Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002564.1 Kokia drynarioides strain JFW-HI SEQ_114762, 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: 39086
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:958 original size:19 final size:19
Alignment explanation
Indices: 915--960 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
905 AAAAATATAG
*
915 ATTTTGAAATTTTTATAAAT
1 ATTTTGAAA-TTTTAAAAAT
935 ATTTTGAAA-TTTAAAAATT
1 ATTTTGAAATTTTAAAAA-T
954 ATTTTGA
1 ATTTTGA
961 TTTTTTTGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 7 0.29
19 8 0.33
20 9 0.38
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (19 bp):
ATTTTGAAATTTTAAAAAT
Found at i:5054 original size:18 final size:18
Alignment explanation
Indices: 5011--5058 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
5001 AGTAAAATCA
5011 AATTAATTCGGTTAACAG
1 AATTAATTCGGTTAACAG
* * *
5029 -ATCGAATTTGGTTAACCG
1 AAT-TAATTCGGTTAACAG
5047 AATTAATTCGGT
1 AATTAATTCGGT
5059 CGGGAGTCGG
Statistics
Matches: 23, Mismatches: 5, Indels: 4
0.72 0.16 0.12
Matches are distributed among these distances:
17 2 0.09
18 19 0.83
19 2 0.09
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.35
Consensus pattern (18 bp):
AATTAATTCGGTTAACAG
Found at i:10645 original size:8 final size:9
Alignment explanation
Indices: 10633--10659 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
10623 GAAAAAACTA
10633 AAAAAAAAT
1 AAAAAAAAT
10642 AAAAAAAAT
1 AAAAAAAAT
10651 AAAAAAAAT
1 AAAAAAAAT
10660 CTTTTACCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:16960 original size:6 final size:6
Alignment explanation
Indices: 16951--17023 Score: 62
Period size: 6 Copynumber: 12.7 Consensus size: 6
16941 TGACCTTTTA
* * * * * *
16951 TTAAAT TTAAA- GTAATT TTAAAT TTAAAA GTAAAC TTAAAC TT-AAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
16997 TTAAAT TTAAAT TTAAA- ATAAAT TTAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAA
17024 TCTTAGAATA
Statistics
Matches: 53, Mismatches: 11, Indels: 6
0.76 0.16 0.09
Matches are distributed among these distances:
5 11 0.21
6 42 0.79
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (6 bp):
TTAAAT
Found at i:16973 original size:17 final size:17
Alignment explanation
Indices: 16951--17041 Score: 87
Period size: 17 Copynumber: 5.3 Consensus size: 17
16941 TGACCTTTTA
*
16951 TTAAATTTAAAGTAATT
1 TTAAATTTAAAGTAAAT
*
16968 TTAAATTTAAAAGTAAAC
1 TTAAATTT-AAAGTAAAT
* **
16986 TTAAACTTAATTTAAAT
1 TTAAATTTAAAGTAAAT
*
17003 TTAAATTTAAAATAAAT
1 TTAAATTTAAAGTAAAT
17020 TT-AATCTTAGAA-TAAAT
1 TTAAAT-TTA-AAGTAAAT
17037 TTAAA
1 TTAAA
17042 AGGGGTCTAC
Statistics
Matches: 61, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
16 3 0.05
17 40 0.66
18 18 0.30
