Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011620.1 Kokia drynarioides strain JFW-HI SEQ_126610, 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: 41192
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Found at i:3429 original size:23 final size:22
Alignment explanation
Indices: 3399--3548 Score: 117
Period size: 23 Copynumber: 6.5 Consensus size: 22
3389 ACGCTAGCGC
3399 GCTTACTG-TTCAGCACTGTGTGT
1 GCTTACTGTTTC-GCACT-TGTGT
*
3422 GCTTACTGTTTCGCATTTTGTGT
1 GCTTACTGTTTCGCA-CTTGTGT
3445 GCTTACTGTTTCGCACCTTGTGT
1 GCTTACTGTTTCGCA-CTTGTGT
* * * *
3468 GCCTACT-TATTTGCGCTATGTGC
1 GCTTACTGT-TTCGCACT-TGTGT
* *
3491 GCCTACTGATT-GCACTGTGTGT
1 GCTTACTGTTTCGCACT-TGTGT
3513 GCTTACTGTTTCCCCAGCACTTGTGT
1 GCTTACTGTTT---C-GCACTTGTGT
3539 GCTTACTGTT
1 GCTTACTGTT
3549 AAGTACTTCG
Statistics
Matches: 104, Mismatches: 13, Indels: 17
0.78 0.10 0.13
Matches are distributed among these distances:
22 20 0.19
23 60 0.58
24 4 0.04
26 15 0.14
27 5 0.05
ACGTcount: A:0.11, C:0.24, G:0.23, T:0.42
Consensus pattern (22 bp):
GCTTACTGTTTCGCACTTGTGT
Found at i:6241 original size:62 final size:62
Alignment explanation
Indices: 6169--6299 Score: 253
Period size: 62 Copynumber: 2.1 Consensus size: 62
6159 TCGAGGGCAT
6169 ACGGGCTAGCACATGGGTGTGTGTCCAGACCATGTGCCATTAAAATAAGCTTCAGAGGACAC
1 ACGGGCTAGCACATGGGTGTGTGTCCAGACCATGTGCCATTAAAATAAGCTTCAGAGGACAC
*
6231 ACGGGCTAGCACATGGGTGTGTGTCCAGACCGTGTGCCATTAAAATAAGCTTCAGAGGACAC
1 ACGGGCTAGCACATGGGTGTGTGTCCAGACCATGTGCCATTAAAATAAGCTTCAGAGGACAC
6293 ACGGGCT
1 ACGGGCT
6300 GTGCCCACGG
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
62 68 1.00
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.21
Consensus pattern (62 bp):
ACGGGCTAGCACATGGGTGTGTGTCCAGACCATGTGCCATTAAAATAAGCTTCAGAGGACAC
Found at i:6855 original size:39 final size:39
Alignment explanation
Indices: 6811--7023 Score: 196
Period size: 39 Copynumber: 5.4 Consensus size: 39
6801 AAACTGGTAA
* *
6811 TGACACTGTAAACATTGCAATGATATACTAAACTAACAG
1 TGACACTGTAAACACTGCAATGATATACTAAACTAGCAG
**
6850 TGACACTGTAAATGCTGCAATGATATA-TATTGAACTAGCAG
1 TGACACTGTAAACACTGCAATGATATACTA---AACTAGCAG
* * **
6891 TGACATTGTAAACACTGTAATGATATACTGCACTAGCAG
1 TGACACTGTAAACACTGCAATGATATACTAAACTAGCAG
** * * * **
6930 TGACACTGTAAACACTGCAATGCCAAACTAAATTGGTGG
1 TGACACTGTAAACACTGCAATGATATACTAAACTAGCAG
* * * * *
6969 TGACACTGTAAACA-TCGCAATGTTATACTGAAGTAGTAA
1 TGACACTGTAAACACT-GCAATGATATACTAAACTAGCAG
7008 TGACACTGTAAACACT
1 TGACACTGTAAACACT
7024 ACTAGACTAT
Statistics
Matches: 139, Mismatches: 29, Indels: 11
0.78 0.16 0.06
Matches are distributed among these distances:
38 3 0.02
39 103 0.74
40 1 0.01
41 31 0.22
42 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (39 bp):
TGACACTGTAAACACTGCAATGATATACTAAACTAGCAG
Found at i:8654 original size:17 final size:17
Alignment explanation
Indices: 8632--8687 Score: 69
Period size: 17 Copynumber: 3.3 Consensus size: 17
8622 TGGACCCCTT
8632 TTAAATTTGTTTTAAGA
1 TTAAATTTGTTTTAAGA
8649 TTAAATTTGTTTTAA-A
1 TTAAATTTGTTTTAAGA
** *
8665 TTTAAATTTAATTTAAGT
1 -TTAAATTTGTTTTAAGA
8683 TTAAA
