Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008635.1 Kokia drynarioides strain JFW-HI SEQ_123315, 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: 95934
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Warning! 36 characters in sequence are not A, C, G, or T
Found at i:37 original size:15 final size:15
Alignment explanation
Indices: 19--67 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
9 CGACCACCAC
19 CACCTCCAAGTACAA
1 CACCTCCAAGTACAA
* ** *
34 CACCACCACCTACAC
1 CACCTCCAAGTACAA
*
49 CATCTCCAAGTACAA
1 CACCTCCAAGTACAA
64 CACC
1 CACC
68 ACCACCACCA
Statistics
Matches: 24, Mismatches: 10, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.37, C:0.47, G:0.04, T:0.12
Consensus pattern (15 bp):
CACCTCCAAGTACAA
Found at i:37 original size:30 final size:30
Alignment explanation
Indices: 1--77 Score: 120
Period size: 30 Copynumber: 2.6 Consensus size: 30
*
1 CAACACCACGACCACCACCACCTCCAAGTA
1 CAACACCACCACCACCACCACCTCCAAGTA
*
31 CAACACCACCACCTA-CACCATCTCCAAGTA
1 CAACACCACCACC-ACCACCACCTCCAAGTA
61 CAACACCACCACCACCA
1 CAACACCACCACCACCA
78 TGTACACCTC
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
29 1 0.02
30 41 0.95
31 1 0.02
ACGTcount: A:0.38, C:0.51, G:0.04, T:0.08
Consensus pattern (30 bp):
CAACACCACCACCACCACCACCTCCAAGTA
Found at i:101 original size:33 final size:33
Alignment explanation
Indices: 64--142 Score: 131
Period size: 33 Copynumber: 2.4 Consensus size: 33
54 CCAAGTACAA
* *
64 CACCACCACCACCATGTACACCTCTGAGGGGAC
1 CACCACCACCACCAAGTACACCTCCGAGGGGAC
97 CACCACCACCACCAAGTACACCTCCGAGGGGAC
1 CACCACCACCACCAAGTACACCTCCGAGGGGAC
*
130 CACCACCTCCACC
1 CACCACCACCACC
143 TCCACCTCCA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.28, C:0.48, G:0.15, T:0.09
Consensus pattern (33 bp):
CACCACCACCACCAAGTACACCTCCGAGGGGAC
Found at i:143 original size:6 final size:6
Alignment explanation
Indices: 132--156 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
122 GAGGGGACCA
132 CCACCT CCACCT CCACCT CCACCT C
1 CCACCT CCACCT CCACCT CCACCT C
157 GGTCATGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.68, G:0.00, T:0.16
Consensus pattern (6 bp):
CCACCT
Found at i:6510 original size:13 final size:13
Alignment explanation
Indices: 6492--6527 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
6482 AAAAGATTCA
6492 TGTCCGACACCTG
1 TGTCCGACACCTG
6505 TGTCCGACACCTG
1 TGTCCGACACCTG
6518 TGTCCGACAC
1 TGTCCGACAC
6528 ATATCAGGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.17, C:0.39, G:0.22, T:0.22
Consensus pattern (13 bp):
TGTCCGACACCTG
Found at i:8456 original size:7 final size:7
Alignment explanation
Indices: 8443--8480 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
8433 CGCAACCCCG
8443 AACCCTTA
1 AACCC-TA
*
8451 AACCTTA
1 AACCCTA
8458 AA-CCTA
1 AACCCTA
8464 AACCCTA
1 AACCCTA
8471 AACCCTA
1 AACCCTA
8478 AAC
1 AAC
8481 TTCACATCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
6 5 0.19
7 18 0.67
