Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013922.1 Kokia drynarioides strain JFW-HI SEQ_128952, 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: 251996
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 286 characters in sequence are not A, C, G, or T
Found at i:10427 original size:2 final size:2
Alignment explanation
Indices: 10422--10452 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
10412 AAATATATTT
10422 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10453 AGTGGATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13738 original size:17 final size:18
Alignment explanation
Indices: 13708--13741 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
13698 GCTTCGGAGA
13708 ATATGCCAAAATCTTCAC
1 ATATGCCAAAATCTTCAC
*
13726 ATAT-CCAAGATCTTCA
1 ATATGCCAAAATCTTCA
13742 TAATTGTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.38, C:0.26, G:0.06, T:0.29
Consensus pattern (18 bp):
ATATGCCAAAATCTTCAC
Found at i:19001 original size:51 final size:51
Alignment explanation
Indices: 18818--19004 Score: 223
Period size: 51 Copynumber: 3.6 Consensus size: 51
18808 TTTCATTTAA
* ** * *
18818 TACTCACGATGACA-TATAGTCATCGGACCTCCTGTTCCATATAGGAATTCATA
1 TACTCACGATGACACT-TAGTCATCGGACCT-TTAATCCATAAAGG-ATTCATT
* * * * *
18871 AACTCACGATGACACTGAGTCATCGGACATTTAATCCATCATGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
* **
18922 TACTCACAATGACACTTAGTCATCGGACCTTTAATCTGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
18973 TACTCACGATGACACTTAGTCATCGGACCTTT
1 TACTCACGATGACACTTAGTCATCGGACCTTT
19005 TCCTTTATAG
Statistics
Matches: 114, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
51 80 0.70
52 8 0.07
53 25 0.22
54 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
Found at i:20766 original size:36 final size:36
Alignment explanation
Indices: 20699--20803 Score: 129
Period size: 36 Copynumber: 2.9 Consensus size: 36
20689 TGATCATTAT
*
20699 TCGTTTTACTCCTTGTTGACCCCAAAAGTCATGATGC
1 TCGTTTTACTCCCTGTTGA-CCCAAAAGTCATGATGC
* * *
20736 TCGTTTTACTCCCTATTGACCCAAAAGTCATTATGT
1 TCGTTTTACTCCCTGTTGACCCAAAAGTCATGATGC
* * * *
20772 TCATTTTTCTTCCTGTTGACCCAAAGGTCATG
1 TCGTTTTACTCCCTGTTGACCCAAAAGTCATG
20804 CCTATTACCA
Statistics
Matches: 58, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
36 41 0.71
37 17 0.29
ACGTcount: A:0.22, C:0.26, G:0.14, T:0.38
Consensus pattern (36 bp):
TCGTTTTACTCCCTGTTGACCCAAAAGTCATGATGC
Found at i:21329 original size:27 final size:27
Alignment explanation
Indices: 21291--21342 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
21281 CTGACACAAA
*
21291 TGGAGGTGGATTAAGTGGCGGCACCTT
1 TGGAGGGGGATTAAGTGGCGGCACCTT
21318 TGGAGGGGGATTAAGTGGCGGCACC
1 TGGAGGGGGATTAAGTGGCGGCACC
21343 AAGGGGTGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.19, C:0.15, G:0.44, T:0.21
Consensus pattern (27 bp):
TGGAGGGGGATTAAGTGGCGGCACCTT
Found at i:21507 original size:14 final size:14
Alignment explanation
Indices: 21490--21526 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
21480 AAGGGAGAGA
*
21490 AGAGAAGAGAGAAG
1 AGAGAAGAAAGAAG
21504 AGAGAAGAAAGAA-
1 AGAGAAGAAAGAAG
21517 AGA-AAGAAAG
1 AGAGAAGAAAG
21527 GTAAATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 7 0.32
13 3 0.14
14 12 0.55
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (14 bp):
AGAGAAGAAAGAAG
Found at i:24536 original size:35 final size:35
Alignment explanation
Indices: 24486--24552 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
24476 TTTATATTAC
* * *
24486 TTACTTACTATTACTAACAAAATAAAATTACTAAT
1 TTACTAACTACTACTAACAAAACAAAATTACTAAT
24521 TTACTAACTACTACTAACAAAACAAAATTACT
1 TTACTAACTACTACTAACAAAACAAAATTACT
24553 TACTAACAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.49, C:0.18, G:0.00, T:0.33
Consensus pattern (35 bp):
TTACTAACTACTACTAACAAAACAAAATTACTAAT
Found at i:24556 original size:31 final size:31
