Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009759.1 Kokia drynarioides strain JFW-HI SEQ_124478, 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: 528391
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 144 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:457999 original size:9 final size:9
Alignment explanation
Indices: 457985--458020 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
457975 TTTAATCTTT
457985 TAAAAATTA
1 TAAAAATTA
457994 TAAAAATTA
1 TAAAAATTA
458003 TAAAAA-TA
1 TAAAAATTA
458011 TAAACAATTA
1 TAAA-AATTA
458021 AAATGGTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 6 0.24
9 17 0.68
10 2 0.08
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (9 bp):
TAAAAATTA
Found at i:461248 original size:25 final size:25
Alignment explanation
Indices: 461186--461249 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 25
461176 TCATACTATT
*
461186 TTTTTAATATTTATGTATTATTTATA
1 TTTTAAATATTT-TGTATTATTTATA
* * *
461212 TTTTATGA-ATTTTGTATTTTTTATC
1 TTTTA-AATATTTTGTATTATTTATA
461237 TTTTAAATATTTT
1 TTTTAAATATTTT
461250 ATAAATTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
24 1 0.03
25 21 0.68
26 8 0.26
27 1 0.03
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.67
Consensus pattern (25 bp):
TTTTAAATATTTTGTATTATTTATA
Found at i:464925 original size:19 final size:18
Alignment explanation
Indices: 464892--464927 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
464882 ATTTATCAAA
*
464892 ATTAATATTCAAAAAATT
1 ATTAAAATTCAAAAAATT
464910 ATTAAAATTACAAAAAAT
1 ATTAAAATT-CAAAAAAT
464928 ATTTTTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (18 bp):
ATTAAAATTCAAAAAATT
Found at i:465207 original size:15 final size:16
Alignment explanation
Indices: 465187--465216 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
465177 CATCGGAACA
465187 CAAATTT-AAAATTTT
1 CAAATTTCAAAATTTT
465202 CAAATTTCAAAATTT
1 CAAATTTCAAAATTT
465217 AGGTTAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (16 bp):
CAAATTTCAAAATTTT
Found at i:466007 original size:22 final size:22
Alignment explanation
Indices: 465951--466009 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
465941 TCTTTATAAT
*
465951 TTTTAAAAGA-TTAAATTAAAA
1 TTTTAAAAAATTTAAATTAAAA
** ** *
465972 TTTTATCATTTTTAATTTAAAA
1 TTTTAAAAAATTTAAATTAAAA
465994 TTTTAAAAAATTTAAA
1 TTTTAAAAAATTTAAA
466010 GGACCTAAAT
Statistics
Matches: 27, Mismatches: 10, Indels: 1
0.71 0.26 0.03
Matches are distributed among these distances:
21 6 0.22
22 21 0.78
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (22 bp):
TTTTAAAAAATTTAAATTAAAA
Found at i:470259 original size:31 final size:31
Alignment explanation
Indices: 470224--470285 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
470214 TTACAAAATG
*
470224 GTCACTAAACTATTCGAAAGTTTTCATTTAA
1 GTCACTAAACTATCCGAAAGTTTTCATTTAA
* *
470255 GTCACTGAACTATCCGAAAGTTTTTATTTAA
