Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011945.1 Kokia drynarioides strain JFW-HI SEQ_126943, 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: 301141
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 61 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:259509 original size:7 final size:6
Alignment explanation
Indices: 259462--259553 Score: 57
Period size: 6 Copynumber: 15.8 Consensus size: 6
259452 TATAATAAGT
* * * *
259462 TTTAAA TTTAAA TATAAA TCTCAA TTTATA -TTAAA TTTAAA TTTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA
** * * * *
259510 -ACAAA TTTAAA TTTAAA -ATAAA TTTATA TTCAAA -ATAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
259554 CCTTAAAATA
Statistics
Matches: 62, Mismatches: 19, Indels: 10
0.68 0.21 0.11
Matches are distributed among these distances:
5 14 0.23
6 42 0.68
7 6 0.10
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:259544 original size:17 final size:17
Alignment explanation
Indices: 259462--259568 Score: 115
Period size: 17 Copynumber: 6.2 Consensus size: 17
259452 TATAATAAGT
259462 TTTAAATTTAAATATAAA
1 TTTAAATTTAAA-ATAAA
* * * *
259480 TCTCAATTTATATTAAA
1 TTTAAATTTAAAATAAA
*
259497 TTTAAATTTTAAAACAAA
1 TTTAAA-TTTAAAATAAA
259515 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
* *
259532 TTTATATTCAAAATAAA
1 TTTAAATTTAAAATAAA
**
259549 TTTAACCTTAAAATAAA
1 TTTAAATTTAAAATAAA
259566 TTT
1 TTT
259569 TGAAATGAGT
Statistics
Matches: 72, Mismatches: 16, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
17 49 0.68
18 23 0.32
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:260688 original size:25 final size:24
Alignment explanation
Indices: 260632--260712 Score: 65
Period size: 25 Copynumber: 3.3 Consensus size: 24
260622 GAATTCAAAG
*
260632 AAAAAAAAGAAAA-AAATTCGAAAT
1 AAAAAAAA-AAAACAAATTCGAATT
**
260656 ATTGAAAAAAAAACAAATTCGAAGTT
1 A-AAAAAAAAAAACAAATTCGAA-TT
* ***
260682 AAAAAAAGAAGGGAAATTCGAATT
1 AAAAAAAAAAAACAAATTCGAATT
260706 AAAAAAA
1 AAAAAAA
260713 TTCCTTCCAA
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
24 14 0.31
25 29 0.64
26 2 0.04
ACGTcount: A:0.67, C:0.05, G:0.12, T:0.16
Consensus pattern (24 bp):
AAAAAAAAAAAACAAATTCGAATT
Found at i:261900 original size:60 final size:59
Alignment explanation
Indices: 261833--261949 Score: 189
Period size: 60 Copynumber: 2.0 Consensus size: 59
261823 TGTTCTGAAT
* * *
261833 CATTATGTGTTTTGTTTGTTAAATGCATCTTTATTTAAATGTTTTGCATTAATACATTTG
1 CATTATGTGTCTTGTTTATTAAATGCATCTTTATTT-AATGTCTTGCATTAATACATTTG
*
261893 CATTATGTGTCTTGTTTATTGAATGCATCTTTATTTAATGTCTTGCATTAATACATT
1 CATTATGTGTCTTGTTTATTAAATGCATCTTTATTTAATGTCTTGCATTAATACATT
261950 AACATCCTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
59 20 0.38
60 33 0.62
ACGTcount: A:0.25, C:0.10, G:0.13, T:0.52
Consensus pattern (59 bp):
CATTATGTGTCTTGTTTATTAAATGCATCTTTATTTAATGTCTTGCATTAATACATTTG
Found at i:262791 original size:19 final size:19
Alignment explanation
Indices: 262753--262791 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
262743 GTCACACGGT
*
262753 CGTACCCCAAATTGTCTGC
1 CGTACCCCAAACTGTCTGC
*
262772 CGTACCCCAAACTGTGTGC
1 CGTACCCCAAACTGTCTGC
262791 C
1 C
262792 AGACCGTGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.38, G:0.18, T:0.23
Consensus pattern (19 bp):
CGTACCCCAAACTGTCTGC
Found at i:263786 original size:80 final size:80
Alignment explanation
Indices: 263607--263835 Score: 260
Period size: 80 Copynumber: 2.8 Consensus size: 80
263597 TAACCAGTAT
* * * * * * ***
263607 ACGATGCTACTCACACAACCTATCAGGAAACTGCAACATATGCAGGATCCCAACCATCGATACAA