Alignment explanation
Indices: 24481--24559 Score: 95
Period size: 35 Copynumber: 2.4 Consensus size: 31
24471 ATTAATTTAT
* * *
24481 ATTACTTACTTACTATTACTAACAAAATAAA
1 ATTACTTACTAACTACTACTAACAAAACAAA
24512 ATTACTAATTTACTAACTACTACTAACAAAACAAA
1 ATTAC----TTACTAACTACTACTAACAAAACAAA
24547 ATTACTTACTAAC
1 ATTACTTACTAAC
24560 AAAATAAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
31 13 0.32
35 28 0.68
ACGTcount: A:0.48, C:0.19, G:0.00, T:0.33
Consensus pattern (31 bp):
ATTACTTACTAACTACTACTAACAAAACAAA
Found at i:27631 original size:4 final size:4
Alignment explanation
Indices: 27622--27646 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
27612 CATCGAGGCA
27622 CAGG CAGG CAGG CAGG CAGG CAGG C
1 CAGG CAGG CAGG CAGG CAGG CAGG C
27647 TCACTCCACA
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:0.24, C:0.28, G:0.48, T:0.00
Consensus pattern (4 bp):
CAGG
Found at i:35006 original size:38 final size:38
Alignment explanation
Indices: 34955--35031 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
34945 AAAGGATACA
34955 AAGAAAGATGCACAAGAAATGTTCCAACAAATGGAAGT
1 AAGAAAGATGCACAAGAAATGTTCCAACAAATGGAAGT
34993 AAGAAAGATGCACAAGAAATGTTCCAACAAATGGAAGT
1 AAGAAAGATGCACAAGAAATGTTCCAACAAATGGAAGT
35031 A
1 A
35032 TATCCATAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.51, C:0.13, G:0.21, T:0.16
Consensus pattern (38 bp):
AAGAAAGATGCACAAGAAATGTTCCAACAAATGGAAGT
Found at i:42765 original size:24 final size:25
Alignment explanation
Indices: 42721--42770 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
42711 GTAACCGTAG
42721 TTAATGAAAACAGTGAATTTTAGTT
1 TTAATGAAAACAGTGAATTTTAGTT
*
42746 TTAATG-AAAC-GTTGAGTTTTAGTT
1 TTAATGAAAACAG-TGAATTTTAGTT
42770 T
1 T
42771 GGAAAAAGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 1 0.04
24 16 0.70
25 6 0.26
ACGTcount: A:0.34, C:0.04, G:0.18, T:0.44
Consensus pattern (25 bp):
TTAATGAAAACAGTGAATTTTAGTT
Found at i:45087 original size:13 final size:13
Alignment explanation
Indices: 45069--45094 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
45059 GAATTGTTCA
45069 ATTAAAGAATTTT
1 ATTAAAGAATTTT
45082 ATTAAAGAATTTT
1 ATTAAAGAATTTT
45095 CTTGATTTGG
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:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
ATTAAAGAATTTT
Found at i:46454 original size:28 final size:30
Alignment explanation
Indices: 46382--46454 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 30
46372 ATAATATTGC
*
46382 TTTAATAAATTTAATATTTATCTAGATAGTAT
1 TTTATTAAA-TTAATATTTATCTAGA-AGTAT
* *
46414 TTTATTAATTTAATATTTATTTAG-A-TAT
1 TTTATTAAATTAATATTTATCTAGAAGTAT
46442 TTTATTAAATTAA
1 TTTATTAAATTAA
46455 ACCTCCAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 15 0.41
29 1 0.03
31 14 0.38
32 7 0.19
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (30 bp):
TTTATTAAATTAATATTTATCTAGAAGTAT
Found at i:52124 original size:34 final size:34
Alignment explanation
Indices: 52043--52124 Score: 80
Period size: 34 Copynumber: 2.4 Consensus size: 34
52033 TACTTCCGTC
* *
52043 TTAT-TACAACTTTATCTTTAAGACGAGTTTCGA
1 TTATGTACAACTTTTTCCTTAAGACGAGTTTCGA
* *
52076 TTATG-AAAAGCTTTTTCCTTAAGGCGAGTTTC-A
1 TTATGTACAA-CTTTTTCCTTAAGACGAGTTTCGA
*
52109 TTGTAGTACAACTTTT
1 TTAT-GTACAACTTTT
52125 ATTTTAATGC
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
33 11 0.28
34 25 0.64
35 3 0.08
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.43
Consensus pattern (34 bp):
TTATGTACAACTTTTTCCTTAAGACGAGTTTCGA
Found at i:54556 original size:30 final size:30
Alignment explanation
Indices: 54520--54580 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
54510 AGCACTACAC
54520 TCAACTGCTGTAACTTTTTCCCCGAATCAG
1 TCAACTGCTGTAACTTTTTCCCCGAATCAG
54550 TCAACTGCTGTAACTTTTTCCCCGAATCAG
1 TCAACTGCTGTAACTTTTTCCCCGAATCAG
54580 T
1 T
54581 TGTCCTTCAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.23, C:0.30, G:0.13, T:0.34
