Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014692.1 Kokia drynarioides strain JFW-HI SEQ_129731, 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: 97672
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:9555 original size:46 final size:46
Alignment explanation
Indices: 9488--9577 Score: 180
Period size: 46 Copynumber: 2.0 Consensus size: 46
9478 TACCTGTATT
9488 GGAAAATTCTAAAAGTTGGAGCTGACTAGTTCTTGTACTATATACA
1 GGAAAATTCTAAAAGTTGGAGCTGACTAGTTCTTGTACTATATACA
9534 GGAAAATTCTAAAAGTTGGAGCTGACTAGTTCTTGTACTATATA
1 GGAAAATTCTAAAAGTTGGAGCTGACTAGTTCTTGTACTATATA
9578 TAACTCTAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.33
Consensus pattern (46 bp):
GGAAAATTCTAAAAGTTGGAGCTGACTAGTTCTTGTACTATATACA
Found at i:17926 original size:30 final size:30
Alignment explanation
Indices: 17890--17962 Score: 76
Period size: 31 Copynumber: 2.4 Consensus size: 30
17880 TTTGATATAT
*
17890 AAACTTTAATTTAGTAT-AATTATACACATA
1 AAACTTTAATTTAGT-TCAAATATACACATA
* * *
17920 AAACTTTGATTGTAGTTCAAATATATACATG
1 AAACTTTAATT-TAGTTCAAATATACACATA
*
17951 AAACTTCAATTT
1 AAACTTTAATTT
17963 TGTAAAGTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
30 12 0.34
31 23 0.66
ACGTcount: A:0.42, C:0.11, G:0.07, T:0.40
Consensus pattern (30 bp):
AAACTTTAATTTAGTTCAAATATACACATA
Found at i:46763 original size:21 final size:22
Alignment explanation
Indices: 46739--46786 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
46729 CATTTTTATC
46739 TTTTTGTC-TTCTTTTTTCCAA
1 TTTTTGTCTTTCTTTTTTCCAA
* * *
46760 TTTTTTTCTTTTTTTTTTTCAA
1 TTTTTGTCTTTCTTTTTTCCAA
46782 TTTTT
1 TTTTT
46787 TTCATTTTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.08, C:0.12, G:0.02, T:0.77
Consensus pattern (22 bp):
TTTTTGTCTTTCTTTTTTCCAA
Found at i:46775 original size:22 final size:22
Alignment explanation
Indices: 46750--46795 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
46740 TTTTGTCTTC
*
46750 TTTTTTCCAATTTTTTTCTTTT
1 TTTTTTCCAATTTTTTTCATTT
*
46772 TTTTTTTCAATTTTTTTCATTT
1 TTTTTTCCAATTTTTTTCATTT
46794 TT
1 TT
46796 CGACTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (22 bp):
TTTTTTCCAATTTTTTTCATTT
Found at i:47759 original size:6 final size:6
Alignment explanation
Indices: 47750--47781 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
47740 AACTAAAAAT
47750 AAATAA AAATAA AAAT-A AAATAA AAATAA AAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAA
47782 AAATGAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:47764 original size:16 final size:16
Alignment explanation
Indices: 47743--47802 Score: 86
Period size: 17 Copynumber: 3.8 Consensus size: 16
47733 CATAGTTAAC
47743 TAAAAATAAATAAAAA
1 TAAAAATAAATAAAAA
47759 TAAAAATAAAATAAAAA
1 TAAAAAT-AAATAAAAA
*
47776 TAAAAA-AAATGAAAA
1 TAAAAATAAATAAAAA
*
47791 TTAAAATAAATA
1 TAAAAATAAATA
47803 TACTAAATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
15 13 0.33
16 11 0.28
17 15 0.38
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (16 bp):
TAAAAATAAATAAAAA
Found at i:47769 original size:21 final size:21
Alignment explanation