8 4 0.15
ACGTcount: A:0.45, C:0.37, G:0.00, T:0.18
Consensus pattern (7 bp):
AACCCTA
Found at i:8479 original size:14 final size:14
Alignment explanation
Indices: 8443--8480 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
8433 CGCAACCCCG
*
8443 AACCCTTAAACCTTA
1 AACCC-TAAACCCTA
8458 AA-CCTAAACCCTA
1 AACCCTAAACCCTA
8471 AACCCTAAAC
1 AACCCTAAAC
8481 TTCACATCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 10 0.48
14 9 0.43
15 2 0.10
ACGTcount: A:0.45, C:0.37, G:0.00, T:0.18
Consensus pattern (14 bp):
AACCCTAAACCCTA
Found at i:13055 original size:6 final size:6
Alignment explanation
Indices: 13044--13068 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
13034 TAGTACTGTC
13044 CCTATA CCTATA CCTATA CCTATA C
1 CCTATA CCTATA CCTATA CCTATA C
13069 ATGTACATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (6 bp):
CCTATA
Found at i:25662 original size:16 final size:16
Alignment explanation
Indices: 25643--25688 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
25633 CAACATAAAT
25643 ATTTAATAATATAATA
1 ATTTAATAATATAATA
25659 ATTT-AT-AT-TAATA
1 ATTTAATAATATAATA
* *
25672 ATTTATTAAAATAATA
1 ATTTAATAATATAATA
25688 A
1 A
25689 ATTATTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 9 0.36
14 3 0.12
15 3 0.12
16 10 0.40
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
ATTTAATAATATAATA
Found at i:25719 original size:34 final size:33
Alignment explanation
Indices: 25644--25723 Score: 90
Period size: 34 Copynumber: 2.4 Consensus size: 33
25634 AACATAAATA
25644 TTTAATAATATAATAATTTATATTAATAATTTAT
1 TTTAATAATA-AATAATTTATATTAATAATTTAT
** * *
25678 TAAAATAATAAATTATTTAATATTACA-ACTTTAT
1 TTTAATAATAAATAATTT-ATATTA-ATAATTTAT
25712 TTTAATAATAAA
1 TTTAATAATAAA
25724 ATTTAAAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
33 7 0.18
34 30 0.79
35 1 0.03
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (33 bp):
TTTAATAATAAATAATTTATATTAATAATTTAT
Found at i:27919 original size:3 final size:3
Alignment explanation
Indices: 27911--27938 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
27901 TCGATCCCTA
27911 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
27939 AGTGTTTGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:32244 original size:225 final size:217
Alignment explanation
Indices: 31821--32463 Score: 728
Period size: 225 Copynumber: 3.0 Consensus size: 217
31811 GCTCTTGCAT
* * * * * * *
31821 TTTACTATGTTCAATGGTTTCAGTAACAGTAGCAACTGCATCAATTCCGTCCTTATTCTTCCTCT
1 TTTACTATGTTCAAGGGTTACAGTCACAGTAGCAACTGCATCAATCCCATCCTT-GTCTTCTTCT
* * * *
31886 TGTGTTTATCTTTCCTAACCTTTTTTGCTTCCCCATTGTTCCCCAAATTCACCACCTTGCTACTT
65 TGTGTTTATCTTTCCTAACCCTTTTTGCTTCCCCATTGTTCTCCAAGTTCATCACCTTGCTACTT
* * * *
31951 TGTTTTTCTGCATTCTCTTTTCCACCTAAATAAGTTTCCATTGAAATCTCTTCAACTACATCTTT
130 TCTTGTTCTGCGTTCTCTTTTCCACCTAAACAAGTTTCCATTGAAATCTCTTCAACTACATCTTT
32016 ACTTTTCTTATGCGCCTTTGGAGATTCCTC
195 ACTTTTCTTAT--GCC-----AGATTCCTC
* * * *