Consensus pattern (30 bp):
TCAACTGCTGTAACTTTTTCCCCGAATCAG
Found at i:66911 original size:17 final size:18
Alignment explanation
Indices: 66889--66923 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
66879 TTTAAATCGT
*
66889 TATGTTATATATA-TATA
1 TATGTTAAATATACTATA
66906 TATGTTAAATATACTATA
1 TATGTTAAATATACTATA
66924 CGTACGGTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.49
Consensus pattern (18 bp):
TATGTTAAATATACTATA
Found at i:68783 original size:20 final size:20
Alignment explanation
Indices: 68742--68784 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
68732 CGTTTAGAAA
* *
68742 TTTTTTATCATATTGATAAT
1 TTTTTTATAATATTAATAAT
68762 TTTTTTATAATAATTAAT-AT
1 TTTTTTATAAT-ATTAATAAT
68782 TTT
1 TTT
68785 AAAATATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (20 bp):
TTTTTTATAATATTAATAAT
Found at i:79667 original size:18 final size:17
Alignment explanation
Indices: 79644--79686 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
79634 TGATGTTTCA
*
79644 TTTTCTAGTTTTTTTAAT
1 TTTTCTAGTTTTGTT-AT
*
79662 TTTTCTTTGTTTTGTTAT
1 TTTTC-TAGTTTTGTTAT
79680 TTTTCTA
1 TTTTCTA
79687 CTACATTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
17 1 0.05
18 12 0.57
19 8 0.38
ACGTcount: A:0.12, C:0.07, G:0.07, T:0.74
Consensus pattern (17 bp):
TTTTCTAGTTTTGTTAT
Found at i:79777 original size:4 final size:4
Alignment explanation
Indices: 79768--79792 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
79758 AGTAGAAGTA
79768 ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC A
79793 ACGAAACAAA
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:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:90662 original size:12 final size:13
Alignment explanation
Indices: 90641--90683 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
90631 CAATTTTTAT
90641 GAAATATTTTCAA
1 GAAATATTTTCAA
*
90654 GAAAGT-TTTT-AC
1 GAAA-TATTTTCAA
90666 GAAATATTTTCAA
1 GAAATATTTTCAA
90679 GAAAT
1 GAAAT
90684 TTATTAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
11 1 0.04
12 9 0.36
13 14 0.56
14 1 0.04
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (13 bp):
GAAATATTTTCAA
Found at i:90662 original size:25 final size:25
Alignment explanation
Indices: 90634--90682 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
90624 TTGAAAACAA
*
90634 TTTTTATGAAATATTTTCAAGAAAG
1 TTTTTACGAAATATTTTCAAGAAAG
90659 TTTTTACGAAATATTTTCAAGAAA
1 TTTTTACGAAATATTTTCAAGAAA
90683 TTTATTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.43
Consensus pattern (25 bp):
TTTTTACGAAATATTTTCAAGAAAG
Found at i:90782 original size:14 final size:15
Alignment explanation
Indices: 90757--90787 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
90747 CAGAAAAGTT
90757 AATCATTTTTTCAGA
1 AATCATTTTTTCAGA
90772 AATCA-TTTTTCAGA
1 AATCATTTTTTCAGA
90786 AA
1 AA
90788 CTATTTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.42
Consensus pattern (15 bp):
AATCATTTTTTCAGA
Found at i:93315 original size:2 final size:2
Alignment explanation
Indices: 93308--93335 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
93298 GTAATATGCG
93308 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
93336 TAGATTAGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:94438 original size:21 final size:20
Alignment explanation
Indices: 94414--94452 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
94404 ACTGTAAGTG
*
94414 CATCACTATTATCTCTTTTAT
1 CATCACTAATAT-TCTTTTAT
*
94435 CATCAGTAATATTCTTTT
1 CATCACTAATATTCTTTT
94453 TTTTTGTAGC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.26, C:0.21, G:0.03, T:0.51
Consensus pattern (20 bp):
CATCACTAATATTCTTTTAT
Found at i:110961 original size:43 final size:43
Alignment explanation
Indices: 110908--111089 Score: 190
Period size: 43 Copynumber: 4.2 Consensus size: 43
110898 TTCTGGAAAG
* * *