Indices: 47745--47800 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 21
47735 TAGTTAACTA
47745 AAAATAAATAAAAATAAAAAT-
1 AAAATAAATAAAAA-AAAAATG
47766 AAAATAAA-AATAAAAAAAATG
1 AAAATAAATAA-AAAAAAAATG
47787 AAAATTAAAATAAA
1 AAAA-T-AAATAAA
47801 TATACTAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
20 8 0.27
21 15 0.50
22 1 0.03
23 4 0.13
24 2 0.07
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (21 bp):
AAAATAAATAAAAAAAAAATG
Found at i:47773 original size:27 final size:27
Alignment explanation
Indices: 47743--47800 Score: 91
Period size: 27 Copynumber: 2.1 Consensus size: 27
47733 CATAGTTAAC
47743 TAAAAATAAATAAAAAT-AAAAATAAAA
1 TAAAAATAAA-AAAAATGAAAAATAAAA
*
47770 TAAAAATAAAAAAAATGAAAATTAAAA
1 TAAAAATAAAAAAAATGAAAAATAAAA
47797 TAAA
1 TAAA
47801 TATACTAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 6 0.21
27 23 0.79
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (27 bp):
TAAAAATAAAAAAAATGAAAAATAAAA
Found at i:47790 original size:6 final size:5
Alignment explanation
Indices: 47745--47800 Score: 53
Period size: 6 Copynumber: 10.6 Consensus size: 5
47735 TAGTTAACTA
47745 AAAAT -AAAT AAAAAT AAAAAT AAAAT AAAAAT AAAA- AAAAT GAAAATT
1 AAAAT AAAAT -AAAAT -AAAAT AAAAT -AAAAT AAAAT AAAAT -AAAA-T
47793 AAAAT AAA
1 AAAAT AAA
47801 TATACTAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
4 8 0.18
5 13 0.29
6 23 0.51
7 1 0.02
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:50970 original size:51 final size:51
Alignment explanation
Indices: 50883--51122 Score: 302
Period size: 51 Copynumber: 4.6 Consensus size: 51
50873 GCTATAAATG
*
50883 AAAGAGTCCGATGACTAAATGTCATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAG-GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* *
50935 AAAGCTCCGGTGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * * *
50986 AAAGGTCCGATGACTAAGTGTTATCGTGAGTAAATGAATCCATGACGAATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * ** **
51037 AAAGGTCCGATGACTCAGTGTCATCGTGAGTATATGAATTTTTATACGGAAC
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTT-TACGGATT
*
51089 AAGGGGGTCCGATGACTATA-TGTCATCGTGAGTA
1 AA--AGGTCCGATGACTA-AGTGTCATCGTGAGTA
51123 TTAAATGAAA
Statistics
Matches: 163, Mismatches: 21, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
51 126 0.77
52 10 0.06
54 26 0.16
55 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
Found at i:59465 original size:28 final size:28
Alignment explanation
Indices: 59434--59487 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
59424 AAGTCTGCGG
* *
59434 AATAACGAATAATGCAATAGAGATTGCA
1 AATAACAAATAATGCAATAAAGATTGCA
*
59462 AATAACAAATAATGCGATAAAGATTG
1 AATAACAAATAATGCAATAAAGATTG
59488 TCAATCCCCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.52, C:0.09, G:0.17, T:0.22
Consensus pattern (28 bp):
AATAACAAATAATGCAATAAAGATTGCA
Found at i:59744 original size:44 final size:43
Alignment explanation
Indices: 59678--59809 Score: 165
Period size: 44 Copynumber: 3.0 Consensus size: 43
59668 ATTCAATATG
* *
59678 CTCTTAATCAATCACATACTTTCAACAATAGAGAAACAATGTTC
1 CTCTCAATCAATCACATACTTTCAATAATAG-GAAACAATGTTC
