 TTCACCTGCC
*
65745 AAATTTTATATATTTTTAATTT
1 AAATTTTATATATTTTTAATAT
*
65767 AAATTTTATGTATTTTT-ATAAT
1 AAATTTTATATATTTTTAAT-AT
65789 AAAT
1 AAAT
65793 ATTAACTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
AAATTTTATATATTTTTAATAT
Found at i:73655 original size:9 final size:9
Alignment explanation
Indices: 73575--73846 Score: 83
Period size: 10 Copynumber: 28.4 Consensus size: 9
73565 ATTTTCAAAT
73575 AAAATTATTA
1 AAAATTA-TA
*
73585 AAAAATA-A
1 AAAATTATA
*
73593 GAAAAATATA
1 -AAAATTATA
*
73603 AAAATATCTA
1 AAAAT-TATA
*
73613 AAAAGTTATT
1 AAAA-TTATA
*
73623 GAAATTAATA
1 AAAATT-ATA
* *
73633 TAAACTTATG
1 -AAAATTATA
73643 AAAATTATAAA
1 AAAATTAT--A
73654 AAAATT-TA
1 AAAATTATA
*
73662 AAACTT-TA
1 AAAATTATA
*
73670 AATATTATAA
1 AAAATTAT-A
73680 AAAATCTA-A
1 AAAAT-TATA
*
73689 TAAAACTA-A
1 -AAAATTATA
*
73698 TAAATTATA
1 AAAATTATA
* *
73707 AAATTTTTA
1 AAAATTATA
73716 TAAAATTAATA
1 -AAAATT-ATA
*
73727 ATAAATATTTA
1 A-AAAT-TATA
*
73738 AAATTTTATA
1 AAA-ATTATA
73748 AAAATGTATA
1 AAAAT-TATA
*
73758 AAAATTCTTA
1 AAAATT-ATA
*
73768 TAAGATTATAA
1 -AAAATTAT-A
*
73779 AAAATCATA
1 AAAATTATA
*
73788 AAAATTATT
1 AAAATTATA
73797 AAAA-TAT-
1 AAAATTATA
*
73804 TAAATTGATA
1 AAAATT-ATA
*
73814 TAAACTTA-A
1 -AAAATTATA
73823 AAAATTTATAA
1 AAAA-TTAT-A
73834 AAAATTATA
1 AAAATTATA
73843 AAAA
1 AAAA
73847 CTTGAATTGG
Statistics
Matches: 194, Mismatches: 39, Indels: 59
0.66 0.13 0.20
Matches are distributed among these distances:
7 3 0.02
8 25 0.13
9 57 0.29
10 70 0.36
11 38 0.20
12 1 0.01
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.35
Consensus pattern (9 bp):
AAAATTATA
Found at i:73693 original size:29 final size:30
Alignment explanation
Indices: 73624--73709 Score: 87
Period size: 29 Copynumber: 3.0 Consensus size: 30
73614 AAAGTTATTG
73624 AAATTAATATAAACTTATGAAAATTATAAAA
1 AAATTAATA-AAACTTATGAAAATTATAAAA
73655 AAATT--TAAAACTT-T-AAATATTAT-AAA
1 AAATTAATAAAACTTATGAAA-ATTATAAAA
*
73681 AAATCTAATAAAACTAAT--AAATTATAAAA
1 AAAT-TAATAAAACTTATGAAAATTATAAAA
73710 TTTTTATAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 14
0.76 0.02 0.22
Matches are distributed among these distances:
26 10 0.21
27 7 0.15
28 11 0.23
29 14 0.29
30 1 0.02
31 5 0.10
ACGTcount: A:0.62, C:0.05, G:0.01, T:0.33
Consensus pattern (30 bp):
AAATTAATAAAACTTATGAAAATTATAAAA
Found at i:73805 original size:11 final size:10
Alignment explanation
Indices: 73701--73805 Score: 54
Period size: 11 Copynumber: 10.1 Consensus size: 10
73691 AAACTAATAA
73701 ATTATAAAATT
1 ATTA-AAAATT
*
73712 TTTATAAAATT
1 ATTA-AAAATT
*
73723 AATAATAAA-T
1 ATTAA-AAATT
*
73733 ATTTAAAATT
1 ATTAAAAATT
*
