Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015380.1 Kokia drynarioides strain JFW-HI SEQ_130427, 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: 614474
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Warning! 461 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:451353 original size:21 final size:22
Alignment explanation
Indices: 451320--451363 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 22
451310 AAAAAAATAT
451320 AAAATTACAAAAA-TATTTAAAA
1 AAAATTACAAAAATTA-TTAAAA
451342 AAAATTAC-AAAATTATTAAAA
1 AAAATTACAAAAATTATTAAAA
451363 A
1 A
451364 TAGAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (22 bp):
AAAATTACAAAAATTATTAAAA
Found at i:453423 original size:18 final size:17
Alignment explanation
Indices: 453381--453429 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
453371 TTATAAATTC
453381 TACTTTTTTTTCCTTAT
1 TACTTTTTTTTCCTTAT
*
453398 TACATTTTTATTCTCTTAT
1 TAC-TTTTTTTTC-CTTAT
453417 T-C-TTTTTTTCCTT
1 TACTTTTTTTTCCTT
453430 CTTAAAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
15 3 0.11
16 7 0.25
17 3 0.11
18 9 0.32
19 6 0.21
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.69
Consensus pattern (17 bp):
TACTTTTTTTTCCTTAT
Found at i:468683 original size:30 final size:30
Alignment explanation
Indices: 468620--468686 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
468610 TATTATTTAT
*
468620 ATTTTTATAATTTTTAAAAATTTAAATTAA
1 ATTTTTATAATTTTTAAAAATTAAAATTAA
* **
468650 ATTTTTATCATTTTTAAAGGTTAAAATGTAA
1 ATTTTTATAATTTTTAAAAATTAAAAT-TAA
*
468681 TTTTTT
1 ATTTTT
468687 TTATTAATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
30 23 0.74
31 8 0.26
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.55
Consensus pattern (30 bp):
ATTTTTATAATTTTTAAAAATTAAAATTAA
Found at i:470407 original size:18 final size:18
Alignment explanation
Indices: 470378--470419 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
470368 TTAAATTAAC
470378 ATTT-AAAAAAT-ATTTA
1 ATTTAAAAAAATAATTTA
470394 ATTTAAAAATAATAATTTA
1 ATTTAAAAA-AATAATTTA
470413 A-TTAAAA
1 ATTTAAAA
470420 TTATGATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 4 0.17
17 4 0.17
18 9 0.39
19 6 0.26
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATTTAAAAAAATAATTTA
Found at i:470902 original size:17 final size:15
Alignment explanation
Indices: 470880--470926 Score: 60
Period size: 17 Copynumber: 3.1 Consensus size: 15
470870 TTTTATGAAC
470880 TTTTTTAAATTTGTTGA
1 TTTTTTAAATTT-TT-A
470897 TTTTTTAAATTTTTA
1 TTTTTTAAATTTTTA
*
470912 TTTTTT-TATTTTTA
1 TTTTTTAAATTTTTA
470926 T
1 T
470927 GTATGATACG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 8 0.28
15 7 0.24
16 2 0.07
17 12 0.41
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.74
Consensus pattern (15 bp):
TTTTTTAAATTTTTA
Found at i:474637 original size:137 final size:137
Alignment explanation
Indices: 474434--474708 Score: 410
Period size: 137 Copynumber: 2.0 Consensus size: 137
474424 TTTCAGAAAA
* * *
474434 TGGCATGTCTTTCATATTGCACTTTCATGTGAACTTGTTATACATGATATTGTTAAATTACTTTT
1 TGGCATATCTTTCATATTGCACTTTCACGTGAACTTATTATACATGATATTGTTAAATTACTTTT
* * * *
474499 GTAGTTAGTGTTATATCCATCTTTTG-TTATTGTTATTTTGAATGTAACACATGCCATAAATGAT