1 GTCACTAAACTATCCGAAAGTTTTCATTTAA
470286 ATCATCGTGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (31 bp):
GTCACTAAACTATCCGAAAGTTTTCATTTAA
Found at i:476957 original size:23 final size:23
Alignment explanation
Indices: 476930--477001 Score: 80
Period size: 22 Copynumber: 3.2 Consensus size: 23
476920 ATATTGTTGT
476930 TTTTGTGCTT-TTTTTTTTTACTA
1 TTTTGTG-TTCTTTTTTTTTACTA
*
476953 TTTTG-GTTCTTTTTTTGTT-GT-
1 TTTTGTGTTCTTTTTTT-TTACTA
*
476974 TTTTGTGTTGTTTTTTTTTACTA
1 TTTTGTGTTCTTTTTTTTTACTA
476997 TTTTG
1 TTTTG
477002 GTTGTTGTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
21 9 0.22
22 20 0.49
23 12 0.29
ACGTcount: A:0.06, C:0.06, G:0.14, T:0.75
Consensus pattern (23 bp):
TTTTGTGTTCTTTTTTTTTACTA
Found at i:476972 original size:44 final size:45
Alignment explanation
Indices: 476923--477038 Score: 164
Period size: 44 Copynumber: 2.5 Consensus size: 45
476913 AAAAATTATA
476923 TTGTTGTTTTTGTGCTT-TTTTTTTTTACTATTTTGGTTCTT-TTT
1 TTGTTGTTTTTGTG-TTGTTTTTTTTTACTATTTTGGTTCTTGTTT
*
476967 TTGTTGTTTTTGTGTTGTTTTTTTTTACTATTTTGGTTGTTGTTT
1 TTGTTGTTTTTGTGTTGTTTTTTTTTACTATTTTGGTTCTTGTTT
*
477012 TCGTGTTGTTTTTGTTGTTATTTTTTT
1 T--TGTTGTTTTTG-TGTTGTTTTTTT
477039 GTTGTTTTGT
Statistics
Matches: 65, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
43 2 0.03
44 37 0.57
45 4 0.06
47 11 0.17
48 11 0.17
ACGTcount: A:0.04, C:0.04, G:0.17, T:0.74
Consensus pattern (45 bp):
TTGTTGTTTTTGTGTTGTTTTTTTTTACTATTTTGGTTCTTGTTT
Found at i:476982 original size:11 final size:11
Alignment explanation
Indices: 476953--477059 Score: 67
Period size: 11 Copynumber: 9.5 Consensus size: 11
476943 TTTTTTACTA
*
476953 TTTTG-GTTCT
1 TTTTGTGTTGT
*
476963 TTTTTTGTTGT
1 TTTTGTGTTGT
476974 TTTTGTGTTGT
1 TTTTGTGTTGT
* *
476985 TTTT-TTTTACT
1 TTTTGTGTT-GT
476996 ATTTTGGTTGTTGT
1 -TTTT-G-TGTTGT
*
477010 TTTCGTGTTGT
1 TTTTGTGTTGT
*
477021 TTTTGTTGTTAT
1 TTTTG-TGTTGT
*
477033 TTTTTTGTTG-
1 TTTTGTGTTGT
*
477043 TTTTGTTGTTAT
1 TTTTG-TGTTGT
477055 TTTTG
1 TTTTG
477060 CTGCTGTTTA
Statistics
Matches: 74, Mismatches: 14, Indels: 16
0.71 0.13 0.15
Matches are distributed among these distances:
10 11 0.15
11 37 0.50
12 19 0.26
13 3 0.04
14 1 0.01
15 3 0.04
ACGTcount: A:0.04, C:0.03, G:0.20, T:0.74
Consensus pattern (11 bp):
TTTTGTGTTGT
Found at i:477005 original size:22 final size:22
Alignment explanation
Indices: 476940--477012 Score: 87
Period size: 22 Copynumber: 3.3 Consensus size: 22
476930 TTTTGTGCTT
*
476940 TTTTTTTTTACTATTTTGGTTC
1 TTTTTTTTTACTATTTTGGTTG
*
476962 TTTTTTTGTT-GT-TTTTGTGTTG
1 TTTTTTT-TTACTATTTTG-GTTG
476984 TTTTTTTTTACTATTTTGGTTG
1 TTTTTTTTTACTATTTTGGTTG
*
477006 TTGTTTT
1 TTTTTTT
477013 CGTGTTGTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
21 7 0.16
22 29 0.67
23 7 0.16
ACGTcount: A:0.05, C:0.04, G:0.15, T:0.75
Consensus pattern (22 bp):
TTTTTTTTTACTATTTTGGTTG
Found at i:477023 original size:23 final size:22
Alignment explanation
