Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013948.1 Kokia drynarioides strain JFW-HI SEQ_128978, 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: 48342
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.35
Found at i:1092 original size:59 final size:59
Alignment explanation
Indices: 886--1231 Score: 227
Period size: 59 Copynumber: 5.9 Consensus size: 59
876 TAAACTATCT
* * * *
886 AAAAATCACATTTTTAC-CCTCGAACATTCC-AAAATTTCA-TTTTGACC-CGAAATTTTTC-
1 AAAAATTACATATTTACACC-CAAAC-TTCCAAAAATCTCATTTTTGACCTCG-AA-TTTTCA
* * * *
944 AAAAATTACATTTTTAC-CCTCGAACTTCCAAAATTC-CATTTTTGACTTCGAATTTTCA
1 AAAAATTACATATTTACACC-CAAACTTCCAAAAATCTCATTTTTGACCTCGAATTTTCA
* * * *
1002 AAAAATTACATTTTTACCCCCAAACTTTCCAAAAATCTCATTTTTGACCTCGATTTTTTCC
1 AAAAATTACATATTTACACCCAAAC-TTCCAAAAATCTCATTTTTGACCTCGA-ATTTTCA
* * * * * *
1063 AAAAA-TACCA-ATTTGCACCCAAACTTCCAAAAATTTCATTTTTGACCTTGAACTCTCT
1 AAAAATTA-CATATTTACACCCAAACTTCCAAAAATCTCATTTTTGACCTCGAATTTTCA
* * * *
1121 AAAAATTATCAT-TTTAC-CCTCGAACTTCCAAAAAT-TCCATTTTTGACCTCGAACTTCCT
1 AAAAATTA-CATATTTACACC-CAAACTTCCAAAAATCT-CATTTTTGACCTCGAATTTTCA
* * * * *
1180 GAAAATTACCAT-TTTAC-CCTCGAACTTCCAAAGATTTCA-TTTTGATCTCGAA
1 AAAAATTA-CATATTTACACC-CAAACTTCCAAAAATCTCATTTTTGACCTCGAA
1232 GTGTTTAAAA
Statistics
Matches: 246, Mismatches: 28, Indels: 28
0.81 0.09 0.09
Matches are distributed among these distances:
57 11 0.04
58 81 0.33
59 114 0.46
60 28 0.11
61 12 0.05
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.36
Consensus pattern (59 bp):
AAAAATTACATATTTACACCCAAACTTCCAAAAATCTCATTTTTGACCTCGAATTTTCA
Found at i:1190 original size:118 final size:118
Alignment explanation
Indices: 886--1222 Score: 300
Period size: 118 Copynumber: 2.9 Consensus size: 118
876 TAAACTATCT
* * * * * * * *
886 AAAAATCACATTTTTACCCTCGAACATTCC-AAAATTTCA-TTTTGACC-CGAAATTTTTCAAAA
1 AAAAATTACATTTTTACCCCCAAACTTTCCAAAAATCTCATTTTTGACCTCGATA-CTTCCAAAA
* * * * *
948 ATTA-CATTTTTACCCTCGAACTTCC-AAAATTCCATTTTTGACTTCGAATTTTCA
65 A-TACCA-ATTTACCCTCAAACTTCCAAAAATTTCATTTTTGACTTCGAACTCTCA
**
1002 AAAAATTACATTTTTACCCCCAAACTTTCCAAAAATCTCATTTTTGACCTCGATTTTTTCCAAAA
1 AAAAATTACATTTTTACCCCCAAACTTTCCAAAAATCTCATTTTTGACCTCGA-TACTTCCAAAA
* *
1067 ATACCAATTTGCACC-CAAACTTCCAAAAATTTCATTTTTGACCTT-GAACTCTCT
65 ATACCAATTTAC-CCTCAAACTTCCAAAAATTTCATTTTTGA-CTTCGAACTCTCA
* *
1121 AAAAATTATCA-TTTTACCCTCGAAC-TTCCAAAAAT-TCCATTTTTGACCTCGA-ACTTCCTGA
1 AAAAATTA-CATTTTTACCCCCAAACTTTCCAAAAATCT-CATTTTTGACCTCGATACTTCC--A
* * * *
1182 AAATTACCATTTTACCCTCGAACTTCCAAAGATTTCATTTT
62 AAAATACCAATTTACCCTCAAACTTCCAAAAATTTCATTTT
1223 GATCTCGAAG
Statistics
Matches: 184, Mismatches: 24, Indels: 24
0.79 0.10 0.10
Matches are distributed among these distances:
116 30 0.16
117 11 0.06
118 81 0.44
119 57 0.31
120 5 0.03
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (118 bp):
AAAAATTACATTTTTACCCCCAAACTTTCCAAAAATCTCATTTTTGACCTCGATACTTCCAAAAA
