Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011886.1 Kokia drynarioides strain JFW-HI SEQ_126883, 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: 42231
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Warning! 3 characters in sequence are not A, C, G, or T
Found at i:829 original size:29 final size:30
Alignment explanation
Indices: 781--1065 Score: 265
Period size: 30 Copynumber: 9.6 Consensus size: 30
771 TTTGTTCAAC
* *
781 AATCTCATTTTTAACCCCAAAAATTCCAAA
1 AATCCCATTTTTAACCCCAAAACTTCCAAA
811 AATCCCATTTTT-ACCCCAAAACTTCCAAA
1 AATCCCATTTTTAACCCCAAAACTTCCAAA
** *
840 AATCCCATTTTT-ACCCCCGAACTTCTAAA
1 AATCCCATTTTTAACCCCAAAACTTCCAAA
* * *
869 AATCCAATTTTTAACCTCGAAACTTCCAAA
1 AATCCCATTTTTAACCCCAAAACTTCCAAA
* * * * * **
899 AGTCCCATTTTTAATCTCGAAGCTTTTAAA
1 AATCCCATTTTTAACCCCAAAACTTCCAAA
* *
929 AATCCCAATTTTAACCCCGAAACTTCCAAA
1 AATCCCATTTTTAACCCCAAAACTTCCAAA
* ** * *
959 AATTCCATTTTT-ACCCCCGAACTACAAAAA
1 AATCCCATTTTTAACCCCAAAACTTC-CAAA
*
989 AATCCCATTTTTAACCCCAAAACTTTCAAA
1 AATCCCATTTTTAACCCCAAAACTTCCAAA
* * * *
1019 AGGT-CTATTTTT-ACCCCCAAACTTCTAAA
1 A-ATCCCATTTTTAACCCCAAAACTTCCAAA
*
1048 AATCCCATTTTTGACCCC
1 AATCCCATTTTTAACCCC
1066 GAATTTTCCC
Statistics
Matches: 207, Mismatches: 42, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
28 1 0.00
29 85 0.41
30 111 0.54
31 10 0.05
ACGTcount: A:0.36, C:0.30, G:0.04, T:0.31
Consensus pattern (30 bp):
AATCCCATTTTTAACCCCAAAACTTCCAAA
Found at i:1079 original size:60 final size:59
Alignment explanation
Indices: 786--1068 Score: 309
Period size: 60 Copynumber: 4.8 Consensus size: 59
776 TCAACAATCT
* * * * *
786 CATTTTTAACCCCAAAAATTCCAAAAATCCCATTTTT-ACCCCAAAACTTCCAAAAATCC
1 CATTTTT-ACCCCCAAACTTCTAAAAATCCCATTTTTAACCCCGAAACTTCCAAAAGTCC
* * *
845 CATTTTTACCCCCGAACTTCTAAAAATCCAATTTTTAACCTCGAAACTTCCAAAAGTCC
1 CATTTTTACCCCCAAACTTCTAAAAATCCCATTTTTAACCCCGAAACTTCCAAAAGTCC
* * * * * * * *
904 CATTTTTAATCTCGAAGCTTTTAAAAATCCCAATTTTAACCCCGAAACTTCCAAAAATTC
1 CATTTTT-ACCCCCAAACTTCTAAAAATCCCATTTTTAACCCCGAAACTTCCAAAAGTCC
* * * * *
964 CATTTTTACCCCCGAACTACAAAAAAATCCCATTTTTAACCCCAAAACTTTCAAAAGGT-C
1 CATTTTTACCCCCAAACTTC-TAAAAATCCCATTTTTAACCCCGAAACTTCCAAAA-GTCC
* *
1024 TATTTTTACCCCCAAACTTCTAAAAATCCCATTTTTGACCCCGAA
1 CATTTTTACCCCCAAACTTCTAAAAATCCCATTTTTAACCCCGAA
1069 TTTTCCCAAA
Statistics
Matches: 183, Mismatches: 37, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
58 24 0.13
59 61 0.33
60 97 0.53
61 1 0.01
ACGTcount: A:0.36, C:0.30, G:0.04, T:0.30
Consensus pattern (59 bp):
CATTTTTACCCCCAAACTTCTAAAAATCCCATTTTTAACCCCGAAACTTCCAAAAGTCC
Found at i:4256 original size:29 final size:29
Alignment explanation
Indices: 4224--4284 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 29
4214 AAAATGAGAC
*
4224 TTTTTGGA-TACTTGGGGGCAAAATGGTAA
1 TTTTTGGACT-CTCGGGGGCAAAATGGTAA
*
4253 -TTTTGGACTCTCGGGGGTAAAATGGTAA
1 TTTTTGGACTCTCGGGGGCAAAATGGTAA
4281 TTTT
1 TTTT
4285 GAGAAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 24 0.86
29 4 0.14
ACGTcount: A:0.25, C:0.08, G:0.30, T:0.38
Consensus pattern (29 bp):
TTTTTGGACTCTCGGGGGCAAAATGGTAA
Found at i:4424 original size:30 final size:29