73743 TTATAAAAATGT
1 AT-TAAAAAT-T
73755 A-TAAAAATT
1 ATTAAAAATT
* *
73764 CTTATAAGATT
1 ATTA-AAAATT
* *
73775 ATAAAAAATC
1 ATTAAAAATT
73785 A-TAAAAATT
1 ATTAAAAATT
73794 ATTAAAATATT
1 ATTAAAA-ATT
73805 A
1 A
73806 AATTGATATA
Statistics
Matches: 70, Mismatches: 16, Indels: 16
0.69 0.16 0.16
Matches are distributed among these distances:
9 11 0.16
10 26 0.37
11 32 0.46
12 1 0.01
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (10 bp):
ATTAAAAATT
Found at i:74467 original size:31 final size:32
Alignment explanation
Indices: 74408--74467 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
74398 CAATTTTAAT
* *
74408 ATTTGTATGATTTTTTATAATTTGTTAAAAAA
1 ATTTGTACGATTTTTTATAAATTGTTAAAAAA
74440 ATTTGTACG-TTTTTTATAAAATT-TTAAA
1 ATTTGTACGATTTTTTAT-AAATTGTTAAA
74468 TATGTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 13 0.52
32 12 0.48
ACGTcount: A:0.37, C:0.02, G:0.08, T:0.53
Consensus pattern (32 bp):
ATTTGTACGATTTTTTATAAATTGTTAAAAAA
Found at i:74475 original size:21 final size:21
Alignment explanation
Indices: 74451--74494 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
74441 TTTGTACGTT
74451 TTTTATAAAATTTTA-AATATG
1 TTTTAT-AAATTTTATAATATG
* *
74472 TTTTATTAATTTTATAATTTG
1 TTTTATAAATTTTATAATATG
74493 TT
1 TT
74495 AAATTTGTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (21 bp):
TTTTATAAATTTTATAATATG
Found at i:74499 original size:37 final size:39
Alignment explanation
Indices: 74452--74564 Score: 112
Period size: 39 Copynumber: 3.0 Consensus size: 39
74442 TTGTACGTTT
*
74452 TTTATA-AAATTTTAAATATGTTTTATTAAT-TTTATAA-
1 TTTATATAAATTTTAAATAT-TTTTAATAATATTTATAAG
* *
74489 TTTGT-TAAATTTGT-TATATTTTTAATAATATTTATAAG
1 TTTATATAAATTT-TAAATATTTTTAATAATATTTATAAG
* *
74527 TTTATATAAATTTTAATTATTTTTCAA-AATTTTTATAA
1 TTTATATAAATTTTAAATATTTTT-AATAATATTTATAA
74565 TGATTTTTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
36 9 0.15
37 21 0.34
38 6 0.10
39 24 0.39
40 2 0.03
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.58
Consensus pattern (39 bp):
TTTATATAAATTTTAAATATTTTTAATAATATTTATAAG
Found at i:75119 original size:31 final size:31
Alignment explanation
Indices: 75082--75215 Score: 102
Period size: 31 Copynumber: 4.5 Consensus size: 31
75072 CCCCAAAAAA
* *
75082 TTTAAGTACCAACTTAAAAAAAATTGTCAAG
1 TTTAAGTACCAAATTAAAAAAAAGTGTCAAG
* **
75113 TTTAAGTATCAAATTAGGAAAAAGTGTCAAG
1 TTTAAGTACCAAATTAAAAAAAAGTGTCAAG
*
75144 TTTGAGTACCAAATTGGACAAAAAAA-----AAG
1 TTTAAGTACCAAATT--A-AAAAAAAGTGTCAAG
* *
75173 TTTAAATACCAAATT-AAAAAAA-TGTCAAA
1 TTTAAGTACCAAATTAAAAAAAAGTGTCAAG
* *
75202 TTCAAGTATCAAAT
1 TTTAAGTACCAAAT
75216 GTTATATTAA
Statistics