1 ACGATGCTGCTCACACAAGCTATCAAGAAACTGCAACATATGTAGGATCTCAGCCATCG-TAGGG
263672 TCCATATTACCCACTC
65 TCCATATTACCCACTC
* * * * *
263688 ACAATGTTGCTCACACAAGCTGTCAAGAATCTGCGACATATGTAGGATCTCAGCCATCGTAGGGT
1 ACGATGCTGCTCACACAAGCTATCAAGAAACTGCAACATATGTAGGATCTCAGCCATCGTAGGGT
* * *
263753 CCATGTTACTCGCTC
66 CCATATTACCCACTC
* * *
263768 ACGATGCTGCTCACACAAGCTATCAAGAAACTGCAACGTATGTAAGATCTCAGCCATCATAGAGG
1 ACGATGCTGCTCACACAAGCTATCAAGAAACTGCAACATATGTAGGATCTCAGCCATCGTAG-GG
263833 TCC
65 TCC
263836 TTACAGTCAG
Statistics
Matches: 122, Mismatches: 25, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
80 69 0.57
81 53 0.43
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (80 bp):
ACGATGCTGCTCACACAAGCTATCAAGAAACTGCAACATATGTAGGATCTCAGCCATCGTAGGGT
CCATATTACCCACTC
Found at i:265523 original size:30 final size:30
Alignment explanation
Indices: 265437--265707 Score: 167
Period size: 30 Copynumber: 9.0 Consensus size: 30
265427 TCTAGTAGGT
* * * *
265437 CCTTAAACTT-TCCAGAAATCATATTTTGAT
1 CCTTAAACTTATCCA-AAATTACATTTTAAC
* * * * *
265467 CCTTAAACTTTTCAAAAATCATATTTTGA-
1 CCTTAAACTTATCCAAAATTACATTTTAAC
*
265496 CCTCTAAACTTATCCAAAATTGCATTTTAAC
1 CCT-TAAACTTATCCAAAATTACATTTTAAC
* *
265527 CCTTAAACTTTTCTAAAATTACATTTTAAC
1 CCTTAAACTTATCCAAAATTACATTTTAAC
* ** *
265557 CCATAATTTTTTTTCCAAAATTACATTTTAAC
1 CCTTAA--ACTTATCCAAAATTACATTTTAAC
* * * **
265589 ACTTAAACTTTTCTAAAATTATGTTTTAAC
1 CCTTAAACTTATCCAAAATTACATTTTAAC
* * * * *
265619 CCCTAAACTTCTCCAAAATCACATCTTGACC
1 CCTTAAACTTATCCAAAATTACAT-TTTAAC
* *
265650 CCTT-AACTT-TCCCAAAATCACTTTTTAA-
1 CCTTAAACTTAT-CCAAAATTACATTTTAAC
*
265678 CCTTAAAACTT-TACCAAAATAACATTTTAA
1 CCTT-AAACTTAT-CCAAAATTACATTTTAA
265708 GAAAATTACA
Statistics
Matches: 195, Mismatches: 37, Indels: 18
0.78 0.15 0.07
Matches are distributed among these distances:
28 4 0.02
29 7 0.04
30 146 0.75
31 13 0.07
32 25 0.13
ACGTcount: A:0.36, C:0.23, G:0.02, T:0.39
Consensus pattern (30 bp):
CCTTAAACTTATCCAAAATTACATTTTAAC
Found at i:265577 original size:32 final size:30
Alignment explanation
Indices: 265470--265707 Score: 174
Period size: 30 Copynumber: 7.9 Consensus size: 30
265460 TTTTGATCCT
* * * *
265470 TAAACTTTTCAAAAATCATATTTTGACCTC-
1 TAAACTTTTCCAAAATTACATTTTAACC-CA
* * *
265500 TAAACTTATCCAAAATTGCATTTTAACCCT
1 TAAACTTTTCCAAAATTACATTTTAACCCA
*
265530 TAAACTTTTCTAAAATTACATTTTAACCCA
1 TAAACTTTTCCAAAATTACATTTTAACCCA
** * *
265560 TAATTTTTTTTCCAAAATTACATTTTAACACT
1 TAA--ACTTTTCCAAAATTACATTTTAACCCA
* ** *
265592 TAAACTTTTCTAAAATTATGTTTTAACCCC
1 TAAACTTTTCCAAAATTACATTTTAACCCA
* * * * *
265622 TAAACTTCTCCAAAATCACATCTTGACCCC
1 TAAACTTTTCCAAAATTACATTTTAACCCA
* * * * *
265652 TTAACTTTCCCAAAATCACTTTTTAA-CCT
1 TAAACTTTTCCAAAATTACATTTTAACCCA
* *
265681 TAAAACTTTACCAAAATAACATTTTAA
1 T-AAACTTTTCCAAAATTACATTTTAA
265708 GAAAATTACA
Statistics
Matches: 164, Mismatches: 40, Indels: 8
0.77 0.19 0.04
Matches are distributed among these distances:
29 4 0.02
30 135 0.82
32 25 0.15
ACGTcount: A:0.37, C:0.22, G:0.02, T:0.39
Consensus pattern (30 bp):
TAAACTTTTCCAAAATTACATTTTAACCCA
Found at i:265771 original size:29 final size:29
Alignment explanation
Indices: 265709--265844 Score: 112
Period size: 29 Copynumber: 4.6 Consensus size: 29
265699 ACATTTTAAG
*
265709 AAAATTACATTTTGAACCCCAAACCTTTTC-
1 AAAATTACATTTT-AACCCTAAA-CTTTTCT
* *
265739 AAAATCACATTTTAACCCTAAACTTCTCT
1 AAAATTACATTTTAACCCTAAACTTTTCT
* * * * * * *
265768 AAAATCACTTTTTGATCCAAAACTTTCCC
1 AAAATTACATTTTAACCCTAAACTTTTCT
* *
265797 AAGATTACATTTTTTACCCCTAAACTTTTCT