Alignment explanation
Indices: 4384--4702 Score: 131
Period size: 30 Copynumber: 10.9 Consensus size: 29
4374 GGACATCCGA
4384 GGGT-AAAATGGTAATTTTGAAAGTTTCG
1 GGGTAAAAATGGTAATTTTGAAAGTTTCG
* * *
4412 GGGTCAAAAATGG-AGTTTTTGGACA-TCAT-G
1 GGGT-AAAAATGGTA-ATTTT-GAAAGT-TTCG
*
4442 AGGT-AAAATGGTAATTTTTGAAAGTTTC-
1 GGGTAAAAATGGTAA-TTTTGAAAGTTTCG
* * *
4470 AGGTAAAAAATGG-AGATTTTGGACA--TCCG
1 GGGT-AAAAATGGTA-ATTTT-GAAAGTTTCG
*
4499 GGG-GAAAATGGTAATTTTTGAAAGTTTCG
1 GGGTAAAAATGGTAA-TTTTGAAAGTTTCG
*
4528 GGGTCAAAAATAGAGT--TTTTGGACA--TTCG
1 GGGT-AAAAAT-G-GTAATTTT-GAAAGTTTCG
* *
4557 AGGGT-AAAATGGTAATTTTTGAAAATTTTG
1 -GGGTAAAAATGGTAA-TTTTGAAAGTTTCG
* * **
4587 GGGTCAAAATTGG-AATTTTTGGAAGTTTAA
1 GGGT-AAAAATGGTAA-TTTTGAAAGTTTCG
*
4617 GGGTAAAAAT-GTAATTTTTAGAAGTTTCG
1 GGGTAAAAATGGTAATTTTGA-AAGTTTCG
*
4646 AGGTTAAAAATGG-AATTTTTGAAAG-TTCGG
1 -GGGTAAAAATGGTAA-TTTTGAAAGTTTC-G
4676 GGGT-AAAAT-GTAATTTTAGAATAGTTT
1 GGGTAAAAATGGTAATTTT-GAA-AGTTT
4703 AGGGACCTCC
Statistics
Matches: 220, Mismatches: 30, Indels: 80
0.67 0.09 0.24
Matches are distributed among these distances:
26 2 0.01
27 17 0.08
28 49 0.22
29 53 0.24
30 72 0.33
31 24 0.11
32 1 0.00
33 2 0.01
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.35
Consensus pattern (29 bp):
GGGTAAAAATGGTAATTTTGAAAGTTTCG
Found at i:4575 original size:59 final size:59
Alignment explanation
Indices: 4253--4702 Score: 370
Period size: 58 Copynumber: 7.7 Consensus size: 59
4243 AAAATGGTAA
* * * * ** *
4253 TTTTGGAC-TCTCGGGGGTAAAATGGTAATTTTGAGAAAATTT-GGAGTTTAAAATGGA-A
1 TTTTGGACAT-TCGAGGGTAAAATGGTAATTTT-TGAAAGTTTCGGGGTCAAAAATGGAGT
* * * * * *** * * * *
4311 TTTTAGACATCCAAGGGTAAGACGGTAATTTTT-ACAAAAATCAGGATCAAAAACGGAAT
1 TTTTGGACATTCGAGGGTAAAATGGTAATTTTTGA-AAGTTTCGGGGTCAAAAATGGAGT
*
4370 TTTTGGACATCCGAGGGTAAAATGGTAA-TTTTGAAAGTTTCGGGGTCAAAAATGGAGT
1 TTTTGGACATTCGAGGGTAAAATGGTAATTTTTGAAAGTTTCGGGGTCAAAAATGGAGT
* * *
4428 TTTTGGACA-TC-ATGAGGTAAAATGGTAATTTTTGAAAGTTTC-AGGTAAAAAATGGAGA
1 TTTTGGACATTCGA-G-GGTAAAATGGTAATTTTTGAAAGTTTCGGGGTCAAAAATGGAGT
* * *
4486 TTTTGGACATCCG-GGGGAAAATGGTAATTTTTGAAAGTTTCGGGGTCAAAAATAGAGT
1 TTTTGGACATTCGAGGGTAAAATGGTAATTTTTGAAAGTTTCGGGGTCAAAAATGGAGT
* * * *
4544 TTTTGGACATTCGAGGGTAAAATGGTAATTTTTGAAAATTTTGGGGTCAAAATTGGAAT
1 TTTTGGACATTCGAGGGTAAAATGGTAATTTTTGAAAGTTTCGGGGTCAAAAATGGAGT
** * * *
4603 TTTTGGA-AGTTTAAGGGTAAAAAT-GTAATTTTT-AGAAGTTTCGAGGTTAAAAATGGAAT
1 TTTTGGACA-TTCGAGGGT-AAAATGGTAATTTTTGA-AAGTTTCGGGGTCAAAAATGGAGT
* * *
4662 TTTT-GAAAGTTCGGGGGTAAAAT-GTAATTTTAGAATAGTTT
1 TTTTGGACA-TTCGAGGGTAAAATGGTAATTTTTGAA-AGTTT
4703 AGGGACCTCC
Statistics
Matches: 319, Mismatches: 55, Indels: 35
0.78 0.13 0.09
Matches are distributed among these distances:
56 2 0.01
57 32 0.10
58 141 0.44
59 139 0.44
60 5 0.02
ACGTcount: A:0.35, C:0.06, G:0.25, T:0.34
Consensus pattern (59 bp):
TTTTGGACATTCGAGGGTAAAATGGTAATTTTTGAAAGTTTCGGGGTCAAAAATGGAGT
Found at i:6673 original size:29 final size:29
Alignment explanation
Indices: 6617--6676 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
6607 ATAATAAATT
*
6617 TTAAATTTAAATATAAATCTAAACTTATA
1 TTAAATTTAAATATAAAACTAAACTTATA
