Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003911.1 Kokia drynarioides strain JFW-HI SEQ_116976, 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: 39205
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:4129 original size:23 final size:24
Alignment explanation
Indices: 4085--4130 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
4075 TCTCACACTT
*
4085 TTTCTTACTCTTTTCCTTTTTGTA
1 TTTCTTACTCTTTTCCATTTTGTA
4109 TTTC-TACTCATTTT-CATTTTGT
1 TTTCTTACTC-TTTTCCATTTTGT
4131 TCTTTTTGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.11, C:0.20, G:0.04, T:0.65
Consensus pattern (24 bp):
TTTCTTACTCTTTTCCATTTTGTA
Found at i:11370 original size:35 final size:35
Alignment explanation
Indices: 11324--11394 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
11314 TCCCATATCA
11324 TTTTGCAGTGTAAAGGTTATTCCTCAATAAGTATG
1 TTTTGCAGTGTAAAGGTTATTCCTCAATAAGTATG
*
11359 TTTTGTAGTGTAAAGGTTATTCCTCAATAAGTATG
1 TTTTGCAGTGTAAAGGTTATTCCTCAATAAGTATG
11394 T
1 T
11395 CTATAGTTCC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.42
Consensus pattern (35 bp):
TTTTGCAGTGTAAAGGTTATTCCTCAATAAGTATG
Found at i:19061 original size:74 final size:74
Alignment explanation
Indices: 18936--19094 Score: 230
Period size: 74 Copynumber: 2.1 Consensus size: 74
18926 GGTGCAATTT
* * *
18936 TCGTCAGTTTATCTAACTAGTGTTGGGCACATATTCGTTGGTTTATTCAACTAAAGCT-GAGCTC
1 TCGTCAGTTTATCTAACTACTGTTGGACACATATTCGTTGGTTTATCCAACTAAAGCTAG-GCTC
19000 ATTAATAATA
65 ATTAATAATA
* * * *
19010 TCGTCAGTTTATTTGACTACTGTTGGATACATATTCGTTGGTTTATCCAACTAGAGCTAGGCTCA
1 TCGTCAGTTTATCTAACTACTGTTGGACACATATTCGTTGGTTTATCCAACTAAAGCTAGGCTCA
19075 TTAATAATA
66 TTAATAATA
*
19084 TCGTCGGTTTA
1 TCGTCAGTTTA
19095 CCCGACTAGC
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
74 75 0.99
75 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.39
Consensus pattern (74 bp):
TCGTCAGTTTATCTAACTACTGTTGGACACATATTCGTTGGTTTATCCAACTAAAGCTAGGCTCA
TTAATAATA
Found at i:19137 original size:74 final size:74
Alignment explanation
Indices: 18936--19121 Score: 223
Period size: 74 Copynumber: 2.5 Consensus size: 74
18926 GGTGCAATTT
* ** * * *
18936 TCGTCAGTTTATCTAACTAGTGTTGGGCACATATTCGTTGGTTTATTCAACTAAAGCTGAGCTCA
1 TCGTCAGTTTACCCGACTAGCGTTGGGCACATATTCGTTGGTTTATCCAACTAGAGCTGAGCTCA
19001 TTAATAATA
66 TTAATAATA
*** **
19010 TCGTCAGTTTATTTGACTA-CTGTTGGATACATATTCGTTGGTTTATCCAACTAGAGCT-AGGCT
1 TCGTCAGTTTACCCGACTAGC-GTTGGGCACATATTCGTTGGTTTATCCAACTAGAGCTGA-GCT
19073 CATTAATAATA
64 CATTAATAATA
* *
19084 TCGTCGGTTTACCCGACTAGCGTTGGGCACACATTCGT
1 TCGTCAGTTTACCCGACTAGCGTTGGGCACATATTCGT
19122 CGATTTACCC
Statistics
Matches: 95, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
73 1 0.01
74 93 0.98
75 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (74 bp):