32046 TTTACCATGTCCAAGGGTTACAGTCACAGTACCAACTGCATTAATCCCATCCTTGTCCTTCTTCT
1 TTTACTATGTTCAAGGGTTACAGTCACAGTAGCAACTGCATCAATCCCATCCTTGT-CTTCTTCT
** * * *
32111 TGTGTTTATCTTTCCCGACCCTTTTTGATTCCCCGTTGTTCTCCAAGTTCATCGCCTTGCTACTT
65 TGTGTTTATCTTTCCTAACCCTTTTTGCTTCCCCATTGTTCTCCAAGTTCATCACCTTGCTACTT
* * * * * *
32176 TCTTGTTCTGTGTTCTTTTTTCCACCTAAACAATTTTGCATTGAAATCTCTTTAACCACATCTTT
130 TCTTGTTCTGCGTTCTCTTTTCCACCTAAACAAGTTTCCATTGAAATCTCTTCAACTACATCTTT
*
32241 ACTTTTC---T--CAGATTCCTT
195 ACTTTTCTTATGCCAGATTCCTC
** * * * *
32259 TTTACTATGTTTGAGGGTTCCAGTCACAGTAGCAACTGCATCGATCTCATCCCTG--TTCTTCTT
1 TTTACTATGTTCAAGGGTTACAGTCACAGTAGCAACTGCATCAATCCCATCCTTGTCTTCTTCTT
* * *
32322 ATGTTTGTCTTTCTTAACCCTTTTTGCTTCCCCATTGTTCTCCAAGTTCATCACCTTGCTACTTT
66 GTGTTTATCTTTCCTAACCCTTTTTGCTTCCCCATTGTTCTCCAAGTTCATCACCTTGCTACTTT
* * *
32387 CTTGTTCTGCGTTCTCTTTTCCATCC-AAACAAGTTTCCACT-AGAATCACTTCAACTGCATCTT
131 CTTGTTCTGCGTTCTCTTTTCCA-CCTAAACAAGTTTCCATTGA-AATCTCTTCAACTACATCTT
*
32450 TACTTGTCTTATGC
194 TACTTTTCTTATGC
32464 TTTTTATGAG
Statistics
Matches: 351, Mismatches: 59, Indels: 26
0.81 0.14 0.06
Matches are distributed among these distances:
209 1 0.00
210 121 0.34
211 2 0.01
213 54 0.15
218 1 0.00
222 1 0.00
224 1 0.00
225 170 0.48
ACGTcount: A:0.19, C:0.28, G:0.11, T:0.43
Consensus pattern (217 bp):
TTTACTATGTTCAAGGGTTACAGTCACAGTAGCAACTGCATCAATCCCATCCTTGTCTTCTTCTT
GTGTTTATCTTTCCTAACCCTTTTTGCTTCCCCATTGTTCTCCAAGTTCATCACCTTGCTACTTT
CTTGTTCTGCGTTCTCTTTTCCACCTAAACAAGTTTCCATTGAAATCTCTTCAACTACATCTTTA
CTTTTCTTATGCCAGATTCCTC
Found at i:32450 original size:210 final size:211
Alignment explanation
Indices: 32059--32454 Score: 528
Period size: 210 Copynumber: 1.9 Consensus size: 211
32049 ACCATGTCCA
* * *
32059 AGGGTTACAGTCACAGTACCAACTGCATTAATCCCATCCTTGTCCTTCTTCTTGTGTTTATCTTT
1 AGGGTTACAGTCACAGTACCAACTGCATCAATCCCATCCCTG--CTTCTTCTTATGTTTATCTTT
* * * *
32124 CCCGACCCTTTTTGATTCCCCGTTGTTCTCCAAGTTCATCGCCTTGCTACTTTCTTGTTCTGTGT
64 CCCAACCCTTTTTGATTCCCCATTGTTCTCCAAGTTCATCACCTTGCTACTTTCTTGTTCTGCGT
* * * * * *
32189 TCTTTTTTCCACCTAAACAATTTTGCATTGAAATCTCTTTAACCACATCTTTACTTTTCTCAGAT
129 TCTCTTTTCCACCTAAACAAGTTTCCATAGAAATCACTTCAACCACATCTTTACTTTTCTCAGAT
32254 TCCTTTTTACTATGTTTG
194 TCCTTTTTACTATGTTTG
* * * * * *
32272 AGGGTTCCAGTCACAGTAGCAACTGCATCGATCTCATCCCTG-TTCTTCTTATGTTTGTCTTTCT
1 AGGGTTACAGTCACAGTACCAACTGCATCAATCCCATCCCTGCTTCTTCTTATGTTTATCTTTCC
* *
32336 TAACCCTTTTTGCTTCCCCATTGTTCTCCAAGTTCATCACCTTGCTACTTTCTTGTTCTGCGTTC
66 CAACCCTTTTTGATTCCCCATTGTTCTCCAAGTTCATCACCTTGCTACTTTCTTGTTCTGCGTTC
**
32401 TCTTTTCCATCC-AAACAAGTTTCCACTAG-AATCACTTCAACTGCATCTTTACTT
131 TCTTTTCCA-CCTAAACAAGTTTCCA-TAGAAATCACTTCAACCACATCTTTACTT
32455 GTCTTATGCT
Statistics
Matches: 158, Mismatches: 23, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
210 118 0.75
211 4 0.03
213 36 0.23
ACGTcount: A:0.18, C:0.28, G:0.11, T:0.42
Consensus pattern (211 bp):
AGGGTTACAGTCACAGTACCAACTGCATCAATCCCATCCCTGCTTCTTCTTATGTTTATCTTTCC
