Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011490.1 Kokia drynarioides strain JFW-HI SEQ_126475, 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: 124121
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 23 characters in sequence are not A, C, G, or T
Found at i:974 original size:28 final size:28
Alignment explanation
Indices: 929--986 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
919 GCAGGAAATG
*
929 AGAAACAACAATTAGAAACATGGAAGAT
1 AGAAACAACAATTAGAAACATGAAAGAT
* * * *
957 AGAAATAACGATTGGAAACGTGAAAGAT
1 AGAAACAACAATTAGAAACATGAAAGAT
985 AG
1 AG
987 GATTTCTTGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.53, C:0.09, G:0.22, T:0.16
Consensus pattern (28 bp):
AGAAACAACAATTAGAAACATGAAAGAT
Found at i:1314 original size:28 final size:28
Alignment explanation
Indices: 1270--1381 Score: 136
Period size: 28 Copynumber: 4.0 Consensus size: 28
1260 TGATAACAAG
*
1270 CATGACC-TTTGGTTCAACAGGGAGTAAA
1 CATGACCTTTTGG-TCAACAAGGAGTAAA
* *
1298 CATGACCTTTTGGTCAATAAGGAGTAAG
1 CATGACCTTTTGGTCAACAAGGAGTAAA
* * *
1326 CATGACCTTTGGGTCAACAGGGAGTAAG
1 CATGACCTTTTGGTCAACAAGGAGTAAA
* *
1354 CATGACCTTTAGGCCAACAAGGAGTAAA
1 CATGACCTTTTGGTCAACAAGGAGTAAA
1382 TCGGATATCA
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
28 68 0.93
29 5 0.07
ACGTcount: A:0.33, C:0.18, G:0.26, T:0.23
Consensus pattern (28 bp):
CATGACCTTTTGGTCAACAAGGAGTAAA
Found at i:1358 original size:56 final size:56
Alignment explanation
Indices: 1267--1380 Score: 183
Period size: 56 Copynumber: 2.0 Consensus size: 56
1257 TACTGATAAC
* * * *
1267 AAGCATGACCTTTGGTTCAACAGGGAGTAAACATGACCTTTTGGTCAATAAGGAGT
1 AAGCATGACCTTTGGGTCAACAGGGAGTAAACATGACCTTTAGGCCAACAAGGAGT
*
1323 AAGCATGACCTTTGGGTCAACAGGGAGTAAGCATGACCTTTAGGCCAACAAGGAGT
1 AAGCATGACCTTTGGGTCAACAGGGAGTAAACATGACCTTTAGGCCAACAAGGAGT
1379 AA
1 AA
1381 ATCGGATATC
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.33, C:0.18, G:0.26, T:0.23
Consensus pattern (56 bp):
AAGCATGACCTTTGGGTCAACAGGGAGTAAACATGACCTTTAGGCCAACAAGGAGT
Found at i:4079 original size:18 final size:17
Alignment explanation
Indices: 4037--4079 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
4027 GTAATATATA
*
4037 TTTTTCTTCTTTTCCCT
1 TTTTTTTTCTTTTCCCT
* *
4054 TTGTTTTTCTTTTTCTCT
1 TTTTTTTTC-TTTTCCCT
4072 TTTTTTTT
1 TTTTTTTT
4080 TATGTGAATG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (17 bp):
TTTTTTTTCTTTTCCCT
Found at i:4661 original size:17 final size:17
Alignment explanation
Indices: 4622--4666 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
4612 TGATATATGG
*
4622 AAATGCAATGACAATGT
1 AAATGCAATGACAATAT
* *
4639 ATATGCAGTGACAATAT
1 AAATGCAATGACAATAT
4656 AAATGCAATGA
1 AAATGCAATGA
4667 AAAAGGAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.47, C:0.11, G:0.18, T:0.24
Consensus pattern (17 bp):
AAATGCAATGACAATAT
Found at i:9690 original size:21 final size:20
Alignment explanation
Indices: 9661--9700 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