1 TTAAA
8688 CTTATATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
16 1 0.03
17 33 0.97
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (17 bp):
TTAAATTTGTTTTAAGA
Found at i:8680 original size:34 final size:33
Alignment explanation
Indices: 8631--8704 Score: 85
Period size: 34 Copynumber: 2.2 Consensus size: 33
8621 CTGGACCCCT
** * * *
8631 TTTAAATTTGTTTTAAGATTAAATTTGTTTTAAA
1 TTTAAATTTAATTTAAGATTAAACTT-ATATAAA
*
8665 TTTAAATTTAATTTAAGTTTAAACTTATATAAA
1 TTTAAATTTAATTTAAGATTAAACTTATATAAA
8698 TTTAAAT
1 TTTAAAT
8705 AAATGTCCAA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
33 12 0.35
34 22 0.65
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.53
Consensus pattern (33 bp):
TTTAAATTTAATTTAAGATTAAACTTATATAAA
Found at i:9454 original size:96 final size:97
Alignment explanation
Indices: 9328--9638 Score: 326
Period size: 96 Copynumber: 3.2 Consensus size: 97
9318 GAAGACATGC
* *
9328 AGGGAAA-ATCTAAGCCGCCACGGCAGATCCAGTACCACGAAGACACAAGGGAAAGATCTAAGCC
1 AGGGAAAGATCTAAGTCGCAACGGCAGATCCAGTACCACGAAGACACAAGGGAAAGATCTAAGCC
*
9392 GTAACGGCGGATCCAATACCACAAAGACAC-A
66 GCAACGGCGGATCCAATACCACAAAGACACAA
* *
9423 AGGGAAAGATCTAAGTCGCAACGG-TGAATCCAGTACCACGAAGACACAAGGGAAATATCTAAGC
1 AGGGAAAGATCTAAGTCGCAACGGCAG-ATCCAGTACCACGAAGACACAAGGGAAAGATCTAAGC
* ***
9487 CGCAACGGCGGATCCAGTACTGGAAAGACACAA
65 CGCAACGGCGGATCCAATACCACAAAGACACAA
* * * * * * * *
9520 AGGGAAAGGTTTAAGTCGCAACGGCA-AACCTTGTACCTC-AGAGACATGAAAGGAAAGATTTAA
1 AGGGAAAGATCTAAGTCGCAACGGCAGATCC-AGTACCACGA-AGACA-CAAGGGAAAGATCTAA
* * * * * *
9583 GCCGCAATGGCGAATCTAGTACCACGAAGGCACAA
63 GCCGCAACGGCGGATCCAATACCACAAAGACACAA
* *
9618 AGGGAAAGGTTTAAGTCGCAA
1 AGGGAAAGATCTAAGTCGCAA
9639 TGACGAACCT
Statistics
Matches: 182, Mismatches: 27, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
95 8 0.04
96 80 0.44
97 34 0.19
98 60 0.33
ACGTcount: A:0.39, C:0.23, G:0.25, T:0.13
Consensus pattern (97 bp):
AGGGAAAGATCTAAGTCGCAACGGCAGATCCAGTACCACGAAGACACAAGGGAAAGATCTAAGCC
GCAACGGCGGATCCAATACCACAAAGACACAA
Found at i:9640 original size:49 final size:48
Alignment explanation
Indices: 9328--9625 Score: 291
Period size: 48 Copynumber: 6.2 Consensus size: 48
9318 GAAGACATGC
*
9328 AGGGAAA-ATCTAAGCCGCCACGGC-AGATCCAGTACCACGAAGACACA
1 AGGGAAAGATCTAAGCCGCAACGGCGA-ATCCAGTACCACGAAGACACA
* * * *
9375 AGGGAAAGATCTAAGCCGTAACGGCGGATCCAATACCACAAAGACACA
1 AGGGAAAGATCTAAGCCGCAACGGCGAATCCAGTACCACGAAGACACA
* *
9423 AGGGAAAGATCTAAGTCGCAACGGTGAATCCAGTACCACGAAGACACA
1 AGGGAAAGATCTAAGCCGCAACGGCGAATCCAGTACCACGAAGACACA
* * **
9471 AGGGAAATATCTAAGCCGCAACGGCGGATCCAGTA-CTGGAAAGACACAA
1 AGGGAAAGATCTAAGCCGCAACGGCGAATCCAGTACCACG-AAGACAC-A
* * * * * * *
9520 AGGGAAAGGTTTAAGTCGCAACGGC-AAACCTTGTACCTC-AGAGACATGA
1 AGGGAAAGATCTAAGCCGCAACGGCGAATCC-AGTACCACGA-AGACA-CA
* * * * *
9569 AAGGAAAGATTTAAGCCGCAATGGCGAATCTAGTACCACGAAGGCACAA
1 AGGGAAAGATCTAAGCCGCAACGGCGAATCCAGTACCACGAAGACAC-A
9618 AGGGAAAG
1 AGGGAAAG
9626 GTTTAAGTCG
Statistics
Matches: 203, Mismatches: 37, Indels: 20
0.78 0.14 0.08
Matches are distributed among these distances:
47 9 0.04
48 118 0.58
49 70 0.34