TCGTCAGTTTACCCGACTAGCGTTGGGCACATATTCGTTGGTTTATCCAACTAGAGCTGAGCTCA
TTAATAATA
Found at i:20065 original size:21 final size:20
Alignment explanation
Indices: 20040--20087 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
20030 ACATAAAAAA
*
20040 ATAAAATAA-AATGACATTAT
1 ATAAAATAACAATG-CAATAT
20060 AGTAAAATAACAATGCAATAT
1 A-TAAAATAACAATGCAATAT
20081 ATAAAAT
1 ATAAAAT
20088 GATAGTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 7 0.28
21 14 0.56
22 4 0.16
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.27
Consensus pattern (20 bp):
ATAAAATAACAATGCAATAT
Found at i:20164 original size:12 final size:11
Alignment explanation
Indices: 20149--20187 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
20139 TAAAAGTATT
20149 AATAATAAAAC
1 AATAATAAAAC
*
20160 AAATAATAATAC
1 -AATAATAAAAC
20172 AATAATAAAAAC
1 AATAAT-AAAAC
20184 AATA
1 AATA
20188 GTGGAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 6 0.25
12 18 0.75
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.21
Consensus pattern (11 bp):
AATAATAAAAC
Found at i:20385 original size:12 final size:12
Alignment explanation
Indices: 20370--20433 Score: 58
Period size: 12 Copynumber: 5.1 Consensus size: 12
20360 AATAATAAAT
20370 AAATAAATAATA
1 AAATAAATAATA
*
20382 AAATGAATATAAAA
1 AAAT-AA-ATAATA
* *
20396 ATAATAGATTATA
1 A-AATAAATAATA
20409 AAATAAATACA-A
1 AAATAAATA-ATA
20421 AAATAAATAATA
1 AAATAAATAATA
20433 A
1 A
20434 TAAAAAAGGT
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
11 1 0.02
12 22 0.54
13 8 0.20
14 7 0.17
15 3 0.07
ACGTcount: A:0.70, C:0.02, G:0.03, T:0.25
Consensus pattern (12 bp):
AAATAAATAATA
Found at i:20401 original size:27 final size:27
Alignment explanation
Indices: 20353--20438 Score: 86
Period size: 27 Copynumber: 3.1 Consensus size: 27
20343 TAAATGACAA
*
20353 AAAAGTAAATA-ATAAATAAATAAATAAT
1 AAAA-TAAATATAAAAAT-AATAAATAAT
* * *
20381 AAAATGAATATAAAAATAATAGATTAT
1 AAAATAAATATAAAAATAATAAATAAT
*
20408 AAAATAAATACAAAAATAA-ATAATAAT
1 AAAATAAATATAAAAATAATA-AATAAT
20435 AAAA
1 AAAA
20439 AAGGTAGACA
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
26 1 0.02
27 38 0.79
28 9 0.19
ACGTcount: A:0.71, C:0.01, G:0.03, T:0.24
Consensus pattern (27 bp):
AAAATAAATATAAAAATAATAAATAAT
Found at i:20438 original size:16 final size:15
Alignment explanation
Indices: 20351--20439 Score: 54
Period size: 15 Copynumber: 5.5 Consensus size: 15
20341 CGTAAATGAC
*
20351 AAAAAAGTAAATAAT
1 AAAAAAATAAATAAT
*
20366 AAATAAATAAATAAT
1 AAAAAAATAAATAAT
20381 AAAATGAATATAAA-AAT
1 AAAA--AA-ATAAATAAT
**
20398 AATAGATTATAAAATAAAT
1 AA-A-AAAAT-AAAT-AAT
*
20417 ACAAAAATAAATAAT
1 AAAAAAATAAATAAT
20432 AATAAAAA
1 AA-AAAAA
20440 AGGTAGACAA
Statistics
Matches: 56, Mismatches: 9, Indels: 17
0.68 0.11 0.21