9651 AACCCAATTC
9661 CATTTTTTATTATTCTTATT
1 CATTTTTTATTATTCTTATT
*
9681 CATTTATTTATTATTTTTAT
1 CATTT-TTTATTATTCTTAT
9701 GAATATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (20 bp):
CATTTTTTATTATTCTTATT
Found at i:9784 original size:63 final size:62
Alignment explanation
Indices: 9676--9840 Score: 264
Period size: 63 Copynumber: 2.7 Consensus size: 62
9666 TTTATTATTC
9676 TTATTCATTTATTTATTATTTTTATGAATATAAATAAAT--A-TAAAATAATATTAATTTTGTT
1 TTATT-ATTTATTTATTA-TTTTATGAATATAAATAAATAAATTAAAATAATATTAATTTTGTT
*
9737 TTATTATTTATTTATTATTGTATGAATATAAATAAATAAATGTAAAATAATATTAATTTTGTT
1 TTATTATTTATTTATTATTTTATGAATATAAATAAATAAAT-TAAAATAATATTAATTTTGTT
*
9800 TTATTATTTATTTATTATTTTATGAATATAGATAAATAAAT
1 TTATTATTTATTTATTATTTTATGAATATAAATAAATAAAT
9841 AAATAAACAA
Statistics
Matches: 97, Mismatches: 3, Indels: 6
0.92 0.03 0.06
Matches are distributed among these distances:
59 19 0.20
60 12 0.12
61 6 0.06
63 60 0.62
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.53
Consensus pattern (62 bp):
TTATTATTTATTTATTATTTTATGAATATAAATAAATAAATTAAAATAATATTAATTTTGTT
Found at i:12325 original size:31 final size:31
Alignment explanation
Indices: 12287--12355 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
12277 TTTCTTGCAT
*
12287 ATGCATTCATAAAATTCCACATCGTATTTTC
1 ATGCATTCATAAAATTCCACATCGCATTTTC
* ***
12318 ATGCATTCATAAAGTTTTGCATCGCATTTTC
1 ATGCATTCATAAAATTCCACATCGCATTTTC
12349 ATGCATT
1 ATGCATT
12356 AAAAGATTGA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.29, C:0.20, G:0.10, T:0.41
Consensus pattern (31 bp):
ATGCATTCATAAAATTCCACATCGCATTTTC
Found at i:17195 original size:50 final size:50
Alignment explanation
Indices: 17092--17215 Score: 158
Period size: 50 Copynumber: 2.5 Consensus size: 50
17082 ATCCTATACC
* * * * *
17092 CCTAAAGCTGTAGAGGAACAGATTGAAGTCACGATGGTGAATCTCATATA
1 CCTAAAGCTGTAGAGGGACAGATTGAAGCCACAATGGTGAATCTCAGACA
* * *
17142 CCTAAAGCTGTAGAGGGACAGATTGAAGCCATAATGGTGAATCTTAGCCA
1 CCTAAAGCTGTAGAGGGACAGATTGAAGCCACAATGGTGAATCTCAGACA
* *
17192 CCTAAAGCTATAGAGGGGCAGATT
1 CCTAAAGCTGTAGAGGGACAGATT
17216 AAAGTTGTAA
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 64 1.00
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.23
Consensus pattern (50 bp):
CCTAAAGCTGTAGAGGGACAGATTGAAGCCACAATGGTGAATCTCAGACA
Found at i:17319 original size:40 final size:40
Alignment explanation
Indices: 17256--17505 Score: 201
Period size: 40 Copynumber: 6.3 Consensus size: 40
17246 AAGCTGAAAT
* *
17256 GGGCAGATTGAAGACCATATGATCTTTTACCCCGACTAGA
1 GGGCAGATTGAAGACCATATGATCTCTTACCCCGACCAGA
* *
17296 GGGTAGATTGAAGACCATTTGATCTCTTACCCCGACCATGA
1 GGGCAGATTGAAGACCATATGATCTCTTACCCCGACCA-GA
* * * * ** *
17337 -GGCAGATTAAAG-CAATCT-AGTCTTTTACCCTAACTAGA
1 GGGCAGATTGAAGACCATATGA-TCTCTTACCCCGACCAGA
*
17375 GGGCAGATTGAAGACCATATGATCTCTTACCTCGACCATG-
1 GGGCAGATTGAAGACCATATGATCTCTTACCCCGACCA-GA
* *** * ** *
17415 GGGCATATTGAAGTA--ATCCAATCTTTTACCCTAACCGGA
1 GGGCAGATTGAAG-ACCATATGATCTCTTACCCCGACCAGA