66 GTAGCTAATGTTATATCCATATTTTGTTTATCGTTATTTTGAATGTAACACATGCCATAAATGAT
474563 TTCATTT
131 TTCATTT
474570 TGGCATATCTTTCATATCT-CACTTTCACGTGAACTTATTACTACATGATATTGTTAAATTACTT
1 TGGCATATCTTTCATAT-TGCACTTTCACGTGAACTTATTA-TACATGATATTGTTAAATTACTT
* * ** *
474634 TTGTAGCTAATGTTATATCCATATTTTGTTTATCGTTGTTTTGAATGTAACGCATTTCATAATTG
64 TTGTAGCTAATGTTATATCCATATTTTGTTTATCGTTATTTTGAATGTAACACATGCCATAAATG
474699 ATTTCATTT
129 ATTTCATTT
474708 T
1 T
474709 TTAGCTGTTT
Statistics
Matches: 124, Mismatches: 12, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
136 35 0.28
137 49 0.40
138 40 0.32
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.48
Consensus pattern (137 bp):
TGGCATATCTTTCATATTGCACTTTCACGTGAACTTATTATACATGATATTGTTAAATTACTTTT
GTAGCTAATGTTATATCCATATTTTGTTTATCGTTATTTTGAATGTAACACATGCCATAAATGAT
TTCATTT
Found at i:475647 original size:31 final size:31
Alignment explanation
Indices: 475612--475676 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
475602 GAGAAACCAA
475612 ATCAATCACGATGAAAGTATAAAATTGTGTG
1 ATCAATCACGATGAAAGTATAAAATTGTGTG
475643 ATCAATCACGATGAAAGTATAAAATTGTGTG
1 ATCAATCACGATGAAAGTATAAAATTGTGTG
475674 ATC
1 ATC
475677 TGTACTGGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.42, C:0.11, G:0.18, T:0.29
Consensus pattern (31 bp):
ATCAATCACGATGAAAGTATAAAATTGTGTG
Found at i:479084 original size:50 final size:50
Alignment explanation
Indices: 479027--479124 Score: 178
Period size: 50 Copynumber: 2.0 Consensus size: 50
479017 CTCAACAAGG
479027 TGGACTGGATACATGTGGATTATTTTAATTGTTTTTGCAGATGCTAATGT
1 TGGACTGGATACATGTGGATTATTTTAATTGTTTTTGCAGATGCTAATGT
* *
479077 TGGACTGGATATATGTGGATTTTTTTAATTGTTTTTGCAGATGCTAAT
1 TGGACTGGATACATGTGGATTATTTTAATTGTTTTTGCAGATGCTAAT
479125 ATTGAGCTGG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.23, C:0.07, G:0.23, T:0.46
Consensus pattern (50 bp):
TGGACTGGATACATGTGGATTATTTTAATTGTTTTTGCAGATGCTAATGT
Found at i:496698 original size:6 final size:6
Alignment explanation
Indices: 496687--496721 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
496677 GTACACCCTC
*
496687 AAAAAT AAAAAT AAAATT AAAAAT AAAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
496722 GAGCCAGGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:500388 original size:51 final size:52
Alignment explanation
Indices: 500312--500414 Score: 190
Period size: 52 Copynumber: 2.0 Consensus size: 52
500302 AATCAAGTCA
500312 AACAAGTAATTCAGTTTTG-GTTTTTTTTTTTATAGTGTAATTCGGTTCCGG
1 AACAAGTAATTCAGTTTTGTGTTTTTTTTTTTATAGTGTAATTCGGTTCCGG
*
500363 AACAAGTAATTCAGTTTTGTTTTTTTTTTTTTATAGTGTAATTCGGTTCCGG
1 AACAAGTAATTCAGTTTTGTGTTTTTTTTTTTATAGTGTAATTCGGTTCCGG
500415 TTAAATAATG
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
51 19 0.38
52 31 0.62
ACGTcount: A:0.21, C:0.10, G:0.18, T:0.50
Consensus pattern (52 bp):
AACAAGTAATTCAGTTTTGTGTTTTTTTTTTTATAGTGTAATTCGGTTCCGG
Found at i:501077 original size:41 final size:40
Alignment explanation
Indices: 500998--501075 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 40
500988 CCAGAAAACA
*
500998 TAAAATAAAAATAATATTATCTAATTAAAGTTGCAAAATC
1 TAAAATAAAAATAATATTATCTAAATAAAGTTGCAAAATC
* *
501038 TAAATATAAAGATAATTTTATCTAAATAAAGTT-CAAAA
