Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168489.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_87, 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: 102453
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.34
Warning! 1000 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:94148 original size:31 final size:31
Alignment explanation
Indices: 94113--94214 Score: 86
Period size: 32 Copynumber: 3.3 Consensus size: 31
94103 TGTCTTTGAT
*
94113 TTTTTATACTATTTTCTTATTATTTTTTTCA
1 TTTTTATTCTATTTTCTTATTATTTTTTTCA
* * *
94144 TTTTT-TTGTATTTTTCATACTAATTTTTTTCA
1 TTTTTATTCTA-TTTTCTTA-TTATTTTTTTCA
*
94176 TTTTGTCATTC-ATTTTCCTT-TTCTTTTTTT-A
1 TTTT-T-ATTCTATTTT-CTTATTATTTTTTTCA
94207 TTTTTATT
1 TTTTTATT
94215 TTTGAGTCAT
Statistics
Matches: 57, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
29 3 0.05
30 4 0.07
31 17 0.30
32 23 0.40
33 5 0.09
34 3 0.05
35 2 0.04
ACGTcount: A:0.16, C:0.11, G:0.02, T:0.72
Consensus pattern (31 bp):
TTTTTATTCTATTTTCTTATTATTTTTTTCA
Found at i:94217 original size:20 final size:20
Alignment explanation
Indices: 94194--94371 Score: 56
Period size: 20 Copynumber: 8.6 Consensus size: 20
94184 TTCATTTTCC
94194 TTTTCTTTTTTTATTTTTAT
1 TTTTCTTTTTTTATTTTTAT
*** **
94214 TTTTGAGTCATTATTTTTTCAT
1 TTTTCTTTTTTTA-TTTTT-AT
* *
94236 TTCTCATTTTTTATTTTTAT
1 TTTTCTTTTTTTATTTTTAT
* * *
94256 TGTATT-TTTGTATATTTTAAAATT
1 T-T-TTCTTTTTTTATTTT--TA-T
** *
94280 TTTTCTTATTGGTATTATT-T
1 TTTTCTT-TTTTTATTTTTAT
* *
94300 TTTTCTTTTTTTGTACTTTAT
1 TTTTCTTTTTTTAT-TTTTAT
** **
94321 TTTT-TTTTTTGCTTAATATT
1 TTTTCTTTTTTTATTTTTA-T
*
94341 TTTTCTTATTTTATTTTTAT
1 TTTTCTTTTTTTATTTTTAT
*
94361 TTTTATTTTTT
1 TTTTCTTTTTT
94372 ATAAATTTTT
Statistics
Matches: 108, Mismatches: 37, Indels: 26
0.63 0.22 0.15
Matches are distributed among these distances:
19 6 0.06
20 43 0.40
21 34 0.31
22 13 0.12
23 4 0.04
24 8 0.07
ACGTcount: A:0.16, C:0.06, G:0.04, T:0.74
Consensus pattern (20 bp):
TTTTCTTTTTTTATTTTTAT
Found at i:94561 original size:18 final size:18
Alignment explanation
Indices: 94540--94578 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
94530 TTTCCTGTGC
* *
94540 TTTCATATTTTTTTTTGT
1 TTTCACATTTTTCTTTGT
*
94558 TTTCACCTTTTTCTTTGT
1 TTTCACATTTTTCTTTGT
94576 TTT
1 TTT
94579 AAAATTTTCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.08, C:0.13, G:0.05, T:0.74
Consensus pattern (18 bp):
TTTCACATTTTTCTTTGT
Found at i:96835 original size:22 final size:22
Alignment explanation
Indices: 96810--96880 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 22
96800 TGGTTTTTTA
96810 TATATGTTTTCTTACTACTTGT
1 TATATGTTTTCTTACTACTTGT
* * ** *
96832 TATATTTTTTAGTT--TTTTTTT
1 TATATGTTTT-CTTACTACTTGT
96853 ATATATGTTTTCTTACTACTTGT