17454 GGGCAGATTGAAGACCAT-TCGATCTCTTACCCCGACCATG-
1 GGGCAGATTGAAGACCATAT-GATCTCTTACCCCGACCA-GA
*
17494 GGGCAAATTGAA
1 GGGCAGATTGAA
17506 ACAATCCAAT
Statistics
Matches: 161, Mismatches: 37, Indels: 24
0.73 0.17 0.11
Matches are distributed among these distances:
38 5 0.03
39 53 0.33
40 97 0.60
41 6 0.04
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.26
Consensus pattern (40 bp):
GGGCAGATTGAAGACCATATGATCTCTTACCCCGACCAGA
Found at i:17411 original size:79 final size:78
Alignment explanation
Indices: 17277--17524 Score: 327
Period size: 79 Copynumber: 3.1 Consensus size: 78
17267 AGACCATATG
** * * *
17277 ATCTTTTACCCCGACTAGAGGGTAGATTGAAGACCATTTGATCTCTTACCCCGACCATGAGGCAG
1 ATCTTTTACCCTAACTAGAGGGCAGATTGAAGACCA-TTGATCTCTTACCCCGACCATGGGGCAA
*
17342 ATTAAAGCAATCTA
65 ATTAAAGCAATCCA
* * *
17356 GTCTTTTACCCTAACTAGAGGGCAGATTGAAGACCATATGATCTCTTACCTCGACCATGGGGCAT
1 ATCTTTTACCCTAACTAGAGGGCAGATTGAAGACCAT-TGATCTCTTACCCCGACCATGGGGCAA
* *
17421 ATTGAAGTAATCCA
65 ATTAAAGCAATCCA
**
17435 ATCTTTTACCCTAACCGGAGGGCAGATTGAAGACCATTCGATCTCTTACCCCGACCATGGGGCAA
1 ATCTTTTACCCTAACTAGAGGGCAGATTGAAGACCATT-GATCTCTTACCCCGACCATGGGGCAA
17500 ATTGAAA-CAATCCA
65 ATT-AAAGCAATCCA
*
17514 ATTTTTTACCC
1 ATCTTTTACCC
17525 CTAAACCTAT
Statistics
Matches: 148, Mismatches: 18, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
78 2 0.01
79 144 0.97
80 2 0.01
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (78 bp):
ATCTTTTACCCTAACTAGAGGGCAGATTGAAGACCATTGATCTCTTACCCCGACCATGGGGCAAA
TTAAAGCAATCCA
Found at i:18225 original size:67 final size:63
Alignment explanation
Indices: 18088--18224 Score: 247
Period size: 63 Copynumber: 2.2 Consensus size: 63
18078 TTTTATCGAT
18088 ATAAATAAATATAAAATAATATTAATTTTGTTTTATTATTTATTTATTATTGTATGAATATAA
1 ATAAATAAATATAAAATAATATTAATTTTGTTTTATTATTTATTTATTATTGTATGAATATAA
* * *
18151 ATAAATAAATGTAAAATAATTTTAATTTTGTTTTATTATTTATTTATTATTTTATGAATATAA
1 ATAAATAAATATAAAATAATATTAATTTTGTTTTATTATTTATTTATTATTGTATGAATATAA
18214 ATAAATAAATA
1 ATAAATAAATA
18225 ACAAACCCAA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 70 1.00
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.50
Consensus pattern (63 bp):
ATAAATAAATATAAAATAATATTAATTTTGTTTTATTATTTATTTATTATTGTATGAATATAA
Found at i:35635 original size:111 final size:110
Alignment explanation
Indices: 35435--35672 Score: 395
Period size: 111 Copynumber: 2.1 Consensus size: 110
35425 TTCAGACGCA
** *
35435 AAAATCGATACTAAATGCAGTGACATTAGTAGCACAAATGGGATAAAATGAAAGAAAATAAGACC
1 AAAAT-GATACTAAATGCAACGACATTAGTAGCACAAATGGGATAAAATGAAAAAAAATAAGACC
35500 ATACAATATTGACTTAGAAAATGCAATTACTAAGTATAAAATGCTG
65 ATACAATATTGACTTAGAAAATGCAATTACTAAGTATAAAATGCTG
35546 AAAACTGATACTAAATGCAACGACATTAGTAGCACAAATGGGATAAAATGAAAAAAAATAAGACC
1 AAAA-TGATACTAAATGCAACGACATTAGTAGCACAAATGGGATAAAATGAAAAAAAATAAGACC
* * *
35611 ATACACTATTGACTTTGAAAATGCAATTACTAAGTATGAAATGCTG
65 ATACAATATTGACTTAGAAAATGCAATTACTAAGTATAAAATGCTG
35657 AAAATGTATACTAAAT