Matches are distributed among these distances:
15 20 0.36
16 11 0.20
17 13 0.23
18 7 0.12
19 5 0.09
ACGTcount: A:0.72, C:0.01, G:0.03, T:0.24
Consensus pattern (15 bp):
AAAAAAATAAATAAT
Found at i:20569 original size:6 final size:6
Alignment explanation
Indices: 20558--20609 Score: 68
Period size: 6 Copynumber: 8.3 Consensus size: 6
20548 TTTAAGGGAT
* *
20558 AAAATA AAAATA GAAAAGA TTAAATA AAAATA AAAATA AAAATA AAAATA
1 AAAATA AAAATA -AAAATA -AAAATA AAAATA AAAATA AAAATA AAAATA
20608 AA
1 AA
20610 GGGACTAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
6 31 0.77
7 9 0.22
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:22333 original size:50 final size:48
Alignment explanation
Indices: 22274--22428 Score: 119
Period size: 50 Copynumber: 3.3 Consensus size: 48
22264 TTCATCTTGC
*
22274 CCCATTGCAACTTCAAGGAGATAAGTTTTGTTTCTGCAGCTTCAATCCGA
1 CCCACTGCAACTTCAAGGAGATAAG-TTTG-TTCTGCAGCTTCAATCCGA
* * * * *
22324 CCCACTGCAACTT-TA-GAGGTATAG---GAT-T-CAGCTTC-ATCTTGC
1 CCCACTGCAACTTCAAGGAGATA-AGTTTGTTCTGCAGCTTCAATC-CGA
* *
22366 CCCATTGCAACTTCAAGGAGATAAGCTTTGCTTCTGCAACTTCAATCCGA
1 CCCACTGCAACTTCAAGGAGATAAG-TTTG-TTCTGCAGCTTCAATCCGA
*
22416 CCCACTGTAACTT
1 CCCACTGCAACTT
22429 TAGAGGTATA
Statistics
Matches: 78, Mismatches: 15, Indels: 24
0.67 0.13 0.21
Matches are distributed among these distances:
41 3 0.04
42 20 0.26
43 4 0.05
44 6 0.08
45 1 0.01
47 1 0.01
48 6 0.08
49 4 0.05
50 30 0.38
51 3 0.04
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.30
Consensus pattern (48 bp):
CCCACTGCAACTTCAAGGAGATAAGTTTGTTCTGCAGCTTCAATCCGA
Found at i:22420 original size:92 final size:92
Alignment explanation
Indices: 22263--22443 Score: 326
Period size: 92 Copynumber: 2.0 Consensus size: 92
22253 AGTAGCACAA
* * *
22263 CTTCATCTTGCCCCATTGCAACTTCAAGGAGATAAGTTTTGTTTCTGCAGCTTCAATCCGACCCA
1 CTTCATCTTGCCCCATTGCAACTTCAAGGAGATAAGCTTTGCTTCTGCAACTTCAATCCGACCCA
22328 CTGCAACTTTAGAGGTATAGGATTCAG
66 CTGCAACTTTAGAGGTATAGGATTCAG
22355 CTTCATCTTGCCCCATTGCAACTTCAAGGAGATAAGCTTTGCTTCTGCAACTTCAATCCGACCCA
1 CTTCATCTTGCCCCATTGCAACTTCAAGGAGATAAGCTTTGCTTCTGCAACTTCAATCCGACCCA
*
22420 CTGTAACTTTAGAGGTATAGGATT
66 CTGCAACTTTAGAGGTATAGGATT
22444 TGGTGTGGTA
Statistics
Matches: 85, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
92 85 1.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (92 bp):
CTTCATCTTGCCCCATTGCAACTTCAAGGAGATAAGCTTTGCTTCTGCAACTTCAATCCGACCCA
CTGCAACTTTAGAGGTATAGGATTCAG
Found at i:22571 original size:50 final size:50
Alignment explanation
Indices: 22517--23248 Score: 294
Period size: 50 Copynumber: 14.6 Consensus size: 50
22507 TTCAAGCTGA
* *
22517 TCCACTACAACTTCAGGGATATAGGATTTGATGTCGTAGCTTCATCTTGC
1 TCCACTACAACTTCAGGGATATAAGATTTGATTTCGTAGCTTCATCTTGC
* * * * * * *