1 -TATATGTTTTCTTACTACTTGT
96876 TATAT
1 TATAT
96881 TACTACTCAT
Statistics
Matches: 35, Mismatches: 10, Indels: 8
0.66 0.19 0.15
Matches are distributed among these distances:
21 6 0.17
22 23 0.66
23 6 0.17
ACGTcount: A:0.20, C:0.08, G:0.07, T:0.65
Consensus pattern (22 bp):
TATATGTTTTCTTACTACTTGT
Found at i:96894 original size:44 final size:44
Alignment explanation
Indices: 96803--96896 Score: 136
Period size: 44 Copynumber: 2.1 Consensus size: 44
96793 TTATCTTTGG
** * *
96803 TTTTTTATATATGTTTTCTTACTACTTGTTATATTTTTTAGTTT
1 TTTTTTATATATGTTTTCTTACTACTTGTTATATTTACTACTAT
96847 TTTTTTATATATGTTTTCTTACTACTTGTTATA-TTACTACTCAT
1 TTTTTTATATATGTTTTCTTACTACTTGTTATATTTACTACT-AT
96891 TTTTTT
1 TTTTTT
96897 CTATTTTGTC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
43 5 0.11
44 40 0.89
ACGTcount: A:0.19, C:0.10, G:0.05, T:0.66
Consensus pattern (44 bp):
TTTTTTATATATGTTTTCTTACTACTTGTTATATTTACTACTAT
Found at i:97142 original size:24 final size:23
Alignment explanation
Indices: 97084--97144 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 23
97074 TTTGCTTTAA
* *
97084 TATTTTATTTTATTTTATTTTTCC
1 TATTATATTTTATTTTATTATT-C
*
97108 TATTATTTTTTATTTTAATTATT-
1 TATTATATTTTATTTT-ATTATTC
97131 TATTGATATTTTAT
1 TATT-ATATTTTAT
97145 AAATTTTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
23 4 0.13
24 22 0.71
25 5 0.16
ACGTcount: A:0.23, C:0.03, G:0.02, T:0.72
Consensus pattern (23 bp):
TATTATATTTTATTTTATTATTC
Found at i:97571 original size:16 final size:15
Alignment explanation
Indices: 97508--97573 Score: 62
Period size: 16 Copynumber: 4.3 Consensus size: 15
97498 TTTTTTCTTC
97508 TTTTA-ATTTTTTAT
1 TTTTATATTTTTTAT
* *
97522 CTTTGATATTTTATAT
1 -TTTTATATTTTTTAT
* *
97538 CTTTATATCTTATTAT
1 TTTTATAT-TTTTTAT
97554 TTCTTATATTTTTTAT
1 TT-TTATATTTTTTAT
97570 TTTT
1 TTTT
97574 TGTTTGTATT
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
15 12 0.30
16 22 0.55
17 6 0.15
ACGTcount: A:0.21, C:0.06, G:0.02, T:0.71
Consensus pattern (15 bp):
TTTTATATTTTTTAT
Found at i:97650 original size:19 final size:20
Alignment explanation
Indices: 97595--97640 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
97585 TATAAACTAA
97595 ATTTTTT-TTA-TATTTTGTC
1 ATTTTTTATTAGT-TTTTGTC
97614 ATTTTTTATTAGTTTTTGT-
1 ATTTTTTATTAGTTTTTGTC
97633 ATTTTTTA
1 ATTTTTTA
97641 ATTTTTTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 15 0.60
20 9 0.36
21 1 0.04
ACGTcount: A:0.17, C:0.02, G:0.07, T:0.74
Consensus pattern (20 bp):
ATTTTTTATTAGTTTTTGTC
Found at i:97690 original size:13 final size:13
Alignment explanation
Indices: 97672--97696 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
97662 ATTTCCTTAC
97672 TTTTTTTTTTTTA
1 TTTTTTTTTTTTA
97685 TTTTTTTTTTTT