* *
6646 TTAAATTTAAATTTTAAAAC-AAATTTATA
1 TTAAATTTAAA-TATAAAACTAAACTTATA
6675 TT
1 TT
6677 CAAAATAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 21 0.78
30 6 0.22
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (29 bp):
TTAAATTTAAATATAAAACTAAACTTATA
Found at i:6686 original size:17 final size:17
Alignment explanation
Indices: 6604--6705 Score: 73
Period size: 17 Copynumber: 5.8 Consensus size: 17
6594 ACTTTCAATA
* *
6604 TTTATAATAAATTTTAAA
1 TTTAAAATAAA-TTTAAC
*
6622 TTTAAATATAAATCTAAAC
1 TTTAAA-ATAAAT-TTAAC
* * *
6641 -TTATATTAAATTTAAAT
1 TTTAAAATAAATTT-AAC
*
6658 TTTAAAACAAATTTATA-
1 TTTAAAATAAATTTA-AC
*
6675 TTCAAAATAAATTTAAC
1 TTTAAAATAAATTTAAC
6692 TTTAAAATAAATTT
1 TTTAAAATAAATTT
6706 TAGAATGAAT
Statistics
Matches: 65, Mismatches: 13, Indels: 13
0.71 0.14 0.14
Matches are distributed among these distances:
16 2 0.03
17 34 0.52
18 21 0.32
19 8 0.12
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TTTAAAATAAATTTAAC
Found at i:10134 original size:6 final size:6
Alignment explanation
Indices: 10125--10197 Score: 80
Period size: 6 Copynumber: 12.7 Consensus size: 6
10115 TGAATTTGTT
* * * *
10125 TTTAAA TTTAAA TTT-AT TTTAAG TTTAAG TTTAAA TTT-AT TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
10171 TTTAAA TTT-AA TTTAAG TTTAAA TTTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTA
10198 TTATCAAATT
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
5 13 0.23
6 44 0.77
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:10146 original size:17 final size:17
Alignment explanation
Indices: 10124--10216 Score: 87
Period size: 17 Copynumber: 5.1 Consensus size: 17
10114 TTGAATTTGT
10124 TTTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
10141 TTTTAAGTTTAAGTTTAAATTTA
1 TTTT-A----AA-TTTAAATTTA
10164 TTTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
* *
10181 ATTTAAGTTTAAATTTA
1 TTTTAAATTTAAATTTA
* *
10198 TTATCAAATTTAAAATTA
1 TT-TTAAATTTAAATTTA
10216 T
1 T
10217 CCTAAATGTA
Statistics
Matches: 63, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
17 30 0.48
18 16 0.25
22 3 0.05
23 14 0.22
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:10151 original size:11 final size:11
Alignment explanation
Indices: 10131--10209 Score: 70
Period size: 11 Copynumber: 6.9 Consensus size: 11
10121 TGTTTTTAAA
10131 TTTAAATTTAT
1 TTTAAATTTAT
* *
10142 TTTAAGTTTAAG
1 TTTAAATTT-AT
10154 TTTAAATTTAT
1 TTTAAATTTAT
*
10165 TTTAAATTTAAA
1 TTTAAATTT-AT
*
10177 TTT-AATTTAAG
1 TTTAAATTT-AT
10188 TTTAAATTTAT
1 TTTAAATTTAT
*
10199 TATCAAATTTA
1 T-TTAAATTTA
10210 AAATTATCCT
Statistics
Matches: 56, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
11 30 0.54
12 26 0.46
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:10151 original size:23 final size:23
Alignment explanation
Indices: 10125--10197 Score: 103
Period size: 23 Copynumber: 3.2 Consensus size: 23
10115 TGAATTTGTT
*
10125 TTTAAATTTAAATTTATTTTAAG
1 TTTAAATTTAAATTTATTTTAAA
*
10148 TTTAAGTTTAAATTTATTTTAAA
1 TTTAAATTTAAATTTATTTTAAA
*
10171 TTTAAATTT-AATTTAAGTTTAAA
1 TTTAAATTTAAATTT-ATTTTAAA
10194 TTTA
1 TTTA
