Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015298.1 Kokia drynarioides strain JFW-HI SEQ_130343, 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: 570056
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 343 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:501100 original size:3 final size:3
Alignment explanation
Indices: 501092--501120 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
501082 ATGAAGATAC
501092 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
501121 AGATAGATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:501195 original size:3 final size:3
Alignment explanation
Indices: 501187--501220 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
501177 TCCCTATATT
501187 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
501221 GATAGATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:501259 original size:99 final size:99
Alignment explanation
Indices: 501092--501285 Score: 361
Period size: 99 Copynumber: 2.0 Consensus size: 99
501082 ATGAAGATAC
*
501092 AAGAAGAAGAAGAAGAAGAAGAAGAAGAAAGATAGATGTAACTGGGTTTATGTTTTGAATTATTG
1 AAGAAGAAGAAGAAGAAGAAGAAGAAGAAAGATAGATATAACTGGGTTTATGTTTTGAATTATTG
501157 TGGTTTTTATAGTATGATTTTCCCTATATTGAAG
66 TGGTTTTTATAGTATGATTTTCCCTATATTGAAG
*
501191 AAGAAGAAGAAGAAGAAGAAGAAGAAGAAGGATAGATATAACTGGGTTTATGTTTTGAATTATTG
1 AAGAAGAAGAAGAAGAAGAAGAAGAAGAAAGATAGATATAACTGGGTTTATGTTTTGAATTATTG
*
501256 TGGTTTTTATAGTATGATTTTGCCTATATT
66 TGGTTTTTATAGTATGATTTTCCCTATATT
501286 TTATCCTTTT
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
99 92 1.00
ACGTcount: A:0.38, C:0.04, G:0.24, T:0.34
Consensus pattern (99 bp):
AAGAAGAAGAAGAAGAAGAAGAAGAAGAAAGATAGATATAACTGGGTTTATGTTTTGAATTATTG
TGGTTTTTATAGTATGATTTTCCCTATATTGAAG
Found at i:507889 original size:25 final size:23
Alignment explanation
Indices: 507844--507889 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
507834 GTTCGGTCTG
* *
507844 TTATAAATTTATAGTACTTTATA
1 TTATAAATTTAAAGCACTTTATA
507867 TTATATAATTTAAAGCACATTTA
1 TTATA-AATTTAAAGCAC-TTTA
507890 AAAAATACAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
24 10 0.53
25 4 0.21
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (23 bp):
TTATAAATTTAAAGCACTTTATA
Found at i:516010 original size:18 final size:17
Alignment explanation
Indices: 515984--516017 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
515974 TACTTATAAC
515984 TTAAATTATTAATTTGTT
1 TTAAATTA-TAATTTGTT
*
516002 TTAATTTATAATTTGT
1 TTAAATTATAATTTGT
516018 AAATATAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (17 bp):
TTAAATTATAATTTGTT
Found at i:516838 original size:31 final size:31
Alignment explanation
Indices: 516797--516876 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 31
516787 TTTGTTTAGA
*
516797 TACCAAATTGAATATTAAAGCCAAACTT-AAG
1 TACCAAATTGAATATTAAAACCAAA-TTCAAG
* * *
516828 TATCAAATTGAACATTAAAATCAAATTCAAG
1 TACCAAATTGAATATTAAAACCAAATTCAAG
516859 TACCAAATT-ATATATTAA
1 TACCAAATTGA-ATATTAA
516877 CCCTCTTTGT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
30 3 0.07
31 38 0.93
ACGTcount: A:0.50, C:0.14, G:0.06, T:0.30
Consensus pattern (31 bp):