Matches: 81, Mismatches: 15, Indels: 16
0.72 0.13 0.14
Matches are distributed among these distances:
25 7 0.09
29 29 0.36
31 39 0.48
33 1 0.01
34 5 0.06
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.28
Consensus pattern (31 bp):
TTTAAGTACCAAATTAAAAAAAAGTGTCAAG
Found at i:75192 original size:90 final size:89
Alignment explanation
Indices: 75032--75215 Score: 237
Period size: 90 Copynumber: 2.1 Consensus size: 89
75022 AATTAGGTAC
*** * *
75032 CAAATTAGGAAAAAAAGTCAAGTTCAGGTACCAAATTGGACCCCAAAAAATTTAAGTACCAACTT
1 CAAATTAGGAAAAAAAGTCAAGTTCAGGTACCAAATTGGACAAAAAAAAATTTAAATACCAAATT
* *
75097 AAAAAAAATTGTCAAGTTTAAGTAT
66 AAAAAAAA-TGTCAAATTCAAGTAT
** *
75122 CAAATTAGGAAAAAGTGTCAAGTT-TGAGTACCAAATTGGACAAAAAAAAAGTTTAAATACCAAA
1 CAAATTAGGAAAAAAAGTCAAGTTCAG-GTACCAAATTGGACAAAAAAAAA-TTTAAATACCAAA
75186 TT-AAAAAAATGTCAAATTCAAGTAT
64 TTAAAAAAAATGTCAAATTCAAGTAT
75211 CAAAT
1 CAAAT
75216 GTTATATTAA
Statistics
Matches: 82, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
89 20 0.24
90 49 0.60
91 13 0.16
ACGTcount: A:0.50, C:0.12, G:0.13, T:0.24
Consensus pattern (89 bp):
CAAATTAGGAAAAAAAGTCAAGTTCAGGTACCAAATTGGACAAAAAAAAATTTAAATACCAAATT
AAAAAAAATGTCAAATTCAAGTAT
Found at i:77177 original size:21 final size:20
Alignment explanation
Indices: 77153--77193 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
77143 TACACAAGGT
*
77153 AATTTGGTGATATACTTTTGA
1 AATTTGGTCATATA-TTTTGA
*
77174 AATTTGTTCATATATTTTGA
1 AATTTGGTCATATATTTTGA
77194 TTAGACTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.29, C:0.05, G:0.15, T:0.51
Consensus pattern (20 bp):
AATTTGGTCATATATTTTGA
Found at i:83533 original size:20 final size:20
Alignment explanation
Indices: 83486--83540 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
83476 TAATTCAATT
*
83486 AATATAAATATTATTATTAA
1 AATATAAATATTATAATTAA
*
83506 AATA-AAATATT-TAAATTTA
1 AATATAAATATTAT-AATTAA
*
83525 AATATAAATAATATAA
1 AATATAAATATTATAA
83541 ATAGATATCA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 1 0.03
19 15 0.52
20 12 0.41
21 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AATATAAATATTATAATTAA
Found at i:91418 original size:63 final size:63
Alignment explanation
Indices: 91319--91445 Score: 254
Period size: 63 Copynumber: 2.0 Consensus size: 63
91309 AATAATTCCC
91319 AACACTTAGTAGAGGTGTGATTGTACTACTTGACACTCCCCTTGTGTGTAGCTTAACAGGCTT
1 AACACTTAGTAGAGGTGTGATTGTACTACTTGACACTCCCCTTGTGTGTAGCTTAACAGGCTT
91382 AACACTTAGTAGAGGTGTGATTGTACTACTTGACACTCCCCTTGTGTGTAGCTTAACAGGCTT
1 AACACTTAGTAGAGGTGTGATTGTACTACTTGACACTCCCCTTGTGTGTAGCTTAACAGGCTT
91445 A
1 A
91446 CATGTGGATA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.33