110908 CGCCGTTAAAGAACATGATCTTTAGCGGCGCTTTTCCCACAAA
1 CGCCGCTAAAGAACATGGTCTTTAGCAGCGCTTTTCCCACAAA
* * * **
110951 CGCCGCTAAAGAACATGGTATTTAGCGGGGC-TTTCGTAACAAGA
1 CGCCGCTAAAGAACATGGTCTTTAGCAGCGCTTTTC-CCACAA-A
*
110995 -GCCGCTAAAGAACATGGTCTTTAGTAGCGCTTTTCCCACAAA
1 CGCCGCTAAAGAACATGGTCTTTAGCAGCGCTTTTCCCACAAA
* * * * *
111037 CGCTGCTATAGATA-ATGTTCTTTAGTAGCGTTTTTCCCACAAA
1 CGCCGCTAAAGA-ACATGGTCTTTAGCAGCGCTTTTCCCACAAA
111080 CGCCGCTAAA
1 CGCCGCTAAA
111090 ATTAACAGAT
Statistics
Matches: 116, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
42 5 0.04
43 105 0.91
44 6 0.05
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (43 bp):
CGCCGCTAAAGAACATGGTCTTTAGCAGCGCTTTTCCCACAAA
Found at i:112250 original size:42 final size:41
Alignment explanation
Indices: 112204--112290 Score: 156
Period size: 42 Copynumber: 2.1 Consensus size: 41
112194 ACGTCGTTAA
*
112204 TGCTCTGATCTTTAGCGGCATTTGCGTTTCCTCATAAATGCC
1 TGCTCTGACCTTTAGCGGCATTTGCGTTTCCTCATAAATG-C
112246 TGCTCTGACCTTTAGCGGCATTTGCGTTTCCTCATAAATGC
1 TGCTCTGACCTTTAGCGGCATTTGCGTTTCCTCATAAATGC
112287 TGCT
1 TGCT
112291 AATACTCTTA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 5 0.11
42 39 0.89
ACGTcount: A:0.16, C:0.26, G:0.20, T:0.38
Consensus pattern (41 bp):
TGCTCTGACCTTTAGCGGCATTTGCGTTTCCTCATAAATGC
Found at i:112675 original size:12 final size:13
Alignment explanation
Indices: 112652--112684 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
112642 CCACGACACC
*
112652 ACTATAAATTAAA
1 ACTATAACTTAAA
112665 A-TATAACTTAAA
1 ACTATAACTTAAA
112677 ACTATAAC
1 ACTATAAC
112685 AATATCTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (13 bp):
ACTATAACTTAAA
Found at i:115067 original size:16 final size:16
Alignment explanation
Indices: 115046--115077 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
115036 TTACATGGTG
115046 TTGAATATATGGTATA
1 TTGAATATATGGTATA
115062 TTGAATATATGGTATA
1 TTGAATATATGGTATA
115078 CTTTGTGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44
Consensus pattern (16 bp):
TTGAATATATGGTATA
Found at i:115627 original size:13 final size:14
Alignment explanation
Indices: 115593--115628 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
115583 CTTCACCCTA
115593 AGTTGTAATCATTC
1 AGTTGTAATCATTC
115607 AGTTGTAATCATTC
1 AGTTGTAATCATTC
115621 A-TTGTAAT
1 AGTTGTAAT
115629 TGAAAACTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.44
Consensus pattern (14 bp):
AGTTGTAATCATTC
Found at i:120067 original size:12 final size:12
Alignment explanation
Indices: 120050--120074 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
120040 TATCCGCATC
120050 CCCAGCCAGCCA
1 CCCAGCCAGCCA
120062 CCCAGCCAGCCA
1 CCCAGCCAGCCA
120074 C
1 C
120075 GTGAGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.60, G:0.16, T:0.00
Consensus pattern (12 bp):
CCCAGCCAGCCA
Found at i:120631 original size:24 final size:24
Alignment explanation
Indices: 120604--120649 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
120594 TTTTAATATT
120604 TAATAAT-TTGATAATTTTTTTATA
1 TAATAATCTT-ATAATTTTTTTATA
* *
120628 TAATCATCTTATTATTTTTTTA
1 TAATAATCTTATAATTTTTTTA
120650 ATGTTTACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 17 0.89
25 2 0.11
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (24 bp):
TAATAATCTTATAATTTTTTTATA
Found at i:121435 original size:29 final size:30
Alignment explanation
Indices: 121403--121466 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
121393 GAGTTTCACA
* * *
121403 TATATAATTGCACA-AAATTAAAGTTCATG
1 TATACAATTACACATAAATTAAAATTCATG
*
121432 TATACAATTACACATTAAATTAAAATTCTTG
1 TATACAATTACACA-TAAATTAAAATTCATG
121463 TATA
1 TATA
121467 ATTTTGATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 12 0.41
31 17 0.59
ACGTcount: A:0.45, C:0.11, G:0.06, T:0.38
Consensus pattern (30 bp):
TATACAATTACACATAAATTAAAATTCATG
Found at i:124285 original size:30 final size:33