TACCAATTTACCCTCAAACTTCCAAAAATTTCATTTTTGACTTCGAACTCTCA
Found at i:1201 original size:30 final size:29
Alignment explanation
Indices: 897--1211 Score: 144
Period size: 30 Copynumber: 10.7 Consensus size: 29
887 AAAATCACAT
*
897 TTTTACCCTCGAACATTCC-AAAATT-TCA
1 TTTTACCCTCGAAC-TTCCAAAAATTACCA
* *
925 TTTTGA-CC-CGAAATTTTTCAAAAATTA-CA
1 TTTT-ACCCTCG-AA-CTTCCAAAAATTACCA
954 TTTTTACCCTCGAACTTCC-AAAATT-CCA
1 -TTTTACCCTCGAACTTCCAAAAATTACCA
* * *
982 TTTTTGA-CTTCGAATTTTCAAAAAATTA-CA
1 -TTTT-ACCCTCGAA-CTTCCAAAAATTACCA
* *
1012 TTTTTACCCCCAAACTTTCCAAAAA-T-CTCA
1 -TTTTACCCTCGAAC-TTCCAAAAATTAC-CA
**
1042 TTTTTGA-CCTCGATTTTTTCCAAAAA-TACCA
1 -TTTT-ACCCTCGA--ACTTCCAAAAATTACCA
* * * *
1073 ATTTGCACC-CAAACTTCCAAAAATT-TCA
1 TTTTAC-CCTCGAACTTCCAAAAATTACCA
* * *
1101 TTTTTGA-CCTTGAACTCTCTAAAAATTATCA
1 -TTTT-ACCCTCGAACT-TCCAAAAATTACCA
1132 TTTTACCCTCGAACTTCCAAAAATT-CCA
1 TTTTACCCTCGAACTTCCAAAAATTACCA
*
1160 TTTTTGA-CCTCGAACTTCCTGAAAATTACCA
1 -TTTT-ACCCTCGAACTTCC-AAAAATTACCA
1191 TTTTACCCTCGAACTTCCAAA
1 TTTTACCCTCGAACTTCCAAA
1212 GATTTCATTT
Statistics
Matches: 220, Mismatches: 32, Indels: 69
0.69 0.10 0.21
Matches are distributed among these distances:
27 2 0.01
28 45 0.20
29 56 0.25
30 93 0.42
31 23 0.10
32 1 0.00
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.37
Consensus pattern (29 bp):
TTTTACCCTCGAACTTCCAAAAATTACCA
Found at i:5602 original size:4 final size:4
Alignment explanation
Indices: 5586--5634 Score: 73
Period size: 4 Copynumber: 12.5 Consensus size: 4
5576 TATATATATA
* *
5586 TATT T-TT TTTT TATT TATA TATT TATT TATT TATT TATT TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT
5633 TA
1 TA
5635 CTGTCACATG
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
3 3 0.07
4 38 0.93
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:6397 original size:20 final size:20
Alignment explanation
Indices: 6369--6435 Score: 52
Period size: 20 Copynumber: 3.4 Consensus size: 20
6359 TCACATCAGC
*
6369 AAATGATTTTAAAATTATTA
1 AAATTATTTTAAAATTATTA
*
6389 AAATTATTTTTTAAAA-TA-AA
1 AAATTA--TTTTAAAATTATTA
6409 AAATTA--TTAAAATTATTTTA
1 AAATTATTTTAAAATTA--TTA
6429 AAATTAT
1 AAATTAT
6436 AATCATCATC
Statistics
Matches: 37, Mismatches: 3, Indels: 13
0.70 0.06 0.25
Matches are distributed among these distances:
16 6 0.16
17 2 0.05
20 19 0.51
21 2 0.05
22 8 0.22
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (20 bp):
AAATTATTTTAAAATTATTA
Found at i:6482 original size:6 final size:6
Alignment explanation
Indices: 6473--6498 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
6463 TTTTTTTCCT
6473 TTCCCC TTCCCC TTCCCC TTCCCC TT
1 TTCCCC TTCCCC TTCCCC TTCCCC TT
6499 ATTTTCTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (6 bp):
TTCCCC
Found at i:7357 original size:9 final size:9
Alignment explanation
Indices: 7333--7396 Score: 52
Period size: 9 Copynumber: 7.7 Consensus size: 9