10198 TTATCAAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
22 5 0.11
23 40 0.89
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (23 bp):
TTTAAATTTAAATTTATTTTAAA
Found at i:10907 original size:3 final size:3
Alignment explanation
Indices: 10889--10926 Score: 58
Period size: 3 Copynumber: 12.0 Consensus size: 3
10879 ATAACGTTAG
10889 TAA TAAA TACA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
10927 AAGATAGTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 27 0.82
4 6 0.18
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:12121 original size:29 final size:29
Alignment explanation
Indices: 12087--12324 Score: 196
Period size: 29 Copynumber: 8.2 Consensus size: 29
12077 AAACTTTTTG
12087 AAAATTACCATTTTACCCTCGAATATCCA
1 AAAATTACCATTTTACCCTCGAATATCCA
* * *
12116 AAAATTACAATTTTACCCTCAAATGTCCA
1 AAAATTACCATTTTACCCTCGAATATCCA
* *
12145 AAAATTA-CATTTTTGACCC-CGAACTTTTCA
1 AAAATTACCA-TTTT-ACCCTCGAA-TATCCA
* * * *
12175 AAAATTACCATTTTTCCCTTGAGTAACCA
1 AAAATTACCATTTTACCCTCGAATATCCA
* * **
12204 AAAATTACCGTTTTACTCTCGAACGTCCA
1 AAAATTACCATTTTACCCTCGAATATCCA
*
12233 AAAATTACCATTTTGA-CCTCGAATGTCCA
1 AAAATTACCATTTT-ACCCTCGAATATCCA
* * * *
12262 AAAAATACTATTTTACCCTAG-ACATCCA
1 AAAATTACCATTTTACCCTCGAATATCCA
* * * * **
12290 AAATTTAACATATTACCCCCGAGCATCCA
1 AAAATTACCATTTTACCCTCGAATATCCA
12319 AAAATT
1 AAAATT
12325 GCATTTTTGA
Statistics
Matches: 163, Mismatches: 38, Indels: 16
0.75 0.18 0.07
Matches are distributed among these distances:
28 21 0.13
29 118 0.72
30 22 0.13
31 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.06, T:0.31
Consensus pattern (29 bp):
AAAATTACCATTTTACCCTCGAATATCCA
Found at i:12161 original size:88 final size:86
Alignment explanation
Indices: 12024--12307 Score: 241
Period size: 88 Copynumber: 3.3 Consensus size: 86
12014 TTCCTGAACA
* * * * * * **
12024 ATCCAAAAATTACATTTAACCC-GAAACTTTCCAAAATTTACCGTTTTGACCTTAAACTTTTTGA
1 ATCCAAAAATTACATTTTACCCTCAAA-TGTCCAAAAATTA-CATTTTGACCTCAAACTTTTCAA
12088 AAATTACCATTTTACCCTCGAAT
64 AAATTACCATTTTACCCTCGAAT
* *
12111 ATCCAAAAATTACAATTTTACCCTCAAATGTCCAAAAATTACATTTTTGACCCCGAACTTTTCAA
1 ATCCAAAAATTAC-ATTTTACCCTCAAATGTCCAAAAATTACA-TTTTGACCTCAAACTTTTCAA
* * *
12176 AAATTACCATTTTTCCCTTGAGT
64 AAATTACCATTTTACCCTCGAAT
* * * * * * * *
12199 AACCAAAAATTACCGTTTTACTCTCGAACGTCCAAAAATTACCATTTTGACCTCGAA-TGTCCAA
1 ATCCAAAAATTA-CATTTTACCCTCAAATGTCCAAAAATTA-CATTTTGACCTCAAACTTTTCAA
* * * *
12263 AAAATACTATTTTACCCTAG-AC
64 AAATTACCATTTTACCCTCGAAT
* *
12285 ATCCAAAATTTAACATATTACCC
1 ATCCAAAAATT-ACATTTTACCC
12308 CCGAGCATCC
Statistics
Matches: 159, Mismatches: 32, Indels: 13
0.78 0.16 0.06
Matches are distributed among these distances:
86 16 0.10
87 36 0.23
88 101 0.64
89 6 0.04
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.33
Consensus pattern (86 bp):
ATCCAAAAATTACATTTTACCCTCAAATGTCCAAAAATTACATTTTGACCTCAAACTTTTCAAAA
ATTACCATTTTACCCTCGAAT
Found at i:13646 original size:29 final size:29
Alignment explanation
Indices: 13604--13662 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
13594 CATATAATGA
*
13604 AGGCGGGTGCTTCAAAAGAGACCTAAGAC