1 AAAATG-ATACTAAAT
35673 ATGATACAAA
Statistics
Matches: 119, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
110 2 0.02
111 116 0.97
112 1 0.01
ACGTcount: A:0.49, C:0.12, G:0.15, T:0.24
Consensus pattern (110 bp):
AAAATGATACTAAATGCAACGACATTAGTAGCACAAATGGGATAAAATGAAAAAAAATAAGACCA
TACAATATTGACTTAGAAAATGCAATTACTAAGTATAAAATGCTG
Found at i:55843 original size:52 final size:52
Alignment explanation
Indices: 55722--55850 Score: 161
Period size: 52 Copynumber: 2.5 Consensus size: 52
55712 AAGAGATTTG
* ** * *
55722 TATACTCACAATGACACAGAGTCATCGGACCTCTTAATCCGTAAAGGATCCA
1 TATACTCACGATGACACTTAGTCATAGGACCTCTTAATCCATAAAGGATCCA
* *
55774 TATACTCATGATGACACTTAGTCATAGGACCT-TTAAATCCATAAAGGATTCA
1 TATACTCACGATGACACTTAGTCATAGGACCTCTT-AATCCATAAAGGATCCA
* *
55826 TTTACTCACGATGACACTTAATCAT
1 TATACTCACGATGACACTTAGTCAT
55851 CGAACCCTTT
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
51 2 0.03
52 64 0.97
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.29
Consensus pattern (52 bp):
TATACTCACGATGACACTTAGTCATAGGACCTCTTAATCCATAAAGGATCCA
Found at i:64438 original size:52 final size:52
Alignment explanation
Indices: 64382--64507 Score: 164
Period size: 52 Copynumber: 2.4 Consensus size: 52
64372 GTATACTTGT
** * * *
64382 GATGACACAGAGTCATCATACCTCTT-AATCCGTAAAGGATCCATATAGTCAC
1 GATGACACTTAGTCATCAGACCT-TTAAATCCATAAAGGATCCATATACTCAC
* *
64434 GATGACACTTAGTCATCAGACCTTTAAATCCATAAAGGATTCATTTACTCAC
1 GATGACACTTAGTCATCAGACCTTTAAATCCATAAAGGATCCATATACTCAC
*
64486 GATGACACTTAGTCATCGGACC
1 GATGACACTTAGTCATCAGACC
64508 CTTTTTCATT
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
51 2 0.03
52 63 0.97
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (52 bp):
GATGACACTTAGTCATCAGACCTTTAAATCCATAAAGGATCCATATACTCAC
Found at i:69890 original size:23 final size:21
Alignment explanation
Indices: 69835--69891 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 21
69825 ACTGAAAAAC
69835 AAAAAACAAAAAAAATATCAG
1 AAAAAACAAAAAAAATATCAG
* *
69856 AAAAAGACCAAAAGACATATCTAG
1 AAAAA-A-CAAAAAAAATATC-AG
69880 ATAAAAACAAAA
1 A-AAAAACAAAA
69892 CACCGTTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
21 5 0.17
22 1 0.03
23 16 0.53
24 4 0.13
25 4 0.13
ACGTcount: A:0.70, C:0.12, G:0.07, T:0.11
Consensus pattern (21 bp):
AAAAAACAAAAAAAATATCAG
Found at i:70920 original size:9 final size:9
Alignment explanation
Indices: 70902--70934 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
70892 GTCAATAAAT
70902 AATT-TTAA
1 AATTATTAA
70910 AATTATTAA
1 AATTATTAA
70919 AATTATTAA
1 AATTATTAA
70928 AATTATT
1 AATTATT
70935 TTTTTAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 4 0.17
9 20 0.83
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
AATTATTAA
Found at i:71075 original size:13 final size:13
Alignment explanation
Indices: 71057--71082 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
71047 TTATTTGATG
71057 ATTTGAAACTTTA
1 ATTTGAAACTTTA
71070 ATTTGAAACTTTA
1 ATTTGAAACTTTA