Consensus pattern (63 bp):
AACACTTAGTAGAGGTGTGATTGTACTACTTGACACTCCCCTTGTGTGTAGCTTAACAGGCTT
Found at i:108015 original size:9 final size:9
Alignment explanation
Indices: 108001--108030 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
107991 ATAACGTGAG
108001 ACCTTTGAA
1 ACCTTTGAA
108010 ACCTTTGAA
1 ACCTTTGAA
*
108019 ACCTTTTAA
1 ACCTTTGAA
108028 ACC
1 ACC
108031 ATGCATCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.33, C:0.27, G:0.07, T:0.33
Consensus pattern (9 bp):
ACCTTTGAA
Found at i:112090 original size:21 final size:21
Alignment explanation
Indices: 112066--112119 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
112056 ATAATTGTGT
112066 TTATTTTCTTTAAATTAA-GGA
1 TTATTTT-TTTAAATTAATGGA
* *
112087 TTATTTTTTTAATTTAATGTA
1 TTATTTTTTTAAATTAATGGA
112108 TTATTTATTTTA
1 TTATTT-TTTTA
112120 TTATCTAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 9 0.31
21 15 0.52
22 5 0.17
ACGTcount: A:0.30, C:0.02, G:0.06, T:0.63
Consensus pattern (21 bp):
TTATTTTTTTAAATTAATGGA
Found at i:113025 original size:7 final size:7
Alignment explanation
Indices: 112990--113071 Score: 51
Period size: 7 Copynumber: 11.7 Consensus size: 7
112980 GGGTATAGGA
*
112990 TTTAGGG
1 TTTAAGG
*
112997 TTTATGG
1 TTTAAGG
113004 TTTAAGG
1 TTTAAGG
**
113011 TTCGAGG
1 TTTAAGG
113018 TTTAAGG
1 TTTAAGG
*
113025 TTTCAA-A
1 TTT-AAGG
113032 TTTAAGG
1 TTTAAGG
113039 TTT-AGG
1 TTTAAGG
**
113045 ATTTTGGG
1 -TTTAAGG
* *
113053 TATAAGA
1 TTTAAGG
113060 TTTAAGG
1 TTTAAGG
113067 TTTAA
1 TTTAA
113072 TTATGTAGTA
Statistics
Matches: 56, Mismatches: 15, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
6 5 0.09
7 47 0.84
8 4 0.07
ACGTcount: A:0.27, C:0.02, G:0.27, T:0.44
Consensus pattern (7 bp):
TTTAAGG
Found at i:113048 original size:14 final size:14
Alignment explanation
Indices: 112985--113070 Score: 61
Period size: 14 Copynumber: 6.1 Consensus size: 14
112975 TGTTTGGGTA
*
112985 TAGGATTTAGGGTT
1 TAGGATTTAAGGTT
112999 TATGG-TTTAAGGTT
1 TA-GGATTTAAGGTT
*
113013 CGAGG-TTTAAGGTT
1 -TAGGATTTAAGGTT
*
113027 TCA-AATTTAAGGTT
1 T-AGGATTTAAGGTT
** *
113041 TAGGATTTTGGGTA
1 TAGGATTTAAGGTT
*
113055 TAAGATTTAAGGTT
1 TAGGATTTAAGGTT
113069 TA
1 TA
113071 ATTATGTAGT
Statistics
Matches: 55, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
13 1 0.02
14 51 0.93
15 3 0.05
ACGTcount: A:0.27, C:0.02, G:0.28, T:0.43
Consensus pattern (14 bp):
TAGGATTTAAGGTT
Found at i:114548 original size:135 final size:135
Alignment explanation
Indices: 114306--114577 Score: 368
Period size: 135 Copynumber: 2.0 Consensus size: 135
114296 GTCAAACCAA
* ** * * * *
