Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005554.1 Kokia drynarioides strain JFW-HI SEQ_119661, 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: 76577
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:1022 original size:31 final size:31
Alignment explanation
Indices: 986--1072 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 31
976 AATATTAAAA
*
986 TTATACATAAATTTTGATTTAATTTGTAATG
1 TTATACATAAATTTTGATTTGATTTGTAATG
* * * *
1017 TTATACGTTAACTTTGATTTGA--TGTAATT
1 TTATACATAAATTTTGATTTGATTTGTAATG
* *
1046 TTATAAATAATATTATGATTTGATTTG
1 TTATACATAA-ATTTTGATTTGATTTG
1073 ATTTTTACTG
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
29 13 0.30
30 10 0.23
31 18 0.42
32 2 0.05
ACGTcount: A:0.33, C:0.03, G:0.11, T:0.52
Consensus pattern (31 bp):
TTATACATAAATTTTGATTTGATTTGTAATG
Found at i:7459 original size:36 final size:34
Alignment explanation
Indices: 7392--7462 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 34
7382 GATTCGCTAA
7392 AATTTTTAAATAAAAAAAATAAAACTAAAATTTT
1 AATTTTTAAATAAAAAAAATAAAACTAAAATTTT
* *
7426 AATTTTTAAA-ACACAAAAAATTAAATCTCAAATTTT
1 AATTTTTAAATA-A-AAAAAA-TAAAACTAAAATTTT
7462 A
1 A
7463 TCATGAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 1 0.03
34 11 0.34
35 6 0.19
36 14 0.44
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (34 bp):
AATTTTTAAATAAAAAAAATAAAACTAAAATTTT
Found at i:8883 original size:17 final size:18
Alignment explanation
Indices: 8851--8886 Score: 56
Period size: 17 Copynumber: 2.0 Consensus size: 18
8841 TTTAAGAGTG
8851 CTTTTGAGTCAAAAAATTA
1 CTTTTGAG-CAAAAAATTA
8870 CTTTTGAG-AAAAAATTA
1 CTTTTGAGCAAAAAATTA
8887 AAATTTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
19 8 0.47
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.36
Consensus pattern (18 bp):
CTTTTGAGCAAAAAATTA
Found at i:10880 original size:8 final size:7
Alignment explanation
Indices: 10837--10879 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
10827 ATGGAAATTA
10837 TTTTA-T
1 TTTTACT
10843 TTTTA-T
1 TTTTACT
10849 TTTTA-T
1 TTTTACT
*
10855 TTTAACT
1 TTTTACT
10862 TTTTACT
1 TTTTACT
10869 TTTTACT
1 TTTTACT
10876 TTTT
1 TTTT
10880 TGCTTATGCA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
6 16 0.47
7 18 0.53
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTACT
Found at i:11899 original size:31 final size:31
Alignment explanation
Indices: 11883--11943 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
11873 TCAATATTTG
*
11883 AAAAGTAAAATGACTAAAATTGACCAATTCA
1 AAAAGTAAAATGACTAAAATTGACAAATTCA
*
11914 AAAAGTACAATGACTAAAATTGATCAAATT
1 AAAAGTAAAATGACTAAAATTGA-CAAATT
11944 AAAGTATATG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 22 0.81
32 5 0.19
ACGTcount: A:0.54, C:0.11, G:0.10, T:0.25
Consensus pattern (31 bp):
AAAAGTAAAATGACTAAAATTGACAAATTCA