Indices: 476997--477100 Score: 95
Period size: 23 Copynumber: 4.7 Consensus size: 22
476987 TTTTTTACTA
*
476997 TTTTGGTTGTTGTTTTCGTGTTG
1 TTTT-GTTGTTATTTTCGTGTTG
**
477020 TTTTTGTTGTTATTTTTTTGTTG
1 -TTTTGTTGTTATTTTCGTGTTG
* *
477043 TTTTGTTGTTATTTTTGCTGCTG
1 TTTTGTTGTTATTTTCG-TGTTG
*
477066 TTTAGTTGTTATTTT--TGTTG
1 TTTTGTTGTTATTTTCGTGTTG
* *
477086 TTTGGATGTTATTTT
1 TTTTGTTGTTATTTT
477101 TTATGCGTTT
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
20 17 0.24
22 16 0.23
23 33 0.47
24 4 0.06
ACGTcount: A:0.06, C:0.03, G:0.22, T:0.69
Consensus pattern (22 bp):
TTTTGTTGTTATTTTCGTGTTG
Found at i:477051 original size:45 final size:47
Alignment explanation
Indices: 476924--477087 Score: 128
Period size: 45 Copynumber: 3.6 Consensus size: 47
476914 AAAATTATAT
* * * *
476924 TGTTGTTTTTG-TGCTT-TTTTTTTTTACTATTTTGGTTCTT-TTTTTGT
1 TGTTGTTTTTGTTG-TTATTTTTTTGT--TATTTTGGTTGTTATTTTCGC
* ** *
476971 TGTT-TTTGTGTTGTT-TTTTTTTACTATTTTGGTTGTTGTTTTCG-
1 TGTTGTTTTTGTTGTTATTTTTTTGTTATTTTGGTTGTTATTTTCGC
* *
477015 TGTTGTTTTTGTTGTTATTTTTTTGTTGTTTT-GTTGTTATTTTTGC
1 TGTTGTTTTTGTTGTTATTTTTTTGTTATTTTGGTTGTTATTTTCGC
* *
477061 TGCTG-TTTAGTTGTTATTTTTGTTGTT
1 TGTTGTTTTTGTTGTTATTTTT-TTGTT
477088 TGGATGTTAT
Statistics
Matches: 98, Mismatches: 13, Indels: 13
0.79 0.10 0.10
Matches are distributed among these distances:
44 16 0.16
45 41 0.42
46 35 0.36
47 6 0.06
ACGTcount: A:0.05, C:0.04, G:0.19, T:0.72
Consensus pattern (47 bp):
TGTTGTTTTTGTTGTTATTTTTTTGTTATTTTGGTTGTTATTTTCGC
Found at i:477075 original size:34 final size:34
Alignment explanation
Indices: 476969--477087 Score: 84
Period size: 34 Copynumber: 3.5 Consensus size: 34
476959 TTCTTTTTTT
* * *
476969 GTTGTT-TTTGTGTTGTT-TTTTT-TTACTATTTTG
1 GTTGTTGTTT-TGTTGTTATTTTTGCTGCTA-TTTA
* * * *
477002 GTTGTTGTTTTCG-TGTTGTTTTTGTTGTTATTTT
1 GTTGTTGTTTT-GTTGTTATTTTTGCTGCTATTTA
* *
477036 TTTGTTGTTTTGTTGTTATTTTTGCTGCTGTTTA
1 GTTGTTGTTTTGTTGTTATTTTTGCTGCTATTTA
*
477070 GTTGTTATTTTTGTTGTT
1 GTTGTT-GTTTTGTTGTT
477088 TGGATGTTAT
Statistics
Matches: 69, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
33 12 0.17
34 43 0.62
35 14 0.20
ACGTcount: A:0.05, C:0.03, G:0.21, T:0.71
Consensus pattern (34 bp):
GTTGTTGTTTTGTTGTTATTTTTGCTGCTATTTA
Found at i:485182 original size:134 final size:132
Alignment explanation
Indices: 484844--485323 Score: 584
Period size: 135 Copynumber: 3.6 Consensus size: 132
484834 AAGAAGAAAG
* * * *
484844 AAAGCTCAAAAATCACATTGCTCAACTC-AAAAACCTAAATCTAAACTT-AACCAGCAACACTGA
1 AAAGCTCAAAAATCACATTGTTCAAATCAAAAAAACTAAATCTAAACTTAAACCAGCAACAATGA
* *
484907 ATCAATAAAAATTCAATTTAGTACATAGAAATCTCAAAGTCAATGCTAGCAAAAAGGAC--AAAA
66 ATCAATAAAAATTCAAATTAGTACATAGAAATCTCAAAGTCAATGCTAGCAAAAACGACAAAAAA
484970 AA
131 AA
** * *
484972 AGGGCTCAAAAATCACATTGTTCAACT-AAAAAAATCTAAATCTAAACTAAAACCAGCAACACA-
1 AAAGCTCAAAAATCACATTGTTCAAATCAAAAAAA-CTAAATCTAAACTTAAACCAGCAACA-AT
*