1 AAAATTACA--TTTTAACCCTAAACTTTTCT
*
265828 AAAATTATATTTTAACC
1 AAAATTACATTTTAACC
265845 TCGAATTCTC
Statistics
Matches: 81, Mismatches: 22, Indels: 7
0.74 0.20 0.06
Matches are distributed among these distances:
28 5 0.06
29 43 0.53
30 12 0.15
31 21 0.26
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.38
Consensus pattern (29 bp):
AAAATTACATTTTAACCCTAAACTTTTCT
Found at i:265824 original size:135 final size:136
Alignment explanation
Indices: 265573--265842 Score: 298
Period size: 135 Copynumber: 2.0 Consensus size: 136
265563 TTTTTTTTCC
** * **
265573 AAAATTACATTTTAACACTTAAACTTTTCTAAAATTATGTTTTAACCCCTAAACTTCTCCAAAAT
1 AAAATTACATTTTAACACCCAAACTTTTCTAAAATCACATTTTAACCCCTAAACTTCTCCAAAAT
** *
265638 CACATCTTGACCCCTTAACTTTCCCAAAATCACTTTTTAACCTTAAAACTTTACCAAAATAACAT
66 CACATCTTGACCCCAAAACTTTCCCAAAATCACTTTTTAACCCTAAAACTTTACCAAAATAACAT
265703 TTTAAG
131 TTTAAG
*
265709 AAAATTACATTTTGAAC-CCCAAACCTTTTC-AAAATCACATTTTAA-CCCTAAACTTCTCTAAA
1 AAAATTACATTTT-AACACCCAAA-CTTTTCTAAAATCACATTTTAACCCCTAAACTTCTCCAAA
* * * * * * * * *
265771 ATCACTTTTTGA-TCCAAAACTTTCCCAAGATTACATTTTTTACCCCT-AAACTTTTCTAAAATT
64 ATCACATCTTGACCCCAAAACTTTCCCAA-AAT-CACTTTTTAACCCTAAAACTTTACCAAAATA
*
265834 ATATTTTAA
127 ACATTTTAA
265843 CCTCGAATTC
Statistics
Matches: 111, Mismatches: 19, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
134 13 0.12
135 49 0.44
136 40 0.36
137 9 0.08
ACGTcount: A:0.37, C:0.23, G:0.02, T:0.37
Consensus pattern (136 bp):
AAAATTACATTTTAACACCCAAACTTTTCTAAAATCACATTTTAACCCCTAAACTTCTCCAAAAT
CACATCTTGACCCCAAAACTTTCCCAAAATCACTTTTTAACCCTAAAACTTTACCAAAATAACAT
TTTAAG
Found at i:274269 original size:49 final size:48
Alignment explanation
Indices: 274216--274551 Score: 170
Period size: 49 Copynumber: 6.8 Consensus size: 48
274206 GACGAACCCA
* * *
274216 GTACCATGAAGATTTAAAGGAAAGGATTGAGGCCACGACAGTGAATCTG
1 GTACCATGAAGATTTAAAGGAAAGG-TTGAGGCTACAACAGTGAACCTG
* * ** * * *
274265 GTACCTTAGAAGATGTGATGGGAAAGGTTAAGGCTGCAACAGTGAACCCG
1 GTACCAT-GAAGAT-TTAAAGGAAAGGTTGAGGCTACAACAGTGAACCTG
* ** * * * *
274315 TTACCATGAAGATACGAAGGGAAAGATTGAGGCAACAACGGTGAACCCT-
1 GTACCATGAAGAT-TTAAAGGAAAGGTTGAGGCTACAACAGTGAA-CCTG
* ** * * * *
274364 ATACCATGAAGATACAAAGGGAAAGGTTGAGGCTGCAACGGCGAACCAG
1 GTACCATGAAGATTTAAA-GGAAAGGTTGAGGCTACAACAGTGAACCTG
* * * * **
274413 GTACCATGAAGATTTGAAGGGAAGGATTGAGGCTGCGACAGTGAATTTG
1 GTACCATGAAGATTTAAAGGAAAGG-TTGAGGCTACAACAGTGAACCTG
* * * * * * * * *
274462 ATACCTTAGAAGATGTAATGAGAAAGGTTGAGGCCATAACGGCGAACCCG
1 GTACCAT-GAAGATTTAAAG-GAAAGGTTGAGGCTACAACAGTGAACCTG
* * ** *
274512 GTGCCTAAGAAGATGTTATGGGAAAGGTTGAGGCCACAAC
1 GTACC-ATGAAGAT-TTAAAGGAAAGGTTGAGGCTACAAC
274552 GACGGACTCG
Statistics
Matches: 213, Mismatches: 64, Indels: 19
0.72 0.22 0.06
Matches are distributed among these distances:
48 10 0.05
49 106 0.50
50 80 0.38
51 17 0.08
ACGTcount: A:0.35, C:0.16, G:0.30, T:0.19
Consensus pattern (48 bp):
GTACCATGAAGATTTAAAGGAAAGGTTGAGGCTACAACAGTGAACCTG
Found at i:274278 original size:99 final size:100
Alignment explanation
Indices: 274138--274705 Score: 366
Period size: 99 Copynumber: 5.8 Consensus size: 100
274128 TGAAGATTTG
* * * * * * * *
274138 AAGGATTGAGGCCACTACGGCGAATC-CAGTACCTTAAAAGATGTGGTGAGAAAGCTTGAGGCCA
1 AAGGATTGAGGCCACAACAGTGAATCTGA-TACCTTAGAAGATGTGATGGGAAAGGTTGAGGCCA
*
274202 TAATGACGAACCCAGTACCATGAAGAT-TTAAAGGA
65 TAACGACGAACCCAGTACCATGAAGATATTAAAGGA
* * * ***
274237 AAGGATTGAGGCCACGACAGTGAATCTGGTACCTTAGAAGATGTGATGGGAAAGGTTAAGGCTGC
1 AAGGATTGAGGCCACAACAGTGAATCTGATACCTTAGAAGATGTGATGGGAAAGGTTGAGGCCAT
* ** *