71083 GTCCCTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (13 bp):
ATTTGAAACTTTA
Found at i:71379 original size:22 final size:22
Alignment explanation
Indices: 71351--71394 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
71341 TCATGAAACT
* *
71351 AGGAACAGCCTCCTCAAAAGCA
1 AGGAACAACCTCCCCAAAAGCA
71373 AGGAACAACCTCCCCAAAAGCA
1 AGGAACAACCTCCCCAAAAGCA
71395 TTATACAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.34, G:0.16, T:0.07
Consensus pattern (22 bp):
AGGAACAACCTCCCCAAAAGCA
Found at i:71789 original size:18 final size:18
Alignment explanation
Indices: 71748--71792 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
71738 AATTGTTAAC
*
71748 TATTTTTTTAAATTTATT
1 TATTTTTTTAAATTTATA
*
71766 TATTTTTTTAAGTTTA-A
1 TATTTTTTTAAATTTATA
*
71783 TACTTTTTTA
1 TATTTTTTTA
71793 CTGACGTGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (18 bp):
TATTTTTTTAAATTTATA
Found at i:73429 original size:381 final size:381
Alignment explanation
Indices: 72726--73488 Score: 1508
Period size: 381 Copynumber: 2.0 Consensus size: 381
72716 GTTCCTCAAG
72726 TTTAAGTCGAAGCAAATTAATAAGAAATGCAATGAAAGTTTGAAGATAATTTGTCGGTGCAATTT
1 TTTAAGTCGAAGCAAATTAATAAGAAATGCAATGAAAGTTTGAAGATAATTTGTCGGTGCAATTT
72791 AAGAAAATTAAAGAAATAAAAACAATGATAATGGAATGGAGGATCTCTGACTTGATAAGTCGACA
66 AAGAAAATTAAAGAAATAAAAACAATGATAATGGAATGGAGGATCTCTGACTTGATAAGTCGACA
72856 AACCATTAAATGTGAGCACAAGGTAAATAATAGATAAATTGTCACCGCAATTAAGCTTAATGAGA
131 AACCATTAAATGTGAGCACAAGGTAAATAATAGATAAATTGTCACCGCAATTAAGCTTAATGAGA
* *
72921 TCTTACCAACTTCGACTTTCTTGTTTATCAAAGACTCAAATACTAACATTAACCACACCTTCCAA
196 TCTTACCAACTTCGACTTTCCTGTTTATCAAAGACTCAAATACTAACATTAACCACACATTCCAA
72986 TGCTGGCAATACTTTGCATTCAAGAATAAGTGGTCAGAATTCCTTCGTTCTCCAAGCAACTTCCG
261 TGCTGGCAATACTTTGCATTCAAGAATAAGTGGTCAGAATTCCTTCGTTCTCCAAGCAACTTCCG
73051 TTGTCTTATTTGTTAATTTAATTTGTCACTGCACTTTCTAGTGTCAATAACTATAA
326 TTGTCTTATTTGTTAATTTAATTTGTCACTGCACTTTCTAGTGTCAATAACTATAA
73107 TTTAAGTCGAAGCAAATTAATAAGAAATGCAATGAAAGTTTGAAGATAATTTGTCGGTGCAATTT
1 TTTAAGTCGAAGCAAATTAATAAGAAATGCAATGAAAGTTTGAAGATAATTTGTCGGTGCAATTT
73172 AAGAAAATTAAAGAAATAAAAACAATGATAATGGAATGGAGGATCTCTGACTTGATAAGTCGACA
66 AAGAAAATTAAAGAAATAAAAACAATGATAATGGAATGGAGGATCTCTGACTTGATAAGTCGACA
73237 AACCATTAAATGTGAGCACAAGGTAAATAATAGATAAATTGTCACCGCAATTAAGCTTAATGAGA
131 AACCATTAAATGTGAGCACAAGGTAAATAATAGATAAATTGTCACCGCAATTAAGCTTAATGAGA
73302 TCTTACCAACTTCGACTTTCCTGTTTATCAAAGACTCAAATACTAACATTAACCACACATTCCAA
196 TCTTACCAACTTCGACTTTCCTGTTTATCAAAGACTCAAATACTAACATTAACCACACATTCCAA
73367 TGCTGGCAATACTTTGCATTCAAGAATAAGTGGTCAGAATTCCTTCGTTCTCCAAGCAACTTCCG
261 TGCTGGCAATACTTTGCATTCAAGAATAAGTGGTCAGAATTCCTTCGTTCTCCAAGCAACTTCCG
73432 TTGTCTTATTTGTTAATTTAATTTGTCACTGCACTTTCTAGTGTCAATAACTATAA
326 TTGTCTTATTTGTTAATTTAATTTGTCACTGCACTTTCTAGTGTCAATAACTATAA
73488 T
1 T
73489 AGCACTTTCG
Statistics
Matches: 380, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
381 380 1.00
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (381 bp):