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (17 bp):
TTAAATTTAAAGTAAAT
Found at i:16984 original size:29 final size:29
Alignment explanation
Indices: 16952--17007 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
16942 GACCTTTTAT
*
16952 TAAATTTAAA-GTAATTTTAAATTTAAAAG
1 TAAACTTAAACGTAA-TTTAAATTTAAAAG
*
16981 TAAACTTAAACTTAATTTAAATTTAAA
1 TAAACTTAAACGTAATTTAAATTTAAA
17008 TTTAAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 21 0.88
30 3 0.12
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.41
Consensus pattern (29 bp):
TAAACTTAAACGTAATTTAAATTTAAAAG
Found at i:17007 original size:23 final size:23
Alignment explanation
Indices: 16969--17023 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
16959 AAAGTAATTT
*
16969 TAAATTTAAAAGTAAACTTAAAC
1 TAAATTTAAAAGTAAACTTAAAA
* ** *
16992 TTAATTTAAATTTAAATTTAAAA
1 TAAATTTAAAAGTAAACTTAAAA
17015 TAAATTTAA
1 TAAATTTAA
17024 TCTTAGAATA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (23 bp):
TAAATTTAAAAGTAAACTTAAAA
Found at i:17687 original size:208 final size:207
Alignment explanation
Indices: 17331--18001 Score: 828
Period size: 209 Copynumber: 3.2 Consensus size: 207
17321 TGGTTTGATG
* * * * *
17331 TCATTGATTTAGTCTACTTCTCAGTATCTCATTAGGAAAATGACCGCATCACTGGCTTTGATCCA
1 TCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCA
* * * * *
17396 --ACTCTGTGTCTCATCAGGAAGACGGATCTGGTTCACTTCTTTGTATCTCTTAAGGAAGGTAAC
66 CTTCTCTGTGTCTCATCAGGAAGACAGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTAAC
17459 CGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGAAAACTAGGGTTCGAAGATTTGCTCA
131 CGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAG-AAACTAGGGTTCGAAGATTTGCTCA
*
17524 CTTTGAGCCTGGT
195 CTTTGAGCTTGGT
* **
17537 TCATTGACTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACTTCATCACTTGTTTTGATCCA
1 TCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCA
*
17602 CTTCTCTGTGTCTCATCAGGAAG-CTAGATCTGGTTCATTTCTCTGTATCTCATCAGGAAGGTAA
66 CTTCTCTGTGTCTCATCAGGAAGAC-AGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTAA
* * * * *
17666 CCGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGTTGGGATTCGAAAATTTACTC
130 CCGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGAAACTAGGG-TTCGAAGATTTGCTC
17731 ACTTTGAGCTTGGTT
194 ACTTTGAGCTTGG-T
* * * * * * ** *
17746 TCATCGAGTTGGTATACTTCTCTGTATCTCATCAAGAAGATGACCGCCTCACTTGTTTCAATCCG
1 TCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCA
* * * * * *
17811 CTTCTCTGTATCTCATCAGGAAGAC-GAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTGA
66 CTTCTCTGTGTCTCATCAGGAAGACAG-ATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTAA
** * * * * * *
17875 CCATTTTATTGCTTCGACCTGCTTCTCAATATATCATTAGGAAGCTGGGGTTCGAAGATTTGCTT