1 TTTTTTTTTTTT
97697 TAGTATTATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.04, C:0.00, G:0.00, T:0.96
Consensus pattern (13 bp):
TTTTTTTTTTTTA
Found at i:97691 original size:14 final size:14
Alignment explanation
Indices: 97672--97698 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
97662 ATTTCCTTAC
97672 TTTTTTTTTTTTAT
1 TTTTTTTTTTTTAT
97686 TTTTTTTTTTTTA
1 TTTTTTTTTTTTA
97699 GTATTATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.00, G:0.00, T:0.93
Consensus pattern (14 bp):
TTTTTTTTTTTTAT
Found at i:98017 original size:24 final size:22
Alignment explanation
Indices: 97963--98017 Score: 65
Period size: 24 Copynumber: 2.4 Consensus size: 22
97953 ATTTGCTTTC
97963 ATTTTTTTTGTTTTAATTTTTT
1 ATTTTTTTTGTTTTAATTTTTT
* * *
97985 ATATATTTTGTATATTCATTTTTT
1 ATTTTTTTTGT-T-TTAATTTTTT
98009 ATTTTTTTT
1 ATTTTTTTT
98018 TGCTTTTTCT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 9 0.35
23 1 0.04
24 16 0.62
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.76
Consensus pattern (22 bp):
ATTTTTTTTGTTTTAATTTTTT
Found at i:98308 original size:24 final size:22
Alignment explanation
Indices: 98273--98374 Score: 84
Period size: 24 Copynumber: 4.5 Consensus size: 22
98263 TGATTCACTA
* *
98273 ATTTTTTATTTTCTTACTTTTTT
1 ATTTTTTGTTTTTTTA-TTTTTT
*
98296 ATTTTTTGCTTTTATTTATTTTTA
1 ATTTTTTG-TTTT-TTTATTTTTT
98320 ATTGTTTTGTTTATTTTATTTTTT
1 ATT-TTTTGTTT-TTTTATTTTTT
* *
98344 ATTTTTAG-TATTTTA--TTTT
1 ATTTTTTGTTTTTTTATTTTTT
*
98363 ATTTTTTCTTTT
1 ATTTTTTGTTTT
98375 ATATTAATAT
Statistics
Matches: 65, Mismatches: 9, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
19 10 0.15
20 2 0.03
21 5 0.08
22 1 0.02
23 11 0.17
24 27 0.42
25 9 0.14
ACGTcount: A:0.15, C:0.04, G:0.04, T:0.77
Consensus pattern (22 bp):
ATTTTTTGTTTTTTTATTTTTT
Found at i:98355 original size:16 final size:14
Alignment explanation
Indices: 98273--98379 Score: 58
Period size: 16 Copynumber: 7.2 Consensus size: 14
98263 TGATTCACTA
98273 ATTTTTTATTTTCTT
1 ATTTTTTATTTT-TT
98288 ACTTTTTTATTTTTT
1 A-TTTTTTATTTTTT
* *
98303 GCTTTTATTTATTTTTA
1 --ATTT-TTTATTTTTT
*
98320 ATTGTTTTGTTTATTTT
1 ATT-TTTT-ATT-TTTT
98337 ATTTTTTA-TTTTT
1 ATTTTTTATTTTTT
*
98350 AGTATTTTA--TTTT
1 A-TTTTTTATTTTTT
* *
98363 ATTTTTTCTTTTAT
1 ATTTTTTATTTTTT
98377 ATT
1 ATT
98380 AATATTTTCT
Statistics
Matches: 72, Mismatches: 10, Indels: 21
0.70 0.10 0.20
Matches are distributed among these distances:
12 5 0.07
13 10 0.14
14 13 0.18
15 8 0.11
16 21 0.29
17 15 0.21
ACGTcount: A:0.16, C:0.04, G:0.04, T:0.77
Consensus pattern (14 bp):
ATTTTTTATTTTTT
Found at i:98364 original size:31 final size:31
Alignment explanation
Indices: 98310--98408 Score: 89
Period size: 31 Copynumber: 3.2 Consensus size: 31