7323 GATGATGATT
7333 ATAATTTTAAA
1 ATAATTTT--A
7344 ATAATTTTA
1 ATAATTTTA
7353 ATAATTTT-
1 ATAATTTTA
7361 AT-ATTTTA
1 ATAATTTTA
*
7369 A-AA---AA
1 ATAATTTTA
7374 ATAATTTTA
1 ATAATTTTA
7383 ATAATTTTA
1 ATAATTTTA
7392 A-AATT
1 ATAATT
7397 ATTTGCTGAT
Statistics
Matches: 45, Mismatches: 2, Indels: 15
0.73 0.03 0.24
Matches are distributed among these distances:
5 2 0.04
6 2 0.04
7 5 0.11
8 8 0.18
9 20 0.44
11 8 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (9 bp):
ATAATTTTA
Found at i:7370 original size:27 final size:29
Alignment explanation
Indices: 7331--7396 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 29
7321 AGGATGATGA
7331 TTATAATTTT-AAAATAATTTTAATAATT
1 TTATAATTTTAAAAATAATTTTAATAATT
7359 TTAT-ATTTTAAAAAAATAATTTTAATAATT
1 TTATAATTTT--AAAAATAATTTTAATAATT
*
7389 TTAAAATT
1 TTATAATT
7397 ATTTGCTGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
27 5 0.15
28 4 0.12
30 21 0.64
31 3 0.09
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (29 bp):
TTATAATTTTAAAAATAATTTTAATAATT
Found at i:7378 original size:21 final size:23
Alignment explanation
Indices: 7352--7394 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 23
7342 AAATAATTTT
7352 AATAATTTT-AT-ATTTTAAAAA
1 AATAATTTTAATAATTTTAAAAA
7373 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
7395 TTATTTGCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 9 0.45
22 2 0.10
23 9 0.45
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
AATAATTTTAATAATTTTAAAAA
Found at i:12267 original size:12 final size:13
Alignment explanation
Indices: 12241--12277 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
12231 ACAAAAAGAA
12241 GCAAAGAATACAG
1 GCAAAGAATACAG
*
12254 GCAAA-AATAGAG
1 GCAAAGAATACAG
12266 GCAAAGAA-ACAG
1 GCAAAGAATACAG
12278 AGTTTTGGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
12 14 0.67
13 7 0.33
ACGTcount: A:0.57, C:0.14, G:0.24, T:0.05
Consensus pattern (13 bp):
GCAAAGAATACAG
Found at i:13701 original size:29 final size:30
Alignment explanation
Indices: 13556--13827 Score: 259
Period size: 30 Copynumber: 9.1 Consensus size: 30
13546 CTCAAGAGGT
* *
13556 CCCC-AAACTTTTCCAAAACTATATTTTGA
1 CCCCTAAACTTTTCCAAAATTACATTTTGA
* * *
13585 CCCCTAAACTTTTCCAAAATCATATTTTAA
1 CCCCTAAACTTTTCCAAAATTACATTTTGA
** * *
13615 CCATTAAATTTTTCCAAAATTACATTTTAA
1 CCCCTAAACTTTTCCAAAATTACATTTTGA
*
13645 CCTCTTAAAC-TTTCCTAAAATTACATTTTGA
1 CC-CCTAAACTTTTCC-AAAATTACATTTTGA
* *
13676 CCCCAAAACTTTT-TAAAATTACATTTT-A
1 CCCCTAAACTTTTCCAAAATTACATTTTGA
* * * * * *
13704 CGCCTTAAAATTTTCTAAACTCACA-TTTAA
1 C-CCCTAAACTTTTCCAAAATTACATTTTGA
*
13734 CTCCTAAACTTTTCCAAAATTACATTTTGA
1 CCCCTAAACTTTTCCAAAATTACATTTTGA
* *
13764 CCCCTCAAACTTTTCCAAAATCATATTTTTGA
1 CCCCT-AAACTTTTCCAAAATTACA-TTTTGA
*
13796 CCCCTAAACTTTT-CAAAATCACATTTTGA
1 CCCCTAAACTTTTCCAAAATTACATTTTGA
13825 CCC
1 CCC
13828 TCGAACTTCT
Statistics