Found at i:14095 original size:20 final size:22
Alignment explanation
Indices: 14062--14102 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
14052 TAAAAATTCA
14062 AAAAATATATAAAAATATTTTT
1 AAAAATATATAAAAATATTTTT
*
14084 AAAAAT-TA-AAAATTATTTT
1 AAAAATATATAAAAATATTTT
14103 GTAATATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 2 0.11
22 6 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
AAAAATATATAAAAATATTTTT
Found at i:14354 original size:12 final size:12
Alignment explanation
Indices: 14337--14361 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
14327 TGATACAAAA
14337 TAAAAATATTTT
1 TAAAAATATTTT
14349 TAAAAATATTTT
1 TAAAAATATTTT
14361 T
1 T
14362 TTTGGATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAAAAATATTTT
Found at i:14962 original size:5 final size:6
Alignment explanation
Indices: 14945--14969 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
14935 AGCAGTGAAG
14945 AGAAAA AGAAAA AGAAAA AGAAAA A
1 AGAAAA AGAAAA AGAAAA AGAAAA A
14970 AGAGATCACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:16539 original size:9 final size:9
Alignment explanation
Indices: 16522--16554 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
16512 GATTGACGTT
*
16522 TTCGGCTTC
1 TTCGTCTTC
16531 TTCGTCTTC
1 TTCGTCTTC
16540 TTCGTCTTC
1 TTCGTCTTC
16549 TTCGTC
1 TTCGTC
16555 GCCGTTGTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.00, C:0.33, G:0.15, T:0.52
Consensus pattern (9 bp):
TTCGTCTTC
Found at i:18844 original size:22 final size:22
Alignment explanation
Indices: 18799--18862 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
18789 GTAGAGTTAG
18799 AAAAATAT-TTTTCATGA-AATTA
1 AAAAATATATTTT-ATGATAA-TA
**
18821 AATTATATATTTTATGATAATA
1 AAAAATATATTTTATGATAATA
*
18843 AAAAATATAATTT-TGATAAT
1 AAAAATATATTTTATGATAAT
18863 TTTAATAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
21 7 0.20
22 22 0.63
23 6 0.17
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.44
Consensus pattern (22 bp):
AAAAATATATTTTATGATAATA
Found at i:18861 original size:9 final size:8
Alignment explanation
Indices: 18848--18889 Score: 50
Period size: 8 Copynumber: 5.1 Consensus size: 8
18838 TAATAAAAAA
18848 TATAATTT
1 TATAATTT
18856 TGATAATTT
1 T-ATAATTT
18865 TAATAA-TT
1 T-ATAATTT
*
18873 TATATTTT
1 TATAATTT
18881 TATAATTT
1 TATAATTT
18889 T
1 T
18890 TAAAATATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
7 3 0.10
8 14 0.48
9 12 0.41
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (8 bp):
TATAATTT
Found at i:23948 original size:95 final size:95
Alignment explanation
Indices: 23605--24158 Score: 653
Period size: 95 Copynumber: 5.9 Consensus size: 95
23595 CCCGCATGCA
* * *
23605 AATGAAGCTGAAACATCGATTCAAAGTTATATACAC-T-TTCAAATTCAATGAAAAATACAGCCG
1 AATGAAGCTGAAAAATCGATTCAAAGTTATATATACATATTCAAATTCAATGGAAAATACAGCCG