CAACCCTTTTTGATTCCCCATTGTTCTCCAAGTTCATCACCTTGCTACTTTCTTGTTCTGCGTTC
TCTTTTCCACCTAAACAAGTTTCCATAGAAATCACTTCAACCACATCTTTACTTTTCTCAGATTC
CTTTTTACTATGTTTG
Found at i:34200 original size:13 final size:14
Alignment explanation
Indices: 34163--34195 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
34153 ATACTATTAG
*
34163 TATTTT-ATTTATT
1 TATTTTGATATATT
34176 TATTTTGATATATT
1 TATTTTGATATATT
34190 TATTTT
1 TATTTT
34196 CTATAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (14 bp):
TATTTTGATATATT
Found at i:41204 original size:19 final size:16
Alignment explanation
Indices: 41182--41222 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 16
41172 AATGATGTTT
41182 ATTTTAAATTGATTCTTAA
1 ATTTTAAATT-ATT-TT-A
41201 ATTTTAAATTATTTTA
1 ATTTTAAATTATTTTA
41217 ATTTTA
1 ATTTTA
41223 TCTCTAAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.32
17 2 0.09
18 3 0.14
19 10 0.45
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (16 bp):
ATTTTAAATTATTTTA
Found at i:41230 original size:29 final size:31
Alignment explanation
Indices: 41180--41250 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 31
41170 ACAATGATGT
* *
41180 TTATTTTAAATTGATTCTTAAA-TTTTAA-A
1 TTATTTTAATTTGATTCTTAAACTATTAAGA
*
41209 TTATTTTAATTTTA-TCTCTAAACTATTAAGA
1 TTATTTTAATTTGATTCT-TAAACTATTAAGA
*
41240 TTATATTAATT
1 TTATTTTAATT
41251 AGGAAATTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
28 3 0.09
29 16 0.46
30 5 0.14
31 11 0.31
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.55
Consensus pattern (31 bp):
TTATTTTAATTTGATTCTTAAACTATTAAGA
Found at i:41861 original size:23 final size:23
Alignment explanation
Indices: 41826--41873 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
41816 AGTCAGATTA
* *
41826 TATTTTACTAAAAAT-GAATAAAT
1 TATTATACAAAAAATAG-ATAAAT
41849 TATTATACAAAAAATAGATAAAT
1 TATTATACAAAAAATAGATAAAT
41872 TA
1 TA
41874 ATCGGTGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 21 0.95
24 1 0.05
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.35
Consensus pattern (23 bp):
TATTATACAAAAAATAGATAAAT
Found at i:47351 original size:19 final size:18
Alignment explanation
Indices: 47306--47351 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
47296 AGTAAATTTG
*
47306 ATTTTTTTTTGTTAAAAA
1 ATTTTTTTTTCTTAAAAA
* *
47324 ATTATTTTTTCTTTAAAA
1 ATTTTTTTTTCTTAAAAA
*
47342 ATTTTGTTTT
1 ATTTTTTTTT
47352 ATATATCACC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.65
Consensus pattern (18 bp):
ATTTTTTTTTCTTAAAAA
Found at i:52772 original size:15 final size:15
Alignment explanation
Indices: 52748--52777 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
52738 TCTATCTGAC
*
52748 AATGTTTCTTACCCA
1 AATGTCTCTTACCCA
52763 AATGTCTCTTACCCA
1 AATGTCTCTTACCCA
52778 GCTCACTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.30, G:0.07, T:0.37
Consensus pattern (15 bp):
AATGTCTCTTACCCA
Found at i:54060 original size:20 final size:20
Alignment explanation