** * *
59722 CTCTCAATCGGTCACATACTTTCAATAATAGGGAAATATTGTTC
1 CTCTCAATCAATCACATACTTTCAATAATA-GGAAACAATGTTC
* * *
59766 CTCTCAATCAATCACATATTTTCAATATTAGGAAACAGTGTTC
1 CTCTCAATCAATCACATACTTTCAATAATAGGAAACAATGTTC
59809 C
1 C
59810 AACTTTCAAA
Statistics
Matches: 75, Mismatches: 12, Indels: 3
0.83 0.13 0.03
Matches are distributed among these distances:
43 12 0.16
44 62 0.83
45 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.10, T:0.33
Consensus pattern (43 bp):
CTCTCAATCAATCACATACTTTCAATAATAGGAAACAATGTTC
Found at i:61522 original size:15 final size:15
Alignment explanation
Indices: 61489--61541 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
61479 ATATCTTATC
* * *
61489 ATCATAACGTATTGG
1 ATCATATCGTATCGT
61504 ATCATATCGTATCGT
1 ATCATATCGTATCGT
** *
61519 ATCATATTATATCAT
1 ATCATATCGTATCGT
61534 ATCATATC
1 ATCATATC
61542 TAACTCATTT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (15 bp):
ATCATATCGTATCGT
Found at i:62545 original size:29 final size:30
Alignment explanation
Indices: 62477--62548 Score: 96
Period size: 29 Copynumber: 2.4 Consensus size: 30
62467 TTTTCCATTT
62477 ATAATTTAATTAAACCTTTAATTAATCAAA
1 ATAATTTAATTAAACCTTTAATTAATCAAA
*
62507 ATTAA-TTAATTAAACC-TTAATTAA-CATA
1 A-TAATTTAATTAAACCTTTAATTAATCAAA
62535 ATAATTGTAATTAA
1 ATAATT-TAATTAA
62549 TCAAAGATAG
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
27 3 0.08
28 5 0.13
29 15 0.39
30 12 0.32
31 3 0.08
ACGTcount: A:0.50, C:0.08, G:0.01, T:0.40
Consensus pattern (30 bp):
ATAATTTAATTAAACCTTTAATTAATCAAA
Found at i:63183 original size:23 final size:23
Alignment explanation
Indices: 63151--63204 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
63141 GACATGGCAT
* * *
63151 CCAGTTAGCAGCTTCTAGAAGAC
1 CCAGTCAGCAACTTCCAGAAGAC
*
63174 CCAGTCAGCAACTTCCAGAAGGC
1 CCAGTCAGCAACTTCCAGAAGAC
*
63197 CTAGTCAG
1 CCAGTCAG
63205 GAAGGATAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.30, C:0.30, G:0.22, T:0.19
Consensus pattern (23 bp):
CCAGTCAGCAACTTCCAGAAGAC
Found at i:70558 original size:13 final size:13
Alignment explanation
Indices: 70540--70569 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
70530 TCGAATAGCA
70540 AAAAAAAAAAAAC
1 AAAAAAAAAAAAC
*
70553 AAAAAAAAAAAGC
1 AAAAAAAAAAAAC
70566 AAAA
1 AAAA
70570 GGTTCGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.90, C:0.07, G:0.03, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAC
Found at i:74394 original size:12 final size:12
Alignment explanation
Indices: 74373--74403 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
74363 TCAGACTCTT
*
74373 ATGCCTAAAGTC
1 ATGCCCAAAGTC
74385 ATGCCCAAAGTC
1 ATGCCCAAAGTC
74397 ATGCCCA
1 ATGCCCA
74404 CTAGCCCAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.19
Consensus pattern (12 bp):
ATGCCCAAAGTC
Found at i:76361 original size:28 final size:28
Alignment explanation
Indices: 76329--76384 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
76319 ATGTGCGAGA
* *
76329 AAGAAAATGGAGGGGACTGGGGGAAGGT
1 AAGAAAATGGAAGGGACTGGAGGAAGGT
76357 AAGAAAATGGAAGGGACTGGAGGAAGGT
