Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003875.1 Kokia drynarioides strain JFW-HI SEQ_116909, 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: 112042
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 89 characters in sequence are not A, C, G, or T
Found at i:2461 original size:11 final size:11
Alignment explanation
Indices: 2445--2475 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
2435 TTTTGTATCT
2445 AAATGAACACG
1 AAATGAACACG
*
2456 AAATGAACCCG
1 AAATGAACACG
2467 AAATGAACA
1 AAATGAACA
2476 TCTATCTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.55, C:0.19, G:0.16, T:0.10
Consensus pattern (11 bp):
AAATGAACACG
Found at i:10343 original size:6 final size:6
Alignment explanation
Indices: 10332--10362 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
10322 TATTACGAAT
10332 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG A
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG A
10363 AGAAATGTGT
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:0.52, C:0.00, G:0.32, T:0.16
Consensus pattern (6 bp):
ATGAAG
Found at i:12989 original size:21 final size:19
Alignment explanation
Indices: 12945--12999 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 19
12935 GTCTTTCAAA
*
12945 ATTTTGAAAATTTTTTTAT
1 ATTTTGAAAATTTTTTTAG
*
12964 TTTTTAGAAAATTTTTATTAG
1 ATTTT-GAAAATTTTT-TTAG
*
12985 ATTTTTTAAAATTTT
1 A-TTTTGAAAATTTT
13000 AAAAAAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 4 0.14
20 10 0.34
21 11 0.38
22 4 0.14
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (19 bp):
ATTTTGAAAATTTTTTTAG
Found at i:29031 original size:31 final size:31
Alignment explanation
Indices: 28993--29053 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
28983 CAGTCCAATA
** **
28993 ATTTAAATAAAATTTTTTGAATAATTTAATG
1 ATTTAAATAAAAACTTTAAAATAATTTAATG
29024 ATTTAAATAAAAACTTTAAAATAATTTAAT
1 ATTTAAATAAAAACTTTAAAATAATTTAAT
29054 AATTATTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (31 bp):
ATTTAAATAAAAACTTTAAAATAATTTAATG
Found at i:29063 original size:22 final size:21
Alignment explanation
Indices: 29038--29079 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
29028 AAATAAAAAC
29038 TTTAAAATAATTTAATAATTAT
1 TTTAAAATAATTTAA-AATTAT
* *
29060 TTTACAATATTTTAAAATTA
1 TTTAAAATAATTTAAAATTA
29080 AATGATCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
TTTAAAATAATTTAAAATTAT
Found at i:30706 original size:24 final size:26
Alignment explanation
Indices: 30664--30713 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 26
30654 TGAATTTCTT
30664 TTAAAAAAAGGAAACACGTAATTGAAA
1 TTAAAAAAA-GAAACACGTAATTGAAA
30691 TTAAAAAAA-AAA-ACGTAATTGAA
1 TTAAAAAAAGAAACACGTAATTGAA
30714 TTCAATGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 11 0.48
25 3 0.13
27 9 0.39
ACGTcount: A:0.62, C:0.06, G:0.12, T:0.20
Consensus pattern (26 bp):
TTAAAAAAAGAAACACGTAATTGAAA
Found at i:31993 original size:22 final size:23