114306 GTTTTGCATGTGAAGGCGTTGCAGAACCAGAAAGGTTTAGTTTCAGTGCCATTGATGATTCAACT
1 GTTTTGCATGTGAAGGCGTCGCAGAACCAGAAAGGAATAGTTCCAATGCCACTGATGATTCAACC
* * *
114371 ATCCCTTGAGATTGTGATGTACATGTTAAGAAAGGTCATGCTGCTAAAGCTGGACTTGGTTGCCT
66 ATCCCTTGAGATTGTAATGTACATGTTAAGAAAGGTCATGCTGCTAAAGCTAGACTTGGCTGCCT
114436 TAGCG
131 TAGCG
* * *
114441 GTTTTGCATGTGAAGGCGTCGCATAACCA-AAAGGGAATAGTTCCAATGCCACTGATGATTTAGC
1 GTTTTGCATGTGAAGGCGTCGCAGAACCAGAAA-GGAATAGTTCCAATGCCACTGATGATTCAAC
* * *
114505 CATCCCTTGAGATTGTAATGTATAT-TCTAAGAAAGGTCGTGCTGCTAAAGTTAGACTTGGCTGC
65 CATCCCTTGAGATTGTAATGTACATGT-TAAGAAAGGTCATGCTGCTAAAGCTAGACTTGGCTGC
114569 CTTAGCG
129 CTTAGCG
114576 GT
1 GT
114578 CTTAGACGTG
Statistics
Matches: 119, Mismatches: 16, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
134 4 0.03
135 115 0.97
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (135 bp):
GTTTTGCATGTGAAGGCGTCGCAGAACCAGAAAGGAATAGTTCCAATGCCACTGATGATTCAACC
ATCCCTTGAGATTGTAATGTACATGTTAAGAAAGGTCATGCTGCTAAAGCTAGACTTGGCTGCCT
TAGCG
Found at i:114866 original size:18 final size:17
Alignment explanation
Indices: 114845--114903 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 17
114835 GCGTCTAATA
*
114845 GGTGGAGGCGAAGAATGT
1 GGTGGAGGCCAAGAA-GT
*
114863 GGTGGATGCCAAGAAGAT
1 GGTGGAGGCCAAGAAG-T
*
114881 GGTGAAGGCCAAGAAGGT
1 GGTGGAGGCCAAGAA-GT
114899 GGTGG
1 GGTGG
114904 TGAGGATAGC
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
17 1 0.03
18 32 0.94
19 1 0.03
ACGTcount: A:0.29, C:0.08, G:0.47, T:0.15
Consensus pattern (17 bp):
GGTGGAGGCCAAGAAGT
Found at i:115383 original size:48 final size:48
Alignment explanation
Indices: 115325--115438 Score: 158
Period size: 48 Copynumber: 2.4 Consensus size: 48
115315 CCTTTTTTAT
* *
115325 ATCTGTCCCTCTGGATTTTGAGG-TATAAAATTGGATGTGGTGGCTTCA
1 ATCTGCCCCTCTGGATTTTG-GGATATAAAACTGGATGTGGTGGCTTCA
* * *
115373 ATCTGCCCCTCTGAATTTTGGGATATAAGACTGGATGTGGTGGCTTTA
1 ATCTGCCCCTCTGGATTTTGGGATATAAAACTGGATGTGGTGGCTTCA
*
115421 ATCTGCCCCTTTGGATTT
1 ATCTGCCCCTCTGGATTT
115439 GTTAGAGTAT
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
47 2 0.03
48 56 0.97
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (48 bp):
ATCTGCCCCTCTGGATTTTGGGATATAAAACTGGATGTGGTGGCTTCA
Found at i:115753 original size:15 final size:16
Alignment explanation
Indices: 115721--115755 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
115711 ACCCAATAAC
115721 CCAAACCCAAAATGAA
1 CCAAACCCAAAATGAA
*
115737 CCAAACCC-AATTGAA
1 CCAAACCCAAAATGAA
115752 CCAA
1 CCAA
115756 GTCCAAACCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.51, C:0.34, G:0.06, T:0.09
Consensus pattern (16 bp):
CCAAACCCAAAATGAA