22567 TCCACTACATCTTCAAGGAGATAAGATTTG-CTTCAATGGCTTCAATC-AGAC
1 TCCACTACAACTTCAGGGATATAAGATTTGATTTC-GTAGCTTC-ATCTTG-C
* * * * *
22618 -CTACTACAACTTTAGGGGTATAAGATTTAAGGTT-GTAGCTTCATCTTGC
1 TCCACTACAACTTCAGGGATATAAGATTTGA-TTTCGTAGCTTCATCTTGC
** * * * *
22667 T-CTGTCACAACTTAATAGAGGATA-AAGATTTGCTTTCGTAGCTTCAATC-CGA
1 TCCACT-ACAACTT--CAG-GGATATAAGATTTGATTTCGTAGCTTC-ATCTTGC
* * * * * * * *
22719 TCCAGTGCAACTTCAAGGATATAGGATTTAATGTCATA-TTTCATCTTGC
1 TCCACTACAACTTCAGGGATATAAGATTTGATTTCGTAGCTTCATCTTGC
* * * ** * * * *
22768 TCCATTGCATCTTTGGGGAGATAAGATTTGCTTTTGTAGC-TCTAT-TAGAC
1 TCCACTACAACTTCAGGGATATAAGATTTGATTTCGTAGCTTC-ATCTTG-C
* * * *
22818 -CCACTATAACTTCAGGCATATAGGATTTGGTGTT-GTAGCTTCATCTTGC
1 TCCACTACAACTTCAGGGATATAAGATTTGAT-TTCGTAGCTTCATCTTGC
* * ** * * * * *
22867 TCTACAACAACTTCAGAAAAAAAAGATTTGTTTTCGTAGCTTCAATC-CGA
1 TCCACTACAACTTCAGGGATATAAGATTTGATTTCGTAGCTTC-ATCTTGC
* * *
22917 TCCACTGCAACTTCAGGGATATAAGATTTGATGTCGTAGCTTCATCTTAC
1 TCCACTACAACTTCAGGGATATAAGATTTGATTTCGTAGCTTCATCTTGC
* ** * * * ** * *
22967 TCCAATGTAACTTTAGGGAGATAAATATTTTCTTTTGTAGCTTTAAT-TTGAC
1 TCCACTACAACTTCAGGGATAT-AAGATTTGATTTCGTAGC-TTCATCTTG-C
* *
23019 -CCACTACAACTTCAAGGG-TATAGGA-TTG-TTTTGTAGCTTCATCTTGC
1 TCCACTACAACTTC-AGGGATATAAGATTTGATTTCGTAGCTTCATCTTGC
* * * *
23066 TCTACAACAACTTCAGAGAGATA-AAGATTTGCTTTTGTAGCTTCAATAC--GAC
1 TCCACTACAACTTCAG-G-GATATAAGATTTGATTTCGTAGCTTC-AT-CTTG-C
* * ** *
23118 -CCATTACAACTTCAAGGG-TATAGGATTTGACTTT-GTATTTTCATCTTAC
1 TCCACTACAACTTC-AGGGATATAAGATTTGA-TTTCGTAGCTTCATCTTGC
* * * * * * *
23167 TCTACTGCAACTTTAGAGATATAATGATTTGCTTTCGTAGCTTCAAT-TCGA
1 TCCACTACAACTTCAGGGATATAA-GATTTGATTTCGTAGCTTC-ATCTTGC
*
23218 TCC-CTGCAACTTCTA-GGATATAAGATTTGAT
1 TCCACTACAACTTC-AGGGATATAAGATTTGAT
23249 GTTGTACTAA
Statistics
Matches: 495, Mismatches: 136, Indels: 103
0.67 0.19 0.14
Matches are distributed among these distances:
47 7 0.01
48 28 0.06
49 101 0.20
50 226 0.46
51 78 0.16
52 44 0.09
53 11 0.02
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (50 bp):
TCCACTACAACTTCAGGGATATAAGATTTGATTTCGTAGCTTCATCTTGC
Found at i:22600 original size:201 final size:201
Alignment explanation
Indices: 22353--23213 Score: 841
Period size: 201 Copynumber: 4.3 Consensus size: 201
22343 TATAGGATTC
* * * * *
22353 AGCTTCATCTTGCCCCATTGCAACTTCAAGGAGATAAGCTTTGCTTCTGCAACTTCAATCCGACC
1 AGCTTCATCTTGCTCCATTGCAACTTCAAGGAGATAAGATTTGCTTCTGTAGCTTCAATCAGACC
** * * * * *
22418 CACTGTAACTTTAGAGGTATAGGATTTGGTGTGGTAGTTTCATCTTGCTCTA-ATGCAACTTTAG
66 CACTACAACTTCAGAGGTATAGGATTTGGTGTTGTAGCTTCATCTTGCTCTACA-ACAACTTCAG
* * * * *
22482 AGAGATAAAGAATTACTTTCGTAGATTCAAGCTGATCCACTACAACTTCAGGGATATAGGATTTG
130 AGAGATAAAGATTTGCTTTCGTAGCTTCAATCCGATCCACTACAACTTCAGGGATATAGGATTTG
22547 ATGTCGT
195 ATGTCGT
* * * ** *