1 TAAA-ATAAAAATAATATTATCTAAATAAAGTTGCAAAA
501076 ATTTAAAGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 9 0.26
41 25 0.74
ACGTcount: A:0.55, C:0.06, G:0.05, T:0.33
Consensus pattern (40 bp):
TAAAATAAAAATAATATTATCTAAATAAAGTTGCAAAATC
Found at i:501491 original size:13 final size:14
Alignment explanation
Indices: 501473--501506 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
501463 GGATTTAAGC
501473 TAATTTAAATATT-
1 TAATTTAAATATTA
*
501486 TAATTTAATTATTA
1 TAATTTAAATATTA
501500 TAATTTA
1 TAATTTA
501507 TAAAAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TAATTTAAATATTA
Found at i:502459 original size:29 final size:28
Alignment explanation
Indices: 502423--502477 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
502413 TTTTTATAAA
*
502423 TTTAGAATTTAAT-TATTGTGTTTTTATT
1 TTTAGAATTTAATCTA-TCTGTTTTTATT
502451 TTTAGGAATTTAATCTATCTGTTTTTA
1 TTTA-GAATTTAATCTATCTGTTTTTA
502478 ATATTTCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 4 0.17
29 18 0.75
30 2 0.08
ACGTcount: A:0.25, C:0.04, G:0.11, T:0.60
Consensus pattern (28 bp):
TTTAGAATTTAATCTATCTGTTTTTATT
Found at i:509783 original size:218 final size:217
Alignment explanation
Indices: 509405--509842 Score: 867
Period size: 218 Copynumber: 2.0 Consensus size: 217
509395 AGGTTATATC
509405 TCTCCCTATTTTGTTACTGATCAAAAGACCCAGAAATGTGTAAGTTCAGATTTGCATTCTTTTTA
1 TCTCCCTATTTTGTTACTGATCAAAAGACCCAGAAATGTGTAAGTTCAGATTTGCATTCTTTTTA
509470 CAATAATTTTTACTCAATATGGTAGGGTACTTGTTTGTTGAACAAAAATGGGGTTTCCAATGTAA
66 CAATAATTTTTACTCAATATGGTAGGGTACTTGTTTGTTGAACAAAAATGGGGTTTCCAATGTAA
509535 ATCCTATGCACAAAATTCATTTTTTCTCTTATTTAAATGTTTTCAATTTGGAGGGGTTCACAGTG
131 ATCCTATGCACAAAATTCATTTTTTCTCTTATTTAAATGTTTTCAATTTGGA-GGGTTCACAGTG
509600 AATTCATGTCATTCTCTTATTTT
195 AATTCATGTCATTCTCTTATTTT
509623 TCTCCCTATTTTGTTACTGATCAAAAGACCCAGAAATGTGTAAGTTCAGATTTGCATTCTTTTTA
1 TCTCCCTATTTTGTTACTGATCAAAAGACCCAGAAATGTGTAAGTTCAGATTTGCATTCTTTTTA
509688 CAATAATTTTTACTCAATATGGTAGGGTACTTGTTTGTTGAACAAAAATGGGGTTTCCAATGTAA
66 CAATAATTTTTACTCAATATGGTAGGGTACTTGTTTGTTGAACAAAAATGGGGTTTCCAATGTAA
509753 ATCCTATGCACAAAATTCATTTTTTCTCTTATTTAAATGTTTTCAATTTGGAGGGTTCACAGTGA
131 ATCCTATGCACAAAATTCATTTTTTCTCTTATTTAAATGTTTTCAATTTGGAGGGTTCACAGTGA
509818 ATTCATGTCATTCTCTTATTTT
196 ATTCATGTCATTCTCTTATTTT
509840 TCT
1 TCT
509843 TAATGTAATT
Statistics
Matches: 220, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
217 38 0.17
218 182 0.83
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (217 bp):
TCTCCCTATTTTGTTACTGATCAAAAGACCCAGAAATGTGTAAGTTCAGATTTGCATTCTTTTTA
CAATAATTTTTACTCAATATGGTAGGGTACTTGTTTGTTGAACAAAAATGGGGTTTCCAATGTAA
ATCCTATGCACAAAATTCATTTTTTCTCTTATTTAAATGTTTTCAATTTGGAGGGTTCACAGTGA
ATTCATGTCATTCTCTTATTTT
Found at i:515879 original size:15 final size:15
Alignment explanation
Indices: 515868--515913 Score: 74
Period size: 15 Copynumber: 3.1 Consensus size: 15
515858 TCTGCTGCAC
*
515868 TTGCTGCTGCTGTTG
1 TTGCTGCTGCTGCTG
*
515883 TTGCTGCTGCTGTTG
1 TTGCTGCTGCTGCTG
515898 TTGCTGCTGCTGCTG
1 TTGCTGCTGCTGCTG
515913 T
1 T
515914 AACATACGCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.00, C:0.22, G:0.33, T:0.46
Consensus pattern (15 bp):
TTGCTGCTGCTGCTG