485035 GAATCAATAAAAATTCAAATTAGTACATAGAAATCTCAAAGTCAATGCTAACAAAAAACGACAAA
64 GAATCAATAAAAATTCAAATTAGTACATAGAAATCTCAAAGTCAATGCTAGC-AAAAACGACAAA
485100 AAAAA
128 AAAAA
*
485105 AAAGCT-AAAAACTCACATTGTTCAAATACAAAAAAAGTAAATCTAAACTTAAACCAGCAACAAT
1 AAAGCTCAAAAA-TCACATTGTTCAAAT-CAAAAAAACTAAATCTAAACTTAAACCAGCAACAAT
* * * * * * *
485169 GAATCAATAAAAATTCAAAAATAGTACATAGAAATCACAGACTCAATACTAGCAAAAACTAAAAA
64 GAATCAATAAAAATTC-AAATTAGTACATAGAAATCTCAAAGTCAATGCTAGCAAAAAC--GACA
485234 AAAAAAA
126 AAAAAAA
* ** *
485241 CAATCAGCTCAAAAGTCACATTGTTC--ATCTCAAAAACTAAATCTAAAC-TAAACCAGCAACAC
1 -AA--AGCTCAAAAATCACATTGTTCAAATCAAAAAAACTAAATCTAAACTTAAACCAGCAACAA
485303 TGAATCAATAAAAATTCAAAT
63 TGAATCAATAAAAATTCAAAT
485324 CAATTCAAAA
Statistics
Matches: 306, Mismatches: 28, Indels: 30
0.84 0.08 0.08
Matches are distributed among these distances:
128 29 0.09
129 13 0.04
130 61 0.20
131 8 0.03
132 5 0.02
133 25 0.08
134 49 0.16
135 67 0.22
136 26 0.08
137 4 0.01
139 15 0.05
140 4 0.01
ACGTcount: A:0.54, C:0.19, G:0.07, T:0.20
Consensus pattern (132 bp):
AAAGCTCAAAAATCACATTGTTCAAATCAAAAAAACTAAATCTAAACTTAAACCAGCAACAATGA
ATCAATAAAAATTCAAATTAGTACATAGAAATCTCAAAGTCAATGCTAGCAAAAACGACAAAAAA
AA
Found at i:485621 original size:2 final size:2
Alignment explanation
Indices: 485614--485644 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
485604 AACCAAACAA
*
485614 AG AG AG AG AG AC AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
485645 AAGCGATGAA
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:0.52, C:0.03, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:489648 original size:22 final size:22
Alignment explanation
Indices: 489622--489663 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
489612 GCAATAAATA
489622 TATATCAATATAGATA-ATATTT
1 TATATCAATA-AGATAGATATTT
*
489644 TATATCGATAAGATAGATAT
1 TATATCAATAAGATAGATAT
489664 ATTAAATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (22 bp):
TATATCAATAAGATAGATATTT
Found at i:492933 original size:30 final size:30
Alignment explanation
Indices: 492899--492961 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
492889 ACGATAAAAA
* *
492899 TTAATAAATATTTTAACT-TAAAAAACTAAT
1 TTAATAAATAATCTAA-TATAAAAAACTAAT
**
492929 TTAATATTTAATCTAATATAAAAAACTAAT
1 TTAATAAATAATCTAATATAAAAAACTAAT
492959 TTA
1 TTA
492962 CTATTTTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 1 0.04
30 27 0.96
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.41
Consensus pattern (30 bp):
TTAATAAATAATCTAATATAAAAAACTAAT
Found at i:493211 original size:22 final size:21
Alignment explanation
Indices: 493161--493211 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
493151 TTGTTACTCT
*
493161 CTACCCTCTTTAACCCTAAAAC
1 CTACCC-CTTTAACCCCAAAAC
* *
493183 CTTCCCCTTTAAACCCCAAACC
1 CTACCCCTTT-AACCCCAAAAC
493205 CTACCCC
1 CTACCCC
493212 AATATCCCCT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.27, C:0.49, G:0.00, T:0.24