274302 AAC-AGTGAACCC-GTTACCATGAAGATACGAAGGGA
66 AACGA-CGAACCCAG-TACCATGAAGATATTAAAGGA
* * * * *** * **
274337 AA-GATTGAGGCAACAACGGTGAACCCT-ATACCAT-GAAGATACAAAGGGAAAGGTTGAGGCTG
1 AAGGATTGAGGCCACAACAGTGAA-TCTGATACCTTAGAAGATGTGATGGGAAAGGTTGAGGCCA
* * * *
274399 CAACGGCGAA-CCAGGTACCATGAAGAT-TTGAAGGG
65 TAACGACGAACCCA-GTACCATGAAGATATTAAAGGA
** * * * *
274434 AAGGATTGAGGCTGCGACAGTGAATTTGATACCTTAGAAGATGTAATGAGAAAGGTTGAGGCCAT
1 AAGGATTGAGGCCACAACAGTGAATCTGATACCTTAGAAGATGTGATGGGAAAGGTTGAGGCCAT
* * * * * **
274499 AACGGCGAACCCGGTGCCTAAGAAGATGTTATGGGA
66 AACGACGAACCCAGTACC-ATGAAGATATTAAAGGA
*
274535 AAGG-TTGAGGCCACAACGACG-GACTC-GATA-CTTAAGAAGATGTGATGGGAAAGGTTGAGGC
1 AAGGATTGAGGCCACAAC-A-GTGAATCTGATACCTT-AGAAGATGTGATGGGAAAGGTTGAGGC
* * ***
274596 CATAACGACGAACCC-GATACCTTAAAAGATGCGATAA-GA
63 CATAACGACGAACCCAG-TACCAT-GAAGATATTA-AAGGA
* * * * * *
274635 AA-GATTGAAG-C-C-ACGGTGAATTTGATACCTT-GAAGATATGAAGGGAAAGGTTGAGGCCAC
1 AAGGATTGAGGCCACAACAGTGAATCTGATACCTTAGAAGATGTGATGGGAAAGGTTGAGGCCAT
274695 AACGACGAACC
66 AACGACGAACC
274706 TAACACCTTA
Statistics
Matches: 365, Mismatches: 80, Indels: 51
0.74 0.16 0.10
Matches are distributed among these distances:
95 1 0.00
96 40 0.11
97 14 0.04
98 71 0.19
99 136 0.37
100 90 0.25
101 12 0.03
102 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.29, T:0.18
Consensus pattern (100 bp):
AAGGATTGAGGCCACAACAGTGAATCTGATACCTTAGAAGATGTGATGGGAAAGGTTGAGGCCAT
AACGACGAACCCAGTACCATGAAGATATTAAAGGA
Found at i:274307 original size:50 final size:50
Alignment explanation
Indices: 274234--274732 Score: 220
Period size: 50 Copynumber: 10.1 Consensus size: 50
274224 AAGATTTAAA
* * * *
274234 GGAAAGGATTGAGGCCACGACAGTGAATCTGGTACCTTAGAAGATGTGATG
1 GGAAAGG-TTGAGGCTACAACAGTGAACCTGATACCTTAGAAGATGTGATG
* * * * * ** *
274285 GGAAAGGTTAAGGCTGCAACAGTGAACCCGTTACCAT-GAAGATACGAAG
1 GGAAAGGTTGAGGCTACAACAGTGAACCTGATACCTTAGAAGATGTGATG
* * * * *** *
274334 GGAAAGATTGAGGCAACAACGGTGAACCCT-ATACCAT-GAAGATACAAAG
1 GGAAAGGTTGAGGCTACAACAGTGAA-CCTGATACCTTAGAAGATGTGATG
* * * * * * * *
274383 GGAAAGGTTGAGGCTGCAACGGCGAACCAGGTACCAT-GAAGATTTGAAG
1 GGAAAGGTTGAGGCTACAACAGTGAACCTGATACCTTAGAAGATGTGATG
* * ** *
274432 GG-AAGGATTGAGGCTGCGACAGTGAATTTGATACCTTAGAAGATGTAATG
1 GGAAAGG-TTGAGGCTACAACAGTGAACCTGATACCTTAGAAGATGTGATG
* * * * * * * * * *
274482 AGAAAGGTTGAGGCCATAACGGCGAACCCGGTGCCTAAGAAGATGTTATG
1 GGAAAGGTTGAGGCTACAACAGTGAACCTGATACCTTAGAAGATGTGATG
*
274532 GGAAAGGTTGAGGCCACAACGACG-G-A-CTCGATA-CTTAAGAAGATGTGATG
1 GGAAAGGTTGAGGCTACAAC-A-GTGAACCT-GATACCTT-AGAAGATGTGATG
* * * * * * *
274582 GGAAAGGTTGAGGCCATAAC-GACGAACCCGATACCTTAAAAGATGCGATA
1 GGAAAGGTTGAGGCTACAACAG-TGAACCTGATACCTTAGAAGATGTGATG
* * * * ** * *
274632 AGAAAGATTGAAGC--C-ACGGTGAATTTGATACCTT-GAAGATATGAAG
1 GGAAAGGTTGAGGCTACAACAGTGAACCTGATACCTTAGAAGATGTGATG
* * * * * *
274678 GGAAAGGTTGAGGCCACAAC-GACGAACCTAACACCTTAGAA-ACGTGACG
1 GGAAAGGTTGAGGCTACAACAG-TGAACCTGATACCTTAGAAGATGTGATG
274727 GGAAAG
1 GGAAAG
274733 ATTAAAGTCA
Statistics
Matches: 338, Mismatches: 90, Indels: 42
0.72 0.19 0.09
Matches are distributed among these distances:
46 18 0.05
47 14 0.04
48 9 0.03
49 135 0.40
50 145 0.43
51 16 0.05
52 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.30, T:0.18
Consensus pattern (50 bp):
GGAAAGGTTGAGGCTACAACAGTGAACCTGATACCTTAGAAGATGTGATG
Found at i:274457 original size:98 final size:99
Alignment explanation
Indices: 274208--274475 Score: 272
Period size: 98 Copynumber: 2.7 Consensus size: 99
274198 GCCATAATGA
* * * * * *
274208 CGAACCCA-GTACCATGAAGATTTAAAGGAAAGGATTGAGGCCACGACAGTGAATCTGGTACCTT