Found at i:121643 original size:20 final size:20
Alignment explanation
Indices: 121615--121666 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
121605 TGATCGACCG
*
121615 TTGATCGTTGACCATTGACT
1 TTGACCGTTGACCATTGACT
121635 TTGACCGTTGACCATTGACT
1 TTGACCGTTGACCATTGACT
121655 TTGACCGTTGAC
1 TTGACCGTTGAC
121667 TTTTTCTGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (20 bp):
TTGACCGTTGACCATTGACT
Found at i:122770 original size:3 final size:3
Alignment explanation
Indices: 122720--122753 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
122710 ACAAATTTAC
122720 ATT ATT -TT A-T ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
122754 TTGATTTTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.14
3 25 0.86
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:125046 original size:168 final size:168
Alignment explanation
Indices: 124735--125258 Score: 708
Period size: 168 Copynumber: 3.1 Consensus size: 168
124725 TCATGTCAAG
* * * * *
124735 GATAAGAGGACAACATCCATCACAACAGATTCAAGCATCAGCTCTGCATACATATTCGGCACAAA
1 GATAGGAGGACAACATCCATCACAACAGATTCAAGCATCAGCTCCGCATACAAATTCAGCACCAA
* * * * *
124800 TAAATAACAATCAGAAGTTGACCAGCTTACAGGCTGGATTAGACTTCAATTTTACAGGTCATCTA
66 TGAATAACAATCAGCAGTTGACCAGCTCACAGGCTGGCTTAGACTTCAATTTTACAGGTCATCCA
* * *
124865 AATAGTACATCTTCTAGACAATGTCCAATACCAGGGGT
131 AATAGTTCATCTTCTAGACCATGTCCAATGCCAGGGGT
* *
124903 GATAGGAGGACAACATCCATCACAACAAATTCAAGCATCAGCTCCGCATACAAATTCAGAACCAA
1 GATAGGAGGACAACATCCATCACAACAGATTCAAGCATCAGCTCCGCATACAAATTCAGCACCAA
* * * * * *
124968 TGAGTAACAATCAGCAGTTGACCAGCTCGCAGGCTGGCTTAGACTTCTATTTTATAGGTCGTCCG
66 TGAATAACAATCAGCAGTTGACCAGCTCACAGGCTGGCTTAGACTTCAATTTTACAGGTCATCCA
*
125033 AATAGTTCATCTTCCAGACCATGTCCAATGCCAGGGGT
131 AATAGTTCATCTTCTAGACCATGTCCAATGCCAGGGGT
* * * *
125071 GATTGAAGGACAAAATCCATCACAATAGATTCAAGCATCAGCTCCGCATACAAATTCAGCACCAA
1 GATAGGAGGACAACATCCATCACAACAGATTCAAGCATCAGCTCCGCATACAAATTCAGCACCAA
* *
125136 TGAATAACGATCAGCAGTTGACCAGCTCAC-GGCTGGCTTAGACTTCAATTTTACAGGTCATTCA
66 TGAATAACAATCAGCAGTTGACCAGCTCACAGGCTGGCTTAGACTTCAATTTTACAGGTCATCCA
*
125200 AATAGTTTATCTTCCAGAGTCCAGACCATGTCCAATGCCAGGGGT
131 AATAGTTCATCTT-C----T--AGACCATGTCCAATGCCAGGGGT
*
125245 GACAGGAGGACAAC
1 GATAGGAGGACAAC
125259 CATCATCTTC
Statistics
Matches: 307, Mismatches: 42, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
167 41 0.13
168 233 0.76
174 33 0.11
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (168 bp):
GATAGGAGGACAACATCCATCACAACAGATTCAAGCATCAGCTCCGCATACAAATTCAGCACCAA
TGAATAACAATCAGCAGTTGACCAGCTCACAGGCTGGCTTAGACTTCAATTTTACAGGTCATCCA
AATAGTTCATCTTCTAGACCATGTCCAATGCCAGGGGT
Done.