Alignment explanation
Indices: 124242--124305 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 33
124232 AATAATATAT
124242 ATTTTTATAATTTTTA-AAAA-ATTAA-ATTAA
1 ATTTTTATAATTTTTATAAAATATTAACATTAA
124272 ATTTTTCAT-ATTTTTATTAAAATATTAACATTAA
1 ATTTTT-ATAATTTTTA-TAAAATATTAACATTAA
124306 TTATCTGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
30 13 0.45
31 2 0.07
32 4 0.14
33 5 0.17
34 5 0.17
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (33 bp):
ATTTTTATAATTTTTATAAAATATTAACATTAA
Found at i:125959 original size:21 final size:20
Alignment explanation
Indices: 125935--125987 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
125925 AATTTACGTT
*
125935 AAAATAAATAGAGAAGGGAGA
1 AAAATAAAAAGAGAA-GGAGA
*
125956 AAAACAAAAAGAGAAGGAGA
1 AAAATAAAAAGAGAAGGAGA
125976 AGAGAATAAAAA
1 A-A-AATAAAAA
125988 AAAGAGGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 6 0.22
21 14 0.52
22 7 0.26
ACGTcount: A:0.68, C:0.02, G:0.25, T:0.06
Consensus pattern (20 bp):
AAAATAAAAAGAGAAGGAGA
Found at i:130295 original size:2 final size:2
Alignment explanation
Indices: 130288--130316 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
130278 AGCCTCGAGA
130288 AT AT 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 AT AT A
130317 GTTTTAATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:133017 original size:6 final size:6
Alignment explanation
Indices: 133002--133042 Score: 75
Period size: 6 Copynumber: 7.0 Consensus size: 6
132992 CGCTGTTTTA
133002 GCTT-G GCTTCG GCTTCG GCTTCG GCTTCG GCTTCG GCTTCG
1 GCTTCG GCTTCG GCTTCG GCTTCG GCTTCG GCTTCG GCTTCG
133043 CCCAATAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.11
6 31 0.89
ACGTcount: A:0.00, C:0.32, G:0.34, T:0.34
Consensus pattern (6 bp):
GCTTCG
Found at i:150217 original size:14 final size:15
Alignment explanation
Indices: 150188--150224 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
150178 TTTTAAAAAG
150188 TATAATATATAATAA
1 TATAATATATAATAA
150203 TATAATATA-AATAA
1 TATAATATATAATAA
*
150217 TTTAATAT
1 TATAATAT
150225 TTTTTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TATAATATATAATAA
Found at i:152258 original size:20 final size:20
Alignment explanation
Indices: 152235--152278 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
152225 TAATTTAGCC
*
152235 ATTTTTATTTTTATTTTAAT
1 ATTTTTATTTTTAATTTAAT
*
152255 ATTTTTGTTTTTAATTTAAT
1 ATTTTTATTTTTAATTTAAT
152275 -TTTT
1 ATTTT
152279 ACATTCTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (20 bp):
ATTTTTATTTTTAATTTAAT
Found at i:159462 original size:48 final size:49
Alignment explanation
Indices: 159341--159465 Score: 130
Period size: 48 Copynumber: 2.6 Consensus size: 49
159331 CTCTCAGTTC
* * * * *
159341 ACAGTGGTTATACAATCACATGTTAAAGTATAACTAGGGCTCCCAATTG
1 ACAGTGATTATGCGATCACAGGTTCAAGTATAACTAGGGCTCCCAATTG
* * * * *
159390 ACAGTGGTTATGCG-TCACGGGTTCAAGTATATCTCGGGC-CCCGATTG
1 ACAGTGATTATGCGATCACAGGTTCAAGTATAACTAGGGCTCCCAATTG
159437 AC-GATGATTATGCGATCACAGGTTCAAGT
1 ACAG-TGATTATGCGATCACAGGTTCAAGT
159466 TTCATGCTAC
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
46 1 0.02
47 18 0.28
48 33 0.52
49 12 0.19
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (49 bp):
ACAGTGATTATGCGATCACAGGTTCAAGTATAACTAGGGCTCCCAATTG
Found at i:165090 original size:40 final size:40
Alignment explanation
Indices: 165035--165112 Score: 156
Period size: 40 Copynumber: 1.9 Consensus size: 40
165025 AATTTAGATT
165035 ACTTAACATAGATGTTGAAATCCATTCGTGGAAACTTATC
1 ACTTAACATAGATGTTGAAATCCATTCGTGGAAACTTATC
165075 ACTTAACATAGATGTTGAAATCCATTCGTGGAAACTTA
1 ACTTAACATAGATGTTGAAATCCATTCGTGGAAACTTA
165113 CTGTCTTAGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (40 bp):
ACTTAACATAGATGTTGAAATCCATTCGTGGAAACTTATC
Found at i:165751 original size:21 final size:21
Alignment explanation
Indices: 165725--165764 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