1 CGAA-CCAGGTACCATGAAGATTTGAAGGGAAGGATTGAGGCAACGACAGTGAACCTGATACCAT
*** *
274272 AGAAGATGTGATGGGAAAGGTTAAGGCTGCAACAG
65 AGAAGATACAAAGGGAAAGGTTAAGGCTGCAACAG
* * * ** * * *
274307 TGAACCCGTTACCATGAAGATACGAAGGGAAAGATTGAGGCAACAACGGTGAACCCT-ATACCAT
1 CGAACCAGGTACCATGAAGATTTGAAGGGAAGGATTGAGGCAACGACAGTGAA-CCTGATACCAT
* *
274371 -GAAGATACAAAGGGAAAGGTTGAGGCTGCAACGG
65 AGAAGATACAAAGGGAAAGGTTAAGGCTGCAACAG
** ** *
274405 CGAACCAGGTACCATGAAGATTTGAAGGGAAGGATTGAGGCTGCGACAGTGAATTTGATACCTTA
1 CGAACCAGGTACCATGAAGATTTGAAGGGAAGGATTGAGGCAACGACAGTGAACCTGATACCATA
274470 GAAGAT
66 GAAGAT
274476 GTAATGAGAA
Statistics
Matches: 132, Mismatches: 33, Indels: 8
0.76 0.19 0.05
Matches are distributed among these distances:
97 1 0.01
98 79 0.60
99 50 0.38
100 2 0.02
ACGTcount: A:0.36, C:0.16, G:0.29, T:0.19
Consensus pattern (99 bp):
CGAACCAGGTACCATGAAGATTTGAAGGGAAGGATTGAGGCAACGACAGTGAACCTGATACCATA
GAAGATACAAAGGGAAAGGTTAAGGCTGCAACAG
Found at i:274637 original size:100 final size:100
Alignment explanation
Indices: 274461--274648 Score: 245
Period size: 100 Copynumber: 1.9 Consensus size: 100
274451 CAGTGAATTT
* * *
274461 GATACCTTAGAAGATGTAATGAGAAAGGTTGAGGCCATAACGGCGAACCCGGTGCCTAAGAAGAT
1 GATACCTTAGAAGATGTAATGAGAAAGGTTGAGGCCATAACGACGAACCCGATACCTAAGAAGAT
** ** * *
274526 GTTATGGGAAAGGTTGAGGCCACAACGACGGACTC
66 GCGATAAGAAAGATTGAAGCCACAACGACGGACTC
* *
274561 GATA-CTTAAGAAGATGTGATGGGAAAGGTTGAGGCCATAACGACGAACCCGATACCTTAA-AAG
1 GATACCTT-AGAAGATGTAATGAGAAAGGTTGAGGCCATAACGACGAACCCGATACC-TAAGAAG
274624 ATGCGATAAGAAAGATTGAAGCCAC
64 ATGCGATAAGAAAGATTGAAGCCAC
274649 GGTGAATTTG
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
99 3 0.04
100 69 0.92
101 3 0.04
ACGTcount: A:0.36, C:0.17, G:0.29, T:0.18
Consensus pattern (100 bp):
GATACCTTAGAAGATGTAATGAGAAAGGTTGAGGCCATAACGACGAACCCGATACCTAAGAAGAT
GCGATAAGAAAGATTGAAGCCACAACGACGGACTC
Found at i:275431 original size:16 final size:16
Alignment explanation
Indices: 275391--275438 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
275381 ATAAACAAAA
* *
275391 TTTAAATTTAAATTTAC
1 TTTAAATTTAAA-ATGC
*
275408 TCTAAATTTAAAATGC
1 TTTAAATTTAAAATGC
275424 TTTAAATTTAAAATG
1 TTTAAATTTAAAATG
275439 TCCCTTTACA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
16 16 0.59
17 11 0.41
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (16 bp):
TTTAAATTTAAAATGC
Found at i:275976 original size:26 final size:23
Alignment explanation
Indices: 275944--276002 Score: 75
Period size: 26 Copynumber: 2.5 Consensus size: 23
275934 TATATCTAAC
*
275944 ATGTATTTATTGTTTATTACATATTA
1 ATGTATTTATTGCTTATT---TATTA
275970 ATGTATTTATTGCTTATTTATTA
1 ATGTATTTATTGCTTATTTATTA
275993 AT-TATTTATT
1 ATGTATTTATT
276003 TCTAAAAGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 8 0.25
23 7 0.22
26 17 0.53
ACGTcount: A:0.29, C:0.03, G:0.07, T:0.61
Consensus pattern (23 bp):
ATGTATTTATTGCTTATTTATTA
Found at i:276993 original size:29 final size:30
Alignment explanation
Indices: 276959--277323 Score: 311
Period size: 30 Copynumber: 12.3 Consensus size: 30
276949 TAAAAATCAT
*
276959 ATTTTAACACTTAAACTTTTCCAAAATTAC
1 ATTTTAACCCTTAAACTTTTCCAAAATTAC
* *
276989 ATTTAAACCCCTAAACTTTTCCAAAATTAC
1 ATTTTAACCCTTAAACTTTTCCAAAATTAC
* *
277019 ATTTTAACCCTTAAACTTTTCCAAAATCAA
1 ATTTTAACCCTTAAACTTTTCCAAAATTAC
* *
277049 ATTTT-ACCCCTAAACTTTTCCAAAATCAC
1 ATTTTAACCCTTAAACTTTTCCAAAATTAC
* * *
277078 ATCTTAACCCTTAAAC-TTTCCAAAATCAT
1 ATTTTAACCCTTAAACTTTTCCAAAATTAC
* *
277107 ATTTTAACCCTAAAAC-TTTCCCAAATTAC
1 ATTTTAACCCTTAAACTTTTCCAAAATTAC
* * * *