98300 TTTGCTTTTA
98310 TTTATTTTTAAT-TGTTT-TGTTTATTTTATTT
1 TTTATTTTTAATAT-TTTAT-TTTATTTTATTT
*
98341 TTTATTTTTAGTATTTTATTTTATTTT-TTCT
1 TTTATTTTTAATATTTTATTTTATTTTATT-T
* * * *
98372 TTTA-TATTAATATTTTCTCTTAATTTATTT
1 TTTATTTTTAATATTTTATTTTATTTTATTT
*
98402 TTCATTT
1 TTTATTT
98409 ATTTTTATTT
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
30 23 0.42
31 30 0.55
32 2 0.04
ACGTcount: A:0.19, C:0.04, G:0.03, T:0.74
Consensus pattern (31 bp):
TTTATTTTTAATATTTTATTTTATTTTATTT
Found at i:98389 original size:18 final size:17
Alignment explanation
Indices: 98354--98410 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
98344 ATTTTTAGTA
* *
98354 TTTTATTTTATTTTTTC
1 TTTTATATTAATTTTTC
98371 TTTTATATTAATATTTTC
1 TTTTATATTAAT-TTTTC
* *
98389 TCTTA-ATTTATTTTTC
1 TTTTATATTAATTTTTC
*
98405 ATTTAT
1 TTTTAT
98411 TTTTATTTAT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
16 8 0.25
17 15 0.47
18 9 0.28
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTATATTAATTTTTC
Found at i:98418 original size:10 final size:10
Alignment explanation
Indices: 98394--98425 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
98384 TTTTCTCTTA
98394 ATTTATTTTT
1 ATTTATTTTT
98404 CATTTATTTTT
1 -ATTTATTTTT
98415 ATTTATTTTT
1 ATTTATTTTT
98425 A
1 A
98426 AAATTTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.52
11 10 0.48
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:98579 original size:18 final size:18
Alignment explanation
Indices: 98558--98617 Score: 72
Period size: 17 Copynumber: 3.4 Consensus size: 18
98548 TATGCTTTCA
98558 TTTTTTATTTGTTTTAAT
1 TTTTTTATTTGTTTTAAT
*
98576 TTTTTCA-TTGTTTTAAT
1 TTTTTTATTTGTTTTAAT
*
98593 TTTTTATATTT-TTTT-TT
1 TTTTT-TATTTGTTTTAAT
98610 TTTTTTAT
1 TTTTTTAT
98618 ATCAAATCTT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
16 3 0.08
17 21 0.57
18 11 0.30
19 2 0.05
ACGTcount: A:0.15, C:0.02, G:0.03, T:0.80
Consensus pattern (18 bp):
TTTTTTATTTGTTTTAAT
Found at i:98581 original size:25 final size:26
Alignment explanation
Indices: 98553--98606 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
98543 TTTCATATGC
*
98553 TTTCATT-TTTTATTTGTTTTA-ATTT
1 TTTCATTGTTTTAATT-TTTTATATTT
98578 TTTCATTGTTTTAATTTTTTATATTT
1 TTTCATTGTTTTAATTTTTTATATTT
98604 TTT
1 TTT
98607 TTTTTTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 12 0.46
26 14 0.54
ACGTcount: A:0.17, C:0.04, G:0.04, T:0.76
Consensus pattern (26 bp):
TTTCATTGTTTTAATTTTTTATATTT
Found at i:98613 original size:34 final size:35
Alignment explanation
Indices: 98530--98619 Score: 94
Period size: 34 Copynumber: 2.6 Consensus size: 35
98520 TTTCTTTCTT
* * *
98530 TTTGCTTTCTTTTTTTCATATGCTTTCATTTTTTA
1 TTTGTTTTATTTTTTTCATATGCTTTAATTTTTTA
* *