TACCAAATTGAATATTAAAACCAAATTCAAG
Found at i:517259 original size:8 final size:8
Alignment explanation
Indices: 517212--517266 Score: 51
Period size: 8 Copynumber: 6.8 Consensus size: 8
517202 GAGTAGAAAA
517212 TTTTCTTTC
1 TTTTC-TTC
517221 GTTTTCTTC
1 -TTTTCTTC
*
517230 -TCTCTTC
1 TTTTCTTC
517237 TCTTT-TTC
1 T-TTTCTTC
*
517245 CTTTCTTC
1 TTTTCTTC
517253 TTTTCTTC
1 TTTTCTTC
517261 TTTTCT
1 TTTTCT
517267 CCGTCGATTG
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
7 9 0.24
8 19 0.50
9 5 0.13
10 5 0.13
ACGTcount: A:0.00, C:0.27, G:0.02, T:0.71
Consensus pattern (8 bp):
TTTTCTTC
Found at i:526754 original size:22 final size:24
Alignment explanation
Indices: 526720--526768 Score: 68
Period size: 22 Copynumber: 2.1 Consensus size: 24
526710 AATTACAAGT
526720 ATGACAAAGTGAAAACAAAA-GAAA
1 ATGACAAAGTGAAAA-AAAAGGAAA
526744 ATGA-AAA-TGAAAAAAAAGGAAA
1 ATGACAAAGTGAAAAAAAAGGAAA
526766 ATG
1 ATG
526769 TTACTCACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.17
22 13 0.54
23 3 0.12
24 4 0.17
ACGTcount: A:0.67, C:0.04, G:0.18, T:0.10
Consensus pattern (24 bp):
ATGACAAAGTGAAAAAAAAGGAAA
Found at i:526760 original size:16 final size:17
Alignment explanation
Indices: 526736--526768 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
526726 AAGTGAAAAC
*
526736 AAAAGAAAATGAAAATG
1 AAAAGAAAAGGAAAATG
526753 AAAA-AAAAGGAAAATG
1 AAAAGAAAAGGAAAATG
526769 TTACTCACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.09
Consensus pattern (17 bp):
AAAAGAAAAGGAAAATG
Found at i:532410 original size:255 final size:256
Alignment explanation
Indices: 531873--532419 Score: 583
Period size: 255 Copynumber: 2.1 Consensus size: 256
531863 GGAATTTCGG
* * * * * *
531873 ATCTTATAAAATATAAAGGAAACCATTCTGTCATACAGGGGATGATATGCAGGCAGTGGTATCAC
1 ATCTTATAAAATATAAAGGAAACCTTTCTGTCATACAAGGGAGGATATGCAAGCAGTGGCATCAA
* * * * * * *
531938 ATACTACGATTAGCTATGAAATACTTCCGATTTTTGATAAATCAAACTACAATGTGATTCAAAGT
66 ACACTACGATAAGCTATGAAACACTTCCCATTTTCGATAAATCAAACTAAAATATGATTCAAAGT
* * * * * *
532003 CTAAACAATATAAAGGAAATCTTTCTTTCAGATGACGTATGATATGCAGGCAGCAGTATCAAACA
131 CTAAACAATAGAAAGGAAATCTTTCTTCCAGATAACGTAGGACATGCAGACAGCAGTATCAAACA
** * * * *
532068 GTATGATTAGCTATGAAACACTATTTGAATTTCGATAAATCTAACTGCAACATTATTCAAA
196 CCATGATTAGCTATGAAACACTATCTGAATTTCGACAAATCTAACTACAACATGATTCAAA
* * * * * * *
532129 ATC-TATGAAGTATAAAAGAGACCTTTCTGTCATATAATGGCGGATATGCAAGCAGTGGCATCAA
1 ATCTTATAAAATATAAAGGAAACCTTTCTGTCATACAAGGGAGGATATGCAAGCAGTGGCATCAA
* *
532193 ACACTATGATAAGCTATGAAACAC-TCCCATATTTCGATGAATCAAACTAAAATATGATTCGAAA
66 ACACTACGATAAGCTATGAAACACTTCCCAT-TTTCGATAAATCAAACTAAAATATGATTC-AAA
** *
532257 -TCTATAA-AATAGAAAGG-AATCTTTTCTGTCCTTA-AACGGT-GGACATGCAGACAG-ATTTA
129 GTCTA-AACAATAGAAAGGAAATC-TTTCT-TCCAGATAAC-GTAGGACATGCAGACAGCA-GTA
* * **
532316 TCGAACACCATGATTAGCTATGAAACAC-CTCTGAATTTCGACGCATC-AATCTACAACATGATT
189 TCAAACACCATGATTAGCTATGAAACACTATCTGAATTTCGACAAATCTAA-CTACAACATGATT
532379 CAAA
253 CAAA
532383 ATCTTATAAAATATAAAGGAAACCTTTCTGTCATACA
1 ATCTTATAAAATATAAAGGAAACCTTTCTGTCATACA
532420 GTTTCCAACA
Statistics
Matches: 236, Mismatches: 46, Indels: 19
0.78 0.15 0.06
Matches are distributed among these distances:
253 2 0.01
254 42 0.18
255 179 0.76
256 13 0.06
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (256 bp):
ATCTTATAAAATATAAAGGAAACCTTTCTGTCATACAAGGGAGGATATGCAAGCAGTGGCATCAA
ACACTACGATAAGCTATGAAACACTTCCCATTTTCGATAAATCAAACTAAAATATGATTCAAAGT
CTAAACAATAGAAAGGAAATCTTTCTTCCAGATAACGTAGGACATGCAGACAGCAGTATCAAACA
CCATGATTAGCTATGAAACACTATCTGAATTTCGACAAATCTAACTACAACATGATTCAAA
Found at i:533739 original size:75 final size:72
Alignment explanation
Indices: 533658--533804 Score: 240
Period size: 75 Copynumber: 2.0 Consensus size: 72
533648 TTATTTCAAG
* *
533658 AATTTAATCTTAGTTTTATGTCCACCAAATGAGTTTTTTTTTTTTTAAATTTCAAAAAATGTCAT
1 AATTTAATCTTAGTTTTATGTCCACCAAATGAG--GTTTTTTTTTT-AATTCCAAAAAATGTCAT
533723 ACTAACAAAT
63 ACTAACAAAT
*
533733 AATTTAATCTTAGTTTTATGTCTACCAAATGAGGTTTTTTTTTTAATTCCAAAAAATGTCATACT
1 AATTTAATCTTAGTTTTATGTCCACCAAATGAGGTTTTTTTTTTAATTCCAAAAAATGTCATACT
533798 AACAAAT
66 AACAAAT
533805 TTAATAGAAG
Statistics
Matches: 69, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
72 27 0.39
73 10 0.14
75 32 0.46
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.44
Consensus pattern (72 bp):
AATTTAATCTTAGTTTTATGTCCACCAAATGAGGTTTTTTTTTTAATTCCAAAAAATGTCATACT
AACAAAT
Found at i:536451 original size:34 final size:34
Alignment explanation
Indices: 536389--536459 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 34
536379 CTTGATCCTC
* *
536389 AAACACATAAATAAATATAAATATAATTATATTT
1 AAACACATAAATAAATATAAATAAAATTATATGT
* * **
536423 AAACACATAATTAAATCTTGATAAAATTATATGT
1 AAACACATAAATAAATATAAATAAAATTATATGT
536457 AAA
1 AAA
536460 TTTATGATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.56, C:0.07, G:0.03, T:0.34
Consensus pattern (34 bp):
AAACACATAAATAAATATAAATAAAATTATATGT
Found at i:536897 original size:36 final size:36
Alignment explanation
Indices: 536851--536932 Score: 110
Period size: 36 Copynumber: 2.3 Consensus size: 36
536841 AGATACATAT
*
536851 ATTTTTATAATATGTAATTTCTTTTATATTTTAAAA
1 ATTTTTATAATATGTAATTTCTTTTAAATTTTAAAA
* * * * *
536887 ATTTATATAATTTTTATTTTCTTTTAAATTTTAAAT
1 ATTTTTATAATATGTAATTTCTTTTAAATTTTAAAA
536923 ATTTTTATAA
1 ATTTTTATAA
536933 AAAACAAATT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.61
Consensus pattern (36 bp):
ATTTTTATAATATGTAATTTCTTTTAAATTTTAAAA
Found at i:546640 original size:13 final size:13
Alignment explanation
Indices: 546622--546652 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
546612 ACTCATTCTC
546622 ACTTTCCCCCAAA
1 ACTTTCCCCCAAA
546635 ACTTTCCCCCAAA
1 ACTTTCCCCCAAA
546648 ACTTT
1 ACTTT
546653 TACCCCCTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.29, C:0.42, G:0.00, T:0.29
Consensus pattern (13 bp):
ACTTTCCCCCAAA
Found at i:547149 original size:18 final size:18
Alignment explanation
Indices: 547103--547149 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
547093 CACATTTTGT
547103 AATATTTATA-T-TATTG
1 AATATTTATATTATATTG
*
547119 AAT-TTTTTAATTATATTG
1 AATATTTAT-ATTATATTG
547137 AATATTTATATTA
1 AATATTTATATTA
547150 AAATTGAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 4 0.16
16 4 0.16
17 1 0.04
18 12 0.48
19 4 0.16