165715 ACCGAAAACA
165725 AAATGATAAG-ATATTTTCCGT
1 AAATGA-AAGTATATTTTCCGT
*
165746 AAATGAAGGTATATTTTCC
1 AAATGAAAGTATATTTTCC
165765 TGTGTTTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.38
Consensus pattern (21 bp):
AAATGAAAGTATATTTTCCGT
Found at i:177031 original size:4 final size:4
Alignment explanation
Indices: 177018--177049 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
177008 TTTAACCCTC
177018 CTTT -TTT CTTT CTTT CTTT CTTT CTTT CTTT C
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT C
177050 ATAATTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.11
4 24 0.89
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
CTTT
Found at i:183597 original size:14 final size:15
Alignment explanation
Indices: 183578--183617 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
183568 GTTTTATTAT
183578 TTATAAATAAA-AAA
1 TTATAAATAAATAAA
183592 TTATAAA-AAATAAA
1 TTATAAATAAATAAA
*
183606 ATA-AAATAAATA
1 TTATAAATAAATA
183618 TTTTTATGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 6 0.26
14 17 0.74
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
TTATAAATAAATAAA
Found at i:196008 original size:6 final size:6
Alignment explanation
Indices: 195997--196027 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
195987 ACCTACGTCC
195997 CTCTCA CTCTCA CTCTCA CTCTCA CTCTCA C
1 CTCTCA CTCTCA CTCTCA CTCTCA CTCTCA C
196028 ACGCACACGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.52, G:0.00, T:0.32
Consensus pattern (6 bp):
CTCTCA
Found at i:196034 original size:6 final size:6
Alignment explanation
Indices: 196025--196052 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
196015 CTCTCACTCT
196025 CACACG CACACG CACACG CACACG CACA
1 CACACG CACACG CACACG CACACG CACA
196053 ATCCTAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.50, G:0.14, T:0.00
Consensus pattern (6 bp):
CACACG
Found at i:196431 original size:22 final size:21
Alignment explanation
Indices: 196404--196450 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
196394 TCAACTAAAT
196404 AATTTGAAAAAATAAAAAAAGA
1 AATTTGAAAAAA-AAAAAAAGA
* **
196426 AATTTGATAAAAGGAAAAAGA
1 AATTTGAAAAAAAAAAAAAGA
196447 AATT
1 AATT
196451 GCTAAAAGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.66, C:0.00, G:0.13, T:0.21
Consensus pattern (21 bp):
AATTTGAAAAAAAAAAAAAGA
Found at i:196456 original size:20 final size:21
Alignment explanation
Indices: 196419--196458 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
196409 GAAAAAATAA
196419 AAAAAGAAATTTGATAAAAGG
1 AAAAAGAAATTTGATAAAAGG
*
196440 AAAAAGAAA-TTGCTAAAAG
1 AAAAAGAAATTTGATAAAAG
196459 ATTCGTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.62, C:0.03, G:0.17, T:0.17
Consensus pattern (21 bp):
AAAAAGAAATTTGATAAAAGG
Found at i:202458 original size:14 final size:14
Alignment explanation
Indices: 202439--202466 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
202429 ATGGAACAAC
202439 AAAAAAAAAAGAAA
1 AAAAAAAAAAGAAA
202453 AAAAAAAAAAGAAA
1 AAAAAAAAAAGAAA
202467 TCATGTGATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAGAAA
Found at i:207971 original size:95 final size:94
Alignment explanation
Indices: 207851--208028 Score: 257
Period size: 95 Copynumber: 1.9 Consensus size: 94
207841 AATACAAGTT
* * * * *
207851 CTGTCAAAAAACCATTTGAATATTTCACATATGCAAAAGAATACAAATTGATGGCTTATGATGTT
1 CTGTCAAAAAACAATTTCAATATTTCACATACGCAAAAGAATACAAATTGATGACTTATAATGTT
207916 TTCTTCAATTAGTATAAAAGGAATATGAA
66 TTCTTCAATTAGTATAAAAGGAATATGAA
* * * *
207945 CTGTCCAAAAAACAATTTCAATATTTCATATACGTAGAGGAATACAAATTGATGACTTATAATGT
1 CTGT-CAAAAAACAATTTCAATATTTCACATACGCAAAAGAATACAAATTGATGACTTATAATGT
*
208010 TTTCTTCAATTAGTGTAAA
65 TTTCTTCAATTAGTATAAA
208029 TTGTAATGAG
Statistics
Matches: 73, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
94 4 0.05
95 69 0.95
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.34