98565 TTTGTTTTAATTTTTTCAT-TGTTTTAATTTTTTA
1 TTTGTTTTATTTTTTTCATATGCTTTAATTTTTTA
* *
98599 TATT-TTTTTTTTTTTTTATAT
1 T-TTGTTTTATTTTTTTCATAT
98620 CAAATCTTTT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
34 26 0.58
35 19 0.42
ACGTcount: A:0.14, C:0.07, G:0.04, T:0.74
Consensus pattern (35 bp):
TTTGTTTTATTTTTTTCATATGCTTTAATTTTTTA
Found at i:98815 original size:22 final size:23
Alignment explanation
Indices: 98775--98834 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
98765 AACTTTTATC
*
98775 TTTTTTA-ATTTTTTGTCTT-TGA
1 TTTTTTATATTGTTT-TCTTATGA
*
98797 TTTTTTATATTGTTTTCTTATTA
1 TTTTTTATATTGTTTTCTTATGA
*
98820 TTTCTTAT-TTGTTTT
1 TTTTTTATATTGTTTT
98835 TCAATTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 18 0.55
23 15 0.45
ACGTcount: A:0.13, C:0.05, G:0.07, T:0.75
Consensus pattern (23 bp):
TTTTTTATATTGTTTTCTTATGA
Found at i:98849 original size:22 final size:22
Alignment explanation
Indices: 98796--98851 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
98786 TTTGTCTTTG
*
98796 ATTTTTTATATTGTTTTCTTATT
1 ATTTTTTAT-TTGTTTTCTAATT
*
98819 ATTTCTTATTTGTTTT-TCAATT
1 ATTTTTTATTTGTTTTCT-AATT
*
98841 TTTTTTTATTT
1 ATTTTTTATTT
98852 TTAAACTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 1 0.04
22 19 0.68
23 8 0.29
ACGTcount: A:0.16, C:0.05, G:0.04, T:0.75
Consensus pattern (22 bp):
ATTTTTTATTTGTTTTCTAATT
Found at i:99014 original size:27 final size:26
Alignment explanation
Indices: 98968--99040 Score: 80
Period size: 26 Copynumber: 2.8 Consensus size: 26
98958 TTATTGTATT
*
98968 TTTGT-TTATTTTTTTCTTTTCT-TA
1 TTTGTATTATTTTTTTCTTTTTTGTA
98992 TTTGTATTAATTTTTTTCTTTTTTGTA
1 TTTGTATT-ATTTTTTTCTTTTTTGTA
*
99019 CTT-TATTTATCTTTTTTCTTTT
1 TTTGTA-TTAT-TTTTTTCTTTT
99041 GCTTTAATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
24 5 0.12
25 2 0.05
26 18 0.43
27 17 0.40
ACGTcount: A:0.11, C:0.08, G:0.04, T:0.77
Consensus pattern (26 bp):
TTTGTATTATTTTTTTCTTTTTTGTA
Found at i:99087 original size:18 final size:17
Alignment explanation
Indices: 99019--99089 Score: 61
Period size: 18 Copynumber: 3.9 Consensus size: 17
99009 CTTTTTTGTA
*
99019 CTTTATTTATCTTTTTT
1 CTTTATTTATATTTTTT
*
99036 CTTTTGCTTTAATATTTTTT
1 C-TTT-ATTT-ATATTTTTT
* *
99056 TTTTATTTTTTATTTCTTT
1 CTTTA-TTTATATTT-TTT
99075 CTTTATTTATATTTT
1 CTTTATTTATATTTT
99090 CATAAATTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
17 2 0.05
18 16 0.38
19 16 0.38
20 8 0.19
ACGTcount: A:0.14, C:0.08, G:0.01, T:0.76
Consensus pattern (17 bp):
CTTTATTTATATTTTTT
Found at i:99134 original size:16 final size:15
Alignment explanation
Indices: 99115--99145 Score: 53
Period size: 15 Copynumber: 2.0 Consensus size: 15
99105 TGTTTTGGAT
99115 TTTTTTGTTTTTTATC
1 TTTTTT-TTTTTTATC