Alignment explanation
Indices: 31950--31993 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
31940 TTAATCTTTT
* *
31950 AAAATTACACTTTTACTATCGTA
1 AAAATTACAATTTAACTATCGTA
31973 AAAATTACAATTTAACT-TCGT
1 AAAATTACAATTTAACTATCGT
31994 CCCCTTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.41, C:0.16, G:0.05, T:0.39
Consensus pattern (23 bp):
AAAATTACAATTTAACTATCGTA
Found at i:32124 original size:15 final size:16
Alignment explanation
Indices: 32092--32125 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
32082 AAGCTAACTA
32092 ATTTATGTCAGTTTGT
1 ATTTATGTCAGTTTGT
32108 ATTTATGTCAG-TTGT
1 ATTTATGTCAGTTTGT
32123 ATT
1 ATT
32126 ATTATCGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.21, C:0.06, G:0.18, T:0.56
Consensus pattern (16 bp):
ATTTATGTCAGTTTGT
Found at i:32384 original size:15 final size:17
Alignment explanation
Indices: 32354--32393 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 17
32344 AAGTTTTTTT
32354 TTATTGTTTAATAAGTA
1 TTATTGTTTAATAAGTA
32371 TTATT-TTT-ATAAGT-
1 TTATTGTTTAATAAGTA
32385 TT-TTGTTTA
1 TTATTGTTTA
32394 CTCTTATAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
13 2 0.10
14 5 0.24
15 6 0.29
16 3 0.14
17 5 0.24
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (17 bp):
TTATTGTTTAATAAGTA
Found at i:36009 original size:30 final size:31
Alignment explanation
Indices: 35973--36031 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
35963 TTTACGAATA
*
35973 ATTTTTAA-AAGATTAAATTAAAATTTTATC
1 ATTTTTAAGAAGATTAAAGTAAAATTTTATC
* *
36003 ATTTTTAAGGAGATTAAAGTATAATTTTA
1 ATTTTTAAGAAGATTAAAGTAAAATTTTA
36032 CTTTTAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 8 0.32
31 17 0.68
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (31 bp):
ATTTTTAAGAAGATTAAAGTAAAATTTTATC
Found at i:36802 original size:50 final size:50
Alignment explanation
Indices: 36740--36925 Score: 228
Period size: 50 Copynumber: 3.7 Consensus size: 50
36730 AGTAAGTGAC
* *
36740 AGTTTATCTGTAAATCAATGGTGGCTTGTCCACCAAGTGTTATCAGTGGC
1 AGTTTATCTGTAAATCAATGGTGGCTTGTCCACAAAGTGTTATCAGTGGT
* * * * * *
36790 AATTTATTTGTAAATTAGTGGTGGTTTGTCCACAAAGTGTTATTAGTGGT
1 AGTTTATCTGTAAATCAATGGTGGCTTGTCCACAAAGTGTTATCAGTGGT
* * * * *
36840 TGTTTATCTGCAAATCAATGGTGACTTATCCACAAAGTGTTATCAGTGAT
1 AGTTTATCTGTAAATCAATGGTGGCTTGTCCACAAAGTGTTATCAGTGGT
* * *
36890 AGTTTATTTGTAAATTAGTGGTGGCTTGTCCACAAA
1 AGTTTATCTGTAAATCAATGGTGGCTTGTCCACAAA
36926 TGGTGTTTCG
Statistics
Matches: 110, Mismatches: 26, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
50 110 1.00
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (50 bp):
AGTTTATCTGTAAATCAATGGTGGCTTGTCCACAAAGTGTTATCAGTGGT
Found at i:36919 original size:100 final size:100
Alignment explanation
Indices: 36741--36925 Score: 298
Period size: 100 Copynumber: 1.9 Consensus size: 100
36731 GTAAGTGACA
* * * * *
36741 GTTTATCTGTAAATCAATGGTGGCTTGTCCACCAAGTGTTATCAGTGGCAATTTATTTGTAAATT