1 AGGCGGGTGCTTCAAAAGAGACCCAAGAC
13633 AGGCGGGTGCTTCAAAAGAGACCCAAGAC
1 AGGCGGGTGCTTCAAAAGAGACCCAAGAC
13662 A
1 A
13663 TAACTAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.36, C:0.22, G:0.31, T:0.12
Consensus pattern (29 bp):
AGGCGGGTGCTTCAAAAGAGACCCAAGAC
Found at i:15484 original size:31 final size:31
Alignment explanation
Indices: 15447--15526 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 31
15437 GGACCCTAAA
* *
15447 AAGTTTAAGTACCAACTTAAAAAAAAGTGTC
1 AAGTTTAAGTACCAAATTAAAAAAAAGTATC
* ** *
15478 AAGTTTAGGTACCAAATTAGGAAATAGTATC
1 AAGTTTAAGTACCAAATTAAAAAAAAGTATC
* *
15509 AAGTTTTAGTATCAAATT
1 AAGTTTAAGTACCAAATT
15527 GGAACAAAAA
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (31 bp):
AAGTTTAAGTACCAAATTAAAAAAAAGTATC
Found at i:15538 original size:90 final size:89
Alignment explanation
Indices: 15392--15573 Score: 201
Period size: 90 Copynumber: 2.0 Consensus size: 89
15382 AAAAAAAAGA
* ** **
15392 TTAGGTACCAAATTAAGAAAAATAGTCAAGTTCAGGTACCAAATTGGACCCTAAAAAGTTTA-AG
1 TTAGGTACCAAATTAAGAAAAATAGTCAAGTTCAGGTACCAAATTGGAACAAAAAAAAATTAGA-
*
15456 TACCAACTTA-AAAAAAAGTGTCAAGT
65 TACCAAATTAGAAAAAAA-T-TCAAGT
* * * *
15482 TTAGGTACCAAATTAGGAAATAGTA-TCAAGTTTTA-GTATCAAATTGGAACAAAAAAAAATTAG
1 TTAGGTACCAAATTAAGAAA-AATAGTCAAG-TTCAGGTACCAAATTGGAACAAAAAAAAATTAG
15545 ATACCAAATTAGAAAAAAATTCAAGT
64 ATACCAAATTAGAAAAAAATTCAAGT
15571 TTA
1 TTA
15574 AACACCAAAT
Statistics
Matches: 78, Mismatches: 10, Indels: 9
0.80 0.10 0.09
Matches are distributed among these distances:
89 9 0.12
90 55 0.71
91 14 0.18
ACGTcount: A:0.48, C:0.12, G:0.14, T:0.26
Consensus pattern (89 bp):
TTAGGTACCAAATTAAGAAAAATAGTCAAGTTCAGGTACCAAATTGGAACAAAAAAAAATTAGAT
ACCAAATTAGAAAAAAATTCAAGT
Found at i:15817 original size:17 final size:17
Alignment explanation
Indices: 15792--15872 Score: 99
Period size: 17 Copynumber: 4.7 Consensus size: 17
15782 GACCCAACAG
15792 AATTTAAATTTATTTTA
1 AATTTAAATTTATTTTA
*
15809 AAATTAAATTTATTTTA
1 AATTTAAATTTATTTTA
* * *
15826 AGTTTAAATTAATTTGA
1 AATTTAAATTTATTTTA
**
15843 AATTTAAATTTATAATA
1 AATTTAAATTTATTTTA
15860 AATTTAAAGTTTA
1 AATTTAAA-TTTA
15873 AATTTATTTA
Statistics
Matches: 53, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
17 49 0.92
18 4 0.08
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.51
Consensus pattern (17 bp):
AATTTAAATTTATTTTA
Found at i:15874 original size:7 final size:6
Alignment explanation
Indices: 15792--15878 Score: 69
Period size: 6 Copynumber: 15.0 Consensus size: 6
15782 GACCCAACAG
* * * *
15792 AATTTA AATTT- ATTTTA AAATTA AATTT- ATTTTA AGTTTA AA-TT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
15836 AATTTGA AATTTA AATTTA TAA--TA AATTTA AAGTTTA AATTTA
1 AATTT-A AATTTA AATTTA -AATTTA AATTTA AA-TTTA AATTTA
15879 TTTAAATAAT
Statistics
Matches: 65, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
4 4 0.06
5 14 0.22
6 34 0.52
7 13 0.20
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (6 bp):
AATTTA
Found at i:16670 original size:9 final size:9
Alignment explanation
Indices: 16658--16700 Score: 61
Period size: 9 Copynumber: 4.8 Consensus size: 9
16648 TAAATATAAC