* *
23668 ACTAAAGGAA-AAAAGAAAA-CCC-AAACCCC
66 ATTAAA-GAAGAAAA-AAAACCCCAAAATCCC
* * * * * *
23697 AATGAAGCTGAAAAATCAATTCATATTTATATATACACATTCAAATTCAATGAAAAATACAGCCA
1 AATGAAGCTGAAAAATCGATTCAAAGTTATATATACATATTCAAATTCAATGGAAAATACAGCCG
*
23762 ATTAAAGGGAAG-AAAAAAA--CAAAAATCCC
66 ATTAAA--GAAGAAAAAAAACCCCAAAATCCC
* * *
23791 AATGAAGCCGAAAAATCGATTAAAAGTTATATATAC--ATTCAAATTCAATGGAAAATGCAGCCG
1 AATGAAGCTGAAAAATCGATTCAAAGTTATATATACATATTCAAATTCAATGGAAAATACAGCCG
**** * *
23854 ATTAAAGAAGGGGGAAACCCCCAAAATCTC
66 ATTAAAGAAGAAAAAAAACCCCAAAATCCC
* *
23884 AATGAAGCTGAAAAGTCGATTCAAAGTTATATATACATATTCATATTCAATGGAAAATACAGCCG
1 AATGAAGCTGAAAAATCGATTCAAAGTTATATATACATATTCAAATTCAATGGAAAATACAGCCG
** *
23949 ATTAAAGAAGAAAATGAACCCAAAAATCCC
66 ATTAAAGAAGAAAAAAAACCCCAAAATCCC
* * * * *
23979 AATAAATCTGAAAAATCGACTCAAAGTTATATATACATATTCAAATTCAATGGAAAATACAACCA
1 AATGAAGCTGAAAAATCGATTCAAAGTTATATATACATATTCAAATTCAATGGAAAATACAGCCG
24044 ATTAAAGAAGAAAAAAGAACCCCAAAATCCC
66 ATTAAAGAAGAAAAAA-AACCCCAAAATCCC
* * *
24075 AATGAAGCTGAAAAATCGATTCGAAGTTATATATACA-AATCAAATTCAATGGAAAACACAGCCG
1 AATGAAGCTGAAAAATCGATTCAAAGTTATATATACATATTCAAATTCAATGGAAAATACAGCCG
*
24139 ATTAAAAACAGAAAATAAAA
66 ATTAAAGA-AGAAAA-AAAA
24159 AGAACCCAAA
Statistics
Matches: 392, Mismatches: 57, Indels: 22
0.83 0.12 0.05
Matches are distributed among these distances:
90 4 0.01
91 3 0.01
92 61 0.16
93 42 0.11
94 71 0.18
95 155 0.40
96 54 0.14
97 2 0.01
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (95 bp):
AATGAAGCTGAAAAATCGATTCAAAGTTATATATACATATTCAAATTCAATGGAAAATACAGCCG
ATTAAAGAAGAAAAAAAACCCCAAAATCCC
Found at i:26225 original size:7 final size:7
Alignment explanation
Indices: 26208--26246 Score: 71
Period size: 7 Copynumber: 5.7 Consensus size: 7
26198 ATGAATACAA
26208 TTAAA-T
1 TTAAATT
26214 TTAAATT
1 TTAAATT
26221 TTAAATT
1 TTAAATT
26228 TTAAATT
1 TTAAATT
26235 TTAAATT
1 TTAAATT
26242 TTAAA
1 TTAAA
26247 ATATGAAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 5 0.16
7 27 0.84
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
TTAAATT
Found at i:28716 original size:16 final size:16
Alignment explanation
Indices: 28695--28729 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
28685 AAACCCGACT
28695 TGAA-CCAAAACTAACA
1 TGAACCCAAAA-TAACA
28711 TGAACCCAAAATAACA
1 TGAACCCAAAATAACA
28727 TGA
1 TGA
28730 GTACGAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.54, C:0.23, G:0.09, T:0.14
Consensus pattern (16 bp):
TGAACCCAAAATAACA
Found at i:43750 original size:12 final size:12
Alignment explanation
Indices: 43733--43757 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43723 ATAACATCCA
43733 AACAATCAAAAT
1 AACAATCAAAAT
43745 AACAATCAAAAT
1 AACAATCAAAAT
43757 A
1 A
43758 GCAGCAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (12 bp):