1 GTTTATCTGCAAATCAATGGTGACTTATCCACAAAGTGTTATCAGTGACAATTTATTTGTAAATT
*
36806 AGTGGTGGTTTGTCCACAAAGTGTTATTAGTGGTT
66 AGTGGTGGCTTGTCCACAAAGTGTTATTAGTGGTT
* *
36841 GTTTATCTGCAAATCAATGGTGACTTATCCACAAAGTGTTATCAGTGATAGTTTATTTGTAAATT
1 GTTTATCTGCAAATCAATGGTGACTTATCCACAAAGTGTTATCAGTGACAATTTATTTGTAAATT
36906 AGTGGTGGCTTGTCCACAAA
66 AGTGGTGGCTTGTCCACAAA
36926 TGGTGTTTCG
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
100 77 1.00
ACGTcount: A:0.26, C:0.13, G:0.22, T:0.38
Consensus pattern (100 bp):
GTTTATCTGCAAATCAATGGTGACTTATCCACAAAGTGTTATCAGTGACAATTTATTTGTAAATT
AGTGGTGGCTTGTCCACAAAGTGTTATTAGTGGTT
Found at i:37929 original size:30 final size:30
Alignment explanation
Indices: 37895--37954 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
37885 AACAGATACC
37895 TTTGGAGTAGTAACTAAAATCTTAGTTTCA
1 TTTGGAGTAGTAACTAAAATCTTAGTTTCA
37925 TTTGGAGTAGTAACTAAAATCTTAGTTTCA
1 TTTGGAGTAGTAACTAAAATCTTAGTTTCA
37955 GTCTTGCTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (30 bp):
TTTGGAGTAGTAACTAAAATCTTAGTTTCA
Found at i:39686 original size:28 final size:26
Alignment explanation
Indices: 39631--39682 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
39621 ATCAAAGCTT
39631 TAGGGACTAAATCATAAAAAAAACCA
1 TAGGGACTAAATCATAAAAAAAACCA
39657 TAGGGACTAAATCATAAAAAAAACCA
1 TAGGGACTAAATCATAAAAAAAACCA
39683 CATAATATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.58, C:0.15, G:0.12, T:0.15
Consensus pattern (26 bp):
TAGGGACTAAATCATAAAAAAAACCA
Found at i:52958 original size:25 final size:24
Alignment explanation
Indices: 52930--52990 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
52920 TAAACTTTTT
* *
52930 TAAAAATTTAATAATTAAATTTAAC
1 TAAAAATATAATAATCAAA-TTAAC
*
52955 TAAAATATATAATGATCAAATTAAC
1 TAAAA-ATATAATAATCAAATTAAC
*
52980 AAAAAATATAA
1 TAAAAATATAA
52991 ACGTTGAAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
24 6 0.19
25 14 0.45
26 11 0.35
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.33
Consensus pattern (24 bp):
TAAAAATATAATAATCAAATTAAC
Found at i:53332 original size:31 final size:30
Alignment explanation
Indices: 53289--53355 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 30
53279 ATCTAAATTT
*
53289 TTTTGTCCAATTTGATA-CTCAAACTTGATAC
1 TTTT-TCCAATTTGATACCT-AAACTTGACAC
* *
53320 TTTTTCCTAATTTGGTACCTAAATTTGACAC
1 TTTTTCC-AATTTGATACCTAAACTTGACAC
53351 TTTTT
1 TTTTT
53356 TTTAAGTTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
30 3 0.10
31 26 0.84
32 2 0.06
ACGTcount: A:0.25, C:0.18, G:0.09, T:0.48
Consensus pattern (30 bp):
TTTTTCCAATTTGATACCTAAACTTGACAC
Found at i:53355 original size:88 final size:88
Alignment explanation
Indices: 53241--53429 Score: 249
Period size: 88 Copynumber: 2.1 Consensus size: 88
53231 TTAATAAAAT
* * * * *
53241 ATTTGGTACTTAAACTTGACATTTTTTTTTAATTTGATATCTAAA-TTTTTTTG-TCCAATTTGA
1 ATTTGGTACCTAAACTTGACACTTTTTTTTAAGTTGAT-GC-AAACTTTTTTGGATCCAATTTGA
53304 TACTCAAACTTGA-TACTTTTTCCTA
64 TACTCAAACTTGACTA-TTTTTCCTA