50 6 0.03
ACGTcount: A:0.39, C:0.23, G:0.26, T:0.12
Consensus pattern (48 bp):
AGGGAAAGATCTAAGCCGCAACGGCGAATCCAGTACCACGAAGACACA
Found at i:10329 original size:6 final size:6
Alignment explanation
Indices: 10315--10419 Score: 94
Period size: 6 Copynumber: 18.2 Consensus size: 6
10305 TTAAATTTGT
* * *
10315 TTTAAA TTTAGA TTT-AT TTTAAA TTTAAA TTTAAA TTT-AT TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * ** *
10361 TTTAAA ATT-AA TTTAAG TTTAAA TTTATT TTTAAA TTTAAA ATT--A
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
10406 TTATAAA TTTAAA T
1 TT-TAAA TTTAAA T
10420 AAATGTCCAA
Statistics
Matches: 77, Mismatches: 16, Indels: 12
0.73 0.15 0.11
Matches are distributed among these distances:
4 2 0.03
5 12 0.16
6 60 0.78
7 3 0.04
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:10329 original size:17 final size:17
Alignment explanation
Indices: 10304--10419 Score: 106
Period size: 17 Copynumber: 6.4 Consensus size: 17
10294 TCGGGCCCCT
*
10304 TTTAAATTTGTTTTAAA
1 TTTAAATTTATTTTAAA
*
10321 TTTAGATTTATTTTAAATTTAAA
1 TTTAAATTTA--TT---TT-AAA
10344 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* * *
10361 TTTAAAATTAATTTAAG
1 TTTAAATTTATTTTAAA
10378 TTTAAATTTATTTTTAAA
1 TTTAAATTTA-TTTTAAA
* *
10396 TTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAA
10413 TTTAAAT
1 TTTAAAT
10420 AAATGTCCAA
Statistics
Matches: 80, Mismatches: 12, Indels: 14
0.75 0.11 0.13
Matches are distributed among these distances:
17 46 0.57
18 16 0.20
19 2 0.03
21 2 0.03
22 2 0.03
23 12 0.15
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:10335 original size:11 final size:11
Alignment explanation
Indices: 10321--10399 Score: 70
Period size: 11 Copynumber: 6.9 Consensus size: 11
10311 TTGTTTTAAA
*
10321 TTTAGATTTAT
1 TTTAAATTTAT
*
10332 TTTAAATTTAAA
1 TTTAAATTT-AT
10344 TTTAAATTTAT
1 TTTAAATTTAT
*
10355 TTTAAATTTAAA
1 TTTAAATTT-AT
* *
10367 ATT-AATTTAAG
1 TTTAAATTT-AT
10378 TTTAAATTTATT
1 TTTAAATTTA-T
10390 TTTAAATTTA
1 TTTAAATTTA
10400 AAATTATTAT
Statistics
Matches: 56, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
11 28 0.50
12 28 0.50
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:10341 original size:23 final size:22
Alignment explanation
Indices: 10315--10387 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 22
10305 TTAAATTTGT
10315 TTTAAATTTAGATTTATTTTAAA
1 TTTAAATTTA-ATTTATTTTAAA
10338 TTTAAATTTAAATTTATTTTAAA
1 TTTAAATTT-AATTTATTTTAAA
* *
10361 TTTAAAATTAATTTAAGTTTAAA
1 TTTAAATTTAATTT-ATTTTAAA
10384 TTTA
1 TTTA
10388 TTTTTAAATT
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
22 5 0.11
23 40 0.87
24 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (22 bp):
TTTAAATTTAATTTATTTTAAA
Found at i:10394 original size:23 final size:23
Alignment explanation
Indices: 10315--10400 Score: 68
Period size: 23 Copynumber: 3.7 Consensus size: 23
10305 TTAAATTTGT
* *
10315 TTTAAATTTAGATTT-ATTTTAAA
1 TTTAATTTTA-ATTTAAGTTTAAA
* *
10338 TTTAAATTTAAATTT-ATTTTAAA
1 TTT-AATTTTAATTTAAGTTTAAA
**
10361 TTTAAAATTAATTTAAGTTTAAA
1 TTTAATTTTAATTTAAGTTTAAA
*