AACAATCAAAAT
Found at i:43778 original size:23 final size:22
Alignment explanation
Indices: 43752--43835 Score: 87
Period size: 23 Copynumber: 3.7 Consensus size: 22
43742 AATAACAATC
43752 AAAATAGCAGCAAAAATAATAAA
1 AAAATAGCA-CAAAAATAATAAA
*
43775 AAAATAGCAACAAAAATAACAATA
1 AAAATAGC-ACAAAAATAATAA-A
* * * *
43799 AAAACAACACCAAAATAGTAAA
1 AAAATAGCACAAAAATAATAAA
*
43821 AAAATAGCACCAAAA
1 AAAATAGCACAAAAA
43836 CAACAATCAA
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
22 14 0.27
23 29 0.57
24 8 0.16
ACGTcount: A:0.69, C:0.14, G:0.06, T:0.11
Consensus pattern (22 bp):
AAAATAGCACAAAAATAATAAA
Found at i:43862 original size:17 final size:17
Alignment explanation
Indices: 43840--43873 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
43830 CCAAAACAAC
*
43840 AATCAAAATAGTAAAAA
1 AATCAAAACAGTAAAAA
43857 AATCAAAACAGTAAAAA
1 AATCAAAACAGTAAAAA
43874 CACAACACCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.71, C:0.09, G:0.06, T:0.15
Consensus pattern (17 bp):
AATCAAAACAGTAAAAA
Found at i:43885 original size:22 final size:23
Alignment explanation
Indices: 43852--43911 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
43842 TCAAAATAGT
*
43852 AAAAAA-ATCAAAACAGT-AAAA
1 AAAAAACACCAAAACAGTAAAAA
* *
43873 ACACAACACCAAAACAGTAAAAA
1 AAAAAACACCAAAACAGTAAAAA
43896 AAAAAACACCAAAACA
1 AAAAAACACCAAAACA
43912 ACAATATAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 4 0.12
22 10 0.31
23 18 0.56
ACGTcount: A:0.72, C:0.20, G:0.03, T:0.05
Consensus pattern (23 bp):
AAAAAACACCAAAACAGTAAAAA
Found at i:44639 original size:21 final size:23
Alignment explanation
Indices: 44606--44667 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 23
44596 AACAATAGTA
* *
44606 AAAAC-GCATAAAAATAACATCC
1 AAAACAGCAGAAAAATAACAACC
44628 -AAACAGC--AAAAATAACAACC
1 AAAACAGCAGAAAAATAACAACC
*
44648 AAAACAGCAGTAAAATAACA
1 AAAACAGCAGAAAAATAACA
44668 GCAAAATAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
20 12 0.35
21 11 0.32
22 2 0.06
23 9 0.26
ACGTcount: A:0.63, C:0.21, G:0.06, T:0.10
Consensus pattern (23 bp):
AAAACAGCAGAAAAATAACAACC
Found at i:44640 original size:20 final size:21
Alignment explanation
Indices: 44615--44802 Score: 77
Period size: 23 Copynumber: 8.8 Consensus size: 21
44605 AAAAACGCAT
*
44615 AAAAATAACATCC-AAACAGC
1 AAAAATAACAACCAAAACAGC
44635 AAAAATAACAACCAAAACAGC
1 AAAAATAACAACCAAAACAGC
* * *
44656 AGTAAAATAAC-AGCAAAATAAC
1 A--AAAATAACAACCAAAACAGC
* * *
44678 ATTAAA-AACAACAAAAATAGCAAC
1 A-AAAATAACAAC-CAAA-A-CAGC
* * *
44702 AAAAATAACAACAAAAATAAC
1 AAAAATAACAACCAAAACAGC
* * *
44723 ACTAAAAAAACAATCAAAACAGT
1 A--AAAATAACAACCAAAACAGC
*
44746 AAAAA-AGGC-ACCAAAACAG-
1 AAAAATA-ACAACCAAAACAGC
* *
44765 TAAAA-AACAACACAAAAACAGT
1 AAAAATAACAAC-C-AAAACAGC
44787 AAAAA-AACAACCAAAA
1 AAAAATAACAACCAAAA