Matches: 203, Mismatches: 30, Indels: 20
0.80 0.12 0.08
Matches are distributed among these distances:
28 2 0.01
29 55 0.27
30 86 0.42
31 49 0.24
32 11 0.05
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.38
Consensus pattern (30 bp):
CCCCTAAACTTTTCCAAAATTACATTTTGA
Found at i:13926 original size:28 final size:28
Alignment explanation
Indices: 13894--13950 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
13884 CCCCTTTTGT
13894 CTTGTTTCTTTTCTCTTCAATGTTCATA
1 CTTGTTTCTTTTCTCTTCAATGTTCATA
*
13922 CTTGTTTCTTTTCTTTTCAATGTTCATA
1 CTTGTTTCTTTTCTCTTCAATGTTCATA
13950 C
1 C
13951 ACAGAATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.14, C:0.21, G:0.07, T:0.58
Consensus pattern (28 bp):
CTTGTTTCTTTTCTCTTCAATGTTCATA
Found at i:15289 original size:32 final size:32
Alignment explanation
Indices: 15252--15315 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
15242 TTCATTTCCA
* *
15252 TTTTTGGATTTC-TTAAGACTTTCTCTATTTTT
1 TTTTTGGATTTCTTTAAAACTTT-TCCATTTTT
**
15284 TTTTTGTTTTTCTTTAAAACTTTTCCATTTTT
1 TTTTTGGATTTCTTTAAAACTTTTCCATTTTT
15316 GAATTTGTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 18 0.67
33 9 0.33
ACGTcount: A:0.16, C:0.12, G:0.06, T:0.66
Consensus pattern (32 bp):
TTTTTGGATTTCTTTAAAACTTTTCCATTTTT
Found at i:15964 original size:23 final size:23
Alignment explanation
Indices: 15921--15966 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
15911 TGTAACAAGA
* *
15921 TTTTAATTTAACATTATTAATTT
1 TTTTAATTTAACATGAATAATTT
15944 TTTTAATTTAAC-TCGAATAATTT
1 TTTTAATTTAACAT-GAATAATTT
15967 CATTCAATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.57
Consensus pattern (23 bp):
TTTTAATTTAACATGAATAATTT
Found at i:26036 original size:6 final size:6
Alignment explanation
Indices: 26025--26074 Score: 100
Period size: 6 Copynumber: 8.3 Consensus size: 6
26015 AAGCATCTTT
26025 GCCATA GCCATA GCCATA GCCATA GCCATA GCCATA GCCATA GCCATA
1 GCCATA GCCATA GCCATA GCCATA GCCATA GCCATA GCCATA GCCATA
26073 GC
1 GC
26075 TGTTAGTATG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.32, C:0.34, G:0.18, T:0.16
Consensus pattern (6 bp):
GCCATA
Found at i:29738 original size:8 final size:8
Alignment explanation
Indices: 29725--29780 Score: 60
Period size: 8 Copynumber: 6.6 Consensus size: 8
29715 GATGGAAAAG
29725 TTTAATTT
1 TTTAATTT
29733 TTTAATTT
1 TTTAATTT
*
29741 TTGT-ACTT
1 TT-TAATTT
29749 TTTAATATT
1 TTTAAT-TT
29758 TTTAATGATT
1 TTTAAT--TT
29768 TTTAATTT
1 TTTAATTT
29776 TTTAA
1 TTTAA
29781 AACAGTGTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
7 1 0.02
8 23 0.55
9 9 0.21
10 9 0.21
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.68
Consensus pattern (8 bp):
TTTAATTT
Found at i:29760 original size:10 final size:9
Alignment explanation
Indices: 29747--29780 Score: 52
Period size: 10 Copynumber: 3.8 Consensus size: 9
29737 ATTTTTGTAC
29747 TTTTTAATA