Consensus pattern (21 bp):
CTACCCCTTTAACCCCAAAAC
Found at i:496127 original size:30 final size:31
Alignment explanation
Indices: 496093--496150 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
496083 TTTTTAGGGA
496093 TAAATAT-TAAACTT-ATACATGAATTTTGTT
1 TAAATATGT-AACTTGATACATGAATTTTGTT
*
496123 TAAATATGTAATTTGATACATGAATTTT
1 TAAATATGTAACTTGATACATGAATTTT
496151 AATTTGGTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 11 0.44
31 14 0.56
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.47
Consensus pattern (31 bp):
TAAATATGTAACTTGATACATGAATTTTGTT
Found at i:497916 original size:263 final size:263
Alignment explanation
Indices: 497499--498202 Score: 1038
Period size: 263 Copynumber: 2.6 Consensus size: 263
497489 GATTAAAATT
*
497499 TTAAATTGGATTTAGAATTTTAGGGTTTAACTTGAACTGGAGTGCTAGAAAAGTATTTTAAATCG
1 TTAAATTGGATTTAGAATTTTAGGGTTTAACTTGAACTGGAGTGCTAGAAAAGTATTTTAAATTG
* * *
497564 AAACTACATTTGGAAGGTTTTTTTTTTCTATTTTAAGATTTGGATTAGCTTGGTTAGTTGAATCT
66 AAACTATATTTGG-AGG---ATTTTTT-TA--TTAAGATTTGAATTAGCTTGGTTAGTTGAATCT
*
497629 TTATTTTTATGAAAATTTCTTTGATTTTCTTGTTTGTAGGATTTGAGTTTAATTTCCTTCACATG
124 TTATTTTTATGAAAATTTCTTTGATTTTCTTGTTTGTAGGATTTGAATTTAATTTCCTTCACATG
497694 TATATTAGTTTTTTTTCTAAGAGTTAGACTCAGATCCAAACTTTTTAGTTTTGAAGGATTAAAAT
189 TATATTAG--TTTTTTCTAAGAGTTAGACTCAGATCCAAACTTTTTAGTTTTGAAGGATT-AAAT
497759 TTT-AAA-TGAAA
251 TTTAAAATTGAAA
* * * *
497770 TTAAATTGGATTTAGACTTTTAGGGTTTAACTTGAACTGGATTGCTAGGAAAGTAATTTAAATTG
1 TTAAATTGGATTTAGAATTTTAGGGTTTAACTTGAACTGGAGTGCTAGAAAAGTATTTTAAATTG
* *
497835 AAACTATAATTGGAGGATTTTTTTA-AAAGATTTGAATTAGCTTGGTTAGTTGAATCTTTATTTT
66 AAACTATATTTGGAGGATTTTTTTATTAAGATTTGAATTAGCTTGGTTAGTTGAATCTTTATTTT
*
497899 TATGAAAAATTCTTTGATTTAT-TTGTTTGTAGGATTTGAATTTAATTTCCTTCACATGTATATT
131 TATGAAAATTTCTTTGATTT-TCTTGTTTGTAGGATTTGAATTTAATTTCCTTCACATGTATATT
* *
497963 AGTTTTTTCTAAGTGTTAGACTCAGATCCAAGCTTTTTAGTTTTGAAGGATTAAATTTTAAAATT
195 AGTTTTTTCTAAGAGTTAGACTCAGATCCAAACTTTTTAGTTTTGAAGGATTAAATTTTAAAATT
498028 GAAA
260 GAAA
*
498032 TTAAATTGGATTTAGAATTTTAGGATTTAACTTGAACTGGAGTGCTAGAAAAGTATTTTAAATTG
1 TTAAATTGGATTTAGAATTTTAGGGTTTAACTTGAACTGGAGTGCTAGAAAAGTATTTTAAATTG
*
498097 AAACTATATTTGAAGGATTTTTTTTATCTTTTTTAAGATTTGAATTAGCTTGGTTAGTTGAATCT
66 AAACTATATTTGGAGGA-TTTTTTTA------TTAAGATTTGAATTAGCTTGGTTAGTTGAATCT
* * * *
498162 TTATTTATATGGAAGTTTCATTGATTTTCTTGTTTGTAGGA
124 TTATTTTTATGAAAATTTCTTTGATTTTCTTGTTTGTAGGA
498203 GTTATGCCCT
Statistics
Matches: 394, Mismatches: 27, Indels: 25
0.88 0.06 0.06
Matches are distributed among these distances:
260 7 0.02
261 51 0.13
262 80 0.20
263 107 0.27
264 1 0.00
266 2 0.01
267 6 0.02
269 1 0.00
270 68 0.17
271 71 0.18
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.46
Consensus pattern (263 bp):
TTAAATTGGATTTAGAATTTTAGGGTTTAACTTGAACTGGAGTGCTAGAAAAGTATTTTAAATTG
AAACTATATTTGGAGGATTTTTTTATTAAGATTTGAATTAGCTTGGTTAGTTGAATCTTTATTTT