1 AAGAAAATGGAAGGGACTGGAGGAAGGT
76385 GCGACTGTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.39, C:0.04, G:0.46, T:0.11
Consensus pattern (28 bp):
AAGAAAATGGAAGGGACTGGAGGAAGGT
Found at i:76609 original size:5 final size:5
Alignment explanation
Indices: 76599--76631 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
76589 TTAATGGCGA
*
76599 AAAAT AAAAT AAAAG AAAAT AAAAT -AAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
76632 ACAGTGGGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:79054 original size:15 final size:15
Alignment explanation
Indices: 79017--79055 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
79007 TTATGTGTGC
*
79017 TTAATTCTTGATTTA
1 TTAATTCTTGATATA
*
79032 GT-ATTCTTGATATA
1 TTAATTCTTGATATA
79046 TTAATTCTTG
1 TTAATTCTTG
79056 TTTGATGTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.26, C:0.08, G:0.10, T:0.56
Consensus pattern (15 bp):
TTAATTCTTGATATA
Found at i:79758 original size:14 final size:13
Alignment explanation
Indices: 79737--79768 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
79727 ATTATTTACA
79737 TTTTTAATTTAAT
1 TTTTTAATTTAAT
79750 TTTTCTAATTTAAT
1 TTTT-TAATTTAAT
79764 TTTTT
1 TTTTT
79769 CCCTCTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTAATTTAAT
Found at i:83594 original size:15 final size:14
Alignment explanation
Indices: 83571--83608 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
83561 TATTATTTAG
83571 AAAAAAAAAGTCGA
1 AAAAAAAAAGTCGA
*
83585 AAAGAAAAAA-TTGA
1 AAA-AAAAAAGTCGA
83599 AAAAAAAAAG
1 AAAAAAAAAG
83609 AATTGAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 6 0.29
14 9 0.43
15 6 0.29
ACGTcount: A:0.76, C:0.03, G:0.13, T:0.08
Consensus pattern (14 bp):
AAAAAAAAAGTCGA
Found at i:83600 original size:14 final size:13
Alignment explanation
Indices: 83570--83646 Score: 54
Period size: 13 Copynumber: 5.8 Consensus size: 13
83560 TTATTATTTA
* *
83570 GAAAAAAAAAGTC
1 GAAAAAAAAAATT
83583 GAAAAGAAAAAATT
1 GAAAA-AAAAAATT
83597 GAAAAAAAAAA--
1 GAAAAAAAAAATT
83608 GAATTGAAAAAAAATT
1 GAA---AAAAAAAATT
*
83624 GAGAAAAAAAA--
1 GAAAAAAAAAATT
83635 GAAAAAGAAAAA
1 GAAAAA-AAAAA
83647 GAAAAAGAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 15
0.74 0.06 0.21
Matches are distributed among these distances:
11 8 0.15
12 5 0.09
13 19 0.36
14 19 0.36
16 2 0.04
ACGTcount: A:0.75, C:0.01, G:0.14, T:0.09
Consensus pattern (13 bp):
GAAAAAAAAAATT
Found at i:83634 original size:16 final size:16
Alignment explanation
Indices: 83584--83621 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
83574 AAAAAAGTCG
*
83584 AAAAGAAAA-AATTGA
1 AAAAAAAAAGAATTGA
83599 AAAAAAAAAGAATTGA
1 AAAAAAAAAGAATTGA
83615 AAAAAAA
1 AAAAAAA
83622 TTGAGAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.11
Consensus pattern (16 bp):
AAAAAAAAAGAATTGA
Found at i:83641 original size:6 final size:6
Alignment explanation
Indices: 83630--83657 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
83620 AATTGAGAAA
83630 AAAAAG AAAAAG AAAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAA
83658 GAGACTAAAG
