Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001528.1 Kokia drynarioides strain JFW-HI SEQ_113094, 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: 46401
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 59 characters in sequence are not A, C, G, or T
Found at i:630 original size:29 final size:29
Alignment explanation
Indices: 598--1034 Score: 309
Period size: 30 Copynumber: 14.8 Consensus size: 29
588 ATTTTTTCCT
* **
598 CGAACTTCTAAAAATTCCATCCTCGACCC
1 CGAACTTCCAAAAATTCCATTTTCGACCC
* * *
627 CGAAATTTCCAAAAAATCCATTTT-TACCC
1 CG-AACTTCCAAAAATTCCATTTTCGACCC
*
656 CTGAACTTCCAAAAAATCCATTTTCGACCC
1 C-GAACTTCCAAAAATTCCATTTTCGACCC
** * *
686 TAAAACTTCCAAAAATCCCATTTT-TACCCC
1 -CGAACTTCCAAAAATTCCATTTTCGA-CCC
*
716 CGAACTTCCAAAAATTCCATTTTTGACCC
1 CGAACTTCCAAAAATTCCATTTTCGACCC
* * *
745 CGAAACTTCCAAAAATTCCCTTTTTG-CCT
1 CG-AACTTCCAAAAATTCCATTTTCGACCC
*
774 TGAACTTCCAAAAATTCCATTTTCGACCC
1 CGAACTTCCAAAAATTCCATTTTCGACCC
* *
803 CAAAACTTCCAAAAATTCCATTTTCGACCT
1 C-GAACTTCCAAAAATTCCATTTTCGACCC
* *
833 CGAAACTCCCAAAAATTCCATTTT-TACCC
1 CG-AACTTCCAAAAATTCCATTTTCGACCC
* * *
862 TCGAACCTCCAAAATTTCCATTTTTGACCC
1 -CGAACTTCCAAAAATTCCATTTTCGACCC
** *
892 CGAAACTTTAAAAAATTACCA--TTCTACCCC
1 CG-AACTTCCAAAAATT-CCATTTTCGA-CCC
* * * * *
922 CGGA-TGTCCAAAAACTCTATTTTCAACCT
1 CGAACT-TCCAAAAATTCCATTTTCGACCC
*
951 CGAAACTT-CAAAAATTCCATTTT-TACTCC
1 CG-AACTTCCAAAAATTCCATTTTCGAC-CC
* ** *
980 CGAA-TGTCTAAAAATTCCATCTTTTAACCT
1 CGAACT-TCCAAAAATTCCAT-TTTCGACCC
*
1010 CGAACTTTCCCAAAATTACCATTTT
1 CGAAC-TTCCAAAAATT-CCATTTT
1035 GCCCCTAGAT
Statistics
Matches: 323, Mismatches: 57, Indels: 54
0.74 0.13 0.12
Matches are distributed among these distances:
27 1 0.00
28 29 0.09
29 123 0.38
30 148 0.46
31 17 0.05
32 5 0.02
ACGTcount: A:0.33, C:0.31, G:0.05, T:0.31
Consensus pattern (29 bp):
CGAACTTCCAAAAATTCCATTTTCGACCC
Found at i:670 original size:59 final size:59
Alignment explanation
Indices: 599--856 Score: 306
Period size: 59 Copynumber: 4.4 Consensus size: 59
589 TTTTTTCCTC
* ** * *
599 GAACTTCTAAAAATTCCATCCTCGACCCCGAAATTTCCAAAAAATCCATTTTTACCCCT
1 GAACTTCCAAAAATTCCATTTTCGACCCCAAAACTTCCAAAAAATCCATTTTTACCCCT
* * *
658 GAACTTCCAAAAAATCCATTTTCGACCCTAAAACTTCC-AAAAATCCCATTTTTACCCCC
1 GAACTTCCAAAAATTCCATTTTCGACCCCAAAACTTCCAAAAAAT-CCATTTTTACCCCT
* * * * * *
717 GAACTTCCAAAAATTCCATTTTTGACCCCGAAACTTCCAAAAATTCCCTTTTT-GCCTT
1 GAACTTCCAAAAATTCCATTTTCGACCCCAAAACTTCCAAAAAATCCATTTTTACCCCT
* * *
775 GAACTTCCAAAAATTCCATTTTCGACCCCAAAACTTCCAAAAATTCCATTTTCGACCTC-
1 GAACTTCCAAAAATTCCATTTTCGACCCCAAAACTTCCAAAAAATCCATTTT-TACCCCT
*
834 GAAACTCCCAAAAATTCCATTTT
1 G-AACTTCCAAAAATTCCATTTT
857 TACCCTCGAA
Statistics
Matches: 169, Mismatches: 25, Indels: 9
0.83 0.12 0.04
Matches are distributed among these distances:
58 57 0.34
59 86 0.51
60 26 0.15