130 CCGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCA-GAAACTAGGGTTCGAAGATTTGCTC
*
17940 ACTTTGAGCTTGATT
194 ACTTTGAGCTTG-GT
* **
17955 TCATTGATTTGGTCTATTTCTTTGTATCTCATCAGGAAGATGACCGC
1 TCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGC
18002 CTCCTTATTT
Statistics
Matches: 399, Mismatches: 57, Indels: 15
0.85 0.12 0.03
Matches are distributed among these distances:
206 57 0.14
207 7 0.02
208 120 0.30
209 208 0.52
210 7 0.02
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.36
Consensus pattern (207 bp):
TCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCA
CTTCTCTGTGTCTCATCAGGAAGACAGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTAAC
CGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGAAACTAGGGTTCGAAGATTTGCTCAC
TTTGAGCTTGGT
Found at i:26550 original size:58 final size:58
Alignment explanation
Indices: 26465--26980 Score: 323
Period size: 59 Copynumber: 8.8 Consensus size: 58
26455 GACACTTTTG
* * *
26465 GGGTAAAATAGTAA-TTTT-CGAAGGTTCGGGGGTAAAAAAAT-AATTTTTGGACATCCGA
1 GGGTAAAATGGTAATTTTTGGGAA-GTT-GGGGGT-AAAAAATGAATTTTTGGACATTCGA
* * * *
26523 GGGT-AAATGGTAATTTTTGGGAAGTTCGGGTTCAAAAATAGAATTTTT-GACATTCGG
1 GGGTAAAATGGTAATTTTTGGGAAGTTGGGGGTAAAAAAT-GAATTTTTGGACATTCGA
* * * **
26580 GGGTAAAATGGT-ATTTTTGGGAAAGTTTGGGTTCAAAAATGGAATTTTTGGATGTTCG-
1 GGGTAAAATGGTAATTTTTGGG-AAGTTGGGGGTAAAAAAT-GAATTTTTGGACATTCGA
* * * * *
26638 GCGGTAAAATGGTAATTTTTGGAAAGTTTGGGGTCAAAATTGGAATTTTTGGACATT-TA
1 G-GGTAAAATGGTAATTTTTGGGAAGTTGGGGGTAAAAAAT-GAATTTTTGGACATTCGA
* * * * *
26697 GGGGTAAAATGGTAA-TTTTGGAAAGTTTGGAGTCAAAAAATGGAATTTTTGGACGTTCGG
1 -GGGTAAAATGGTAATTTTTGGGAAGTTGGGGGT-AAAAAAT-GAATTTTTGGACATTCGA
* * * ** *
26757 GGGTAAAATGGTAA-TTTTGGGAAAGTTCGTGATGTAAAATGGAATTTTTGGACATTCAA
1 GGGTAAAATGGTAATTTTTGGG-AAGTTGGGGGTAAAAAAT-GAATTTTTGGACATTCGA
* * * *
26816 GGGTAAAATGGTAA-TTTTGGGAAAGTTTGGGGTCAAAAATGGGA-TTTTGGA-AATCTGA
1 GGGTAAAATGGTAATTTTTGGG-AAGTTGGGGGTAAAAAAT-GAATTTTTGGACATTC-GA
* * * *
26874 GGGT-AAATGGTAATTTTAT--GAAGTTCGGGGGT-GATAATGTAATTTTTGCA-ATGTTCAA
1 GGGTAAAATGGTAATTTT-TGGGAAGTT-GGGGGTAAAAAATG-AATTTTTGGACA--TTCGA
* * * * *
26932 GGGTTAAAAT-ATAATTTTTGGAAAGTTTGGGGGTTAAAATTTAATTTTT
1 GGG-TAAAATGGTAATTTTTGGGAAG-TTGGGGGTAAAAAATGAATTTTT
26981 TGGAAAGTTT
Statistics
Matches: 376, Mismatches: 54, Indels: 54
0.78 0.11 0.11
Matches are distributed among these distances:
55 1 0.00
56 16 0.04
57 57 0.15
58 88 0.23
59 173 0.46
60 36 0.10
61 5 0.01
ACGTcount: A:0.32, C:0.05, G:0.28, T:0.35
Consensus pattern (58 bp):
GGGTAAAATGGTAATTTTTGGGAAGTTGGGGGTAAAAAATGAATTTTTGGACATTCGA
Found at i:26570 original size:30 final size:30
Alignment explanation
Indices: 26527--26863 Score: 185
Period size: 31 Copynumber: 11.4 Consensus size: 30
26517 ATCCGAGGGT
*
26527 AAATGGTAATTTTTGGGAAGTTCGGGTTCAA