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:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:83645 original size:27 final size:26
Alignment explanation
Indices: 83583--83646 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 26
83573 AAAAAAAGTC
83583 GAAAAG-AAAAAATTGAAAAAAAAAA
1 GAAAAGAAAAAAATTGAAAAAAAAAA
** *
83608 GAATTGAAAAAAAATTGAGAAAAAAAA
1 GAAAAG-AAAAAAATTGAAAAAAAAAA
83635 GAAAAAGAAAAA
1 G-AAAAGAAAAA
83647 GAAAAAGAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
25 4 0.13
27 24 0.77
28 3 0.10
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (26 bp):
GAAAAGAAAAAAATTGAAAAAAAAAA
Found at i:84707 original size:23 final size:25
Alignment explanation
Indices: 84681--84726 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
84671 CAAATTAGGG
84681 AATTAT-TGTTTAG-ATTTAATTCA
1 AATTATCTGTTTAGAATTTAATTCA
*
84704 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
84727 TGGATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCA
Found at i:85143 original size:15 final size:15
Alignment explanation
Indices: 85106--85144 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
85096 TCATGTGTGC
*
85106 TTAATTCTTGATTTA
1 TTAATTCTTGATATA
*
85121 GT-ATTCTTGATATA
1 TTAATTCTTGATATA
85135 TTAATTCTTG
1 TTAATTCTTG
85145 TTTGATGTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.26, C:0.08, G:0.10, T:0.56
Consensus pattern (15 bp):
TTAATTCTTGATATA
Found at i:87876 original size:25 final size:23
Alignment explanation
Indices: 87839--87965 Score: 103
Period size: 23 Copynumber: 5.4 Consensus size: 23
87829 ACACTAGCGC
87839 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGTTTAGCACTGTCT-GT
*
87862 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG-T-TTAGCACTGTCTGT
** * *
87887 GCTCTCTAATTAGCACTTTGTGT
1 GCTCTCTGTTTAGCACTGTCTGT
* * * * *
87910 GCTCTCTGATTAGAATTTTGTGT
1 GCTCTCTGTTTAGCACTGTCTGT
** *
87933 GCTCTCAATTTAGCACTGTTTGT
1 GCTCTCTGTTTAGCACTGTCTGT
87956 GCTCTCTGTT
1 GCTCTCTGTT
87966 GCCCAGCACT
Statistics
Matches: 85, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
23 65 0.76
24 1 0.01
25 16 0.19
26 3 0.04
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.44
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTGTCTGT
Found at i:88510 original size:22 final size:22
Alignment explanation
Indices: 88485--88529 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
88475 TATGTAATAC
88485 TTCTATATCGGGTTTATACGTG
1 TTCTATATCGGGTTTATACGTG
88507 TTCTATATCGGGTTTATACGTG
1 TTCTATATCGGGTTTATACGTG
88529 T
1 T
88530 GAACTGGGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.18, C:0.13, G:0.22, T:0.47
Consensus pattern (22 bp):
TTCTATATCGGGTTTATACGTG
Found at i:89328 original size:42 final size:42
Alignment explanation
Indices: 89280--89416 Score: 113
Period size: 42 Copynumber: 3.2 Consensus size: 42
89270 CCCTTTCGGT
89280 TTCTGGAGGTGGCATGCCATCAAAAGGATTCTCCTCTTCCGA
1 TTCTGGAGGTGGCATGCCATCAAAAGGATTCTCCTCTTCCGA
* * * *
89322 TTCTGGAGATGTTGCCTCCCCTGAACTCAAAA-G-TAC-CCT-TTCCG-
1 TTCTGGAG--GTGGCAT-GCC---A-TCAAAAGGATTCTCCTCTTCCGA
* *
89366 TTTTCGGAGGTGGCATGCCATCAAACGGATTCTCCTCTTCCGA