ACGTcount: A:0.34, C:0.31, G:0.05, T:0.30
Consensus pattern (59 bp):
GAACTTCCAAAAATTCCATTTTCGACCCCAAAACTTCCAAAAAATCCATTTTTACCCCT
Found at i:728 original size:88 final size:88
Alignment explanation
Indices: 624--1034 Score: 315
Period size: 88 Copynumber: 4.6 Consensus size: 88
614 CCATCCTCGA
* * *
624 CCCCGAAATTTCCAAAAAATCCATTTTTACCCCTG-AACTTCCAAAAAATCCATTTTCGACCCTA
1 CCCCG-AACTTCCAAAAATTCCATTTTTACCCC-GAAACTTCCAAAAATTCCATTTTCGACCCTA
*
688 AAACTTCCAAAAATCCCATTTTTAC
64 AAACTTCCAAAAATTCCATTTTTAC
* * **
713 CCCCGAACTTCCAAAAATTCCATTTTTGACCCCGAAACTTCCAAAAATTCCCTTTTTG--CCTTG
1 CCCCGAACTTCCAAAAATTCCATTTTT-ACCCCGAAACTTCCAAAAATTCCATTTTCGACCCTAA
*
776 AACTTCCAAAAATTCCATTTTCGAC
65 AACTTCCAAAAATTCCATTTT-TAC
** * * * * **
801 CCCAAAACTTCCAAAAATTCCATTTTCGACCTCGAAACTCCCAAAAATTCCATTTT-TACCCTCG
1 CCCCGAACTTCCAAAAATTCCATTTT-TACCCCGAAACTTCCAAAAATTCCATTTTCGACCCTAA
* *
865 AACCTCCAAAATTTCCATTTTTGA-
65 AACTTCCAAAAATTCCATTTTT-AC
** * * * * *
889 CCCCGAAACTTTAAAAAATTACCA-TTCTACCCCCG-GA-TGTCCAAAAACTCTATTTTC-AACC
1 CCCCG-AACTTCCAAAAATT-CCATTTTTA-CCCCGAAACT-TCCAAAAATTCCATTTTCGACCC
*
950 TCGAAACTT-CAAAAATTCCATTTTTAC
62 T-AAAACTTCCAAAAATTCCATTTTTAC
* * * *
977 TCCCGAA-TGTCTAAAAATTCCATCTTTTAACCTCG-AACTTTCCCAAAATTACCATTTT
1 CCCCGAACT-TCCAAAAATTCCAT-TTTT-ACCCCGAAAC-TTCCAAAAATT-CCATTTT
1035 GCCCCTAGAT
Statistics
Matches: 256, Mismatches: 45, Indels: 41
0.75 0.13 0.12
Matches are distributed among these distances:
86 4 0.02
87 35 0.14
88 122 0.48
89 85 0.33
90 10 0.04
ACGTcount: A:0.33, C:0.31, G:0.05, T:0.31
Consensus pattern (88 bp):
CCCCGAACTTCCAAAAATTCCATTTTTACCCCGAAACTTCCAAAAATTCCATTTTCGACCCTAAA
ACTTCCAAAAATTCCATTTTTAC
Found at i:885 original size:59 final size:58
Alignment explanation
Indices: 578--1034 Score: 301
Period size: 59 Copynumber: 7.8 Consensus size: 58
568 CTAAACTGTT
* ** * * ** *
578 CAAAAATTACATTTT-TTCCTCG-AACTTCTAAAAATTCCATCCTCGACCCCGAAATTTC
1 CAAAAATTCCATTTTCGACCTCGAAACTTCCAAAAATTCCAT-TTTTACCCCG-AACTTC
* * * * * **
636 CAAAAAATCCATTTT-TACCCCTG-AACTTCCAAAAAATCCATTTTCGACCCTAAAACTTC
1 CAAAAATTCCATTTTCGACCTC-GAAACTTCCAAAAATTCCATTTT-TACCC-CGAACTTC
* * *
695 CAAAAATCCCATTTT-TACCCCCG-AACTTCCAAAAATTCCATTTTTGACCCCGAAACTTC
1 CAAAAATTCCATTTTCGA-CCTCGAAACTTCCAAAAATTCCATTTTT-ACCCCG-AACTTC
* * * * *
754 CAAAAATTCCCTTTTTG-CCTTG-AACTTCCAAAAATTCCATTTTCGACCCCAAAACTTC
1 CAAAAATTCCATTTTCGACCTCGAAACTTCCAAAAATTCCATTTT-TACCCC-GAACTTC
* *
812 CAAAAATTCCATTTTCGACCTCGAAACTCCCAAAAATTCCATTTTTACCCTCGAACCTC
1 CAAAAATTCCATTTTCGACCTCGAAACTTCCAAAAATTCCATTTTTACCC-CGAACTTC
* * * ** * *
871 CAAAATTTCCATTTTTGACCCCGAAACTTTAAAAAATTACCA-TTCTACCCCCGGA-TGTC
1 CAAAAATTCCATTTTCGACCTCGAAACTTCCAAAAATT-CCATTTTTA-CCCCGAACT-TC
* * *
930 CAAAAACTCTATTTTCAACCTCGAAACTT-CAAAAATTCCATTTTTACTCCCGAA-TGTC
1 CAAAAATTCCATTTTCGACCTCGAAACTTCCAAAAATTCCATTTTTAC-CCCGAACT-TC
* ** *