44803 TAGTTAAAAA
Statistics
Matches: 132, Mismatches: 21, Indels: 30
0.72 0.11 0.16
Matches are distributed among these distances:
18 1 0.01
19 7 0.05
20 30 0.23
21 30 0.23
22 23 0.17
23 31 0.23
24 10 0.08
ACGTcount: A:0.68, C:0.19, G:0.05, T:0.09
Consensus pattern (21 bp):
AAAAATAACAACCAAAACAGC
Found at i:44651 original size:12 final size:12
Alignment explanation
Indices: 44629--44741 Score: 60
Period size: 12 Copynumber: 9.8 Consensus size: 12
44619 ATAACATCCA
*
44629 AACAGCAAAAAT
1 AACAACAAAAAT
* *
44641 AACAACCAAAAC
1 AACAACAAAAAT
* **
44653 AGCAGTA-AAAT
1 AACAACAAAAAT
*
44664 AACAGC-AAAAT
1 AACAACAAAAAT
** *
44675 AACATTAAAAAC
1 AACAACAAAAAT
44687 AAC-A-A-AAAT
1 AACAACAAAAAT
*
44696 AGCAACAAAAAT
1 AACAACAAAAAT
44708 AACAACAAAAAT
1 AACAACAAAAAT
44720 AAC-ACTAAAAA-
1 AACAAC-AAAAAT
44731 AACAATCAAAA
1 AACAA-CAAAA
44742 CAGTAAAAAA
Statistics
Matches: 76, Mismatches: 17, Indels: 16
0.70 0.16 0.15
Matches are distributed among these distances:
9 5 0.07
10 2 0.03
11 21 0.28
12 47 0.62
13 1 0.01
ACGTcount: A:0.68, C:0.18, G:0.04, T:0.10
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:44711 original size:24 final size:23
Alignment explanation
Indices: 44681--44741 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 23
44671 AAATAACATT
*
44681 AAAAACAACAAAAATAGCAAC-AA
1 AAAAACAACAAAAATAAC-ACTAA
44704 AAATAACAACAAAAATAACACTAA
1 AAA-AACAACAAAAATAACACTAA
44728 AAAAACAATCAAAA
1 AAAAACAA-CAAAA
44742 CAGTAAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
23 10 0.29
24 24 0.71
ACGTcount: A:0.74, C:0.16, G:0.02, T:0.08
Consensus pattern (23 bp):
AAAAACAACAAAAATAACACTAA
Found at i:44718 original size:33 final size:34
Alignment explanation
Indices: 44629--44741 Score: 95
Period size: 33 Copynumber: 3.3 Consensus size: 34
44619 ATAACATCCA
* * *
44629 AACAGCAAAAATAACAACCAAAACAGCAGTAAAAT
1 AACAACAAAAATAACAACAAAAACAACAG-AAAAT
* **
44664 AACAGC-AAAATAACATTAAAAACAACA-AAAAT
1 AACAACAAAAATAACAACAAAAACAACAGAAAAT
* * * *
44696 AGCAACAAAAATAACAACAAAAATAACACTAAAAA
1 AACAACAAAAATAACAACAAAAACAACA-GAAAAT
44731 AACAATCAAAA
1 AACAA-CAAAA
44742 CAGTAAAAAA
Statistics
Matches: 63, Mismatches: 11, Indels: 7
0.78 0.14 0.09
Matches are distributed among these distances:
32 9 0.14
33 18 0.29
34 17 0.27
35 14 0.22
36 5 0.08
ACGTcount: A:0.68, C:0.18, G:0.04, T:0.10
Consensus pattern (34 bp):
AACAACAAAAATAACAACAAAAACAACAGAAAAT
Found at i:44811 original size:20 final size:19
Alignment explanation
Indices: 44727--44813 Score: 95
Period size: 20 Copynumber: 4.3 Consensus size: 19
44717 AATAACACTA
*
44727 AAAAAACAATCAAAACAGT
1 AAAAAACAACCAAAACAGT
44746 AAAAAAGGC-ACCAAAACAGT
1 AAAAAA--CAACCAAAACAGT
44766 AAAAAACAACACAAAAACAGT
1 AAAAAACAAC-C-AAAACAGT
*
44787 AAAAAAACAACCAAAATAGTT
1 -AAAAAACAACCAAAACAG-T
44808 AAAAAA
1 AAAAAA
44814 AAATAGCACC