TTTAAGTCGAAGCAAATTAATAAGAAATGCAATGAAAGTTTGAAGATAATTTGTCGGTGCAATTT
AAGAAAATTAAAGAAATAAAAACAATGATAATGGAATGGAGGATCTCTGACTTGATAAGTCGACA
AACCATTAAATGTGAGCACAAGGTAAATAATAGATAAATTGTCACCGCAATTAAGCTTAATGAGA
TCTTACCAACTTCGACTTTCCTGTTTATCAAAGACTCAAATACTAACATTAACCACACATTCCAA
TGCTGGCAATACTTTGCATTCAAGAATAAGTGGTCAGAATTCCTTCGTTCTCCAAGCAACTTCCG
TTGTCTTATTTGTTAATTTAATTTGTCACTGCACTTTCTAGTGTCAATAACTATAA
Found at i:80692 original size:17 final size:17
Alignment explanation
Indices: 80670--80708 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
80660 ACAACCTAAT
80670 GTTTCAATACTTTTGTC
1 GTTTCAATACTTTTGTC
80687 GTTTCAATACTTTTGTC
1 GTTTCAATACTTTTGTC
80704 GTTTC
1 GTTTC
80709 CATGAAGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.15, C:0.18, G:0.13, T:0.54
Consensus pattern (17 bp):
GTTTCAATACTTTTGTC
Found at i:90170 original size:18 final size:18
Alignment explanation
Indices: 90149--90196 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
90139 AGTTGAAACC
90149 TGAGGAGAAGAAAGAAAA
1 TGAGGAGAAGAAAGAAAA
*
90167 TGAGGA-AGAGAAGGAAAA
1 TGAGGAGA-AGAAAGAAAA
*
90185 AGAGGAGAAGAA
1 TGAGGAGAAGAA
90197 TGAAGAGAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 1 0.04
18 24 0.92
19 1 0.04
ACGTcount: A:0.58, C:0.00, G:0.38, T:0.04
Consensus pattern (18 bp):
TGAGGAGAAGAAAGAAAA
Found at i:91167 original size:9 final size:9
Alignment explanation
Indices: 91150--91200 Score: 57
Period size: 9 Copynumber: 5.6 Consensus size: 9
91140 TCATTTATAA
91150 AAAAAAAAG
1 AAAAAAAAG
*
91159 AAAAGAAAG
1 AAAAAAAAG
91168 AAAAAAAAG
1 AAAAAAAAG
**
91177 AAGGAAAAG
1 AAAAAAAAG
*
91186 AGAAAAGAAG
1 A-AAAAAAAG
91196 AAAAA
1 AAAAA
91201 GGAAATATAT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
9 28 0.82
10 6 0.18
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:91173 original size:16 final size:16
Alignment explanation
Indices: 91152--91205 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 16
91142 ATTTATAAAA
91152 AAAAAAGAAAAGAAAG
1 AAAAAAGAAAAGAAAG
*
91168 --AAAA-AAAAGAAGG
1 AAAAAAGAAAAGAAAG
*
91181 AAAAGAGAAAAG-AAG
1 AAAAAAGAAAAGAAAG
*
91196 AAAAAGGAAA
1 AAAAAAGAAA
91206 TATATGCTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
13 8 0.27
14 4 0.13
15 13 0.43
16 5 0.17
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (16 bp):
AAAAAAGAAAAGAAAG
Found at i:91177 original size:13 final size:14
Alignment explanation
Indices: 91154--91199 Score: 51
Period size: 13 Copynumber: 3.3 Consensus size: 14
91144 TTATAAAAAA
91154 AAAAGAAAAGAAAG
1 AAAAGAAAAGAAAG
*
91168 AAAA-AAAAGAAGG
1 AAAAGAAAAGAAAG
91181 AAAAGAGAAA-AGAAG
1 AAAAGA-AAAGA-AAG
91196 AAAA
1 AAAA
91200 AGGAAATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 12 0.44
14 6 0.22
15 9 0.33
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAGAAAG
Found at i:95406 original size:17 final size:17
Alignment explanation
Indices: 95395--95433 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
95385 CAAATGCATT
95395 GACAAATAAAATGCAAA