988 TAAAAATTCCATCTTTTAACCTCG-AACTTTCCCAAAATTACCATTTT
1 CAAAAATTCCAT-TTTCGACCTCGAAAC-TTCCAAAAATT-CCATTTT
1035 GCCCCTAGAT
Statistics
Matches: 324, Mismatches: 54, Indels: 39
0.78 0.13 0.09
Matches are distributed among these distances:
57 4 0.01
58 100 0.31
59 175 0.54
60 38 0.12
61 7 0.02
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.32
Consensus pattern (58 bp):
CAAAAATTCCATTTTCGACCTCGAAACTTCCAAAAATTCCATTTTTACCCCGAACTTC
Found at i:963 original size:147 final size:145
Alignment explanation
Indices: 600--1034 Score: 412
Period size: 147 Copynumber: 2.9 Consensus size: 145
590 TTTTTCCTCG
* * * * * **
600 AACTTCTAAAAATTCCATCCT-CGACCCCGAAATTTCCAAAAAATCCATTTT-TACCCCTGAACT
1 AACTTCAAAAAATTCCATTCTAC--CCCCG-AACTTCCAAAAACTCCATTTTCAACCCCAAAACT
* * * *
663 TCCAAAAAATCCATTTTCGACCCTAAAACTTCCAAAAATCCCATTTTTACCCCCGAACTTCCAAA
63 TCCAAAAATTCCATTTTCGACCC-GAAAC-TCCAAAAATTCCATTTTTACCCTCGAACTTCCAAA
*
728 AATTCCATTTTTGACCCCGA
126 ATTTCCATTTTTGACCCCGA
* * * ** ** * *
748 AACTTCCAAAAATTCCCTTTTTGCCTTGAACTTCCAAAAATTCCATTTTCGACCCCAAAACTTCC
1 AACTTCAAAAAATTCCATTCTACCCCCGAACTTCCAAAAACTCCATTTTCAACCCCAAAACTTCC
*
813 AAAAATTCCATTTTCGACCTCGAAACTCCCAAAAATTCCATTTTTACCCTCGAACCTCCAAAATT
66 AAAAATTCCATTTTCGACC-CGAAACT-CCAAAAATTCCATTTTTACCCTCGAACTTCCAAAATT
878 TCCATTTTTGACCCCGA
129 TCCATTTTTGACCCCGA
* * * * *
895 AACTTTAAAAAATTACCATTCTACCCCCGGA-TGTCCAAAAACTCTATTTTCAACCTCGAAACTT
1 AACTTCAAAAAATT-CCATTCTACCCCCGAACT-TCCAAAAACTCCATTTTCAACCCCAAAACTT
* ** * *
959 -CAAAAATTCCATTTTTAC-TCCCGAATGTCTAAAAATTCCATCTTTTAACCTCGAACTTTCCCA
64 CCAAAAATTCCA-TTTT-CGACCCGAAACTCCAAAAATTCCAT-TTTTACCCTCGAAC-TT-CCA
*
1022 AAATTACCATTTT
124 AAATTTCCATTTT
1035 GCCCCTAGAT
Statistics
Matches: 237, Mismatches: 39, Indels: 21
0.80 0.13 0.07
Matches are distributed among these distances:
146 32 0.14
147 129 0.54
148 60 0.25
149 16 0.07
ACGTcount: A:0.33, C:0.31, G:0.05, T:0.31
Consensus pattern (145 bp):
AACTTCAAAAAATTCCATTCTACCCCCGAACTTCCAAAAACTCCATTTTCAACCCCAAAACTTCC
AAAAATTCCATTTTCGACCCGAAACTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAATTTC
CATTTTTGACCCCGA
Found at i:4983 original size:46 final size:46
Alignment explanation
Indices: 4916--5010 Score: 172
Period size: 46 Copynumber: 2.1 Consensus size: 46
4906 GTAATTATTA
* *
4916 TTAGATTATAGCATATTTATGATCAGGGGCGAAGTTAGGAAAAAAT
1 TTAGATTATAGCATATTTATGATCAGGGACGAAGTTAGAAAAAAAT
4962 TTAGATTATAGCATATTTATGATCAGGGACGAAGTTAGAAAAAAAT
1 TTAGATTATAGCATATTTATGATCAGGGACGAAGTTAGAAAAAAAT
5008 TTA
1 TTA
5011 AAGGGGCTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.41, C:0.06, G:0.21, T:0.32
Consensus pattern (46 bp):
TTAGATTATAGCATATTTATGATCAGGGACGAAGTTAGAAAAAAAT
Found at i:8826 original size:10 final size:10
Alignment explanation
Indices: 8811--8847 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
8801 TCCATTTCCT
*