Statistics
Matches: 59, Mismatches: 2, Indels: 13
0.80 0.03 0.18
Matches are distributed among these distances:
18 1 0.02
19 8 0.14
20 29 0.49
21 11 0.19
22 10 0.17
ACGTcount: A:0.69, C:0.16, G:0.07, T:0.08
Consensus pattern (19 bp):
AAAAAACAACCAAAACAGT
Found at i:46175 original size:18 final size:18
Alignment explanation
Indices: 46152--46186 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
46142 GGAAGAAATG
46152 TAAGTTTGATTAATTTTT
1 TAAGTTTGATTAATTTTT
*
46170 TAAGTTTGGTTAATTTT
1 TAAGTTTGATTAATTTT
46187 AAATTTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.14, T:0.60
Consensus pattern (18 bp):
TAAGTTTGATTAATTTTT
Found at i:46383 original size:21 final size:20
Alignment explanation
Indices: 46357--46399 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
46347 TAATTTACTT
46357 TAATTTAAATTTGTTAGTTAG
1 TAATTTAAATTTGTTAG-TAG
* *
46378 TAATTTTATTTTGTTAGTAG
1 TAATTTAAATTTGTTAGTAG
46398 TA
1 TA
46400 GTAAGTAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.56
Consensus pattern (20 bp):
TAATTTAAATTTGTTAGTAG
Found at i:49113 original size:49 final size:48
Alignment explanation
Indices: 49039--49179 Score: 204
Period size: 45 Copynumber: 3.0 Consensus size: 48
49029 CCTTAGCTCG
*
49039 TCAAGCCAA-GAATAT-T-AGGCTCAGTTTGACGAGCCACCGTAATAC
1 TCAAGCCAAGGAATATATCAGGCTCAGTTTGACGAGCCACCGCAATAC
*
49084 TCAAGCCAAGGATATATATCAGGCTCAGTTTGACGAGCCACTGCAATAC
1 TCAAGCCAAGGA-ATATATCAGGCTCAGTTTGACGAGCCACCGCAATAC
*
49133 TCAAGCCAAGG---ATATCAGGCTCAGTTTGACGAGCCATCGCAATAC
1 TCAAGCCAAGGAATATATCAGGCTCAGTTTGACGAGCCACCGCAATAC
49178 TC
1 TC
49180 TACTCCTCCC
Statistics
Matches: 88, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
45 43 0.49
46 2 0.02
47 4 0.05
48 1 0.01
49 38 0.43
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.22
Consensus pattern (48 bp):
TCAAGCCAAGGAATATATCAGGCTCAGTTTGACGAGCCACCGCAATAC
Found at i:49197 original size:21 final size:21
Alignment explanation
Indices: 49171--49216 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
49161 ACGAGCCATC
*
49171 GCAATACTCTACTCCTCCCGG
1 GCAATACTCTACTCCTCCAGG
49192 GCAATACTCTACTCCTCCAGG
1 GCAATACTCTACTCCTCCAGG
49213 GCAA
1 GCAA
49217 ATGGACCATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.24, C:0.39, G:0.15, T:0.22
Consensus pattern (21 bp):
GCAATACTCTACTCCTCCAGG
Found at i:49731 original size:26 final size:26
Alignment explanation
Indices: 49701--49752 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
49691 TTCAAAACCA
*
49701 AAATACAAATATAAAAATTATTAATT
1 AAATACAAATATAAAAATAATTAATT
**
49727 AAATACAAATATTGAAATAATTAATT
1 AAATACAAATATAAAAATAATTAATT
49753 TTAAATTCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (26 bp):
AAATACAAATATAAAAATAATTAATT
Found at i:52344 original size:19 final size:19
Alignment explanation