*
53329 ATTTGGTACCTAAATTTGACACTTTTTTTTAAGTTGATGCAAACTTTTTTGGATCCAATTTGATA
1 ATTTGGTACCTAAACTTGACACTTTTTTTTAAGTTGATGCAAACTTTTTTGGATCCAATTTGATA
** *
53394 CTTGAACTTGACTATTTTTTCTA
66 CTCAAACTTGACTATTTTTCCTA
53417 ATTTGGTACCTAA
1 ATTTGGTACCTAA
53430 TTTTTTTTTA
Statistics
Matches: 89, Mismatches: 9, Indels: 6
0.86 0.09 0.06
Matches are distributed among these distances:
86 3 0.03
87 8 0.09
88 76 0.85
89 2 0.02
ACGTcount: A:0.27, C:0.14, G:0.11, T:0.49
Consensus pattern (88 bp):
ATTTGGTACCTAAACTTGACACTTTTTTTTAAGTTGATGCAAACTTTTTTGGATCCAATTTGATA
CTCAAACTTGACTATTTTTCCTA
Found at i:53635 original size:18 final size:20
Alignment explanation
Indices: 53612--53651 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
53602 AAGCTTAAAT
53612 ACCAAATT-AA-AAAAAAAA
1 ACCAAATTGAACAAAAAAAA
53630 ACCAAATTGAATCAAAAAAAA
1 ACCAAATTGAA-CAAAAAAAA
53651 A
1 A
53652 GTTTAAGTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.42
19 2 0.11
21 9 0.47
ACGTcount: A:0.72, C:0.12, G:0.03, T:0.12
Consensus pattern (20 bp):
ACCAAATTGAACAAAAAAAA
Found at i:53707 original size:60 final size:60
Alignment explanation
Indices: 53632--53756 Score: 173
Period size: 60 Copynumber: 2.1 Consensus size: 60
53622 AAAAAAAAAC
53632 CAAATTGAATCAAAAAAAAAG-TTTAAGTACGAAATT-AAAAAAAGTATCAAGTTCAAATAT
1 CAAATTGAATC--AAAAAAAGTTTTAAGTACGAAATTAAAAAAAAGTATCAAGTTCAAATAT
* * * * *
53692 TAAATTGGATCAAAAAAAGTTTTAAGTACTAAATTAAAAAAAAGTGTCAAGTTCAAGTAT
1 CAAATTGAATCAAAAAAAGTTTTAAGTACGAAATTAAAAAAAAGTATCAAGTTCAAATAT
53752 CAAAT
1 CAAAT
53757 ATTATATTAA
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
58 8 0.14
59 14 0.25
60 35 0.61
ACGTcount: A:0.54, C:0.08, G:0.11, T:0.27
Consensus pattern (60 bp):
CAAATTGAATCAAAAAAAGTTTTAAGTACGAAATTAAAAAAAAGTATCAAGTTCAAATAT
Found at i:57328 original size:63 final size:63
Alignment explanation
Indices: 57257--57379 Score: 210
Period size: 63 Copynumber: 2.0 Consensus size: 63
57247 TAAATCTTTT
* *
57257 TCATTTTATTTTAATTTCTTTCAGAACAGATGATCAAATACTAACAAGCATTTAAATAAGTAC
1 TCATTTTATTTTAAATTCTTTCAGAACAGATGATCAAATACTAACAAACATTTAAATAAGTAC
**
57320 TCATTTTATTTTAAATTCTTTCTTAACAGATGATCAAATACTAACAAACATTTAAATAAG
1 TCATTTTATTTTAAATTCTTTCAGAACAGATGATCAAATACTAACAAACATTTAAATAAG
57380 CACCAGATAC
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 56 1.00
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.39
Consensus pattern (63 bp):
TCATTTTATTTTAAATTCTTTCAGAACAGATGATCAAATACTAACAAACATTTAAATAAGTAC
Found at i:57923 original size:21 final size:20
Alignment explanation
Indices: 57886--57928 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
57876 GGAGTAAAAG
57886 AAGAAATTGAAAACGAAGAA
1 AAGAAATTGAAAACGAAGAA
* *
57906 AAGAAAGTTGAGATCGAAGAA
1 AAGAAA-TTGAAAACGAAGAA
57927 AA
1 AA
57929 TTTTTAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.60, C:0.05, G:0.23, T:0.12
Consensus pattern (20 bp):
AAGAAATTGAAAACGAAGAA
Found at i:58466 original size:18 final size:18