1 GACAAATAAAATGCAAA
*
95412 GACAATTAAAATG-AAA
1 GACAAATAAAATGCAAA
95428 TGACAA
1 -GACAA
95434 CTATATGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.62, C:0.10, G:0.13, T:0.15
Consensus pattern (17 bp):
GACAAATAAAATGCAAA
Found at i:95858 original size:12 final size:12
Alignment explanation
Indices: 95837--95882 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
95827 TCGCTGCAAA
*
95837 TTCTTCTTCTTT
1 TTCTTCTTCTCT
*
95849 TTCTTTTTCTCT
1 TTCTTCTTCTCT
95861 TTCTTCTTCTCT
1 TTCTTCTTCTCT
95873 CTTC-TCTTCT
1 -TTCTTCTTCT
95883 TCCTCCTCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
12 27 0.90
13 3 0.10
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (12 bp):
TTCTTCTTCTCT
Found at i:95879 original size:19 final size:17
Alignment explanation
Indices: 95857--95893 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
95847 TTTTCTTTTT
95857 CTCTT-TCTTCTT-CT-
1 CTCTTCTCTTCTTCCTC
95871 CTCTTCTCTTCTTCCTC
1 CTCTTCTCTTCTTCCTC
95888 CTCTTC
1 CTCTTC
95894 CTCAGCACCC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 5 0.25
15 7 0.35
16 2 0.10
17 6 0.30
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (17 bp):
CTCTTCTCTTCTTCCTC
Found at i:104217 original size:18 final size:18
Alignment explanation
Indices: 104194--104237 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
104184 GCAAGCTAAA
104194 GAAGAAGAAGAAGACCCT
1 GAAGAAGAAGAAGACCCT
*
104212 GAAGAAGAAGAAGATCCT
1 GAAGAAGAAGAAGACCCT
*
104230 GAGGAAGA
1 GAAGAAGA
104238 TCCTGTGGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.50, C:0.11, G:0.32, T:0.07
Consensus pattern (18 bp):
GAAGAAGAAGAAGACCCT
Found at i:107700 original size:26 final size:28
Alignment explanation
Indices: 107671--107728 Score: 84
Period size: 26 Copynumber: 2.1 Consensus size: 28
107661 GCATAGGAAT
* *
107671 TTAATTTAGTTTAGCTTTA-AC-TTAGA
1 TTAATTTAGTTTAGATTAATACTTTAGA
107697 TTAATTTAGTTTAGATTAATACTTTAGA
1 TTAATTTAGTTTAGATTAATACTTTAGA
107725 TTAA
1 TTAA
107729 CATCCTTTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 17 0.61
27 2 0.07
28 9 0.32
ACGTcount: A:0.34, C:0.05, G:0.10, T:0.50
Consensus pattern (28 bp):
TTAATTTAGTTTAGATTAATACTTTAGA
Found at i:112229 original size:36 final size:36
Alignment explanation
Indices: 112178--112248 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
112168 TCTAATGAAC
112178 ACTCAAAAAACGCTATGCAAGGACTAAAGAACCAAT
1 ACTCAAAAAACGCTATGCAAGGACTAAAGAACCAAT
*
112214 ACTCAAAAAAGGCTATGCAAGGACTAAAGAACCAA
1 ACTCAAAAAACGCTATGCAAGGACTAAAGAACCAA
112249 CCTTTTCCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.51, C:0.21, G:0.15, T:0.13
Consensus pattern (36 bp):
ACTCAAAAAACGCTATGCAAGGACTAAAGAACCAAT
Found at i:124093 original size:2 final size:2
Alignment explanation
Indices: 124086--124121 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
124076 CTTTAATTTC
124086 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
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
Done.