Indices: 52320--52358 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
52310 TTTACAATCA
*
52320 AAATAAAATTAACACACAC
1 AAATAAAATAAACACACAC
52339 AAATAAAATAAACACACAC
1 AAATAAAATAAACACACAC
52358 A
1 A
52359 CGGCATAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.67, C:0.21, G:0.00, T:0.13
Consensus pattern (19 bp):
AAATAAAATAAACACACAC
Found at i:54826 original size:16 final size:15
Alignment explanation
Indices: 54772--54844 Score: 51
Period size: 16 Copynumber: 4.7 Consensus size: 15
54762 GTTTTCCCAT
*
54772 TCATTTTAAATCCAA
1 TCATTTTAAATCGAA
*
54787 CCCA-TTTAAATC-ACA
1 -TCATTTTAAATCGA-A
*
54802 TCAAATTTAAATCGAA
1 TC-ATTTTAAATCGAA
* *
54818 TTCTTTTTAAATTGAA
1 -TCATTTTAAATCGAA
54834 TCATTTTAAAT
1 TCATTTTAAAT
54845 TTATTAACTT
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
14 2 0.04
15 20 0.43
16 21 0.46
17 3 0.07
ACGTcount: A:0.40, C:0.16, G:0.03, T:0.41
Consensus pattern (15 bp):
TCATTTTAAATCGAA
Found at i:54842 original size:15 final size:16
Alignment explanation
Indices: 54807--54845 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
54797 TCACATCAAA
* *
54807 TTTAAATCGAATTCTT
1 TTTAAATTGAATTCAT
54823 TTTAAATTGAA-TCAT
1 TTTAAATTGAATTCAT
54838 TTTAAATT
1 TTTAAATT
54846 TATTAACTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.36, C:0.08, G:0.05, T:0.51
Consensus pattern (16 bp):
TTTAAATTGAATTCAT
Found at i:59778 original size:2 final size:2
Alignment explanation
Indices: 59771--59807 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
59761 GGTACGCTAA
59771 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
59808 GCCTTAGGTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:64559 original size:6 final size:6
Alignment explanation
Indices: 64548--64574 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
64538 CTTTCCCACC
64548 ATACAT ATACAT ATACAT ATACAT ATA
1 ATACAT ATACAT ATACAT ATACAT ATA
64575 GTAATGTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (6 bp):
ATACAT
Found at i:64877 original size:6 final size:6
Alignment explanation
Indices: 64866--64916 Score: 93
Period size: 6 Copynumber: 8.5 Consensus size: 6
64856 AGTTTTAGCC
*
64866 ATACAT ATACAT ATACAT ACACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
64914 ATA
1 ATA
64917 AGTTTTGTGG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.51, C:0.18, G:0.00, T:0.31
Consensus pattern (6 bp):
ATACAT
Found at i:68938 original size:7 final size:7
Alignment explanation
Indices: 68926--68953 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
68916 TTAAATTATA
68926 TGAACAT
1 TGAACAT
68933 TGAACAT
1 TGAACAT
68940 TGAACAT
1 TGAACAT
68947 TGAACAT
1 TGAACAT
68954 AAAATTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (7 bp):
TGAACAT
Found at i:72603 original size:13 final size:13
Alignment explanation