22554 AGCTTCATCTTGCTCCACTACATCTTCAAGGAGATAAGATTTGCTTCAATGGCTTCAATCAGACC
1 AGCTTCATCTTGCTCCATTGCAACTTCAAGGAGATAAGATTTGCTTCTGTAGCTTCAATCAGACC
* * * * * * *
22619 TACTACAACTTTAGGGGTATAAGATTTAAG-GTTGTAGCTTCATCTTGCTCTGTC-ACAACTTAA
66 CACTACAACTTCAGAGGTATAGGATTT-GGTGTTGTAGCTTCATCTTGCTCT-ACAACAACTTCA
* * * *
22682 TAGAGGATAAAGATTTGCTTTCGTAGCTTCAATCCGATCCAGTGCAACTTCAAGGATATAGGATT
129 GAGA-GATAAAGATTTGCTTTCGTAGCTTCAATCCGATCCACTACAACTTCAGGGATATAGGATT
* *
22747 TAATGTCAT
193 TGATGTCGT
* * *** * * *
22756 A-TTTCATCTTGCTCCATTGCATCTTTGGGGAGATAAGATTTGCTTTTGTAGC-TCTATTAGACC
1 AGCTTCATCTTGCTCCATTGCAACTTCAAGGAGATAAGATTTGCTTCTGTAGCTTCAATCAGACC
* *
22819 CACTATAACTTCAG-GCATATAGGATTTGGTGTTGTAGCTTCATCTTGCTCTACAACAACTTCAG
66 CACTACAACTTCAGAG-GTATAGGATTTGGTGTTGTAGCTTCATCTTGCTCTACAACAACTTCAG
* * * * *
22883 A-AAAAAAAGATTTGTTTTCGTAGCTTCAATCCGATCCACTGCAACTTCAGGGATATAAGATTTG
130 AGAGATAAAGATTTGCTTTCGTAGCTTCAATCCGATCCACTACAACTTCAGGGATATAGGATTTG
22947 ATGTCGT
195 ATGTCGT
* * * * * * * * * **
22954 AGCTTCATCTTACTCCAATGTAACTTTAGGGAGATAAATATTTTCTTTTGTAGCTTTAATTTGAC
1 AGCTTCATCTTGCTCCATTGCAACTTCAAGGAGAT-AAGATTTGCTTCTGTAGCTTCAATCAGAC
*
23019 CCACTACAACTTCA-AGGGTATAGGA-TT-GTTTTGTAGCTTCATCTTGCTCTACAACAACTTCA
65 CCACTACAACTTCAGA-GGTATAGGATTTGGTGTTGTAGCTTCATCTTGCTCTACAACAACTTCA
* * * *
23081 GAGAGATAAAGATTTGCTTTTGTAGCTTCAATACGACCCATTACAACTTCAAGGG-TATAGGATT
129 GAGAGATAAAGATTTGCTTTCGTAGCTTCAATCCGATCCACTACAACTTC-AGGGATATAGGATT
*
23145 TGACT-TTGT
193 TGA-TGTCGT
** * * * * *
23154 ATTTTCATCTTACTCTACTGCAACTT-TAGAGATATAATGATTTGCTT-TCGTAGCTTCAAT
1 AGCTTCATCTTGCTCCATTGCAACTTCAAG-GAGATAA-GATTTGCTTCT-GTAGCTTCAAT
23214 TCGATCCCTG
Statistics
Matches: 545, Mismatches: 97, Indels: 37
0.80 0.14 0.05
Matches are distributed among these distances:
198 62 0.11
199 71 0.13
200 172 0.32
201 178 0.33
202 62 0.11
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (201 bp):
AGCTTCATCTTGCTCCATTGCAACTTCAAGGAGATAAGATTTGCTTCTGTAGCTTCAATCAGACC
CACTACAACTTCAGAGGTATAGGATTTGGTGTTGTAGCTTCATCTTGCTCTACAACAACTTCAGA
GAGATAAAGATTTGCTTTCGTAGCTTCAATCCGATCCACTACAACTTCAGGGATATAGGATTTGA
TGTCGT
Found at i:23127 original size:51 final size:49
Alignment explanation
Indices: 22873--23131 Score: 140
Period size: 51 Copynumber: 5.2 Consensus size: 49
22863 TTGCTCTACA
* * *
22873 ACAACTTCAGA-AAAAAAAGATTTGTTTTCGTAGCTTCAATCCGATCCACT
1 ACAACTTCAGAGAGATAAAGATTTGTTTT-GTAGCTTCAAT-CGACCCACT
* * * * *
22923 GCAACTTCAG-G-GATATAAGATTTGATGTCGTAGCTTC-ATCTTACTCCAAT
1 ACAACTTCAGAGAGATA-AAGATTTG-TTTTGTAGCTTCAATC-GAC-CCACT
** * * * * * *
22973 GTAACTTTAGGGAGATAAATATTTTCTTTTGTAGCTTTAATTTGACCCACT
1 ACAACTTCAGAGAGATAAAGA-TTTGTTTTGTAGCTTCAA-TCGACCCACT
* * * *
23024 ACAACTTCA-AG-GGTATAGGA-TTGTTTTGTAGCTTC-ATCTTG-CTCTACA
1 ACAACTTCAGAGAGATA-AAGATTTGTTTTGTAGCTTCAATC--GAC-CCACT
*