1 AAATGG-AATTTTTGGGAAGTTCGGGGTCAA
*
26558 AAATAGAATTTTT--GACA-TTCGGGGGT--A
1 AAATGGAATTTTTGGGA-AGTTC-GGGGTCAA
* * *
26585 AAATGGTATTTTTGGGAAAGTTTGGGTTCAA
1 AAATGGAATTTTTGGG-AAGTTCGGGGTCAA
*
26616 AAATGGAATTTTT-GGATGTTCGGCGGT--A
1 AAATGGAATTTTTGGGAAGTTCGG-GGTCAA
* *
26644 AAATGGTAATTTTTGGAAAGTTTGGGGTCAA
1 AAATGG-AATTTTTGGGAAGTTCGGGGTCAA
* * *
26675 AATTGGAATTTTT-GGACATTTAGGGGT--A
1 AAATGGAATTTTTGGGA-AGTTCGGGGTCAA
* * *
26703 AAATGGTAA-TTTTGGAAAGTTTGGAGTCAAA
1 AAATGG-AATTTTTGGGAAGTTCGGGGTC-AA
*
26734 AAATGGAATTTTT-GGACGTTCGGGGGT--A
1 AAATGGAATTTTTGGGAAGTTC-GGGGTCAA
* * **
26762 AAATGGTAA-TTTTGGGAAAGTTCGTGATGTA
1 AAATGG-AATTTTTGGG-AAGTTCGGGGTCAA
*
26793 AAATGGAATTTTT-GGACA-TTCAAGGGT--A
1 AAATGGAATTTTTGGGA-AGTTC-GGGGTCAA
*
26821 AAATGGTAA-TTTTGGGAAAGTTTGGGGTCAA
1 AAATGG-AATTTTTGGG-AAGTTCGGGGTCAA
*
26852 AAATGGGATTTT
1 AAATGGAATTTT
26864 GGAAATCTGA
Statistics
Matches: 235, Mismatches: 35, Indels: 72
0.69 0.10 0.21
Matches are distributed among these distances:
27 12 0.05
28 51 0.22
29 53 0.23
30 59 0.25
31 60 0.26
ACGTcount: A:0.31, C:0.05, G:0.29, T:0.35
Consensus pattern (30 bp):
AAATGGAATTTTTGGGAAGTTCGGGGTCAA
Found at i:26664 original size:59 final size:58
Alignment explanation
Indices: 26464--26890 Score: 433
Period size: 59 Copynumber: 7.3 Consensus size: 58
26454 AGACACTTTT
* * * * * *
26464 GGGGTAAAATAGTAA-TTTTCGAAGGTTCGGGGGTAAAAAAAT--AATTTTTGGACATCC
1 GGGGTAAAATGGTAATTTTTGGAAAGTT-TGGGGT-CAAAAATGGAATTTTTGGACATTC
* * * *
26521 GAGGGT-AAATGGTAATTTTTGGGAAGTTCGGGTTCAAAAATAGAATTTTT-GACATTC
1 G-GGGTAAAATGGTAATTTTTGGAAAGTTTGGGGTCAAAAATGGAATTTTTGGACATTC
* **
26578 GGGGGTAAAATGGT-ATTTTTGGGAAAGTTTGGGTTCAAAAATGGAATTTTTGGATGTTC
1 -GGGGTAAAATGGTAATTTTT-GGAAAGTTTGGGGTCAAAAATGGAATTTTTGGACATTC
* *
26637 GGCGGTAAAATGGTAATTTTTGGAAAGTTTGGGGTCAAAATTGGAATTTTTGGACATTTA
1 GG-GGTAAAATGGTAATTTTTGGAAAGTTTGGGGTCAAAAATGGAATTTTTGGACA-TTC
* *
26697 GGGGTAAAATGGTAA-TTTTGGAAAGTTTGGAGTCAAAAAATGGAATTTTTGGACGTTC
1 GGGGTAAAATGGTAATTTTTGGAAAGTTTGGGGTC-AAAAATGGAATTTTTGGACATTC
* * * * **
26755 GGGGGTAAAATGGTAATTTTGGGAAAGTTCGTGATGTAAAATGGAATTTTTGGACATTC
1 -GGGGTAAAATGGTAATTTTTGGAAAGTTTGGGGTCAAAAATGGAATTTTTGGACATTC
* * * *
26814 AAGGGTAAAATGGTAATTTTGGGAAAGTTTGGGGTCAAAAATGGGA-TTTTGGA-AATC
1 -GGGGTAAAATGGTAATTTTTGGAAAGTTTGGGGTCAAAAATGGAATTTTTGGACATTC
26871 TGAGGGT-AAATGGTAATTTT
1 -G-GGGTAAAATGGTAATTTT
26891 ATGAAGTTCG
Statistics
Matches: 314, Mismatches: 41, Indels: 30
0.82 0.11 0.08
Matches are distributed among these distances:
56 6 0.02
57 45 0.14
58 88 0.28
59 152 0.48
60 23 0.07
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.34
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTTGGAAAGTTTGGGGTCAAAAATGGAATTTTTGGACATTC
Found at i:26984 original size:31 final size:30