1 TTTTTAATA
29756 TTTTTAATGA
1 TTTTTAAT-A
29766 TTTTTAAT-
1 TTTTTAATA
29774 TTTTTAA
1 TTTTTAA
29781 AACAGTGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 7 0.29
9 8 0.33
10 9 0.38
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (9 bp):
TTTTTAATA
Found at i:30983 original size:30 final size:28
Alignment explanation
Indices: 30947--31033 Score: 93
Period size: 30 Copynumber: 3.0 Consensus size: 28
30937 TATTTAATTA
30947 ATTTTTTAAAATTTTAAAATATTAAAAAAT
1 ATTTTTTAAAATTTT-AAAT-TTAAAAAAT
* * * *
30977 ATTTTTTAATGATTTTTTATTTTTAAAAAT
1 ATTTTTTAA--AATTTTAAATTTAAAAAAT
*
31007 ATTTTTTTAAATTTTAAATTTAAAAAA
1 ATTTTTTAAAATTTTAAATTTAAAAAA
31034 ATAATTAAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
28 14 0.30
30 25 0.54
31 2 0.04
32 5 0.11
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (28 bp):
ATTTTTTAAAATTTTAAATTTAAAAAAT
Found at i:31173 original size:16 final size:17
Alignment explanation
Indices: 31146--31184 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
31136 TAACAAAAAT
*
31146 ATAAATTTAAAAATTAA
1 ATAAAATTAAAAATTAA
31163 A-AAAATTAAAAATTAA
1 ATAAAATTAAAAATTAA
31179 ATAAAA
1 ATAAAA
31185 AACTAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
ATAAAATTAAAAATTAA
Found at i:32185 original size:29 final size:29
Alignment explanation
Indices: 32153--32211 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
32143 AATCAACAAA
* * *
32153 TTAAAAA-AAGAATTTAATAATATTAAATT
1 TTAAAAATAAAAATATAAAAAT-TTAAATT
32182 TTAAAAATAAAAATATAAAAATTTAAATT
1 TTAAAAATAAAAATATAAAAATTTAAATT
32211 T
1 T
32212 AAATTTGTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (29 bp):
TTAAAAATAAAAATATAAAAATTTAAATT
Found at i:32214 original size:22 final size:22
Alignment explanation
Indices: 32163--32214 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
32153 TTAAAAAAAG
* * *
32163 AATTTAATAATATTAAATTTTA
1 AATTTAAAAATATAAAAATTTA
**
32185 AAAATAAAAATATAAAAATTTA
1 AATTTAAAAATATAAAAATTTA
32207 AATTTAAA
1 AATTTAAA
32215 TTTGTAAAAA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
AATTTAAAAATATAAAAATTTA
Found at i:33776 original size:2 final size:2
Alignment explanation
Indices: 33765--33808 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
33755 TCTATCTCTA
33765 AT AT -T AT AT AT AT 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 AT AT AT AT AT AT AT
33806 AT A
1 AT A
33809 AGAATTAATC
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34637 original size:28 final size:28
Alignment explanation
Indices: 34584--34637 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
34574 ACTAAAATTT
* * *
34584 AAAAATTAAAACCAAAGTGATTAAAAAA
1 AAAAATTAAAACCAAAATAATAAAAAAA
*
34612 AAAAATTAAGACCAAAATAATAAAAA
1 AAAAATTAAAACCAAAATAATAAAAA
34638 TGAGTAAACA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.70, C:0.07, G:0.06, T:0.17
Consensus pattern (28 bp):
AAAAATTAAAACCAAAATAATAAAAAAA