Alignment explanation
Indices: 58445--58513 Score: 75
Period size: 18 Copynumber: 3.7 Consensus size: 18
58435 TTAAAAATAA
*
58445 TTTAATATTTTTTATATT
1 TTTAATAATTTTTATATT
* *
58463 TTTAATAATGTTAATAATTT
1 TTTAATAATTTTTAT-A-TT
58483 ATTTAATAATTTTTATATT
1 -TTTAATAATTTTTATATT
*
58502 TTTAAAAATTTT
1 TTTAATAATTTT
58514 CAATATTAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
18 23 0.55
19 3 0.07
20 3 0.07
21 13 0.31
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (18 bp):
TTTAATAATTTTTATATT
Found at i:62087 original size:2 final size:2
Alignment explanation
Indices: 62080--62116 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
62070 TGTTATAGGA
62080 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
62117 TGAGGATACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:62814 original size:12 final size:12
Alignment explanation
Indices: 62797--62822 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
62787 TGTGTAAGGT
62797 TTTATAATGTTG
1 TTTATAATGTTG
62809 TTTATAATGTTG
1 TTTATAATGTTG
62821 TT
1 TT
62823 ATACTTCGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.15, T:0.62
Consensus pattern (12 bp):
TTTATAATGTTG
Found at i:65366 original size:22 final size:21
Alignment explanation
Indices: 65338--65385 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 21
65328 GAAAAAATAC
*
65338 AAAATTATAAAAAATATTTAAA
1 AAAATTACAAAAAATA-TTAAA
*
65360 AAAATTACAAAAAGTATTAAA
1 AAAATTACAAAAAATATTAAA
65381 AAAAT
1 AAAAT
65386 AAAAATATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (21 bp):
AAAATTACAAAAAATATTAAA
Found at i:65371 original size:21 final size:22
Alignment explanation
Indices: 65338--65385 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
65328 GAAAAAATAC
65338 AAAATTATAAAAAA-TATTTAAA
1 AAAATTATAAAAAAGTA-TTAAA
*
65360 AAAATTA-CAAAAAGTATTAAA
1 AAAATTATAAAAAAGTATTAAA
65381 AAAAT
1 AAAAT
65386 AAAAATATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (22 bp):
AAAATTATAAAAAAGTATTAAA
Found at i:67748 original size:21 final size:22
Alignment explanation
Indices: 67712--67754 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
67702 GTTTGGCCTT
67712 TTTAATTTTATAAAAATTTTAA
1 TTTAATTTTATAAAAATTTTAA
*
67734 TTTAA-TTTATTAAAATTTTAA
1 TTTAATTTTATAAAAATTTTAA
67755 AAATTTTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTAATTTTATAAAAATTTTAA
Found at i:72026 original size:18 final size:18
Alignment explanation
Indices: 72003--72052 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
71993 TCCAAAAAAA
72003 TTATATTTTTAAATTAAT
1 TTATATTTTTAAATTAAT
* **
72021 TTATATTTTAAAAAGAAT
1 TTATATTTTTAAATTAAT
*
72039 TT-TATTTTTTAATT
1 TTATATTTTTAAATT
72053 TATGTTCGTC
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (18 bp):
TTATATTTTTAAATTAAT
Found at i:73500 original size:60 final size:57
Alignment explanation
Indices: 73417--73587 Score: 191
Period size: 60 Copynumber: 2.9 Consensus size: 57
73407 AAATTGATTC
* * * *