10384 TTTATTTTTAAATTTAA
1 TTTAATTTT-AATTTAA
10401 AATTATTATA
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
22 8 0.16
23 31 0.61
24 12 0.24
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
TTTAATTTTAATTTAAGTTTAAA
Found at i:11097 original size:3 final size:3
Alignment explanation
Indices: 11089--11174 Score: 84
Period size: 3 Copynumber: 28.3 Consensus size: 3
11079 ACCTTTAGTC
*
11089 ATA ATA ATA ATA AT- ATCG ATA ATAA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA AT-A ATA AT-A ATA ATA ATA ATA ATA ATA ATA
* * * * **
11135 ATA ACA TTA ATA ATA TTA ATG ACG ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
11175 ATATTATTAA
Statistics
Matches: 69, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
2 2 0.03
3 62 0.90
4 5 0.07
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:12321 original size:29 final size:29
Alignment explanation
Indices: 12287--12885 Score: 276
Period size: 29 Copynumber: 20.4 Consensus size: 29
12277 CAAAAATCAT
* *
12287 ATTTTTACCCTCGAACTTTCTAAAATTTC
1 ATTTTTACCCTCGAACTTTCCAAAATTAC
* * *
12316 ATTTTTAACCCT-AAACTTTTCAAAAATTAA
1 ATTTTT-ACCCTCGAAC-TTTCCAAAATTAC
* * *
12346 AATTTTACCC-CAAAACTTTCCAAAATTCC
1 ATTTTTACCCTC-GAACTTTCCAAAATTAC
* * *
12375 ATTTTAACCC-CTATCTTTCCAAAAATTACC
1 ATTTTTACCCTCGAACTTTCC-AAAATTA-C
* *
12405 A-TTTTACCATCGAACTTTCCAAAATTTC
1 ATTTTTACCCTCGAACTTTCCAAAATTAC
* *
12433 ATTTTTA-CCTTGAACTTTCTAAAAATTAC
1 ATTTTTACCCTCGAACTTTC-CAAAATTAC
* *
12462 ATTTTTACCCTCGAACTTTCTAAAATTCC
1 ATTTTTACCCTCGAACTTTCCAAAATTAC
*
12491 ATTTTTAACCC-CGATCTTTCCAAAATTAC
1 ATTTTT-ACCCTCGAACTTTCCAAAATTAC
12520 -TATTTTACCCTCGAACTTTCCAAAATT-C
1 AT-TTTTACCCTCGAACTTTCCAAAATTAC
* **
12548 TATTTTTGA-CCTTGAACTTTTTGAAAATTAC
1 -ATTTTT-ACCCTCGAAC-TTTCCAAAATTAC
* *
12579 ATATTTACCCTCGAAC-TTCCAAAAATTCC
1 ATTTTTACCCTCGAACTTTCC-AAAATTAC
* * **
12608 ATTTTTAGACCTTGATTTTTCCAAAAGTTACC
1 ATTTTTA-CCCTCGAACTTTCCAAAA-TTA-C
* * * *
12640 A-TTTTCCCCCCGAACTTT-AAAAATTCC
1 ATTTTTACCCTCGAACTTTCCAAAATTAC
*** *
12667 ATTTTTGACCC-C-TTTTTTCAAAAAATTACC
1 ATTTTT-ACCCTCGAACTTTC-CAAAATTA-C
*
12697 A-TTTTACCC-CTAAAC-TTCCTAAAATT-C
1 ATTTTTACCCTC-GAACTTTCC-AAAATTAC
* * *
12724 TATTTTTGACCC-CGATTCTTTTCATAATTACC
1 -ATTTTT-ACCCTCGA-ACTTTCCAAAATTA-C
* * *
12756 A-TTTTACCCCCAAAC-TTCCAAAAATTTC
1 ATTTTTACCCTCGAACTTTCC-AAAATTAC
* *
12784 ATTTTTGATCC-CGATCCTTTCCAAAAATTACC
1 ATTTTT-ACCCTCGA-ACTTTCC-AAAATTA-C
* * * *
12816 A-TTTTACCCCCGAAC-GTCTAAAATTTC
1 ATTTTTACCCTCGAACTTTCCAAAATTAC
* *
12843 ATTTTTTAACCCCCGAACTTTCCCAAGATTACC
1 A-TTTTT-ACCCTCGAACTTT-CCAAAATTA-C
12876 A-TTTTACCCT
1 ATTTTTACCCT
12886 TGGATACCCA
Statistics
Matches: 434, Mismatches: 83, Indels: 105
0.70 0.13 0.17
Matches are distributed among these distances:
27 8 0.02
28 51 0.12
29 195 0.45
30 129 0.30
31 38 0.09
32 11 0.03
33 2 0.00
ACGTcount: A:0.31, C:0.26, G:0.04, T:0.39
Consensus pattern (29 bp):
ATTTTTACCCTCGAACTTTCCAAAATTAC
Found at i:12363 original size:59 final size:58
Alignment explanation
Indices: 12289--12884 Score: 360
Period size: 59 Copynumber: 10.1 Consensus size: 58
12279 AAAATCATAT