8811 TTCTTTTTTC
1 TTCTTTTCTC
8821 TTCTTTTCTC
1 TTCTTTTCTC
*
8831 TTCTCTTCTC
1 TTCTTTTCTC
8841 TTCTTTT
1 TTCTTTT
8848 TCCCTTCCCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (10 bp):
TTCTTTTCTC
Found at i:8854 original size:21 final size:20
Alignment explanation
Indices: 8805--8861 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
8795 AAATTTTCCA
* * *
8805 TTTCCTTTCTTTTTTCTTCT
1 TTTCCCTTCTCTTCTCTTCT
*
8825 TTTCTCTTCTCTTCTCTTCTT
1 TTTCCCTTCTCTTCTCTTC-T
*
8846 TTTCCCTTCCCTTCTC
1 TTTCCCTTCTCTTCTC
8862 CTCTCTTCTC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTCCCTTCTCTTCTCTTCT
Found at i:8872 original size:5 final size:5
Alignment explanation
Indices: 8819--8873 Score: 56
Period size: 5 Copynumber: 10.8 Consensus size: 5
8809 CTTTCTTTTT
* * * * *
8819 TCTTC TTTTC TCTTC TCTTC TCTTC TTTTTC CCTTC CCTTC TCCTC TCTTC
1 TCTTC TCTTC TCTTC TCTTC TCTTC -TCTTC TCTTC TCTTC TCTTC TCTTC
8870 TCTT
1 TCTT
8874 TGTTTGGTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
5 37 0.90
6 4 0.10
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (5 bp):
TCTTC
Found at i:15632 original size:23 final size:23
Alignment explanation
Indices: 15606--15650 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
15596 TTACTGTTGG
15606 ATTGAAAT-TTCTTAATGTTTTAT
1 ATTGAAATGTT-TTAATGTTTTAT
*
15629 ATTGGAATGTTTTAATGTTTTA
1 ATTGAAATGTTTTAATGTTTTA
15651 CTTAATTTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.29, C:0.02, G:0.13, T:0.56
Consensus pattern (23 bp):
ATTGAAATGTTTTAATGTTTTAT
Found at i:16957 original size:21 final size:21
Alignment explanation
Indices: 16933--16975 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
16923 TAGGGATAAA
16933 GAGAAGAAGAAGAAAAAGAAG
1 GAGAAGAAGAAGAAAAAGAAG
* *
16954 GAGAAGAAGAAGGAAGAGAAG
1 GAGAAGAAGAAGAAAAAGAAG
16975 G
1 G
16976 CAAAGGCGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (21 bp):
GAGAAGAAGAAGAAAAAGAAG
Found at i:16958 original size:15 final size:16
Alignment explanation
Indices: 16934--16974 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
16924 AGGGATAAAG
*
16934 AGAAGAAGAAGAA-AA
1 AGAAGGAGAAGAAGAA
16949 AGAAGGAGAAGAAGAA
1 AGAAGGAGAAGAAGAA
*
16965 GGAA-GAGAAG
1 AGAAGGAGAAG
16975 GCAAAGGCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 18 0.78
16 5 0.22
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (16 bp):
AGAAGGAGAAGAAGAA
Found at i:16973 original size:12 final size:13
Alignment explanation
Indices: 16934--16974 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 13
16924 AGGGATAAAG
16934 AGAAGAA-GAAGA
1 AGAAGAAGGAAGA
*
16946 AAAAGAAGG-AGA
1 AGAAGAAGGAAGA
16958 AGAAGAAGGAAG-
1 AGAAGAAGGAAGA
16970 AGAAG
1 AGAAG
16975 GCAAAGGCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 22 0.88
13 3 0.12
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (13 bp):