TATGAAAATTTCTTTGATTTTCTTGTTTGTAGGATTTGAATTTAATTTCCTTCACATGTATATTA
GTTTTTTCTAAGAGTTAGACTCAGATCCAAACTTTTTAGTTTTGAAGGATTAAATTTTAAAATTG
AAA
Found at i:506777 original size:4 final size:4
Alignment explanation
Indices: 506768--506794 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
506758 AACAATCAAA
506768 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
506795 GCAAAATCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:508656 original size:269 final size:269
Alignment explanation
Indices: 508174--508710 Score: 993
Period size: 269 Copynumber: 2.0 Consensus size: 269
508164 AATTTCTAGA
508174 TTAAGTTATTTTAAGCTTTACTTTTAAAGTCACATCTGACTAAAACAAAAATTTGTTTTTTTTTT
1 TTAAGTTATTTTAAGCTTTACTTTTAAAGTCACATCTGACTAAAACAAAAATTTGTTTTTTTTTT
508239 TAATATATTAGTATGATTATATGATAATATGTATTCATACTTTCTTAATCCTTCAATAAAGCACA
66 TAATATATTAGTATGATTATATGATAATATGTATTCATACTTTCTTAATCCTTCAATAAAGCACA
508304 CACACCTTACACACACAGACGCTCGAATCCAGGACTTTTAAGATGAACAACATTAGATTTTTCAC
131 CACACCTTACACACACAGACGCTCGAATCCAGGACTTTTAAGATGAACAACATTAGATTTTTCAC
*
508369 TATAATCACTTGTTAGGTTCGAAATTTGTTCTAAAATGTTCATGTTTAAGACTTATTTTGGGAAA
196 TATAATCACTTATTAGGTTCGAAATTTGTTCTAAAATGTTCATGTTTAAGACTTATTTTGGGAAA
508434 GATTGTTTT
261 GATTGTTTT
508443 TTAAGTTATTTTAAGCTTTACTTTTAAAGTCACATCTGACTAAAACAAAAATTTGTTTTTTTTTT
1 TTAAGTTATTTTAAGCTTTACTTTTAAAGTCACATCTGACTAAAACAAAAATTTGTTTTTTTTTT
* *
508508 TAATATATTAGTATGATTATATGATAGTATGTATTCATACTTTCTTAATCCTTCGATAAAGCACA
66 TAATATATTAGTATGATTATATGATAATATGTATTCATACTTTCTTAATCCTTCAATAAAGCACA
* * **
508573 CACACCTTGCACACACAGGCGCTCGAATCCAGGACTTTTAAGATGAACAACATTATCTTTTTCAC
131 CACACCTTACACACACAGACGCTCGAATCCAGGACTTTTAAGATGAACAACATTAGATTTTTCAC
* *
508638 TATAATCACTTATTAGGTTCGAAATTTGTTTTAAAATGTTCGTGTTTAAGACTTATTTTGGGAAA
196 TATAATCACTTATTAGGTTCGAAATTTGTTCTAAAATGTTCATGTTTAAGACTTATTTTGGGAAA
508703 GATTGTTT
261 GATTGTTT
508711 ATGCTTCCAT
Statistics
Matches: 259, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
269 259 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.41
Consensus pattern (269 bp):
TTAAGTTATTTTAAGCTTTACTTTTAAAGTCACATCTGACTAAAACAAAAATTTGTTTTTTTTTT
TAATATATTAGTATGATTATATGATAATATGTATTCATACTTTCTTAATCCTTCAATAAAGCACA
CACACCTTACACACACAGACGCTCGAATCCAGGACTTTTAAGATGAACAACATTAGATTTTTCAC
TATAATCACTTATTAGGTTCGAAATTTGTTCTAAAATGTTCATGTTTAAGACTTATTTTGGGAAA
GATTGTTTT
Found at i:511501 original size:2 final size:2
Alignment explanation
Indices: 511494--511545 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
511484 TACACTCATC
511494 AT AT AT 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
511536 AT AT AT AT AT
1 AT AT AT AT AT
511546 GCATATTGGT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:515514 original size:31 final size:31
Alignment explanation
Indices: 515479--515541 Score: 110
Period size: 31 Copynumber: 2.0 Consensus size: 31
515469 AACCCAATAT
515479 CTTAAATGAAAAC-TTTCGAATAGTTCAATGA