Indices: 54035--54081 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
54025 ATATCCTTGA
54035 GTTTATGATTTATAAGCTAG
1 GTTTATGATTTATAAGCTAG
54055 GTTTATGATTTATAAGCTAG
1 GTTTATGATTTATAAGCTAG
*
54075 GTCTATG
1 GTTTATG
54082 TTTTCTCACA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.28, C:0.06, G:0.21, T:0.45
Consensus pattern (20 bp):
GTTTATGATTTATAAGCTAG
Found at i:59261 original size:22 final size:22
Alignment explanation
Indices: 59236--59279 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
59226 TACATCCAGC
59236 TTTAAATTCCTAAACATATATA
1 TTTAAATTCCTAAACATATATA
59258 TTTAAATTCCTAAACATATATA
1 TTTAAATTCCTAAACATATATA
59280 AGATATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (22 bp):
TTTAAATTCCTAAACATATATA
Found at i:59287 original size:2 final size:2
Alignment explanation
Indices: 59273--59317 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
59263 ATTCCTAAAC
*
59273 AT AT AT A- AG 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
59314 AT AT
1 AT AT
59318 TTCAATAGCT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:70877 original size:2 final size:2
Alignment explanation
Indices: 70870--70898 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
70860 TACTCTATTA
70870 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
70899 AGTGCTTAAC
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:71218 original size:21 final size:21
Alignment explanation
Indices: 71189--71256 Score: 86
Period size: 22 Copynumber: 3.2 Consensus size: 21
71179 GTTTTTTTGC
71189 TGTTGTTGGTGTGTGTTTTTAT
1 TGTT-TTGGTGTGTGTTTTTAT
71211 TGTTTTGGT-TGTTGTTTTTTAT
1 TGTTTTGGTGTG-TG-TTTTTAT
*
71233 TGTTTTGGTGT-TGTTTTTAC
1 TGTTTTGGTGTGTGTTTTTAT
71253 TGTT
1 TGTT
71257 ATTTTTCTTG
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
20 12 0.29
21 9 0.21
22 20 0.48
23 1 0.02
ACGTcount: A:0.04, C:0.01, G:0.26, T:0.68
Consensus pattern (21 bp):
TGTTTTGGTGTGTGTTTTTAT
Found at i:71268 original size:42 final size:44
Alignment explanation
Indices: 71189--71271 Score: 109
Period size: 42 Copynumber: 1.9 Consensus size: 44
71179 GTTTTTTTGC
* *
71189 TGTTGTTGGTGTGTGTTTTTATTGTTTTGGTTGTTGTTTTTTAT
1 TGTTGTTGGTGTGTGTTTTTACTGTTTTGGTTCTTGTTTTTTAT
*
71233 TGTT-TTGGTGT-TGTTTTTACTGTTATT-TTTCTTGTTTTT
1 TGTTGTTGGTGTGTGTTTTTACTGTT-TTGGTTCTTGTTTTT
71272 GTTGATATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
42 22 0.63
43 9 0.26
44 4 0.11
ACGTcount: A:0.05, C:0.02, G:0.23, T:0.70
Consensus pattern (44 bp):
TGTTGTTGGTGTGTGTTTTTACTGTTTTGGTTCTTGTTTTTTAT
Found at i:92600 original size:12 final size:12
Alignment explanation
Indices: 92579--92610 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
92569 GTCTTTGTTA
92579 TCATCATCATCG
1 TCATCATCATCG
*
92591 TCATCGTCATCG
1 TCATCATCATCG
92603 TCATCATC
1 TCATCATC
92611 TGCATCTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.22, C:0.34, G:0.09, T:0.34
Consensus pattern (12 bp):
TCATCATCATCG
Done.