1 TTCT-GGAGGTGGCATGCCATCAAAAGGATTCTCCTCTTCCGA
89409 TTCTGGAG
1 TTCTGGAG
89417 ATGCTGCCTT
Statistics
Matches: 71, Mismatches: 11, Indels: 26
0.66 0.10 0.24
Matches are distributed among these distances:
38 5 0.07
39 2 0.03
40 2 0.03
41 3 0.04
42 19 0.27
43 8 0.11
44 8 0.11
45 11 0.15
46 3 0.04
47 2 0.03
48 2 0.03
49 6 0.08
ACGTcount: A:0.20, C:0.28, G:0.23, T:0.30
Consensus pattern (42 bp):
TTCTGGAGGTGGCATGCCATCAAAAGGATTCTCCTCTTCCGA
Found at i:89375 original size:87 final size:87
Alignment explanation
Indices: 89228--89491 Score: 388
Period size: 87 Copynumber: 3.0 Consensus size: 87
89218 AGAGCTTCTA
* *
89228 CTTCCGATTCTGGGGATGCTGCCTCCCCTGAACTCAAAAGTACCCTTT-CGGTTTCTGGAGGTGG
1 CTTCCGATTCTGGAGATGCTGCCTCCCCTGAACTCAAAAGTACCCTTTCCGCTTTC-GGAGGTGG
89292 CATGCCATCAAAAGGATTCTCCT
65 CATGCCATCAAAAGGATTCTCCT
* *
89315 CTTCCGATTCTGGAGATGTTGCCTCCCCTGAACTCAAAAGTACCCTTTCCGTTTTCGGAGGTGGC
1 CTTCCGATTCTGGAGATGCTGCCTCCCCTGAACTCAAAAGTACCCTTTCCGCTTTCGGAGGTGGC
*
89380 ATGCCATCAAACGGATTCTCCT
66 ATGCCATCAAAAGGATTCTCCT
* * * * * *
89402 CTTCCGATTCTGGAGATGCTGCCTTCCCTGAACTCAAAAGTACCCTTTCGGCTTCCAGAGATGGT
1 CTTCCGATTCTGGAGATGCTGCCTCCCCTGAACTCAAAAGTACCCTTTCCGCTTTCGGAGGTGGC
*
89467 A-CCTCATCAAAAGGATTCTCCT
66 ATGC-CATCAAAAGGATTCTCCT
89489 CTT
1 CTT
89492 GTCCTACTAC
Statistics
Matches: 161, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
86 1 0.01
87 154 0.96
88 6 0.04
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (87 bp):
CTTCCGATTCTGGAGATGCTGCCTCCCCTGAACTCAAAAGTACCCTTTCCGCTTTCGGAGGTGGC
ATGCCATCAAAAGGATTCTCCT
Found at i:91673 original size:16 final size:18
Alignment explanation
Indices: 91641--91674 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
91631 TAAGTGATAT
91641 TAAATAAATACTTAAATA
1 TAAATAAATACTTAAATA
91659 TAAA-AAATA-TTAAATA
1 TAAATAAATACTTAAATA
91675 CTCAATCTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 5 0.31
18 4 0.25
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (18 bp):
TAAATAAATACTTAAATA
Found at i:93794 original size:87 final size:87
Alignment explanation
Indices: 93540--93799 Score: 369
Period size: 87 Copynumber: 3.0 Consensus size: 87
93530 CTTCTACTTC
* *
93540 CGATTCTGGGGATGCTGCCTCCCTTGAACTCAAAAGTACCCTTTCGGTTTCCGGAGGTGGCATGC
1 CGATTCTGGAGATGCTGCCTCCCCTGAACTCAAAAGTACCCTTTCGGTTTCCGGAGGTGGCATGC
*
93605 CATCAAAAGGATTCTTCTCTTT
66 CATCAAAAGGATTCTCCTCTTT
* **
93627 CGATTCTGGAGGTGCTGCCTCCCCTGAACTCAAAAGTACCCTTTCGGTTTTTGGAGGTGGCATGC
1 CGATTCTGGAGATGCTGCCTCCCCTGAACTCAAAAGTACCCTTTCGGTTTCCGGAGGTGGCATGC
*
93692 CATCAAACGGATTCTCCTCTTT
66 CATCAAAAGGATTCTCCTCTTT
* * * * * * *
93714 CGATTCTGGAAATGCTACCTCCCCTGAACTCAAAAGTACCCTTTCAGCTTCCGGAGATGGTA-AC
1 CGATTCTGGAGATGCTGCCTCCCCTGAACTCAAAAGTACCCTTTCGGTTTCCGGAGGTGGCATGC
*
93778 TCATCAAAAGGATTCTCTTCTT
66 -CATCAAAAGGATTCTCCTCTT
93800 GTCCTATTAC
Statistics
Matches: 153, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
86 1 0.01
87 152 0.99
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.30
Consensus pattern (87 bp):
CGATTCTGGAGATGCTGCCTCCCCTGAACTCAAAAGTACCCTTTCGGTTTCCGGAGGTGGCATGC
CATCAAAAGGATTCTCCTCTTT
Done.