Consensus pattern (94 bp):
CTGTCAAAAAACAATTTCAATATTTCACATACGCAAAAGAATACAAATTGATGACTTATAATGTT
TTCTTCAATTAGTATAAAAGGAATATGAA
Found at i:220089 original size:12 final size:12
Alignment explanation
Indices: 220053--220082 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
220043 CAAGACTCGA
*
220053 ACTACTACAACT
1 ACTACAACAACT
220065 ACTACAACAACT
1 ACTACAACAACT
220077 ACTACA
1 ACTACA
220083 GCCACTAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.20
Consensus pattern (12 bp):
ACTACAACAACT
Found at i:221014 original size:3 final size:3
Alignment explanation
Indices: 221008--221034 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
220998 AATAATAATA
221008 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
221035 TTGGTATTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:224592 original size:16 final size:16
Alignment explanation
Indices: 224573--224607 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
224563 ATCATTTTGA
224573 ATTTGAATTATTTCAG
1 ATTTGAATTATTTCAG
* *
224589 ATTTGTATTATTTTAG
1 ATTTGAATTATTTCAG
224605 ATT
1 ATT
224608 CTAAATTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.03, G:0.11, T:0.57
Consensus pattern (16 bp):
ATTTGAATTATTTCAG
Found at i:225402 original size:22 final size:22
Alignment explanation
Indices: 225375--225431 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
225365 CAGTCGAAAG
*
225375 AACCAAAGATTTTTATAATCCA
1 AACCAAAGATTTATATAATCCA
225397 AACCAAAGATTTATATAATCCA
1 AACCAAAGATTTATATAATCCA
225419 AACCAAAGATTTA
1 AACCAAAGATTTA
225432 ACACAAGTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.49, C:0.18, G:0.05, T:0.28
Consensus pattern (22 bp):
AACCAAAGATTTATATAATCCA
Found at i:230029 original size:20 final size:20
Alignment explanation
Indices: 230004--230046 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
229994 TTTATAAAAG
230004 TTTTAGATGCAATGCCTAAA
1 TTTTAGATGCAATGCCTAAA
* *
230024 TTTTAGATGCGATTCCTAAA
1 TTTTAGATGCAATGCCTAAA
230044 TTT
1 TTT
230047 ATCCATTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (20 bp):
TTTTAGATGCAATGCCTAAA
Found at i:231390 original size:57 final size:56
Alignment explanation
Indices: 231283--231395 Score: 165
Period size: 57 Copynumber: 2.0 Consensus size: 56
231273 AGTCACAATA
231283 TTTTTATTCATGTACTTATTTAAACAATCAGAGTTTTTACTTCTTCTTTTTTAAGGG
1 TTTTTATTCATGTACTTATTTAAACAATCAGAGTTTTT-CTTCTTCTTTTTTAAGGG
* * * *
231340 TTTTTATTCATGTATTTATTTAAACAATC-GAGTTTTTGTTTTTTTTTTTTTAAGGG
1 TTTTTATTCATGTACTTATTTAAACAATCAGAGTTTTT-CTTCTTCTTTTTTAAGGG
231396 AGATACATAT
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
56 23 0.45
57 28 0.55
ACGTcount: A:0.23, C:0.09, G:0.12, T:0.57
Consensus pattern (56 bp):
TTTTTATTCATGTACTTATTTAAACAATCAGAGTTTTTCTTCTTCTTTTTTAAGGG
Found at i:232834 original size:29 final size:29
Alignment explanation
Indices: 232780--232836 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
232770 AAACAAATTA
232780 ATTAAATCTAAATTTTCTTAAGAAATTTC
1 ATTAAATCTAAATTTTCTTAAGAAATTTC
* *
232809 ATTAACTCTTAAATTTTTTTAA-AAATTT
1 ATTAAATC-TAAATTTTCTTAAGAAATTT
232837 GCAAAAACCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (29 bp):
ATTAAATCTAAATTTTCTTAAGAAATTTC
Found at i:233370 original size:24 final size:23
Alignment explanation
Indices: 233342--233389 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
233332 ATTTATATAA
233342 AAATTTATTAATATA-AAAATACAT
1 AAATTTA--AATATATAAAATACAT
233366 AAATTTAAATATATTAAAATACAT
1 AAATTTAAATATA-TAAAATACAT
233390 TATTCTCATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 6 0.27
24 16 0.73
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (23 bp):
AAATTTAAATATATAAAATACAT
Found at i:235832 original size:30 final size:29
Alignment explanation
Indices: 235731--236040 Score: 226
Period size: 30 Copynumber: 10.4 Consensus size: 29
235721 AATGGTAATT
* *