16658 ATTAATATT
1 ATTAATATT
16667 ATTAATATT
1 ATTAATATT
16676 ATTAATATT
1 ATTAATATT
*
16685 AAATAATATT
1 -ATTAATATT
16695 -TTAATA
1 ATTAATA
16701 AAAAAGAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
8 5 0.16
9 18 0.58
10 8 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
ATTAATATT
Found at i:16673 original size:36 final size:36
Alignment explanation
Indices: 16609--16689 Score: 90
Period size: 36 Copynumber: 2.2 Consensus size: 36
16599 TTAATAATGG
** * *
16609 TAATAAATATATTATTTATTTTAATAATAATACTAA
1 TAATAAATATAACATTAATATTAATAATAATACTAA
* * *
16645 TAATAAATATAACATTAATATTATTAATATTATTAA
1 TAATAAATATAACATTAATATTAATAATAATACTAA
*
16681 TATTAAATA
1 TAATAAATA
16690 ATATTTTAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (36 bp):
TAATAAATATAACATTAATATTAATAATAATACTAA
Found at i:16679 original size:18 final size:19
Alignment explanation
Indices: 16612--16700 Score: 71
Period size: 18 Copynumber: 4.9 Consensus size: 19
16602 ATAATGGTAA
*
16612 TAAAT-ATATTATTTAT-T
1 TAAATAATATTATTAATAT
* * * *
16629 TTAATAATAATACTAATAA
1 TAAATAATATTATTAATAT
**
16648 TAAAT-ATAACATTAATAT
1 TAAATAATATTATTAATAT
*
16666 T-ATTAATATTATTAATAT
1 TAAATAATATTATTAATAT
16684 TAAATAATATT-TTAATA
1 TAAATAATATTATTAATA
16701 AAAAAGAAAA
Statistics
Matches: 55, Mismatches: 13, Indels: 7
0.73 0.17 0.09
Matches are distributed among these distances:
17 6 0.11
18 37 0.67
19 12 0.22
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
TAAATAATATTATTAATAT
Found at i:17825 original size:30 final size:29
Alignment explanation
Indices: 17789--18171 Score: 182
Period size: 29 Copynumber: 13.1 Consensus size: 29
17779 CCCAAGGTCT
* * *
17789 CTAAACTATCCAAAAAATACATTTTAGCCC
1 CTAAACTTTCCAAAAATTACATTTT-GACC
*
17819 CTAAACTTTCCAAAAATTATATTTTGACC
1 CTAAACTTTCCAAAAATTACATTTTGACC
* * *
17848 CAAAACTTTCTAAAAATTACATTTTTATCC
1 CTAAACTTTCCAAAAATTACATTTTGA-CC
*
17878 C-GAACTTTCCAAAAATCT-CATTTTTGACC
1 CTAAACTTTCCAAAAAT-TACA-TTTTGACC
* ** * *
17907 C-GATTTTTCAAAAAATCACCATTTT-ACTC
1 CTAAACTTTCCAAAAATTA-CATTTTGAC-C
* * * * *
17936 CCAAAC-TTCCAAATATTCCATTTTTAAC
1 CTAAACTTTCCAAAAATTACATTTTGACC
* * *
17964 CTCGATCTTGCCAAAAATTACCATTTT-ACC
1 CT-AAACTTTCCAAAAATTA-CATTTTGACC
* *
17994 CTCGAAC-TTCCAAAAATTCCATTTTGACC
1 CT-AAACTTTCCAAAAATTACATTTTGACC
* *
18023 CT-GATTTCTCCAAAAATTACCATTTT-ACC
1 CTAAACTT-TCCAAAAATTA-CATTTTGACC
* * *
18052 CATGAAC-TTCCAAAAATTCCATTTTTAACC
1 C-TAAACTTTCCAAAAATTACA-TTTTGACC
** * *
18082 CCGATCTTTCCAAAAGTTAGCATTTT-ACC
1 CTAAACTTTCCAAAAATTA-CATTTTGACC
* * *
18111 CTCAAAC-TTCAAAAAATTCCATTTTTAACC
1 CT-AAACTTTCCAAAAATTACA-TTTTGACC
*
18141 CT-AATTTTCCAAAAAATTACCATTTT-ACC
1 CTAAACTTTCC-AAAAATTA-CATTTTGACC
18170 CT
1 CT
18172 CGAATGTCTA
Statistics
Matches: 274, Mismatches: 52, Indels: 55
0.72 0.14 0.14
Matches are distributed among these distances:
27 1 0.00
28 23 0.08
29 144 0.53
30 95 0.35
31 11 0.04
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.35
Consensus pattern (29 bp):
CTAAACTTTCCAAAAATTACATTTTGACC
Found at i:17930 original size:59 final size:58
Alignment explanation
Indices: 17826--18223 Score: 388
Period size: 59 Copynumber: 6.8 Consensus size: 58