73417 TAAAAAAAATTTAAGTGCCAAATTAGGAAAAAATGCCAAGTTCAGGTACCAAATTGGA
1 TAAAAAAAATTTAGGTACCAAATTA-GAAAAAATGTCAAGTTTAGGTACCAAATTGGA
** *
73475 TCCAAAAAAAATTTAGGTACCAAATTAAGAAAATGTGTCAAGTTTAGGTACCAAATTGGG
1 T--AAAAAAAATTTAGGTACCAAATT-AGAAAAAATGTCAAGTTTAGGTACCAAATTGGA
* * * *
73535 T-GAAAAAATTTAGATACCAAATTAAAAAAAAGTGTCAAGTTTAAGTACCAAAT
1 TAAAAAAAATTTAGGTACCAAATTAGAAAAAA-TGTCAAGTTTAGGTACCAAAT
73588 GTTATATTAA
Statistics
Matches: 96, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
56 5 0.05
57 40 0.42
58 1 0.01
60 49 0.51
61 1 0.01
ACGTcount: A:0.48, C:0.11, G:0.16, T:0.25
Consensus pattern (57 bp):
TAAAAAAAATTTAGGTACCAAATTAGAAAAAATGTCAAGTTTAGGTACCAAATTGGA
Found at i:73570 original size:57 final size:58
Alignment explanation
Indices: 73419--73587 Score: 191
Period size: 57 Copynumber: 2.9 Consensus size: 58
73409 ATTGATTCTA
* * * *
73419 AAAAAAATTTA-AGTGCCAAATTAGGAAAAAA-TGCCAAGTTCAGGTACCAAATTGGATCC
1 AAAAAAATTTAGA-TACCAAATTA-AAAAAAAGTGTCAAGTTTAGGTACCAAATTGGAT-C
* * * *
73478 AAAAAAAATTTAGGTACCAAATTAAGAAAATGTGTCAAGTTTAGGTACCAAATTGGGT-
1 -AAAAAAATTTAGATACCAAATTAAAAAAAAGTGTCAAGTTTAGGTACCAAATTGGATC
* *
73536 GAAAAAATTTAGATACCAAATTAAAAAAAAGTGTCAAGTTTAAGTACCAAAT
1 AAAAAAATTTAGATACCAAATTAAAAAAAAGTGTCAAGTTTAGGTACCAAAT
73588 GTTATATTAA
Statistics
Matches: 94, Mismatches: 13, Indels: 7
0.82 0.11 0.06
Matches are distributed among these distances:
57 47 0.50
59 4 0.04
60 43 0.46
ACGTcount: A:0.48, C:0.11, G:0.16, T:0.25
Consensus pattern (58 bp):
AAAAAAATTTAGATACCAAATTAAAAAAAAGTGTCAAGTTTAGGTACCAAATTGGATC
Found at i:74111 original size:30 final size:31
Alignment explanation
Indices: 74066--74130 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
74056 ATATAAGGGT
*
74066 AAATGACAAAACAAT-C-ACTCAACTTTCAAA
1 AAATAACAAAACAATCCTACT-AACTTTCAAA
*
74096 AAATAACAAATCAATCCTACTAACTTTCAAA
1 AAATAACAAAACAATCCTACTAACTTTCAAA
74127 AAAT
1 AAAT
74131 CAGACACCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 13 0.42
31 15 0.48
32 3 0.10
ACGTcount: A:0.54, C:0.22, G:0.02, T:0.23
Consensus pattern (31 bp):
AAATAACAAAACAATCCTACTAACTTTCAAA
Found at i:74943 original size:14 final size:14
Alignment explanation
Indices: 74924--74952 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
74914 GCCAAAGATG
74924 GTTGTGGCGGAGGC
1 GTTGTGGCGGAGGC
74938 GTTGTGGCGGAGGC
1 GTTGTGGCGGAGGC
74952 G
1 G
74953 GTGACGGCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.14, G:0.59, T:0.21
Consensus pattern (14 bp):
GTTGTGGCGGAGGC
Found at i:75711 original size:20 final size:17
Alignment explanation
Indices: 75686--75722 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
75676 ACATTAAAAT
75686 TTTAATAATTCAACCAG
1 TTTAATAATTCAACCAG
75703 TTTAATAATTCAACCAG
1 TTTAATAATTCAACCAG
75720 TTT
1 TTT
75723 TTCCATATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.41
Consensus pattern (17 bp):
TTTAATAATTCAACCAG
Found at i:79563 original size:45 final size:45
Alignment explanation