1 CTTAAATGAAAACATTT-GAATAGTTCAATGA
515510 CTTAAATGAAAACATTTGAATAGTTCAATGA
1 CTTAAATGAAAACATTTGAATAGTTCAATGA
515541 C
1 C
515542 CATCTTGTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 28 0.90
32 3 0.10
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.32
Consensus pattern (31 bp):
CTTAAATGAAAACATTTGAATAGTTCAATGA
Found at i:518490 original size:9 final size:8
Alignment explanation
Indices: 518459--518508 Score: 52
Period size: 8 Copynumber: 6.5 Consensus size: 8
518449 AGTTGAGTTG
518459 TTTTAT-T
1 TTTTATAT
518466 TTTT-TA-
1 TTTTATAT
518472 TTTTATAT
1 TTTTATAT
518480 TTTTAATAT
1 TTTT-ATAT
*
518489 TTTTATAA
1 TTTTATAT
*
518497 TTATATAT
1 TTTTATAT
518505 TTTT
1 TTTT
518509 GAATATTTAG
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
6 5 0.14
7 6 0.17
8 16 0.46
9 8 0.23
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTTATAT
Found at i:518503 original size:25 final size:25
Alignment explanation
Indices: 518462--518516 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
518452 TGAGTTGTTT
* *
518462 TATTTTTTTATTTTATATTTTT-AA
1 TATTTTTTAATTATATATTTTTGAA
518486 TATTTTTATAATTATATATTTTTGAA
1 TATTTTT-TAATTATATATTTTTGAA
518512 TATTT
1 TATTT
518517 AGAATAATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 7 0.26
25 13 0.48
26 7 0.26
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (25 bp):
TATTTTTTAATTATATATTTTTGAA
Found at i:518955 original size:8 final size:7
Alignment explanation
Indices: 518937--518991 Score: 53
Period size: 6 Copynumber: 8.0 Consensus size: 7
518927 AATTTCTTAA
518937 ATAAAAT
1 ATAAAAT
*
518944 A-AAATT
1 ATAAAAT
518950 ATAAAAT
1 ATAAAAT
518957 AT-AAAT
1 ATAAAAT
518963 AT-AAAT
1 ATAAAAT
518969 ATAAAACT
1 ATAAAA-T
*
518977 AATAAAGT
1 -ATAAAAT
518985 ATAAAAT
1 ATAAAAT
518992 TTATTTTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
6 17 0.43
7 16 0.40
8 2 0.05
9 5 0.12
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (7 bp):
ATAAAAT
Found at i:518962 original size:19 final size:18
Alignment explanation
Indices: 518935--518974 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
518925 AAAATTTCTT
518935 AAATAAAATA-AAATTATA
1 AAATAAAATATAAA-TATA
518953 AAATATAAATATAAATATA
1 AAATA-AAATATAAATATA
518972 AAA
1 AAA
518975 CTAATAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 5 0.25
19 12 0.60
20 3 0.15
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (18 bp):
AAATAAAATATAAATATA
Found at i:518966 original size:21 final size:23
Alignment explanation
Indices: 518936--518992 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 23
518926 AAATTTCTTA
518936 AATAAA-ATAAAATTATAAAA-T
1 AATAAATATAAAATTATAAAACT
518957 -ATAAATAT-AAA-TATAAAACT
1 AATAAATATAAAATTATAAAACT
518977 AATAAAGTATAAAATT
1 AATAAA-TATAAAATT
518993 TATTTTTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
19 7 0.23
20 9 0.30
21 7 0.23
22 3 0.10
23 3 0.10
24 1 0.03
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (23 bp):