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.57
Consensus pattern (18 bp):
AATATTTATATTATATTG
Found at i:549655 original size:38 final size:40
Alignment explanation
Indices: 549560--549663 Score: 124
Period size: 42 Copynumber: 2.6 Consensus size: 40
549550 GAAAATGACA
* *
549560 AGTTTAATCATAAAAAGTCA-AGATTGAAATAGCAACTCACTT
1 AGTTTAATCATAAAAAGTCAGA-ATTAAAATAACAACT-AC-T
* *
549602 AATTTAATCATAAAAAGTTAGAATTAAAATAACAACT-C-
1 AGTTTAATCATAAAAAGTCAGAATTAAAATAACAACTACT
549640 AGTTTAATCATAAAAAGTCAGAAT
1 AGTTTAATCATAAAAAGTCAGAAT
549664 CTCACCTCAA
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
38 22 0.40
40 1 0.02
42 31 0.56
43 1 0.02
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.29
Consensus pattern (40 bp):
AGTTTAATCATAAAAAGTCAGAATTAAAATAACAACTACT
Found at i:549660 original size:19 final size:20
Alignment explanation
Indices: 549603--549661 Score: 59
Period size: 19 Copynumber: 3.0 Consensus size: 20
549593 AACTCACTTA
*
549603 ATTTAATCATAAAAAGTTAG
1 ATTTAATCATAAAAAGTCAG
* * * *
549623 AATTAA-AATAACAACTCAG
1 ATTTAATCATAAAAAGTCAG
549642 -TTTAATCATAAAAAGTCAG
1 ATTTAATCATAAAAAGTCAG
549661 A
1 A
549662 ATCTCACCTC
Statistics
Matches: 28, Mismatches: 9, Indels: 4
0.68 0.22 0.10
Matches are distributed among these distances:
18 4 0.14
19 19 0.68
20 5 0.18
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.29
Consensus pattern (20 bp):
ATTTAATCATAAAAAGTCAG
Found at i:562455 original size:35 final size:36
Alignment explanation
Indices: 562406--562483 Score: 95
Period size: 35 Copynumber: 2.2 Consensus size: 36
562396 TTTTTTACAT
* * **
562406 CGTCTTAAGTCAACCTTAAAAAGGTTGGGATAGACC
1 CGTCTAAAGTCAACCTTAAAAAGATTAAGATAGACC
*
562442 CGTCTAAAG-CAACCTTACAAAGATTAAGATAGACC
1 CGTCTAAAGTCAACCTTAAAAAGATTAAGATAGACC
*
562477 CATCTAA
1 CGTCTAA
562484 GGTTGGGATA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
35 28 0.78
36 8 0.22
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23
Consensus pattern (36 bp):
CGTCTAAAGTCAACCTTAAAAAGATTAAGATAGACC
Found at i:563049 original size:13 final size:14
Alignment explanation
Indices: 563031--563063 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
563021 TGAACCTCAA
563031 GGTTTAGGCTTT-G
1 GGTTTAGGCTTTGG
*
563044 GGTTTAGGGTTTGG
1 GGTTTAGGCTTTGG
563058 GGTTTA
1 GGTTTA
563064 ATGTTTATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.09, C:0.03, G:0.42, T:0.45
Consensus pattern (14 bp):
GGTTTAGGCTTTGG
Found at i:563070 original size:21 final size:21
Alignment explanation
Indices: 563045--563090 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
563035 TAGGCTTTGG
*
563045 GTTTAGGGTTTGGGGTTT-AAT
1 GTTTA-GGTTTAGGGTTTAAAT
*
563066 GTTTATGTTTAGGGTTTAAAT
1 GTTTAGGTTTAGGGTTTAAAT
563087 GTTT
1 GTTT
563091 GCAGTTATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.17, C:0.00, G:0.30, T:0.52
Consensus pattern (21 bp):
GTTTAGGTTTAGGGTTTAAAT
Found at i:563080 original size:20 final size:21
Alignment explanation
Indices: 563052--563090 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
563042 TGGGTTTAGG
*
563052 GTTTGGGGTTT-AATGTTTAT
1 GTTTAGGGTTTAAATGTTTAT
563072 GTTTAGGGTTTAAATGTTT
1 GTTTAGGGTTTAAATGTTT