99131 TTTTTTTTTTTTATC
1 TTTTTTTTTTTTATC
99146 ATTGTTGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.06, C:0.06, G:0.03, T:0.84
Consensus pattern (15 bp):
TTTTTTTTTTTTATC
Found at i:99757 original size:20 final size:18
Alignment explanation
Indices: 99719--99771 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
99709 ATTTCCTTAC
99719 TTTTTTATTTTTTCT-ATT
1 TTTTTTATTTTTT-TAATT
99737 TTGCTTTTATTTTTTTAATT
1 TT--TTTTATTTTTTTAATT
*
99757 TTTTTTCTTTTTTTA
1 TTTTTTATTTTTTTA
99772 GTACTTATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
18 14 0.45
19 1 0.03
20 16 0.52
ACGTcount: A:0.11, C:0.06, G:0.02, T:0.81
Consensus pattern (18 bp):
TTTTTTATTTTTTTAATT
Found at i:100095 original size:17 final size:17
Alignment explanation
Indices: 100075--100139 Score: 69
Period size: 17 Copynumber: 3.7 Consensus size: 17
100065 AATTGGACTA
*
100075 TTTTATTTATTGCTTAT
1 TTTTATTTATTACTTAT
*
100092 TTTTATTTATTTATTTA-
1 TTTTATTTA-TTACTTAT
*
100109 TTTTATTGATTACTTAT
1 TTTTATTTATTACTTAT
100126 TAGTTTATTTATTA
1 T--TTTATTTATTA
100140 TTTTGGATTG
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
16 6 0.15
17 18 0.46
18 5 0.13
19 10 0.26
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (17 bp):
TTTTATTTATTACTTAT
Found at i:100110 original size:12 final size:11
Alignment explanation
Indices: 100076--100142 Score: 52
Period size: 11 Copynumber: 6.3 Consensus size: 11
100066 ATTGGACTAT
*
100076 TTTATTTATTG
1 TTTATTTATTA
*
100087 CTTATTT-TTA
1 TTTATTTATTA
100097 TTTATTTATT-
1 TTTATTTATTA
*
100107 TAT-TTTATTGA
1 TTTATTTATT-A
*
100118 -TTACTTATTA
1 TTTATTTATTA
100128 GTTTATTTATTA
1 -TTTATTTATTA
100140 TTT
1 TTT
100143 TGGATTGTAT
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
9 6 0.14
10 12 0.28
11 16 0.37
12 9 0.21
ACGTcount: A:0.22, C:0.03, G:0.04, T:0.70
Consensus pattern (11 bp):
TTTATTTATTA
Found at i:100111 original size:34 final size:34
Alignment explanation
Indices: 100073--100142 Score: 97
Period size: 34 Copynumber: 2.0 Consensus size: 34
100063 ACAATTGGAC
* *
100073 TATTTTATTTATTGCTTATT-TTTATTTATTTATT
1 TATTTTATTGATTACTTATTATTTATTTA-TTATT
100107 TATTTTATTGATTACTTATTAGTTTATTTATTATT
1 TATTTTATTGATTACTTATTA-TTTATTTATTATT
100142 T
1 T
100143 TGGATTGTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
34 18 0.56
35 6 0.19
36 8 0.25
ACGTcount: A:0.23, C:0.03, G:0.04, T:0.70
Consensus pattern (34 bp):
TATTTTATTGATTACTTATTATTTATTTATTATT
Found at i:100531 original size:16 final size:16
Alignment explanation
Indices: 100512--100542 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
100502 TTCTTTTCCT
100512 TTTTTTTAGCTTTTTG
1 TTTTTTTAGCTTTTTG
*
100528 TTTTTTTTGCTTTTT
1 TTTTTTTAGCTTTTT