Found at i:35602 original size:13 final size:13
Alignment explanation
Indices: 35563--35603 Score: 52
Period size: 11 Copynumber: 3.4 Consensus size: 13
35553 CTCAATTTGG
35563 TAAAATAAATTAT
1 TAAAATAAATTAT
35576 T-AAA-AAATTA-
1 TAAAATAAATTAT
*
35586 TAAAATAAAATAT
1 TAAAATAAATTAT
35599 TAAAA
1 TAAAA
35604 ATTCGATTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
10 1 0.04
11 9 0.38
12 8 0.33
13 6 0.25
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TAAAATAAATTAT
Found at i:47248 original size:32 final size:32
Alignment explanation
Indices: 47200--47274 Score: 100
Period size: 32 Copynumber: 2.4 Consensus size: 32
47190 GAAGGAAAAA
*
47200 AGAAAGAAAAAAGAGAAAGAAA-GGAAGAAAGA
1 AGAAGGAAAAAAGAG-AAGAAAGGGAAGAAAGA
* *
47232 AGAAGGAAGAAGGAGAAGAAAGGGAAGAAAG-
1 AGAAGGAAAAAAGAGAAGAAAGGGAAGAAAGA
47263 AGAAGGAAAAAA
1 AGAAGGAAAAAA
47275 AAAAGGTAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
31 16 0.43
32 21 0.57
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (32 bp):
AGAAGGAAAAAAGAGAAGAAAGGGAAGAAAGA
Found at i:47259 original size:18 final size:16
Alignment explanation
Indices: 47199--47267 Score: 70
Period size: 17 Copynumber: 4.2 Consensus size: 16
47189 TGAAGGAAAA
* *
47199 AAGAAAGAAAAAAGAG
1 AAGAAAGGAAGAAGAG
47215 AAAGAAAGGAAGAA-AG
1 -AAGAAAGGAAGAAGAG
47231 AAG-AAGGAAGAAGGAG
1 AAGAAAGGAAGAA-GAG
47247 AAGAAAGGGAAGAAAGAG
1 AAGAAA-GGAAG-AAGAG
47265 AAG
1 AAG
47268 GAAAAAAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
14 9 0.20
15 3 0.07
16 7 0.16
17 13 0.29
18 11 0.24
19 2 0.04
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (16 bp):
AAGAAAGGAAGAAGAG
Found at i:47951 original size:29 final size:30
Alignment explanation
Indices: 47919--48017 Score: 98
Period size: 29 Copynumber: 3.4 Consensus size: 30
47909 TAAACTTAGC
47919 TAATTAATTATCAAAATATAATAT-AAAAA
1 TAATTAATTATCAAAATATAATATAAAAAA
**** *
47948 TAATTAATTATC-AAA-ATAATATCCCCAT
1 TAATTAATTATCAAAATATAATATAAAAAA
*
47976 TATATT-ATTGTCCAAAATATAATATAAAAAA
1 TA-ATTAATTAT-CAAAATATAATATAAAAAA
48007 TAATTAATTAT
1 TAATTAATTAT
48018 GAAATTTTGT
Statistics
Matches: 53, Mismatches: 11, Indels: 10
0.72 0.15 0.14
Matches are distributed among these distances:
27 7 0.13
28 10 0.19
29 16 0.30
30 6 0.11
31 14 0.26
ACGTcount: A:0.54, C:0.08, G:0.01, T:0.37
Consensus pattern (30 bp):
TAATTAATTATCAAAATATAATATAAAAAA
Found at i:47965 original size:16 final size:16
Alignment explanation
Indices: 47919--47967 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
47909 TAAACTTAGC
47919 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
*
47935 T-A-TAA-TATAAAAA
1 TAATTAATTATCAAAA
47948 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
47964 TAAT
1 TAAT
47968 ATCCCCATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
13 8 0.29
14 4 0.14
15 4 0.14
16 12 0.43
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Done.