17816 CCCCTAAACT
* * * *
17826 TTCCAAAAATT--ATATTTTGACCCAAAACTTTCTAAAAATTA-CATTTTTATCC-CGAAC
1 TTCCAAAAATTCCAT-TTTTGACCC-GATCTTTCCAAAAATTACCA-TTTTACCCTCGAAC
* * * *
17883 TTTCCAAAAA-TCTCATTTTTGACCCGATTTTTCAAAAAATCACCATTTTACTCC-CAAAC
1 -TTCCAAAAATTC-CATTTTTGACCCGATCTTTCCAAAAATTACCATTTTAC-CCTCGAAC
* * *
17942 TTCCAAATATTCCATTTTTAACCTCGATCTTGCCAAAAATTACCATTTTACCCTCGAAC
1 TTCCAAAAATTCCATTTTTGACC-CGATCTTTCCAAAAATTACCATTTTACCCTCGAAC
18001 TTCCAAAAATTCCA-TTTTGACCCTGAT-TTCTCCAAAAATTACCATTTTACCCAT-GAAC
1 TTCCAAAAATTCCATTTTTGACCC-GATCTT-TCCAAAAATTACCATTTTACCC-TCGAAC
* * * *
18059 TTCCAAAAATTCCATTTTTAACCCCGATCTTTCCAAAAGTTAGCATTTTACCCTCAAAC
1 TTCCAAAAATTCCATTTTTGA-CCCGATCTTTCCAAAAATTACCATTTTACCCTCGAAC
* * *
18118 TTCAAAAAATTCCATTTTTAACCCTAAT-TTTCCAAAAAATTACCATTTTACCCTCGAA-
1 TTCCAAAAATTCCATTTTTGACCC-GATCTTTCC-AAAAATTACCATTTTACCCTCGAAC
* * * *
18176 TGTCTAAAAATTCTATTTTTGACCCGAACTTTCC-CAAATTACCATTTT
1 T-TCCAAAAATTCCATTTTTGACCCGATCTTTCCAAAAATTACCATTTT
18224 GCCACTGAGC
Statistics
Matches: 289, Mismatches: 32, Indels: 39
0.80 0.09 0.11
Matches are distributed among these distances:
57 17 0.06
58 106 0.37
59 159 0.55
60 7 0.02
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (58 bp):
TTCCAAAAATTCCATTTTTGACCCGATCTTTCCAAAAATTACCATTTTACCCTCGAAC
Found at i:18187 original size:29 final size:29
Alignment explanation
Indices: 17917--18175 Score: 214
Period size: 29 Copynumber: 8.8 Consensus size: 29
17907 CGATTTTTCA
* *
17917 AAAAATCACCATTTTACTCC-CAAACTTCC
1 AAAAATTACCATTTTAC-CCTCGAACTTCC
* * *
17946 AAATATT-CCATTTTTAACCTCGATCTTGCC
1 AAAAATTACCA-TTTTACCCTCGAACTT-CC
17976 AAAAATTACCATTTTACCCTCGAACTTCC
1 AAAAATTACCATTTTACCCTCGAACTTCC
**
18005 AAAAATT-CCATTTTGACCCT-GATTTCTCC
1 AAAAATTACCATTTT-ACCCTCGAACT-TCC
18034 AAAAATTACCATTTTACCCAT-GAACTTCC
1 AAAAATTACCATTTTACCC-TCGAACTTCC
*
18063 AAAAATT-CCATTTTTAACCC-CGATCTTTCC
1 AAAAATTACCA-TTTT-ACCCTCGAAC-TTCC
* * * *
18093 AAAAGTTAGCATTTTACCCTCAAACTTCA
1 AAAAATTACCATTTTACCCTCGAACTTCC
*
18122 AAAAATT-CCATTTTTAACCCT--AATTTTCC
1 AAAAATTACCA-TTTT-ACCCTCGAA-CTTCC
18151 AAAAAATTACCATTTTACCCTCGAA
1 -AAAAATTACCATTTTACCCTCGAA
18176 TGTCTAAAAA
Statistics
Matches: 187, Mismatches: 22, Indels: 40
0.75 0.09 0.16
Matches are distributed among these distances:
28 22 0.12
29 85 0.45
30 70 0.37
31 10 0.05
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (29 bp):
AAAAATTACCATTTTACCCTCGAACTTCC
Found at i:18202 original size:117 final size:116
Alignment explanation
Indices: 17888--18223 Score: 407
Period size: 117 Copynumber: 2.9 Consensus size: 116
17878 CGAACTTTCC
* * * *
17888 AAAAA-TCTCATTTTTGACCC-GATTTTTCAAAAAATCACCATTTTACTCC-CAAACTTCCAAAT
1 AAAAATTC-CATTTTTGACCCTGATTTTCCAAAAAATTACCATTTTAC-CCTCGAACTTCCAAAA
* * *
17950 ATTCCATTTTTAACCTCGATCTTGCCAAAAATTACCATTTTACCCTCGAACTTCC
64 ATTCCATTTTTAACC-CGATCTTTCC-AAAATTACCATTTTACCCTCAAACTTCA
18005 AAAAATTCCA-TTTTGACCCTGATTTCTCC-AAAAATTACCATTTTACCCAT-GAACTTCCAAAA
1 AAAAATTCCATTTTTGACCCTGATTT-TCCAAAAAATTACCATTTTACCC-TCGAACTTCCAAAA
*
18067 ATTCCATTTTTAACCCCGATCTTTCCAAAAGTTAGCATTTTACCCTCAAACTTCA
64 ATTCCATTTTTAA-CCCGATCTTTCCAAAA-TTACCATTTTACCCTCAAACTTCA