Indices: 72585--72612 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
72575 TTTCAGTTTG
72585 TTATTTAATTATT
1 TTATTTAATTATT
72598 TTATTTAATTATT
1 TTATTTAATTATT
72611 TT
1 TT
72613 TTGCTTTTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTATTTAATTATT
Found at i:75941 original size:199 final size:192
Alignment explanation
Indices: 75505--76024 Score: 567
Period size: 199 Copynumber: 2.7 Consensus size: 192
75495 AACCCTTTAA
*
75505 CAATAAAAAAGTTAGCTTCCTGAT-AAGATACTGAGAAGTGGACCAAATTCGTCTT-C-C-TG-A
1 CAATAAAAAGGTTAGCTTCCTGATGAA-ATACTGAGAAGTGGACCAAATTCGTCTTCCTCATGAA
* ** * *
75565 T---GA-AAGTGGATTGAAACAAGTGAGGCGGTCATCTTCTTGATGAGATACAGAGAAGTATACC
65 TACAGAGAAGCGGATTGAAACAAACGAGGCAGTCATCTTCCTGATGAGATACAGAGAAGTATACC
* *
75626 AACTCAATGTGAACAAATCTTCGAACCCCAGCTTCCTGATAGATACTGAGAAGTAGGGCAAAG
130 AACTCAATGTGAACAAATCTTCGAACCCCAGCTTCCTGATAGATACGGAGAAGCAGGGCAAAG
* * * *
75689 TAATAAAAAGGTTAGCTTCCTGATGAGACACTGAGAAGTGGACCAACTTCGTCTTCCTCATGAAA
1 CAATAAAAAGGTTAGCTTCCTGATGAAATACTGAGAAGTGGACCAAATTCGTCTTCCTCATG-AA
* * * *
75754 TACAGAGAAGCAGATTGAAATAAACGGGGCAGTTATCTTCCTG-TGAGATACAGAGAAGTATACC
65 TACAGAGAAGCGGATTGAAACAAACGAGGCAGTCATCTTCCTGATGAGATACAGAGAAGTATACC
* * * *
75818 AACTCAGGGCTCGATGTAGCAAATCTTCGAATCCCAGCTTCCTGATGAGATACGGAGAAGCAGGT
130 AACTCA---AT-G-TG-AACAAATCTTCGAACCCCAGCTTCCTGAT-AGATACGGAGAAGCAGGG
*
75883 CGAAG
188 CAAAG
* * * *
75888 CAATAAAATGGTTAGCTTCCTGATGAAATACTGAGAAGTAGACCAAATTCGTCTTCCTGATGAGG
1 CAATAAAAAGGTTAGCTTCCTGATGAAATACTGAGAAGTGGACCAAATTCGTCTTCCTCATGA-A
* * ** * * *
75953 TACAGAGAAGCGGATTGAAACAAGCAATACGGTCATCTTCCTGATAAGATACTA-AGAAGTAGAC
65 TACAGAGAAGCGGATTGAAACAAACGAGGCAGTCATCTTCCTGATGAGATAC-AGAGAAGTATAC
*
76017 CAAATCAA
129 CAACTCAA
76025 CGACACCAAA
Statistics
Matches: 274, Mismatches: 42, Indels: 27
0.80 0.12 0.08
Matches are distributed among these distances:
184 48 0.18
185 2 0.01
186 1 0.00
187 2 0.01
189 2 0.01
192 29 0.11
193 27 0.10
195 1 0.00
196 1 0.00
197 2 0.01
198 28 0.10
199 108 0.39
200 22 0.08
201 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (192 bp):
CAATAAAAAGGTTAGCTTCCTGATGAAATACTGAGAAGTGGACCAAATTCGTCTTCCTCATGAAT
ACAGAGAAGCGGATTGAAACAAACGAGGCAGTCATCTTCCTGATGAGATACAGAGAAGTATACCA
ACTCAATGTGAACAAATCTTCGAACCCCAGCTTCCTGATAGATACGGAGAAGCAGGGCAAAG
Found at i:76396 original size:17 final size:17
Alignment explanation
Indices: 76342--76412 Score: 70
Period size: 17 Copynumber: 4.2 Consensus size: 17
76332 AATAAGTTTG
* *
76342 AATTTATTTTAAATTCA
1 AATTTACTTTAAATTTA
* * * *
76359 AATTCACTTTGAGTTTG
1 AATTTACTTTAAATTTA
76376 AATTTACTTTAAATTTA
1 AATTTACTTTAAATTTA
* *
76393 AATTTATTTTAAATTAA
1 AATTTACTTTAAATTTA
76410 AAT
1 AAT
76413 AAAATTAAAA
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 42 1.00
ACGTcount: A:0.39, C:0.06, G:0.04, T:0.51
Consensus pattern (17 bp):
AATTTACTTTAAATTTA
Done.