AGAAGAAGGAAGA
Found at i:18184 original size:3 final size:3
Alignment explanation
Indices: 18176--18216 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
18166 TTGAGAATGT
18176 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG -AG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
18217 CTGTGGTGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:18581 original size:14 final size:14
Alignment explanation
Indices: 18564--18595 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
18554 GATTTCGAAA
18564 TTTTGATTTTTTGT
1 TTTTGATTTTTTGT
*
18578 TTTTGTTTTTTTGT
1 TTTTGATTTTTTGT
18592 TTTT
1 TTTT
18596 TTCACTTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.03, C:0.00, G:0.12, T:0.84
Consensus pattern (14 bp):
TTTTGATTTTTTGT
Found at i:20954 original size:45 final size:45
Alignment explanation
Indices: 20867--20956 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
20857 ATGATTAAAA
** *
20867 TAGAAATATTATTAAAAATGTTATTTATCCAACTTAATAAAGAGC
1 TAGAAATATTATTAAAAATGTTATTTATCCAAAATAAGAAAGAGC
*
20912 TAGAAATATTATTATAAATGTTATTTATCCAAAATAAGAAAGAGC
1 TAGAAATATTATTAAAAATGTTATTTATCCAAAATAAGAAAGAGC
20957 AATGTTGTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.48, C:0.08, G:0.10, T:0.34
Consensus pattern (45 bp):
TAGAAATATTATTAAAAATGTTATTTATCCAAAATAAGAAAGAGC
Found at i:25532 original size:42 final size:42
Alignment explanation
Indices: 25452--25537 Score: 136
Period size: 42 Copynumber: 2.0 Consensus size: 42
25442 GAGACCTCCT
* *
25452 CCTTCGCCTATAGCTGATTGGTGATCTTGACATGGACCTTGA
1 CCTTCGCCTATAACTGATTGGTGATCTAGACATGGACCTTGA
* *
25494 CCTTCGCCTATAACTGATTGGTGATCTAGACTTTGACCTTGA
1 CCTTCGCCTATAACTGATTGGTGATCTAGACATGGACCTTGA
25536 CC
1 CC
25538 GTCTTCGATA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.20, C:0.26, G:0.21, T:0.34
Consensus pattern (42 bp):
CCTTCGCCTATAACTGATTGGTGATCTAGACATGGACCTTGA
Found at i:25549 original size:42 final size:42
Alignment explanation
Indices: 25455--25549 Score: 109
Period size: 42 Copynumber: 2.3 Consensus size: 42
25445 ACCTCCTCCT
* * * *
25455 TCGCCTATAGCTGATTGGTGATCTTGACATGGACCTTGACCT
1 TCGCCGATAACTGATTGGTGATCTAGACATGGACCTTGACCG
* * *
25497 TCGCCTATAACTGATTGGTGATCTAGACTTTGACCTTGACCG
1 TCGCCGATAACTGATTGGTGATCTAGACATGGACCTTGACCG
**
25539 TCTTCGATAAC
1 TCGCCGATAAC
25550 CAAGGGGTGA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (42 bp):
TCGCCGATAACTGATTGGTGATCTAGACATGGACCTTGACCG
Found at i:36035 original size:27 final size:27
Alignment explanation
Indices: 35966--36036 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
35956 TTAATTATTG
* *
35966 TTTTAATGTATTAAAGTTACACAATTATA
1 TTTTAATGTATT-AA-TAAAACAATTATA
* *
35995 TTTTTAT-TATTTAATAAAACATTTATA
1 TTTTAATGTA-TTAATAAAACAATTATA
36022 TTTTAATGTATTAAT
1 TTTTAATGTATTAAT