Indices: 79507--79594 Score: 106
Period size: 47 Copynumber: 1.9 Consensus size: 45
79497 ATCATTAAAT
**
79507 ATTTGTAATTAA-ATACTAACACGGTTGTATTATTTTAATTTTTTA
1 ATTTGTAATTAAGATACTAACACAATTGTATTATTTT-ATTTTTTA
* **
79552 ATTTTTAATTAATGATTTTAACACAATTGTATTATTTTATTTT
1 ATTTGTAATTAA-GATACTAACACAATTGTATTATTTTATTTT
79595 AAAATATAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
45 11 0.31
46 5 0.14
47 20 0.56
ACGTcount: A:0.33, C:0.06, G:0.07, T:0.55
Consensus pattern (45 bp):
ATTTGTAATTAAGATACTAACACAATTGTATTATTTTATTTTTTA
Found at i:81956 original size:19 final size:19
Alignment explanation
Indices: 81933--82001 Score: 79
Period size: 20 Copynumber: 3.6 Consensus size: 19
81923 AAAATTACAA
*
81933 AAAAAATCAAAATAATTTT
1 AAAAATTCAAAATAATTTT
*
81952 CAAAAATTAAAAATAATTTT
1 -AAAAATTCAAAATAATTTT
*
81972 -AAAATTCTAAAT-ATTTAT
1 AAAAATTCAAAATAATTT-T
81990 AAAAATTCAAAA
1 AAAAATTCAAAA
82002 ATTTTTATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
17 4 0.10
18 11 0.26
19 10 0.24
20 17 0.40
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:81983 original size:18 final size:18
Alignment explanation
Indices: 81942--82006 Score: 64
Period size: 18 Copynumber: 3.6 Consensus size: 18
81932 AAAAAAATCA
*
81942 AAATAATTTTCAAAAATTAA
1 AAATAATTTT-AAAAATT-C
81962 AAATAATTTT-AAAATTC
1 AAATAATTTTAAAAATTC
81979 TAAAT-ATTTATAAAAATTC
1 -AAATAATTT-TAAAAATTC
81998 AAA-AATTTT
1 AAATAATTTT
82007 TATTTTTAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
17 5 0.12
18 18 0.45
19 7 0.17
20 10 0.25
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (18 bp):
AAATAATTTTAAAAATTC
Found at i:82010 original size:24 final size:25
Alignment explanation
Indices: 81983--82031 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
81973 AAATTCTAAA
81983 TATTTAT-AAAAATTCA-AAAATTTT
1 TATTTATAAAAAATT-ATAAAATTTT
*
82007 TATTTTTAAAAAATTATAAAATTTT
1 TATTTATAAAAAATTATAAAATTTT
82032 AAAAAAATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (25 bp):
TATTTATAAAAAATTATAAAATTTT
Found at i:82286 original size:23 final size:23
Alignment explanation
Indices: 82243--82288 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
82233 TGTAACAAAA
*
82243 TTTTAATTTAACATTATTAATTT
1 TTTTAATTTAACATTAATAATTT
82266 TTTTAATTTAAC-TTGAATAATTT
1 TTTTAATTTAACATT-AATAATTT
82289 CACTCGATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 2 0.10
23 19 0.90
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (23 bp):
TTTTAATTTAACATTAATAATTT
Found at i:88755 original size:31 final size:31
Alignment explanation
Indices: 88720--88782 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
88710 AAGAAAATAT
88720 TTAGCCCTCAAAACTCGAGCCATTAACGATG
1 TTAGCCCTCAAAACTCGAGCCATTAACGATG
88751 TTAGCCCTCAAAACTCGAGCCATTAACGATG
1 TTAGCCCTCAAAACTCGAGCCATTAACGATG
88782 T
1 T
88783 AGGATGCATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.24
Consensus pattern (31 bp):
TTAGCCCTCAAAACTCGAGCCATTAACGATG
Done.