235731 TTTTTGGAAGTGTCGGGGTCAAAAAATGAGA
1 TTTTTGGAAGTTTCGGGGT--AAAAATGGGA
*
235762 TTTTTGGAAG-TTCGGGGGT-AAAATGGTAA
1 TTTTTGGAAGTTTC-GGGGTAAAAATGG-GA
* *
235791 TTTTTGAAAGTTTCGAGGTAAAAAATGGGA
1 TTTTTGGAAGTTTCGGGGT-AAAAATGGGA
* * *
235821 CTTTTGGAAGTTTGGGGGT-AAAATGGTAA
1 TTTTTGGAAGTTTCGGGGTAAAAATGG-GA
* *
235850 TTTTTGAAAGTTTCGGGGTCAAAGATGGGA
1 TTTTTGGAAGTTTCGGGGT-AAAAATGGGA
*
235880 TTTTTGGAAG-TTCGAGGGT-AAAATGGTAA
1 TTTTTGGAAGTTTCG-GGGTAAAAATGG-GA
* **
235909 TTTTAGGAAGTTTCGATGTCAAAAATGGGA
1 TTTTTGGAAGTTTCGGGGT-AAAAATGGGA
* **
235939 TTTTTGGAAGTTTAGGGGT-AAAATGATAA
1 TTTTTGGAAGTTTCGGGGTAAAAATG-GGA
*
235968 TTTTTGGAAGGTTT-GGGGTCAAAATTGGTG-
1 TTTTTGGAA-GTTTCGGGGT-AAAAATGG-GA
*
235998 TTTTTGGAAG-TTCGGGGGT-AAAATGGTAA
1 TTTTTGGAAGTTTC-GGGGTAAAAATGG-GA
236027 TTTTTGGATAGTTT
1 TTTTTGGA-AGTTT
236041 AGGGACCTCC
Statistics
Matches: 222, Mismatches: 34, Indels: 46
0.74 0.11 0.15
Matches are distributed among these distances:
28 34 0.15
29 71 0.32
30 75 0.34
31 42 0.19
ACGTcount: A:0.29, C:0.04, G:0.31, T:0.36
Consensus pattern (29 bp):
TTTTTGGAAGTTTCGGGGTAAAAATGGGA
Found at i:236033 original size:59 final size:59
Alignment explanation
Indices: 235717--236040 Score: 427
Period size: 59 Copynumber: 5.4 Consensus size: 59
235707 ACATCCAGGA
* *
235717 GTAAAATGGTAATTTTTTTGGAAGTGTCGGGGTCAAAAAATGAGATTTTTGGAAGTTCGGGG
1 GTAAAATGGTAA--TTTTTGGAAGTTTCGGGGTC-AAAAATGGGATTTTTGGAAGTTCGGGG
* * * * *
235779 GTAAAATGGTAATTTTTGAAAGTTTCGAGGTAAAAAATGGGACTTTTGGAAGTTTGGGG
1 GTAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGG
* * *
235838 GTAAAATGGTAATTTTTGAAAGTTTCGGGGTCAAAGATGGGATTTTTGGAAGTTCGAGG
1 GTAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGG
* ** **
235897 GTAAAATGGTAATTTTAGGAAGTTTCGATGTCAAAAATGGGATTTTTGGAAGTTTAGGG
1 GTAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGG
* *
235956 GTAAAATGATAATTTTTGGAAGGTTT-GGGGTCAAAATTGGTG-TTTTTGGAAGTTCGGGG
1 GTAAAATGGTAATTTTTGGAA-GTTTCGGGGTCAAAAATGG-GATTTTTGGAAGTTCGGGG
236015 GTAAAATGGTAATTTTTGGATAGTTT
1 GTAAAATGGTAATTTTTGGA-AGTTT
236041 AGGGACCTCC
Statistics
Matches: 230, Mismatches: 29, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
59 196 0.85
60 22 0.10
62 12 0.05
ACGTcount: A:0.30, C:0.04, G:0.31, T:0.36
Consensus pattern (59 bp):
GTAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGG
Found at i:237768 original size:6 final size:6
Alignment explanation
Indices: 237757--237806 Score: 70
Period size: 6 Copynumber: 8.8 Consensus size: 6
237747 AATTTCGAAA
*
237757 TTAAAT TTAAAT TTAAA- TTAAAT TTAAAT TTAGA- TT-AAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
237802 TTAAA
1 TTAAA
237807 ATAAATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
4 1 0.03
5 9 0.23
6 29 0.74
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (6 bp):
TTAAAT
Found at i:237776 original size:17 final size:17
Alignment explanation
Indices: 237754--237813 Score: 95
Period size: 17 Copynumber: 3.6 Consensus size: 17
237744 TTTAATTTCG
237754 AAATTAAATTTAAATTT
1 AAATTAAATTTAAATTT
237771 AAATTAAATTTAAATTT
1 AAATTAAATTTAAATTT
*
237788 AGATT-AATTTAAATTT
1 AAATTAAATTTAAATTT
*
237804 AAAATAAATT
1 AAATTAAATT
237814 AAAAAGGGCC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
16 14 0.36
17 25 0.64
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (17 bp):
AAATTAAATTTAAATTT
Found at i:237777 original size:11 final size:11
Alignment explanation
Indices: 237757--237813 Score: 62
Period size: 11 Copynumber: 5.1 Consensus size: 11
237747 AATTTCGAAA
237757 TTAAATTTAAAT
1 TTAAA-TTAAAT
237769 TTAAATTAAAT
1 TTAAATTAAAT
*
237780 TTAAATTTAGA-
1 TTAAA-TTAAAT
*
237791 TTAATTTAAAT
1 TTAAATTAAAT
*
237802 TTAAAATAAAT
1 TTAAATTAAAT
237813 T
1 T
237814 AAAAAGGGCC
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
10 4 0.11
11 25 0.66
12 9 0.24
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (11 bp):
TTAAATTAAAT
Done.