36037 GTTAAAATGT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
27 21 0.60
28 6 0.17
29 8 0.23
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.52
Consensus pattern (27 bp):
TTTTAATGTATTAATAAAACAATTATA
Found at i:36553 original size:24 final size:24
Alignment explanation
Indices: 36503--36554 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
36493 AATCAATATC
* * **
36503 AAATATATTATGCTAATAAATGTT
1 AAATATATTATACTAAAAAATACT
36527 AAATATATTATACTAAAAAATACT
1 AAATATATTATACTAAAAAATACT
36551 AAAT
1 AAAT
36555 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAAAAAATACT
Found at i:42111 original size:24 final size:24
Alignment explanation
Indices: 42079--42134 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
42069 AGCTTAATTT
* *
42079 TAATCAATGTCAAATATATTATGC
1 TAATAAATGTCAAATATATTATAC
* *
42103 TAATAAATGTTAAATGTATTATAC
1 TAATAAATGTCAAATATATTATAC
42127 TAATAAAT
1 TAATAAAT
42135 ATTAAATCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (24 bp):
TAATAAATGTCAAATATATTATAC
Found at i:42139 original size:24 final size:24
Alignment explanation
Indices: 42090--42141 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
42080 AATCAATGTC
* *
42090 AAATATATTATGCTAATAAATGTT
1 AAATATATTATACTAATAAATATT
*
42114 AAATGTATTATACTAATAAATATT
1 AAATATATTATACTAATAAATATT
42138 AAAT
1 AAAT
42142 CTTCCATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.04, G:0.06, T:0.40
Consensus pattern (24 bp):
AAATATATTATACTAATAAATATT
Found at i:44322 original size:15 final size:15
Alignment explanation
Indices: 44302--44332 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
44292 ATTTCTATAC
44302 GTAGGAAAGCATTTG
1 GTAGGAAAGCATTTG
44317 GTAGGAAAGCATTTG
1 GTAGGAAAGCATTTG
44332 G
1 G
44333 AAGTAAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.35, T:0.26
Consensus pattern (15 bp):
GTAGGAAAGCATTTG
Found at i:45701 original size:23 final size:23
Alignment explanation
Indices: 45681--45734 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
45671 TTTATTTTTG
45681 TTTTATTA-TTTATATTTTTTTAAT
1 TTTTATTATTTTA-ATTTTTTT-AT
*
45705 TTTTA-TATTTTAATTTTTTTCT
1 TTTTATTATTTTAATTTTTTTAT
45727 CTTTTATT
1 -TTTTATT
45735 TGCTTCTAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 1 0.04
23 15 0.58
24 10 0.38
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (23 bp):
TTTTATTATTTTAATTTTTTTAT
Found at i:45709 original size:17 final size:18
Alignment explanation
Indices: 45669--45715 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
45659 TTTAGAAATT
*
45669 TTTTTAT-TTTTGTTTTA
1 TTTTTATATTTTGTTTAA
45686 TTATTTATATTTT-TTTAA
1 TT-TTTATATTTTGTTTAA
45704 TTTTTATATTTT
1 TTTTTATATTTT
45716 AATTTTTTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 12 0.44
18 11 0.41
19 4 0.15
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (18 bp):
TTTTTATATTTTGTTTAA
Done.