AATAAATATAAAATTATAAAACT
Found at i:519090 original size:12 final size:13
Alignment explanation
Indices: 519070--519102 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
519060 ATATTTAAAA
519070 TATTATTATTTAT
1 TATTATTATTTAT
519083 TATT-TTATTTAT
1 TATTATTATTTAT
*
519095 TTTTATTA
1 TATTATTA
519103 AAATATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (13 bp):
TATTATTATTTAT
Found at i:519109 original size:18 final size:17
Alignment explanation
Indices: 519064--519115 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
519054 CCTTTTATAT
519064 TTAAAATATTATTATTTA
1 TTAAAATATTATT-TTTA
***
519082 TTATTTTATTTATTTTTA
1 TTAAAATA-TTATTTTTA
519100 TTAAAATATTATTTTT
1 TTAAAATATTATTTTT
519116 TATACATAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
17 8 0.30
18 14 0.52
19 5 0.19
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTAAAATATTATTTTTA
Found at i:521798 original size:16 final size:16
Alignment explanation
Indices: 521766--521795 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
521756 TATGAAATGA
521766 TGAAAAAAGAAATAAT
1 TGAAAAAAGAAATAAT
521782 TGAAAAAA-AAATAA
1 TGAAAAAAGAAATAA
521796 ATTAAACATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.17
Consensus pattern (16 bp):
TGAAAAAAGAAATAAT
Found at i:521808 original size:2 final size:2
Alignment explanation
Indices: 521803--521838 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
521793 TAAATTAAAC
521803 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
521839 TATTATACTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:523121 original size:19 final size:20
Alignment explanation
Indices: 523089--523146 Score: 73
Period size: 19 Copynumber: 2.9 Consensus size: 20
523079 TATATTTTAT
*
523089 ATTAATATTAAAATTTTACA
1 ATTAATATTAAAATTTAACA
*
523109 ATTAAT-TTGAAATTTAACA
1 ATTAATATTAAAATTTAACA
*
523128 ATTTATTATTAAAATTTAA
1 A-TTAATATTAAAATTTAA
523147 TTCAAGTCGA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 12 0.38
20 10 0.31
21 10 0.31
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (20 bp):
ATTAATATTAAAATTTAACA
Found at i:527405 original size:2 final size:2
Alignment explanation
Indices: 527398--527435 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
527388 TTGGATCATC
* *
527398 TA TA TA TA TC TA TA TA TA TC TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
527436 GGAATAGGAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:527410 original size:10 final size:10
Alignment explanation
Indices: 527395--527435 Score: 73
Period size: 10 Copynumber: 4.1 Consensus size: 10
527385 AAGTTGGATC
527395 ATCTATATAT
1 ATCTATATAT
527405 ATCTATATAT
1 ATCTATATAT
527415 ATCTATATAT
1 ATCTATATAT
*
527425 ATATATATAT
1 ATCTATATAT
527435 A
1 A
527436 GGAATAGGAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
10 30 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (10 bp):
ATCTATATAT
Done.