Alignment explanation
Indices: 26650--27009 Score: 130
Period size: 30 Copynumber: 12.2 Consensus size: 30
26640 GGTAAAATGG
*
26650 TAATTTTTGGAAAGTTTG-GGGTCAAAAT-
1 TAATTTTTGGAAAGTTTGAGGGTTAAAATA
* * *
26678 TGGAATTTTTGGACA-TTT-AGGGGTAAAATGG
1 T--AATTTTTGGAAAGTTTGAGGGTTAAAAT-A
* * *
26709 TAA-TTTTGGAAAGTTTG-GAGTCAAAAAA
1 TAATTTTTGGAAAGTTTGAGGGTTAAAATA
* * * *
26737 TGGAATTTTTGG-ACGTTCG-GGGGTAAAATGG
1 T--AATTTTTGGAAAGTTTGAGGGTTAAAAT-A
* * *
26768 TAATTTTGGGAAAGTTCGTGA-TG-TAAAATG
1 TAATTTTTGGAAAGTT--TGAGGGTTAAAATA
* * ** *
26798 GAATTTTTGGACA-TTCAAGGG-TAAAATGG
1 TAATTTTTGGAAAGTTTGAGGGTTAAAAT-A
* *
26827 TAATTTTGGGAAAGTTTG-GGGTCAAAA-A
1 TAATTTTTGGAAAGTTTGAGGGTTAAAATA
* * *
26855 TGGGA-TTTTGGAAA-TCTGAGGG-T-AAATGG
1 T--AATTTTTGGAAAGTTTGAGGGTTAAAAT-A
* * * * *
26884 TAATTTTAT-G-AAGTTCGGGGGTGATAATG
1 TAATTTT-TGGAAAGTTTGAGGGTTAAAATA
* * **
26913 TAATTTTTGCAATGTTCAAGGGTTAAAATA
1 TAATTTTTGGAAAGTTTGAGGGTTAAAATA
* *
26943 TAATTTTTGGAAAGTTTGGGGGTTAAAATT
1 TAATTTTTGGAAAGTTTGAGGGTTAAAATA
26973 TAATTTTTTGGAAAGTTTGAGGGTTAAAATA
1 TAA-TTTTTGGAAAGTTTGAGGGTTAAAATA
*
27004 TGATTT
1 TAATTT
27010 CTAGACACTC
Statistics
Matches: 240, Mismatches: 60, Indels: 62
0.66 0.17 0.17
Matches are distributed among these distances:
27 7 0.03
28 31 0.13
29 67 0.28
30 92 0.38
31 41 0.17
32 2 0.01
ACGTcount: A:0.32, C:0.04, G:0.28, T:0.37
Consensus pattern (30 bp):
TAATTTTTGGAAAGTTTGAGGGTTAAAATA
Found at i:27528 original size:30 final size:31
Alignment explanation
Indices: 27492--27557 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 31
27482 ATTTTTCATA
*
27492 AAAAAAATATCATTCCC-TACCATTTCTTTC
1 AAAAAAATATCATTCCCTTACCATTTCTCTC
* * * *
27522 AAAAAAATTTCCTTCCCTTCCCTTTTCTCTC
1 AAAAAAATATCATTCCCTTACCATTTCTCTC
27553 AAAAA
1 AAAAA
27558 CCGTCGCTCC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 15 0.50
31 15 0.50
ACGTcount: A:0.35, C:0.29, G:0.00, T:0.36
Consensus pattern (31 bp):
AAAAAAATATCATTCCCTTACCATTTCTCTC
Found at i:28106 original size:9 final size:9
Alignment explanation
Indices: 28092--28170 Score: 58
Period size: 9 Copynumber: 9.0 Consensus size: 9
28082 TTTTTTATTT
28092 TATTATTAA
1 TATTATTAA
28101 TATTATTAA
1 TATTATTAA
*
28110 TA-TAATAA
1 TATTATTAA
28118 TA--A-TAA
1 TATTATTAA
* *
28124 TAATAATAA
1 TATTATTAA
*
28133 TAATTATTAT
1 T-ATTATTAA
*
28143 TATTATTAT
1 TATTATTAA
*
28152 TGTTATTTAA
1 TATTA-TTAA
28162 TATTATTAA
1 TATTATTAA
28171 AACGTTATTT
Statistics
Matches: 58, Mismatches: 7, Indels: 10
0.77 0.09 0.13
Matches are distributed among these distances:
6 5 0.09
7 1 0.02
8 8 0.14
9 31 0.53
10 13 0.22
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (9 bp):
TATTATTAA
Found at i:28308 original size:11 final size:11
Alignment explanation