277136 ATTTTCA-CCTCAAAATTTTTCCAAAATTAT
1 ATTTTAACCCT-TAAACTTTTCCAAAATTAC
* * * *
277166 ATTTTGACCCCTAAACTTCTCTAAAATTAC
1 ATTTTAACCCTTAAACTTTTCCAAAATTAC
* * *
277196 ATTTTAA-CCTCTAAAC-CTTCTCGAAATCAC
1 ATTTTAACCCT-TAAACTTTTC-CAAAATTAC
* * * * * *
277226 ATTTTGACAC-AAAACTTCTCGAAAATCAC
1 ATTTTAACCCTTAAACTTTTCCAAAATTAC
277255 ATTTTAACCC-TAAAC-TTTCCTAAAATTAC
1 ATTTTAACCCTTAAACTTTTCC-AAAATTAC
* * *
277284 ATTTTTACACC-TAAACATTTT-TAAAATTAT
1 ATTTTAAC-CCTTAAAC-TTTTCCAAAATTAC
277314 ATTTTAACCC
1 ATTTTAACCC
277324 CAAATTCTCT
Statistics
Matches: 271, Mismatches: 52, Indels: 25
0.78 0.15 0.07
Matches are distributed among these distances:
28 6 0.02
29 115 0.42
30 144 0.53
31 3 0.01
32 3 0.01
ACGTcount: A:0.38, C:0.25, G:0.01, T:0.37
Consensus pattern (30 bp):
ATTTTAACCCTTAAACTTTTCCAAAATTAC
Found at i:277085 original size:59 final size:58
Alignment explanation
Indices: 276937--277323 Score: 300
Period size: 59 Copynumber: 6.6 Consensus size: 58
276927 TTTAGTAAGT
* ** * * * * *
276937 CCCTAAATTTTTTAAAAATCATATTTTAACACTTAAACTTTTCCAAAATTACATTTAAAC
1 CCCTAAACTTTTCCAAAATCACATTTTAACCCTTAAAC-TTTCCAAAATCAAATTT-TAC
*
276997 CCCTAAACTTTTCCAAAATTACATTTTAACCCTTAAACTTTTCCAAAATCAAATTTTAC
1 CCCTAAACTTTTCCAAAATCACATTTTAACCCTTAAAC-TTTCCAAAATCAAATTTTAC
* * *
277056 CCCTAAACTTTTCCAAAATCACATCTTAACCCTTAAACTTTCCAAAATCATATTTTAA
1 CCCTAAACTTTTCCAAAATCACATTTTAACCCTTAAACTTTCCAAAATCAAATTTTAC
* * * * * * *
277114 CCCTAAAAC-TTTCCCAAATTACATTTTCA-CCTCAAAATTTTTCCAAAATTATATTTTGAC
1 CCCT-AAACTTTTCCAAAATCACATTTTAACCCT-TAAA-CTTTCCAAAATCAAATTTT-AC
* * * * * *
277174 CCCTAAACTTCTCTAAAATTACATTTTAA-CCTCTAAACCTTCTCGAAATCACATTTTGA-
1 CCCTAAACTTTTCCAAAATCACATTTTAACCCT-TAAACTTTC-CAAAATCAAATTTT-AC
* * * * * *
277233 CACAAAACTTCTCGAAAATCACATTTTAACCC-TAAACTTTCCTAAAATTACATTTTTAC
1 CCCTAAACTTTTCCAAAATCACATTTTAACCCTTAAACTTTCC-AAAATCA-AATTTTAC
* * * *
277292 ACCTAAACATTTT-TAAAATTATATTTTAACCC
1 CCCTAAAC-TTTTCCAAAATCACATTTTAACCC
277324 CAAATTCTCT
Statistics
Matches: 269, Mismatches: 47, Indels: 23
0.79 0.14 0.07
Matches are distributed among these distances:
57 4 0.01
58 55 0.20
59 116 0.43
60 94 0.35
ACGTcount: A:0.38, C:0.24, G:0.01, T:0.37
Consensus pattern (58 bp):
CCCTAAACTTTTCCAAAATCACATTTTAACCCTTAAACTTTCCAAAATCAAATTTTAC
Found at i:279876 original size:14 final size:14
Alignment explanation
Indices: 279859--279888 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
279849 TTTAAACTCT
*
279859 AAAAGATAAATCTA
1 AAAAGATAAATATA
279873 AAAAGATAAATATA
1 AAAAGATAAATATA
279887 AA
1 AA
279889 TTAAATATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.70, C:0.03, G:0.07, T:0.20
Consensus pattern (14 bp):
AAAAGATAAATATA
Found at i:285206 original size:17 final size:17
Alignment explanation
Indices: 285180--285263 Score: 82
Period size: 17 Copynumber: 4.9 Consensus size: 17
285170 TTAATTTATT
*
285180 TTTAAGTTTAAATTTAG
1 TTTAAATTTAAATTTAG
* *
285197 TATAAATTTAAATTTAT
1 TTTAAATTTAAATTTAG
* **
285214 TTTGAATTTAAATGCA-
1 TTTAAATTTAAATTTAG
285230 TTCTAAATTTAAATTT-G
1 TT-TAAATTTAAATTTAG
285247 TTTTAAATTTAAATTTA
1 -TTTAAATTTAAATTTA
285264 ATTAAAAATT
Statistics
Matches: 53, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
16 2 0.04
17 49 0.92
18 2 0.04
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.52
Consensus pattern (17 bp):
TTTAAATTTAAATTTAG
Found at i:285207 original size:34 final size:34
Alignment explanation
Indices: 285172--285263 Score: 112
Period size: 34 Copynumber: 2.7 Consensus size: 34
285162 TTTAATTTTT
285172 AATTTATTTTTAAGTTTAAATTTAGTATAAATTTA
1 AATTTATTTTTAA-TTTAAATTTAGTATAAATTTA