Found at i:515890 original size:18 final size:18
Alignment explanation
Indices: 515869--515913 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
515859 CTGCTGCACT
* *
515869 TGCTGCTGCTGTTGTTGC
1 TGCTGCTGTTGTTGCTGC
515887 TGCTGCTGTTGTTGCTGC
1 TGCTGCTGTTGTTGCTGC
515905 TGCTGCTGT
1 TGCTGCTGT
515914 AACATACGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.00, C:0.22, G:0.33, T:0.44
Consensus pattern (18 bp):
TGCTGCTGTTGTTGCTGC
Found at i:515932 original size:3 final size:3
Alignment explanation
Indices: 515869--515912 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
515859 CTGCTGCACT
* * * *
515869 TGC TGC TGC TGT TGT TGC TGC TGC TGT TGT TGC TGC TGC TGC TG
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
515913 TAACATACGC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.00, C:0.23, G:0.34, T:0.43
Consensus pattern (3 bp):
TGC
Found at i:517801 original size:27 final size:27
Alignment explanation
Indices: 517763--517817 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
517753 GTCGAAACAG
517763 GAGCAAAAAGATGGATCTAAGCAACCT
1 GAGCAAAAAGATGGATCTAAGCAACCT
517790 GAGCAAAAAGATGGATCTAAGCAACCT
1 GAGCAAAAAGATGGATCTAAGCAACCT
517817 G
1 G
517818 CAAAATGATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (27 bp):
GAGCAAAAAGATGGATCTAAGCAACCT
Found at i:520106 original size:26 final size:26
Alignment explanation
Indices: 520070--520120 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
520060 AAATTTTTAA
*
520070 GAATCATTTGTCAACAGATATCAAAT
1 GAATCATTTGTCAACAGAGATCAAAT
*
520096 GAATTATTTGTCAACAGAGATCAAA
1 GAATCATTTGTCAACAGAGATCAAA
520121 ATTCTTTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (26 bp):
GAATCATTTGTCAACAGAGATCAAAT
Found at i:521253 original size:23 final size:23
Alignment explanation
Indices: 521238--521366 Score: 88
Period size: 23 Copynumber: 5.6 Consensus size: 23
521228 TTAATGTTCA
521238 CGAACATGTTCATTTAACTTAAT
1 CGAACATGTTCATTTAACTTAAT
**
521261 CGAACATGTTCA-CGAACATTAAT
1 CGAACATGTTCATTTAAC-TTAAT
* **
521284 CGAACATTTTCA-CGAACATTAAT
1 CGAACATGTTCATTTAAC-TTAAT
**
521307 CGAACATGTTCA-CGAACATTAAAT
1 CGAACATGTTCATTTAAC-TT-AAT
*
521331 -GAACATGTTCA-TGAACATATAAT
1 CGAACATGTTCATTTAAC-T-TAAT
*
521354 TGAACATGTTCAT
1 CGAACATGTTCAT
521367 GAATAATAAA
Statistics
Matches: 96, Mismatches: 5, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
22 3 0.03
23 78 0.81
24 15 0.16
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.31
Consensus pattern (23 bp):
CGAACATGTTCATTTAACTTAAT
Found at i:521278 original size:12 final size:11
Alignment explanation
Indices: 521261--521326 Score: 55
Period size: 12 Copynumber: 5.7 Consensus size: 11
521251 TTAACTTAAT
521261 CGAACATGTTCA
1 CGAACAT-TTCA
*
521273 CGAACA-TTAA
1 CGAACATTTCA
521283 TCGAACATTTTCA
1 -CGAACA-TTTCA
*
521296 CGAACA-TTAA
1 CGAACATTTCA
521306 TCGAACATGTTCA
1 -CGAACAT-TTCA
521319 CGAACATT
1 CGAACATT
521327 AAATGAACAT
Statistics
Matches: 44, Mismatches: 4, Indels: 13
0.72 0.07 0.21
Matches are distributed among these distances:
10 6 0.14
11 13 0.30
12 19 0.43
13 6 0.14
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (11 bp):
CGAACATTTCA
Found at i:521290 original size:46 final size:47
Alignment explanation