**
12289 TTTTACCCTCGAACTTTCTAAAATTTCATTTTTAACCCTAAACTTTTCAAAAATTAAAA
1 TTTTACCC-CGAACTTTCTAAAATTTCATTTTTAACCCTAAACTTTTCAAAAATTACCA
* * * * *
12348 TTTTACCCCAAAACTTTCCAAAATTCCA-TTTTAACCCCT-ATCTTTCCAAAAATTACCA
1 TTTTACCCC-GAACTTTCTAAAATTTCATTTTTAA-CCCTAAACTTTTCAAAAATTACCA
* * * *
12406 TTTTACCATCGAACTTTCCAAAATTTCATTTTT-ACCTTGAAC-TTTCTAAAAATTA-CA
1 TTTTACC-CCGAACTTTCTAAAATTTCATTTTTAACCCTAAACTTTTC-AAAAATTACCA
* ** * * *
12463 TTTTTACCCTCGAACTTTCTAAAATTCCATTTTTAACCCCGATC-TTTCCAAAATTACTA
1 -TTTTACCC-CGAACTTTCTAAAATTTCATTTTTAACCCTAAACTTTTCAAAAATTACCA
* * * * **
12522 TTTTACCCTCGAACTTTCCAAAA-TTCTATTTTTGACCTTGAACTTTTTGAAAATTA-CA
1 TTTTACCC-CGAACTTTCTAAAATTTC-ATTTTTAACCCTAAACTTTTCAAAAATTACCA
* * * ** * *
12580 TATTTACCCTCGAACTTCCAAAAATTCCATTTTTAGA-CCTTGATTTTTCCAAAAGTTACCA
1 T-TTTACCC-CGAACTTTCTAAAATTTCATTTTTA-ACCCTAAACTTTT-CAAAAATTACCA
* * * * *
12641 TTTTCCCCCCGAACTTT-AAAAATTCCATTTTTGACCCCT---TTTTTCAAAAAATTACCA
1 TTTT-ACCCCGAACTTTCTAAAATTTCATTTTT-AACCCTAAACTTTTC-AAAAATTACCA
* * * * ** *
12698 TTTTACCCCTAAACTTCCTAAAA-TTCTATTTTTGACCCCGATTCTTTTC-ATAATTACCA
1 TTTTACCCC-GAACTTTCTAAAATTTC-ATTTTT-AACCCTAAACTTTTCAAAAATTACCA
* * * * * ** *
12757 TTTTACCCCCAAACTTCCAAAAATTTCATTTTTGATCCCGATCCTTTCCAAAAATTACCA
1 TTTTA-CCCCGAACTTTCTAAAATTTCATTTTT-AACCCTAAACTTTTCAAAAATTACCA
* ** * * *
12817 TTTTACCCCCGAAC-GTCTAAAATTTCATTTTTTAACCCCCGAACTTTCCCAAGATTACCA
1 TTTTA-CCCCGAACTTTCTAAAATTTCA-TTTTTAA-CCCTAAACTTTTCAAAAATTACCA
12877 TTTTACCC
1 TTTTACCC
12885 TTGGATACCC
Statistics
Matches: 436, Mismatches: 69, Indels: 64
0.77 0.12 0.11
Matches are distributed among these distances:
56 5 0.01
57 36 0.08
58 144 0.33
59 160 0.37
60 80 0.18
61 11 0.03
ACGTcount: A:0.31, C:0.26, G:0.04, T:0.39
Consensus pattern (58 bp):
TTTTACCCCGAACTTTCTAAAATTTCATTTTTAACCCTAAACTTTTCAAAAATTACCA
Found at i:12409 original size:58 final size:58
Alignment explanation
Indices: 12289--12884 Score: 432
Period size: 58 Copynumber: 10.1 Consensus size: 58
12279 AAAATCATAT
* * * * **
12289 TTTTACCCTCGAACTTTCTAAAATTTCATTTTTAA-CCCTAAACTTTTCAAAAATTAAAA
1 TTTTACCC-CGAACTTTCCAAAATTCCATTTTTAACCCCT-ATCTTTCCAAAAATTACCA
*
12348 TTTTACCCCAAAACTTTCCAAAATTCCA-TTTTAACCCCTATCTTTCCAAAAATTACCA
1 TTTTACCCC-GAACTTTCCAAAATTCCATTTTTAACCCCTATCTTTCCAAAAATTACCA
* * * * *
12406 TTTTACCATCGAACTTTCCAAAATTTCATTTTT-A-CCTTGAACTTTCTAAAAATTA-CA
1 TTTTACC-CCGAACTTTCCAAAATTCCATTTTTAACCCCT-ATCTTTCCAAAAATTACCA
* * *
12463 TTTTTACCCTCGAACTTTCTAAAATTCCATTTTTAACCCCGATCTTTCC-AAAATTACTA
1 -TTTTACCC-CGAACTTTCCAAAATTCCATTTTTAACCCCTATCTTTCCAAAAATTACCA
* * * * ***
12522 TTTTACCCTCGAACTTTCCAAAATTCTATTTTTGA-CCTTGAACTTTTTGAAAATTA-CA
1 TTTTACCC-CGAACTTTCCAAAATTCCATTTTTAACCCCT-ATCTTTCCAAAAATTACCA
* * *
12580 TATTTACCCTCGAAC-TTCCAAAAATTCCATTTTTAGA-CCTTGATTTTTCCAAAAGTTACCA
1 T-TTTACCC-CGAACTTTCC-AAAATTCCATTTTTA-ACCCCT-ATCTTTCCAAAAATTACCA
* * * * *
12641 TTTTCCCCCCGAACTTT-AAAAATTCCATTTTTGACCCCT-TTTTTCAAAAAATTACCA
1 TTTT-ACCCCGAACTTTCCAAAATTCCATTTTTAACCCCTATCTTTCCAAAAATTACCA
* * * * * *
12698 TTTTACCCCTAAAC-TTCCTAAAATTCTATTTTTGACCCCGATTCTTTTC-ATAATTACCA
1 TTTTACCCC-GAACTTTCC-AAAATTCCATTTTTAACCCCTA-TCTTTCCAAAAATTACCA