* ** * *
285207 AATTTATTTTGAATTTAAATGCATTCTAAATTTA
1 AATTTATTTTTAATTTAAATTTAGTATAAATTTA
* *
285241 AATTTGTTTTAAATTTAAATTTA
1 AATTTATTTTTAATTTAAATTTA
285264 ATTAAAAATT
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
34 36 0.75
35 12 0.25
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.53
Consensus pattern (34 bp):
AATTTATTTTTAATTTAAATTTAGTATAAATTTA
Found at i:285276 original size:34 final size:33
Alignment explanation
Indices: 285172--285276 Score: 102
Period size: 34 Copynumber: 3.1 Consensus size: 33
285162 TTTAATTTTT
* *
285172 AATTTATTTTTAAGTTTAAATTTAGTATAAATTTA
1 AATTTA-TTTTAAATTTAAATTTATTA-AAATTTA
* ** *
285207 AATTTATTTTGAATTTAAATGCATTCTAAATTTA
1 AATTTATTTTAAATTTAAATTTATT-AAAATTTA
* *
285241 AATTTGTTTTAAATTTAAATTTAATTAAAAATTA
1 AATTTATTTTAAATTTAAATTT-ATTAAAATTTA
285275 AA
1 AA
285277 AGAAAGTCCA
Statistics
Matches: 56, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
34 47 0.84
35 9 0.16
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (33 bp):
AATTTATTTTAAATTTAAATTTATTAAAATTTA
Found at i:287050 original size:30 final size:30
Alignment explanation
Indices: 287018--287074 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
287008 GAACTGTCCA
*
287018 AAAATCATATTTTAA-CCCTAAACTTTTCC
1 AAAATCACATTTTAACCCCTAAACTTTTCC
*
287047 AAAATTACATTTTAACCCCTAAACTTTT
1 AAAATCACATTTTAACCCCTAAACTTTT
287075 TTTAAATCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.39
Consensus pattern (30 bp):
AAAATCACATTTTAACCCCTAAACTTTTCC
Found at i:287089 original size:30 final size:30
Alignment explanation
Indices: 287018--287096 Score: 88
Period size: 30 Copynumber: 2.7 Consensus size: 30
287008 GAACTGTCCA
*
287018 AAAATCATATTTTAA-CCCTAAACTTTTCC
1 AAAATCAAATTTTAACCCCTAAACTTTTCC
* * **
287047 AAAATTACATTTTAACCCCTAAACTTTTTT
1 AAAATCAAATTTTAACCCCTAAACTTTTCC
* *
287077 TAAATCAAATTTTTACCCCT
1 AAAATCAAATTTTAACCCCT
287097 CGAACTTCAA
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 13 0.32
30 28 0.68
ACGTcount: A:0.37, C:0.23, G:0.00, T:0.41
Consensus pattern (30 bp):
AAAATCAAATTTTAACCCCTAAACTTTTCC
Found at i:287119 original size:30 final size:29
Alignment explanation
Indices: 287085--287233 Score: 165
Period size: 29 Copynumber: 5.1 Consensus size: 29
287075 TTTAAATCAA
* *
287085 ATTTTTACCCCTCGAACTTCAAAAAATTAT
1 ATTTTT-CCCCTCGAACTTCCAAAAATTAC
** * *
287115 ATTTTTAACCTAGAATTTCCAAAAATTAC
1 ATTTTTCCCCTCGAACTTCCAAAAATTAC
287144 ATTTTTGCCCC-CGAACTTCCAAAAATTAC
1 ATTTTT-CCCCTCGAACTTCCAAAAATTAC
** *
287173 ATTTTTGTCCTCAAACTTCCAAAAAATTAC
1 ATTTTTCCCCTCGAACTTCC-AAAAATTAC
* *
287203 ATTTTTGCCCTCGAACTTCCAAAAATCAC
1 ATTTTTCCCCTCGAACTTCCAAAAATTAC
287232 AT
1 AT
287234 ACCTTGAATT
Statistics
Matches: 100, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
28 2 0.02
29 63 0.63
30 35 0.35
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.35
Consensus pattern (29 bp):
ATTTTTCCCCTCGAACTTCCAAAAATTAC
Found at i:287200 original size:59 final size:58
Alignment explanation
Indices: 287085--287233 Score: 192
Period size: 59 Copynumber: 2.5 Consensus size: 58
287075 TTTAAATCAA
* * * *
287085 ATTTTTACCCCTCGAACTTCAAAAAATTATATTTTTAACCTAGAATTTCCAAAAATTAC
1 ATTTTTGCCCC-CGAACTTCCAAAAATTACATTTTTAACCTAGAACTTCCAAAAATTAC
**
287144 ATTTTTGCCCCCGAACTTCCAAAAATTACATTTTTGTCCTCA-AACTTCCAAAAAATTAC
1 ATTTTTGCCCCCGAACTTCCAAAAATTACATTTTTAACCT-AGAACTTCC-AAAAATTAC
* *
287203 ATTTTTGCCCTCGAACTTCCAAAAATCACAT
1 ATTTTTGCCCCCGAACTTCCAAAAATTACAT
287234 ACCTTGAATT
Statistics
Matches: 80, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