Indices: 521238--521365 Score: 181
Period size: 46 Copynumber: 2.7 Consensus size: 47
521228 TTAATGTTCA
*
521238 CGAACATGTTCATTTAAC-TTAATCGAACATGTTCACGAACATT-AAT
1 CGAACATGTTCA-TGAACATTAATCGAACATGTTCACGAACATTAAAT
* *
521284 CGAACATTTTCACGAACATTAATCGAACATGTTCACGAACATTAAAT
1 CGAACATGTTCATGAACATTAATCGAACATGTTCACGAACATTAAAT
*
521331 -GAACATGTTCATGAACATATAATTGAACATGTTCA
1 CGAACATGTTCATGAACAT-TAATCGAACATGTTCA
521366 TGAATAATAA
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
45 3 0.04
46 52 0.71
47 18 0.25
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.30
Consensus pattern (47 bp):
CGAACATGTTCATGAACATTAATCGAACATGTTCACGAACATTAAAT
Found at i:521382 original size:23 final size:23
Alignment explanation
Indices: 521262--521376 Score: 108
Period size: 23 Copynumber: 5.0 Consensus size: 23
521252 TAACTTAATC
* *
521262 GAACATGTTCACGAAC-ATTAAT
1 GAACATGTTCATGAACAATAAAT
* * *
521284 CGAACATTTTCACGAAC-ATTAAT
1 -GAACATGTTCATGAACAATAAAT
* *
521307 CGAACATGTTCACGAACATTAAAT
1 -GAACATGTTCATGAACAATAAAT
*
521331 GAACATGTTCATGAACATATAATT
1 GAACATGTTCATGAACA-ATAAAT
*
521355 GAACATGTTCATGAATAATAAA
1 GAACATGTTCATGAACAATAAA
521377 CAAACAAACA
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
23 57 0.70
24 24 0.30
ACGTcount: A:0.43, C:0.17, G:0.12, T:0.29
Consensus pattern (23 bp):
GAACATGTTCATGAACAATAAAT
Found at i:531021 original size:13 final size:14
Alignment explanation
Indices: 530998--531028 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
530988 ATTGTGGTGT
530998 TTTTGTATTTTTTA
1 TTTTGTATTTTTTA
531012 TTTT-TATTTTTTA
1 TTTTGTATTTTTTA
531025 TTTT
1 TTTT
531029 CATACAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.84
Consensus pattern (14 bp):
TTTTGTATTTTTTA
Found at i:536177 original size:2 final size:2
Alignment explanation
Indices: 536170--536198 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
536160 CAATGTTCAT
536170 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
536199 AGGGTGTGAA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:537272 original size:8 final size:8
Alignment explanation
Indices: 537259--537287 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
537249 TTTACAAACC
537259 AAAAAAGA
1 AAAAAAGA
537267 AAAAAA-A
1 AAAAAAGA
537274 AAAAAAGA
1 AAAAAAGA
537282 AAAAAA
1 AAAAAA
537288 AATCCAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:537297 original size:16 final size:15
Alignment explanation
Indices: 537259--537289 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
537249 TTTACAAACC
537259 AAAAAAGAAAAAAAA
1 AAAAAAGAAAAAAAA
537274 AAAAAAGAAAAAAAA
1 AAAAAAGAAAAAAAA
537289 A
1 A
537290 TCCAAAGACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAAAAAA
Found at i:540899 original size:12 final size:12
Alignment explanation
Indices: 540869--540893 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
540859 GTTGTAATTT
540869 AGCTAAGCTGTG
1 AGCTAAGCTGTG
540881 AGCTAAGCTGTG
1 AGCTAAGCTGTG
540893 A
1 A
540894 AGTAAGTAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.16, G:0.32, T:0.24
Consensus pattern (12 bp):
AGCTAAGCTGTG
Found at i:549713 original size:3 final size:3
Alignment explanation
Indices: 549705--549730 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