* * * * *
12757 TTTTACCCCCAAAC-TTCCAAAAATTTCATTTTTGATCCCGATCCTTTCCAAAAATTACCA
1 TTTTA-CCCCGAACTTTCC-AAAATTCCATTTTTAACCCCTAT-CTTTCCAAAAATTACCA
* * * * * * *
12817 TTTTACCCCCGAAC-GTCTAAAATTTCATTTTTTAACCCCCGAACTTTCCCAAGATTACCA
1 TTTTA-CCCCGAACTTTCCAAAATTCCA-TTTTTAA-CCCCTATCTTTCCAAAAATTACCA
12877 TTTTACCC
1 TTTTACCC
12885 TTGGATACCC
Statistics
Matches: 441, Mismatches: 67, Indels: 58
0.78 0.12 0.10
Matches are distributed among these distances:
56 6 0.01
57 30 0.07
58 160 0.36
59 148 0.34
60 84 0.19
61 13 0.03
ACGTcount: A:0.31, C:0.26, G:0.04, T:0.39
Consensus pattern (58 bp):
TTTTACCCCGAACTTTCCAAAATTCCATTTTTAACCCCTATCTTTCCAAAAATTACCA
Found at i:12703 original size:176 final size:174
Alignment explanation
Indices: 12289--12884 Score: 559
Period size: 176 Copynumber: 3.4 Consensus size: 174
12279 AAAATCATAT
* * ** * **
12289 TTTTACCCTCGAACTTTCTAAAATTTCATTTTTAACCCTAAACTTTTCAAAAATTAAAATTTTAC
1 TTTTACCCCCGAAC-TT-TAAAATTCCATTTTTAACCCCGATC-TTTCAAAAATTACCATTTTAC
* * * * * *
12354 CCCAAAACTTTCC-AAAATTCCA-TTTTAACCCCTA-TCTTTCCAAAAATTACCATTTTACCATC
63 CCCTAAAC-TTCCTAAAATTCTATTTTTGACCCCGACTCTTTTC-AAAATTACCATTTTACCCTC
* *
12416 GAACTTTCC-AAAATTTCATTTTT-ACCTTGAACTTTCTAAAAATTA-CA
126 GAAC-TTCCAAAAATTTCATTTTTGACCTTGATCTTTCCAAAAATTACCA
* * *
12463 TTTTTACCCTCGAACTTTCTAAAATTCCATTTTTAACCCCGATCTTTCCAAAATTACTATTTTA-
1 -TTTTACCCCCGAAC-TT-TAAAATTCCATTTTTAACCCCGATCTTTCAAAAATTACCATTTTAC
* ** *
12527 CCCTCGAACTTTCC-AAAATTCTATTTTTGACCTTGAACT-TTTTGAAAATTA-CATATTTACCC
63 CCCT-AAAC-TTCCTAAAATTCTATTTTTGACCCCG-ACTCTTTTCAAAATTACCAT-TTTACCC
* * *
12589 TCGAACTTCCAAAAATTCCATTTTTAGACCTTGATTTTTCCAAAAGTTACCA
124 TCGAACTTCCAAAAATTTCATTTTT-GACCTTGATCTTTCCAAAAATTACCA
* * * *
12641 TTTTCCCCCCGAACTTTAAAAATTCCATTTTTGACCCC-TTTTTTCAAAAAATTACCATTTTACC
1 TTTTACCCCCGAACTTT-AAAATTCCATTTTTAACCCCGATCTTTC-AAAAATTACCATTTTACC
* * * *
12705 CCTAAACTTCCTAAAATTCTATTTTTGACCCCGATTCTTTTCATAATTACCATTTTACCCCCAAA
64 CCTAAACTTCCTAAAATTCTATTTTTGACCCCGACTCTTTTCAAAATTACCATTTTACCCTCGAA
*
12770 CTTCCAAAAATTTCATTTTTGATCC-CGATCCTTTCCAAAAATTACCA
129 CTTCCAAAAATTTCATTTTTGA-CCTTGAT-CTTTCCAAAAATTACCA
* * * * *
12817 TTTTACCCCCGAACGTCTAAAATTTCATTTTTTAACCCCCGAACTTTCCCAAGATTACCATTTTA
1 TTTTACCCCCGAAC-TTTAAAATTCCA-TTTTTAA-CCCCGATCTTT-CAAAAATTACCATTTTA
12882 CCC
62 CCC
12885 TTGGATACCC
Statistics
Matches: 349, Mismatches: 50, Indels: 40
0.79 0.11 0.09
Matches are distributed among these distances:
173 3 0.01
174 40 0.11
175 95 0.27
176 138 0.40
177 46 0.13
178 6 0.02
179 20 0.06
180 1 0.00
ACGTcount: A:0.31, C:0.26, G:0.04, T:0.39
Consensus pattern (174 bp):
TTTTACCCCCGAACTTTAAAATTCCATTTTTAACCCCGATCTTTCAAAAATTACCATTTTACCCC
TAAACTTCCTAAAATTCTATTTTTGACCCCGACTCTTTTCAAAATTACCATTTTACCCTCGAACT
TCCAAAAATTTCATTTTTGACCTTGATCTTTCCAAAAATTACCA
Found at i:18170 original size:29 final size:28
Alignment explanation
Indices: 18138--18234 Score: 81
Period size: 29 Copynumber: 3.4 Consensus size: 28
18128 AATAATTGCT
*
18138 AACTTTTAAATG-TCAAAATTTATTTTATC
1 AACTTTTAAA-GATCAAAATTT-TTTTATA
* ** *
18167 AACTTTTAAGAAGTTTTAAATTTTTTT-TT