23072 ACAACTTCAGAGAGATAAAGATTTGCTTTTGTAGCTTCAATACGACCCATT
1 ACAACTTCAGAGAGATAAAGATTTG-TTTTGTAGCTTCAAT-CGACCCACT
23123 ACAACTTCA
1 ACAACTTCA
23132 AGGGTATAGG
Statistics
Matches: 153, Mismatches: 35, Indels: 41
0.67 0.15 0.18
Matches are distributed among these distances:
46 1 0.01
47 2 0.01
48 27 0.18
49 13 0.08
50 46 0.30
51 49 0.32
52 13 0.08
53 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (49 bp):
ACAACTTCAGAGAGATAAAGATTTGTTTTGTAGCTTCAATCGACCCACT
Found at i:23131 original size:300 final size:296
Alignment explanation
Indices: 22405--23250 Score: 775
Period size: 300 Copynumber: 2.8 Consensus size: 296
22395 GCTTCTGCAA
** * * *
22405 CTTCAATCCGACCCACTGTAACTT-TAGAGGTATAGGATTTGGTGTGGTAGTTTCATCTTGCTCT
1 CTTCAATCCGACCCACTACAACTTCAAG-GGTATAGGA-TT-GTATTGTAGTTTCATCTTGCTCT
* * * * * *
22469 AATGCAACTTTAGAGAGATAAAGAATTACTTTCGTAGATTCAA-GCTGATCCACTACAACTTCAG
63 AA-GCAACTTTAGAGAGATAAAGATTTGCTTTTGTAGCTTCAATAC-GACCCACTACAACTTCA-
* * * * * *
22533 GGATATAGGATTTGATGTCGTAGCTTCATCTTGCTCCACTACATCTTCA-AGGAGATAAGATTTG
125 GGATATAGGATTTGATGTTGTAGCTTCATCTTGCTCTACTACAACTTCAGAGAAAAAAAGATTTG
* * * * * * * * * *
22597 CTTCAATGGCTTCAATCAGA-CCTACTACAACTTTAGGGGTATAAGATTTAAGGTTGTAGCTTCA
190 TTTC-GTAGCTTCAATCCGATCC-ACTGCAACTTCAGGGATATAAGATTTGATGTCGTAGCTTCA
*
22661 TCTTGCTCTGTCACAACTTAATAGAGGATAAAGATTTGCTTTCGTAG
253 TCTTACTCTGT--CAACTT-ATAGAGGATAAAGATTTGCTTTCGTAG
* * * * * * *
22708 CTTCAATCCGATCCAGTGCAACTTCAAGGATATAGGATT-TAATGTCATATTTCATCTTGCTCCA
1 CTTCAATCCGACCCACTACAACTTCAAGGGTATAGGATTGTATTGT-A-GTTTCATCTTGCTCTA
* * * * * *
22772 TTGCATCTTTGGGGAGAT-AAGATTTGCTTTTGTAGC-TCTATTA-GACCCACTATAACTTCAGG
64 -AGCAACTTTAGAGAGATAAAGATTTGCTTTTGTAGCTTC-AATACGACCCACTACAACTTCAGG
* *
22834 CATATAGGATTTGGTGTTGTAGCTTCATCTTGCTCTACAACAACTTCAGA-AAAAAAAGATTTGT
127 -ATATAGGATTTGATGTTGTAGCTTCATCTTGCTCTACTACAACTTCAGAGAAAAAAAGATTTG-
22898 TTTCGTAGCTTCAATCCGATCCACTGCAACTTCAGGGATATAAGATTTGATGTCGTAGCTTCATC
190 TTTCGTAGCTTCAATCCGATCCACTGCAACTTCAGGGATATAAGATTTGATGTCGTAGCTTCATC
* * * *
22963 TTACTCCAATGT-AACTT-TAGGGAGATAAATATTTTCTTTTGTAG
255 TTACT-C--TGTCAACTTATAGAG-GATAAAGATTTGCTTTCGTAG
* ** * *
23007 CTTTAATTTGACCCACTACAACTTCAAGGGTATAGGATTGTTTTGTAGCTTCATCTTGCTCTACA
1 CTTCAATCCGACCCACTACAACTTCAAGGGTATAGGATTGTATTGTAGTTTCATCTTGCTCTA-A
* * * *
23072 ACAACTTCAGAGAGATAAAGATTTGCTTTTGTAGCTTCAATACGACCCATTACAACTTCAAGGGT
65 GCAACTTTAGAGAGATAAAGATTTGCTTTTGTAGCTTCAATACGACCCACTACAACTTC-AGGAT
** * * * * * *
23137 ATAGGATTTGACT-TTGTATTTTCATCTTACTCTACTGCAACTTTAGAGATATAATGATTTGCTT
129 ATAGGATTTGA-TGTTGTAGCTTCATCTTGCTCTACTACAACTTCAGAGAAAAAAAGATTTG-TT
*
23201 TCGTAGCTTCAATTCGATCC-CTGCAACTTCTA-GGATATAAGATTTGATGT
192 TCGTAGCTTCAATCCGATCCACTGCAACTTC-AGGGATATAAGATTTGATGT
23251 TGTACTAATC
Statistics
Matches: 441, Mismatches: 80, Indels: 47