563091 GCAGTTATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.18, C:0.00, G:0.28, T:0.54
Consensus pattern (21 bp):
GTTTAGGGTTTAAATGTTTAT
Found at i:563662 original size:126 final size:124
Alignment explanation
Indices: 563388--563703 Score: 330
Period size: 126 Copynumber: 2.5 Consensus size: 124
563378 TTCCAACTCT
* * * **
563388 TATACAAAGAGTTGGCCAAAGCATATGTCGGCAAATCTATCCCATCAAGTGTCGACCCAAAAGTG
1 TATACAAAGAGTTGGCCAAAGCATATGTCAGCAAATCTATCCCAAC-ACT-T--A--GGAAAGTG
* * * * * * * *
563453 TCGGCATAGTGTTGGACAATTGACTCTTGTTTAAGCATTGCCTTAGGCATACATATCCTAACCCT
60 TCGGCATAGTGTTAGACAATAGACTCTTATTTAAACATTCCCTTAGACATACATATCCCAACCCC
* * *
563518 TATAAAAAGAGTTGGCCAAAGCATATGTCAGCAACTCTATCCCAACACTTAGGAAATTGTCGGCA
1 TATACAAAGAGTTGGCCAAAGCATATGTCAGCAAATCTATCCCAACACTTAGGAAAGTGTCGGCA
* *
563583 TAGTGTTAGACAA-AGCCAACTCTTATTTAAACGTTCCCTTAGACATGCATATCCCAACCCC
66 TAGTGTTAGACAATAG---ACTCTTATTTAAACATTCCCTTAGACATACATATCCCAACCCC
* * * *
563644 TATACAAAGTGTTGGCCAAAGCGTATG-CTGACAAGTCTATCCCAACACTTAGGAAAGTGT
1 TATACAAAGAGTTGGCCAAAGCATATGTCAG-CAAATCTATCCCAACACTTAGGAAAGTGT
563704 TGCCCAAAAG
Statistics
Matches: 158, Mismatches: 24, Indels: 12
0.81 0.12 0.06
Matches are distributed among these distances:
123 1 0.01
124 23 0.15
125 2 0.01
126 87 0.55
128 1 0.01
129 2 0.01
130 42 0.27
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.26
Consensus pattern (124 bp):
TATACAAAGAGTTGGCCAAAGCATATGTCAGCAAATCTATCCCAACACTTAGGAAAGTGTCGGCA
TAGTGTTAGACAATAGACTCTTATTTAAACATTCCCTTAGACATACATATCCCAACCCC
Found at i:563895 original size:141 final size:139
Alignment explanation
Indices: 563575--563997 Score: 451
Period size: 139 Copynumber: 3.0 Consensus size: 139
563565 CTTAGGAAAT
* * *
563575 TGTCGGCATAGTGTTAGACAAAGCCAACTCTTATTTAAACGTTCCCTTAGACATGCATATCCCAA
1 TGTCGGCATAGTGTTGGACAAAGCCAACTCTTATTTAAGCGTTTCCTTAGACATGCATATCCCAA
* ** * * *
563640 CCCCTATACAAAGTGTTGGCCAAAGCGTATGCTGACAAGTCTATCCCAACACTTAGGAAAGTGTT
66 CCCCTATACAAAGAGTTAACAAAAGCGCATGCTGACAAGTCTATCCCAACACTTAGGAAAGTGTC
563705 GCCCAAAAG
131 GCCCAAAAG
* * * *
563714 TGTCGCCATAGTGTTGGAAAAAGCTAACTCTTATTTAAGCGTTTCCTTAGGCATGCATATCCCAA
1 TGTCGGCATAGTGTTGGACAAAGCCAACTCTTATTTAAGCGTTTCCTTAGACATGCATATCCCAA
* * *
563779 CCCTTTTATA-AAAGAGTTAACAAAAGCGCATG-TCGGCAAGTCTATTCCAACACTTAGGAAAGT
66 CCC--CTATACAAAGAGTTAACAAAAGCGCATGCT-GACAAGTCTATCCCAACACTTAGGAAAGT
*
563842 GTCGCCCCAAAGG
128 GTCG-CCCAAAAG
* * * * *
563855 TGTTGGCAAAGTGTTGGACAAAGCCAACTCTTATTCAAGCGTGT-CTTAGACATGCATATCTCAA
1 TGTCGGCATAGTGTTGGACAAAGCCAACTCTTATTTAAGCGTTTCCTTAGACATGCATATCCCAA
** ** ** ** * * *
563919 CCGTTATACAAAGAGTTGGCCAAAA-CATATATTGGCAAGTCTATCCCAACACCT-GGAAAATTG
66 CCCCTATACAAAGAGTT-AACAAAAGCGCATGCTGACAAGTCTATCCCAACACTTAGG-AAAGTG
563982 TCGCCGCAAAAG
129 TCGCC-CAAAAG
563994 TGTC
1 TGTC
563998 ATATTAGGAC
Statistics
Matches: 238, Mismatches: 37, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
138 9 0.04
139 108 0.45
140 73 0.31
141 48 0.20
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (139 bp):
TGTCGGCATAGTGTTGGACAAAGCCAACTCTTATTTAAGCGTTTCCTTAGACATGCATATCCCAA
CCCCTATACAAAGAGTTAACAAAAGCGCATGCTGACAAGTCTATCCCAACACTTAGGAAAGTGTC
GCCCAAAAG
Done.