1 AACTTTT-A-AAGATCAAAATTTTTTTATA
*
18196 AGCTTTTAAAGATCCAAAATTTTTTTATA
1 AACTTTTAAAGAT-CAAAATTTTTTTATA
18225 AACTTTTAAA
1 AACTTTTAAA
18235 AGACTTAAAT
Statistics
Matches: 54, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
27 4 0.07
28 11 0.20
29 24 0.44
30 6 0.11
31 9 0.17
ACGTcount: A:0.37, C:0.08, G:0.05, T:0.49
Consensus pattern (28 bp):
AACTTTTAAAGATCAAAATTTTTTTATA
Found at i:18244 original size:29 final size:28
Alignment explanation
Indices: 18153--18271 Score: 105
Period size: 28 Copynumber: 4.1 Consensus size: 28
18143 TTAAATGTCA
**
18153 AAATTTATTTTATCAACTTTTAAGAAGTTTT
1 AAATTT-TTTT-TCAACTTTTAA-AAGACTT
* * **
18184 AAATTTTTTTTTAGCTTTT-AAAGATCCA
1 AAATTTTTTTTCAACTTTTAAAAGA-CTT
*
18212 AAATTTTTTTATAAACTTTTAAAAGACTT
1 AAATTTTTTT-TCAACTTTTAAAAGACTT
* *
18241 AAATTTTTTTCCAACTTTTAAAAAACTT
1 AAATTTTTTTTCAACTTTTAAAAGACTT
18269 AAA
1 AAA
18272 ACTCTATTTT
Statistics
Matches: 72, Mismatches: 13, Indels: 9
0.77 0.14 0.10
Matches are distributed among these distances:
27 3 0.04
28 29 0.40
29 25 0.35
30 9 0.12
31 6 0.08
ACGTcount: A:0.39, C:0.09, G:0.04, T:0.48
Consensus pattern (28 bp):
AAATTTTTTTTCAACTTTTAAAAGACTT
Found at i:20636 original size:62 final size:60
Alignment explanation
Indices: 20545--20709 Score: 208
Period size: 62 Copynumber: 2.8 Consensus size: 60
20535 TCTCTAGCGT
*
20545 AAAAATCAGCAAAAAAAAATTTCGGGTACTGAAAAAGGTGGTGCCAACCATCAATAGGGAA
1 AAAAACCAGCAAAAAAAAATTTCGGGTACTGAAAAAGGTGGTGCCAACCATCAATAGGG-A
* * * ** *
20606 AAAAACTAGCAAAAAAATAATTTTGGGTACTGAAAAAGGTGATGCCGGCCATCAATAGGGC
1 AAAAACCAGCAAAAAAA-AATTTCGGGTACTGAAAAAGGTGGTGCCAACCATCAATAGGGA
* * *
20667 AAAAACCAG-AAAAAAAAA-ATCGAGTATTGAAAAAGGTGGTGCC
1 AAAAACCAGCAAAAAAAAATTTCGGGTACTGAAAAAGGTGGTGCC
20710 GATTGATAGG
Statistics
Matches: 90, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
58 20 0.22
59 2 0.02
60 7 0.08
61 23 0.26
62 38 0.42
ACGTcount: A:0.47, C:0.14, G:0.22, T:0.17
Consensus pattern (60 bp):
AAAAACCAGCAAAAAAAAATTTCGGGTACTGAAAAAGGTGGTGCCAACCATCAATAGGGA
Found at i:21997 original size:16 final size:16
Alignment explanation
Indices: 21972--22006 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
21962 TATCTCTATT
*
21972 ATTTAAAATAATCATA
1 ATTTAAAATAATAATA
*
21988 ATTTATAATAATAATA
1 ATTTAAAATAATAATA
22004 ATT
1 ATT
22007 ATTATTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
ATTTAAAATAATAATA
Found at i:24290 original size:18 final size:18
Alignment explanation
Indices: 24264--24306 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
24254 CATGAAATTT
*
24264 TTAAATAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
24282 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
24300 TTAATTA
1 TTAATTA
24307 CAATTGAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:25664 original size:20 final size:19
Alignment explanation
Indices: 25636--25674 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
25626 ATACTAATCG
25636 AATTAAAATTTAATTTAAAT
1 AATTAAAATTTAA-TTAAAT
*
25656 AATTTAAATTTAATTAAAT
1 AATTAAAATTTAATTAAAT
25675 GGAGTTGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AATTAAAATTTAATTAAAT