0.78 0.14 0.08
Matches are distributed among these distances:
298 28 0.06
299 74 0.17
300 217 0.49
301 59 0.13
302 29 0.07
303 32 0.07
304 2 0.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.36
Consensus pattern (296 bp):
CTTCAATCCGACCCACTACAACTTCAAGGGTATAGGATTGTATTGTAGTTTCATCTTGCTCTAAG
CAACTTTAGAGAGATAAAGATTTGCTTTTGTAGCTTCAATACGACCCACTACAACTTCAGGATAT
AGGATTTGATGTTGTAGCTTCATCTTGCTCTACTACAACTTCAGAGAAAAAAAGATTTGTTTCGT
AGCTTCAATCCGATCCACTGCAACTTCAGGGATATAAGATTTGATGTCGTAGCTTCATCTTACTC
TGTCAACTTATAGAGGATAAAGATTTGCTTTCGTAG
Found at i:23163 original size:200 final size:201
Alignment explanation
Indices: 22435--23254 Score: 724
Period size: 200 Copynumber: 4.1 Consensus size: 201
22425 ACTTTAGAGG
* * * * * *
22435 TATAGGATTTGGTGTGGTAGTTTCATCTTGCTCTA-ATGCAACTTTAGAGAGATAAAGAATTACT
1 TATAGGATTTGGTGTTGTAGCTTCATCTTGCTCTACA-ACAACTTCAGAGAGATAAAGATTTGCT
* * * * * * **
22499 TTCGTAGATTCAAGCTGATCCACTACAACTTC-AGGGATATAGGATTTGATGTCGTAGCTTCATC
65 TTTGTAGCTTCAATCCGATCCACTGCAACTTCAAGGG-TATAGGATTTGAT-TTGTATTTTCATC
* * * * * * * *** * * * *
22563 TTGCTCCACTACATCTTCAAGGAGAT-AAGATTTGCTTCAATGGCTTCAATCAGACCTACTACAA
128 TTACTCCAATGCAACTTTAGGGAGATAAATATTTGCTTTTGTAGCTTTAATTAGACCCACTACAA
* **
22627 CTTTAGGGG
193 CTTCAGGCA
* * * * *
22636 TATAAGATTTAAG-GTTGTAGCTTCATCTTGCTCTGTC-ACAACTTAATAGAGGATAAAGATTTG
1 TATAGGATTT-GGTGTTGTAGCTTCATCTTGCTCT-ACAACAACTTCAGAGA-GATAAAGATTTG
* * * *
22699 CTTTCGTAGCTTCAATCCGATCCAGTGCAACTTCAAGGATATAGGATTT-A-ATGTCATATTTCA
63 CTTTTGTAGCTTCAATCCGATCCACTGCAACTTCAAGGGTATAGGATTTGATTTGT-AT-TTTCA
* * * * * * *
22762 TCTTGCTCCATTGCATCTTTGGGGAGAT-AAGATTTGCTTTTGTAGCTCT-ATTAGACCCACTAT
126 TCTTACTCCAATGCAACTTTAGGGAGATAAATATTTGCTTTTGTAGCTTTAATTAGACCCACTAC
22825 AACTTCAGGCA
191 AACTTCAGGCA
* *
22836 TATAGGATTTGGTGTTGTAGCTTCATCTTGCTCTACAACAACTTCAGA-AAAAAAAGATTTG-TT
1 TATAGGATTTGGTGTTGTAGCTTCATCTTGCTCTACAACAACTTCAGAGAGATAAAGATTTGCTT
* * **
22899 TTCGTAGCTTCAATCCGATCCACTGCAACTTC-AGGGATATAAGATTTGATGTCGTAGCTTCATC
66 TT-GTAGCTTCAATCCGATCCACTGCAACTTCAAGGG-TATAGGATTTGAT-TTGTATTTTCATC
* * *
22963 TTACTCCAATGTAACTTTAGGGAGATAAATATTTTCTTTTGTAGCTTTAATTTGACCCACTACAA
128 TTACTCCAATGCAACTTTAGGGAGATAAATATTTGCTTTTGTAGCTTTAATTAGACCCACTACAA
*
23028 CTTCAAGG-G
193 CTTC-AGGCA
*
23037 TATAGGA-TT-GTTTTGTAGCTTCATCTTGCTCTACAACAACTTCAGAGAGATAAAGATTTGCTT
1 TATAGGATTTGGTGTTGTAGCTTCATCTTGCTCTACAACAACTTCAGAGAGATAAAGATTTGCTT
* * * *
23100 TTGTAGCTTCAATACGACCCATTACAACTTCAAGGGTATAGGATTTGACTTTGTATTTTCATCTT
66 TTGTAGCTTCAATCCGATCCACTGCAACTTCAAGGGTATAGGATTTGA-TTTGTATTTTCATCTT
* * * * * * *
23165 ACTCTACTGCAACTTTA--GAGATATAATGATTTGCTTTCGTAGCTTCAATTCGATCC-CTGCAA
130 ACTCCAATGCAACTTTAGGGAGATA-AAT-ATTTGCTTTTGTAGCTTTAATTAGACCCACTACAA
23227 CTTCTAGG-A
193 CTTC-AGGCA
* *
23236 TATAAGATTTGATGTTGTA
1 TATAGGATTTGGTGTTGTA