549695 TAACATTTAA
549705 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
549731 ACTGTCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:558013 original size:3 final size:3
Alignment explanation
Indices: 558005--558036 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
557995 TTATTAACCC
558005 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
558037 AAATGGGTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:571655 original size:19 final size:20
Alignment explanation
Indices: 571618--571655 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
571608 AAAATTTAAA
**
571618 TTAAATATATAAATTATATT
1 TTAAATATATAAAAAATATT
571638 TTAAATA-ATAAAAAATAT
1 TTAAATATATAAAAAATAT
571656 AAGCACTACA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 9 0.56
20 7 0.44
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TTAAATATATAAAAAATATT
Found at i:580185 original size:2 final size:2
Alignment explanation
Indices: 580180--580208 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
580170 GTTTATCTGT
580180 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
580209 GGGGTTTGCG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:594733 original size:2 final size:2
Alignment explanation
Indices: 594728--594758 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
594718 ATATATGATA
*
594728 TG TG TG TG TG TG TG TG TG TG TG TG CG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
594759 TCATGATGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.03, G:0.48, T:0.48
Consensus pattern (2 bp):
TG
Found at i:599709 original size:5 final size:5
Alignment explanation
Indices: 599699--599725 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
599689 CACATTAAAT
599699 TTTGA TTTGA TTTGA TTTGA TTTGA TT
1 TTTGA TTTGA TTTGA TTTGA TTTGA TT
599726 CAATCCTCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.63
Consensus pattern (5 bp):
TTTGA
Found at i:600947 original size:86 final size:86
Alignment explanation
Indices: 600802--600973 Score: 308
Period size: 86 Copynumber: 2.0 Consensus size: 86
600792 TAAGTAGGTT
* *
600802 CTTACTGCCTAATGAAGAGGTGAGCATTTTCTCAGCATGATGGCGTCCATGTAGATCTCGGGTGC
1 CTTACTGCCTAATGAAAAGGTGAGCATTTTCTCAGCATGATGGCGTCCATGGAGATCTCGGGTGC
600867 CAACCCCACCCAATCATCGGC
66 CAACCCCACCCAATCATCGGC
* *
600888 CTTACTGCCTAATGAAAAGGTGAGCATTTTCTCAGCATGATGGTGTCCATGGAGATCTCGTGTGC
1 CTTACTGCCTAATGAAAAGGTGAGCATTTTCTCAGCATGATGGCGTCCATGGAGATCTCGGGTGC
600953 CAACCCCACCCAATCATCGGC
66 CAACCCCACCCAATCATCGGC
600974 GGTGGGTTCA
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
86 82 1.00
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (86 bp):
CTTACTGCCTAATGAAAAGGTGAGCATTTTCTCAGCATGATGGCGTCCATGGAGATCTCGGGTGC
CAACCCCACCCAATCATCGGC
Found at i:608281 original size:25 final size:25
Alignment explanation
Indices: 608253--608300 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
608243 TTATATTGGT
608253 ATAATACAAAGATTTGAAAGAACCA
1 ATAATACAAAGATTTGAAAGAACCA
608278 ATAATACAAAGATTTGAAAGAAC
1 ATAATACAAAGATTTGAAAGAAC
608301 AACGGTGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.56, C:0.10, G:0.12, T:0.21
Consensus pattern (25 bp):
ATAATACAAAGATTTGAAAGAACCA
Done.