Found at i:27930 original size:6 final size:6
Alignment explanation
Indices: 27909--27944 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
27899 TATGTATAGA
*
27909 GAGAGG GA-ATG GAGAGG GAGAGG GAGAGG GAGAGG G
1 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG G
27945 TACCTTGAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 4 0.15
6 23 0.85
ACGTcount: A:0.33, C:0.00, G:0.64, T:0.03
Consensus pattern (6 bp):
GAGAGG
Found at i:28166 original size:6 final size:6
Alignment explanation
Indices: 28153--28196 Score: 61
Period size: 6 Copynumber: 7.3 Consensus size: 6
28143 TTAATCAAAA
* * *
28153 AAGATG ATGATG ATGATG AAGAGG AAGATG AAGATG AAGATG AA
1 AAGATG AAGATG AAGATG AAGATG AAGATG AAGATG AAGATG AA
28197 AGTGACACAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.48, C:0.00, G:0.34, T:0.18
Consensus pattern (6 bp):
AAGATG
Found at i:33098 original size:30 final size:29
Alignment explanation
Indices: 33064--33322 Score: 172
Period size: 30 Copynumber: 8.8 Consensus size: 29
33054 TTGACCTCTA
* *
33064 AACTTTTTAAAAGTTCAAATTTAACCTCCT
1 AACTTTTCAAAAATTCAAATTTAA-CTCCT
*
33094 AACTTTTCAAAAATTCAAATTTGACTCCT
1 AACTTTTCAAAAATTCAAATTTAACTCCT
* * * *
33123 AAATTTTCCAAAAAATT-GAATTTGAC-CTCA
1 AACTTTT-C-AAAAATTCAAATTTAACTC-CT
* ** * *
33153 AACTTTCCAAAAATTTGAATTTAACCCCA
1 AACTTTTCAAAAATTCAAATTTAACTCCT
* * *
33182 AACTTTCCAAAAATTCAAATTTGACCCCT
1 AACTTTTCAAAAATTCAAATTTAACTCCT
* *
33211 AAACTTTCCAAAAATTCAAATTTGAC-CCT
1 -AACTTTTCAAAAATTCAAATTTAACTCCT
*
33240 CAAACTTTTCAAAAATTCTAA-TTAAC-CCT
1 --AACTTTTCAAAAATTCAAATTTAACTCCT
*
33269 CAAATTTTCCAAAAATT-ATAATTTAAC-CCTT
1 -AACTTTT-CAAAAATTCA-AATTTAACTCC-T
**
33300 AAACTTCCCAAAAATTCAAATTT
1 -AACTTTTCAAAAATTCAAATTT
33323 GACCCGATTT
Statistics
Matches: 194, Mismatches: 23, Indels: 24
0.80 0.10 0.10
Matches are distributed among these distances:
28 13 0.07
29 68 0.35
30 100 0.52
31 13 0.07
ACGTcount: A:0.41, C:0.22, G:0.03, T:0.34
Consensus pattern (29 bp):
AACTTTTCAAAAATTCAAATTTAACTCCT
Found at i:33409 original size:3 final size:3
Alignment explanation
Indices: 33401--33435 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
33391 TTATCTTGTT
33401 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
33436 TAATCTCTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:33496 original size:19 final size:20
Alignment explanation
Indices: 33460--33498 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
33450 TGCATATGTA
**
33460 TTTTATTTTATTTGTTTATT
1 TTTTATTTTATTCATTTATT
33480 TTTTA-TTTATTCATTTATT
1 TTTTATTTTATTCATTTATT
33499 CGGTTATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.77
Consensus pattern (20 bp):
TTTTATTTTATTCATTTATT
Found at i:33951 original size:10 final size:11
Alignment explanation
Indices: 33926--33952 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
33916 GCGATTTAAT
33926 TTTTTCTCAAA
1 TTTTTCTCAAA
33937 TTTTTCTCAAA
1 TTTTTCTCAAA
33948 TTTTT
1 TTTTT
33953 AATTTTCAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.15, G:0.00, T:0.63
Consensus pattern (11 bp):
TTTTTCTCAAA
Done.