23255 CTAATCTCTT
Statistics
Matches: 506, Mismatches: 88, Indels: 50
0.79 0.14 0.08
Matches are distributed among these distances:
197 6 0.01
198 53 0.10
199 90 0.18
200 178 0.35
201 123 0.24
202 53 0.10
203 3 0.01
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (201 bp):
TATAGGATTTGGTGTTGTAGCTTCATCTTGCTCTACAACAACTTCAGAGAGATAAAGATTTGCTT
TTGTAGCTTCAATCCGATCCACTGCAACTTCAAGGGTATAGGATTTGATTTGTATTTTCATCTTA
CTCCAATGCAACTTTAGGGAGATAAATATTTGCTTTTGTAGCTTTAATTAGACCCACTACAACTT
CAGGCA
Found at i:25288 original size:44 final size:44
Alignment explanation
Indices: 25080--25294 Score: 306
Period size: 44 Copynumber: 4.9 Consensus size: 44
25070 GACTTGGTGA
* *
25080 TTATTAAATGGAAGACTTATGTCTCGAGTAGAGCATAAGATTGT
1 TTATGAAATGGAAGACTTATGTCTCGGGTAGAGCATAAGATTGT
25124 TTATGAAATGGAAGACTTATGTCTCGGGTAGAGCATAAGATTGT
1 TTATGAAATGGAAGACTTATGTCTCGGGTAGAGCATAAGATTGT
*
25168 TTATGAAATGGAATACTTATGTCTCGGGTAGAGCATAAGATTGT
1 TTATGAAATGGAAGACTTATGTCTCGGGTAGAGCATAAGATTGT
** ***
25212 TTATGAAATGGAAGACTTATGTCTCGACTAGAGCATAAGATAAA
1 TTATGAAATGGAAGACTTATGTCTCGGGTAGAGCATAAGATTGT
* * * *
25256 TTGT-AAATGGAAGAACTTATGACTCGGTTAGAGTATAAG
1 TTATGAAATGGAAG-ACTTATGTCTCGGGTAGAGCATAAG
25295 GTTAAATGCG
Statistics
Matches: 156, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
43 9 0.06
44 147 0.94
ACGTcount: A:0.35, C:0.09, G:0.24, T:0.32
Consensus pattern (44 bp):
TTATGAAATGGAAGACTTATGTCTCGGGTAGAGCATAAGATTGT
Found at i:30322 original size:20 final size:21
Alignment explanation
Indices: 30289--30327 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
30279 ACACGAAATT
30289 TGAAACAACAAAAA-TAAAAG
1 TGAAACAACAAAAAGTAAAAG
30309 TGAAACAA-ATAAAAGTAAA
1 TGAAACAACA-AAAAGTAAA
30328 TAAAAAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 1 0.06
20 12 0.71
21 4 0.24
ACGTcount: A:0.69, C:0.08, G:0.10, T:0.13
Consensus pattern (21 bp):
TGAAACAACAAAAAGTAAAAG
Found at i:36369 original size:12 final size:12
Alignment explanation
Indices: 36360--36385 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
36350 ATACCGACGT
36360 AGATGTCGACCC
1 AGATGTCGACCC
36372 AGATGTCGACCC
1 AGATGTCGACCC
36384 AG
1 AG
36386 CAATCGATCG
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:0.27, C:0.31, G:0.27, T:0.15
Consensus pattern (12 bp):
AGATGTCGACCC
Found at i:39029 original size:18 final size:17
Alignment explanation
Indices: 39008--39060 Score: 52
Period size: 18 Copynumber: 3.0 Consensus size: 17
38998 TTTTTAATAA
39008 TTTTTAAATTTTAAACTT
1 TTTTTAAATTTTAAA-TT
* ** *
39026 TTTTAAAAAATTATATT
1 TTTTTAAATTTTAAATT
39043 TTTTTAAAATTTTAAATT
1 TTTTT-AAATTTTAAATT
39061 ATAAAAAATT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
17 6 0.23
18 20 0.77
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTTTAAATTTTAAATT
Done.