Indices: 28292--28321 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
28282 TGGACATTAG
28292 AGTAATAAGCA
1 AGTAATAAGCA
28303 AGTAATAAGCA
1 AGTAATAAGCA
28314 AGTAATAA
1 AGTAATAA
28322 ATGTACCTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.57, C:0.07, G:0.17, T:0.20
Consensus pattern (11 bp):
AGTAATAAGCA
Found at i:28905 original size:6 final size:6
Alignment explanation
Indices: 28896--29004 Score: 75
Period size: 6 Copynumber: 18.8 Consensus size: 6
28886 TGACCTTTTA
* * * * * *
28896 TTAAAT TT-AAT GTAATT TTAAAT TTAAAA GTAAAC TTAAAC TTAAA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
** * *
28942 TTAAAT TTAAAT TTAAA- ACAAAT TTAAAT TTAAAA ATAAAT TT-AAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
28988 CTTAAA- ATAAAT TTAAA
1 -TTAAAT TTAAAT TTAAA
29005 AATGATCTAG
Statistics
Matches: 79, Mismatches: 18, Indels: 12
0.72 0.17 0.11
Matches are distributed among these distances:
5 19 0.24
6 58 0.73
7 2 0.03
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (6 bp):
TTAAAT
Found at i:28951 original size:17 final size:17
Alignment explanation
Indices: 28896--29004 Score: 121
Period size: 17 Copynumber: 6.3 Consensus size: 17
28886 TGACCTTTTA
** *
28896 TTAAATTTAATGTAATT
1 TTAAATTTAAAATAAAT
*
28913 TTAAATTTAAAAGTAAAC
1 TTAAATTTAAAA-TAAAT
* *
28931 TTAAACTTAAATTAAAT
1 TTAAATTTAAAATAAAT
*
28948 TTAAATTTAAAACAAAT
1 TTAAATTTAAAATAAAT
28965 TTAAATTTAAAAATAAAT
1 TTAAATTT-AAAATAAAT
28983 TT-AATCTTAAAATAAAT
1 TTAAAT-TTAAAATAAAT
29000 TTAAA
1 TTAAA
29005 AATGATCTAG
Statistics
Matches: 77, Mismatches: 11, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
17 50 0.65
18 27 0.35
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (17 bp):
TTAAATTTAAAATAAAT
Found at i:28951 original size:35 final size:35
Alignment explanation
Indices: 28912--29004 Score: 118
Period size: 35 Copynumber: 2.7 Consensus size: 35
28902 TTAATGTAAT
* *
28912 TTTAAATTTAAAAGTAAACTTAAACTT-AAATTAAA
1 TTTAAATTTAAAA-TAAATTTAAACTTAAAAATAAA
* *
28947 TTTAAATTTAAAACAAATTTAAATTTAAAAATAAA
1 TTTAAATTTAAAATAAATTTAAACTTAAAAATAAA
28982 TTT-AATCTTAAAATAAATTTAAA
1 TTTAAAT-TTAAAATAAATTTAAA
29005 AATGATCTAG
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
34 13 0.25
35 38 0.75
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (35 bp):
TTTAAATTTAAAATAAATTTAAACTTAAAAATAAA
Found at i:36544 original size:19 final size:19
Alignment explanation
Indices: 36520--36562 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
36510 TCAATTGGGT
36520 GCGAAGTGAGGCGGGCCTC
1 GCGAAGTGAGGCGGGCCTC
36539 GCGAAGTGAGGCGGGCCTC
1 GCGAAGTGAGGCGGGCCTC
36558 GCGAA
1 GCGAA
36563 ACCCGCCCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.19, C:0.26, G:0.47, T:0.09
Consensus pattern (19 bp):
GCGAAGTGAGGCGGGCCTC
Done.