58 31 0.39
59 49 0.61
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.35
Consensus pattern (58 bp):
ATTTTTGCCCCCGAACTTCCAAAAATTACATTTTTAACCTAGAACTTCCAAAAATTAC
Found at i:287426 original size:15 final size:15
Alignment explanation
Indices: 287399--287440 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
287389 TGATTCATGA
287399 TTCGTAT-TTTATTT
1 TTCGTATATTTATTT
*
287413 TTCTTATATTTA-TT
1 TTCGTATATTTATTT
287427 TTCGTATATTTATT
1 TTCGTATATTTATT
287441 CATTTGTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 19 0.79
15 5 0.21
ACGTcount: A:0.19, C:0.07, G:0.05, T:0.69
Consensus pattern (15 bp):
TTCGTATATTTATTT
Found at i:292970 original size:50 final size:51
Alignment explanation
Indices: 292889--293044 Score: 140
Period size: 50 Copynumber: 3.1 Consensus size: 51
292879 TGACATCCAT
* * *
292889 TAACTCTCATGATTAGTT-TAGTTTGCATCATAAATAATGACATGCATTAAG
1 TAACTCACATG-TTAGTTAAAGTATGCATCATAAATAATGACATGCATTAAG
* ** *
292940 TAACTTACATGTTAGTTAAA-TATGCATCATAAATCCT-ATCATGCATTATG
1 TAACTCACATGTTAGTTAAAGTATGCATCATAAATAATGA-CATGCATTAAG
* * * * *
292990 TAACTCCCATGTTAGTTAAAGTTTGCATCTTTAAATCAA-GTCATGCATTTAG
1 TAACTCACATGTTAGTTAAAGTATGCATC-ATAAAT-AATGACATGCATTAAG
293042 TAA
1 TAA
293045 TCCATTAGTT
Statistics
Matches: 83, Mismatches: 16, Indels: 11
0.75 0.15 0.10
Matches are distributed among these distances:
49 1 0.01
50 48 0.58
51 17 0.20
52 17 0.20
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (51 bp):
TAACTCACATGTTAGTTAAAGTATGCATCATAAATAATGACATGCATTAAG
Found at i:297320 original size:15 final size:15
Alignment explanation
Indices: 297301--297360 Score: 66
Period size: 16 Copynumber: 3.8 Consensus size: 15
297291 TACATTCAAC
*
297301 TTTTTTATATAATTTA
1 TTTTTAATATAA-TTA
297317 TTTTTAATATAATTA
1 TTTTTAATATAATTA
**
297332 TTCTTCTTTTATAATTA
1 TT-TT-TAATATAATTA
297349 TTTTTAATATAA
1 TTTTTAATATAA
297361 AATTTCAATA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
15 11 0.30
16 15 0.41
17 11 0.30
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTTTAATATAATTA
Found at i:298819 original size:15 final size:15
Alignment explanation
Indices: 298799--298830 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
298789 CAATATAGTG
298799 TATGTGTTTCCATAC
1 TATGTGTTTCCATAC
298814 TATGTGTTTCCATAC
1 TATGTGTTTCCATAC
298829 TA
1 TA
298831 ACATTCATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.22, C:0.19, G:0.12, T:0.47
Consensus pattern (15 bp):
TATGTGTTTCCATAC
Found at i:299524 original size:22 final size:21
Alignment explanation
Indices: 299469--299540 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
299459 ACAAAACATT
299469 ATGTTTGTAACTCTCCTCATA
1 ATGTTTGTAACTCTCCTCATA
299490 ATGTTTGTAACTCTCCTCATA
1 ATGTTTGTAACTCTCCTCATA
* *
299511 ATGTTTAGTAACTCTCTTCATT
1 ATGTTT-GTAACTCTCCTCATA
299533 ATGTTTGT
1 ATGTTTGT
299541 TTTAAATTTC
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
21 29 0.60
22 19 0.40
ACGTcount: A:0.22, C:0.19, G:0.11, T:0.47
Consensus pattern (21 bp):
ATGTTTGTAACTCTCCTCATA
Found at i:300144 original size:15 final size:15
Alignment explanation
Indices: 300124--300182 Score: 66
Period size: 15 Copynumber: 4.0 Consensus size: 15
300114 TCGTATTTAG
*
300124 GGGTTCATACATATA
1 GGGTTCACACATATA
* *
300139 GGGTTCGCACATGTA
1 GGGTTCACACATATA
*
300154 GGGTTCACACAT-TT
1 GGGTTCACACATATA
*
300168 GGGTTCGCACATATA
1 GGGTTCACACATATA
300183 AAGTTTGCAC
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
14 12 0.33
15 24 0.67
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (15 bp):
GGGTTCACACATATA
Done.