* * *
18122 AAAAATTCCATTTTTAACCCTAATTTTCCAAAAAATTACCATTTTACCCTCGAA-TGTCTAAAAA
1 AAAAATTCCATTTTTGACCCTGATTTTCCAAAAAATTACCATTTTACCCTCGAACT-TCCAAAAA
* * * *
18186 TTCTATTTTTGACCCGAACTTTCCCAAATTACCATTTT
65 TTCCATTTTTAACCCGATCTTTCCAAAATTACCATTTT
18224 GCCACTGAGC
Statistics
Matches: 192, Mismatches: 16, Indels: 23
0.83 0.07 0.10
Matches are distributed among these distances:
116 24 0.12
117 110 0.57
118 58 0.30
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.36
Consensus pattern (116 bp):
AAAAATTCCATTTTTGACCCTGATTTTCCAAAAAATTACCATTTTACCCTCGAACTTCCAAAAAT
TCCATTTTTAACCCGATCTTTCCAAAATTACCATTTTACCCTCAAACTTCA
Found at i:24864 original size:114 final size:117
Alignment explanation
Indices: 24662--24893 Score: 389
Period size: 116 Copynumber: 2.0 Consensus size: 117
24652 TTGGATTGTG
*
24662 GGACCACTCAATCTTTTTATTGTTAACAAACCACACTCCTATCTTGTCCAATTTCACACTCAACT
1 GGACCACTCAATCTTTTTATTGTTAACAAACCACAC-CCTATCGTGTCCAATTTCACACTCAACT
*
24727 TTCGACTTTGATTTTGTTTTG-TTTTTT-ATGGTATATATTATGAATGGTAAT
65 TTCGACTTTGATTTTGTTTTGTTTTTTTAATGGTATATATTATAAATGGTAAT
* * *
24778 GGACCACTCAATCTTTTTATTGTTAATAAACCACA-CCTATCGTGTCCAATTTGACATTCAACTT
1 GGACCACTCAATCTTTTTATTGTTAACAAACCACACCCTATCGTGTCCAATTTCACACTCAACTT
24842 TCGACTTTGATTTTGTTTTGTTTTTTTAATGGTATATATTATAAATGGTAAT
66 TCGACTTTGATTTTGTTTTGTTTTTTTAATGGTATATATTATAAATGGTAAT
24894 TATTCTAAAA
Statistics
Matches: 109, Mismatches: 5, Indels: 4
0.92 0.04 0.03
Matches are distributed among these distances:
114 46 0.42
115 6 0.06
116 57 0.52
ACGTcount: A:0.27, C:0.17, G:0.12, T:0.44
Consensus pattern (117 bp):
GGACCACTCAATCTTTTTATTGTTAACAAACCACACCCTATCGTGTCCAATTTCACACTCAACTT
TCGACTTTGATTTTGTTTTGTTTTTTTAATGGTATATATTATAAATGGTAAT
Found at i:25276 original size:52 final size:52
Alignment explanation
Indices: 25196--25295 Score: 121
Period size: 52 Copynumber: 1.9 Consensus size: 52
25186 AAATTAGGCT
**
25196 CTTTAAAAATTTTAAAATGTTAAATTAATAAAA-ATAAAATTATATTTTGTTC
1 CTTTAAAAATGATAAAATGTTAAATTAATAAAATA-AAAATTATATTTTGTTC
* * * **
25248 CTTTAAAAATGATAAAATTTTGATTTAATAATTTAAAAATTATATTTT
1 CTTTAAAAATGATAAAATGTTAAATTAATAAAATAAAAATTATATTTT
25296 TACTATCCTA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
52 39 0.98
53 1 0.03
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (52 bp):
CTTTAAAAATGATAAAATGTTAAATTAATAAAATAAAAATTATATTTTGTTC
Found at i:34342 original size:2 final size:2
Alignment explanation
Indices: 34335--34365 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
34325 CACATACATT
34335 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
34366 GCATGACAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:41181 original size:19 final size:19
Alignment explanation
Indices: 41140--41183 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
41130 TCACGTGATT
41140 TTTTTTTAATATCACAGGAA
1 TTTTTTTAATA-CACAGGAA
*
41160 TTTTTTTAATA-ACTAGGTA
1 TTTTTTTAATACAC-AGGAA
41179 TTTTT
1 TTTTT
41184 AGTCTATACA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 2 0.09
19 9 0.41
20 11 0.50
ACGTcount: A:0.30, C:0.07, G:0.09, T:0.55
Consensus pattern (19 bp):
TTTTTTTAATACACAGGAA
Done.