100543 ATGCATTTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.03, C:0.06, G:0.10, T:0.81
Consensus pattern (16 bp):
TTTTTTTAGCTTTTTG
Found at i:100531 original size:17 final size:16
Alignment explanation
Indices: 100511--100542 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
100501 TTTCTTTTCC
100511 TTTTTTTTAGCTTTTTG
1 TTTTTTTT-GCTTTTTG
100528 TTTTTTTTGCTTTTT
1 TTTTTTTTGCTTTTT
100543 ATGCATTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.03, C:0.06, G:0.09, T:0.81
Consensus pattern (16 bp):
TTTTTTTTGCTTTTTG
Found at i:100873 original size:7 final size:7
Alignment explanation
Indices: 100856--100962 Score: 58
Period size: 7 Copynumber: 14.9 Consensus size: 7
100846 CATGCTTTCT
100856 TTTTTTA
1 TTTTTTA
100863 -TTTTTA
1 TTTTTTA
100869 TTTTTTA
1 TTTTTTA
*
100876 TTTTGTA
1 TTTTTTA
***
100883 -TTAACA
1 TTTTTTA
100889 TTTTTCT-
1 TTTTT-TA
*
100896 TCTTTTAA
1 T-TTTTTA
100904 TTTTTTA
1 TTTTTTA
*
100911 TTATCTTGA
1 TT-T-TTTA
100920 TTTTTTA
1 TTTTTTA
*
100927 TATTTTA
1 TTTTTTA
100934 TTTCTTTTA
1 -TT-TTTTA
* *
100943 TCTTATA
1 TTTTTTA
100950 TTTTTTA
1 TTTTTTA
100957 TTTTTT
1 TTTTTT
100963 GTTTGTATTT
Statistics
Matches: 74, Mismatches: 17, Indels: 18
0.68 0.16 0.17
Matches are distributed among these distances:
6 9 0.12
7 46 0.62
8 9 0.12
9 10 0.14
ACGTcount: A:0.18, C:0.06, G:0.02, T:0.75
Consensus pattern (7 bp):
TTTTTTA
Found at i:100907 original size:28 final size:26
Alignment explanation
Indices: 100862--100913 Score: 68
Period size: 28 Copynumber: 1.9 Consensus size: 26
100852 TTCTTTTTTT
100862 ATTTTTATTTTTTATTTTGTATTAAC
1 ATTTTTATTTTTTATTTTGTATTAAC
* *
100888 ATTTTTCTTCTTTTAATTTTTTATTA
1 ATTTTTATT-TTTT-ATTTTGTATTA
100914 TCTTGATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 8 0.36
27 4 0.18
28 10 0.45
ACGTcount: A:0.21, C:0.06, G:0.02, T:0.71
Consensus pattern (26 bp):
ATTTTTATTTTTTATTTTGTATTAAC
Found at i:100922 original size:16 final size:16
Alignment explanation
Indices: 100903--100958 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
100893 TCTTCTTTTA
*
100903 ATTTTTTATTATCTTG
1 ATTTTTTATTATCTTT
100919 ATTTTTTA-TAT-TTT
1 ATTTTTTATTATCTTT
*
100933 ATTTCTT-TTATCTTAT
1 ATTTTTTATTATCTT-T
100949 ATTTTTTATT
1 ATTTTTTATT
100959 TTTTGTTTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
14 11 0.33
15 5 0.15
16 15 0.45
17 2 0.06
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (16 bp):
ATTTTTTATTATCTTT
Found at i:100955 original size:23 final size:22
Alignment explanation
Indices: 100903--100959 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
100893 TCTTCTTTTA
* *
100903 ATTTTTTATTATCTTGATTTTTT
1 ATTTTTTATT-TCTTGATCTTAT
* *
100926 ATATTTTATTTCTTTTATCTTAT
1 ATTTTTTATTTC-TTGATCTTAT
100949 ATTTTTTATTT
1 ATTTTTTATTT
100960 TTTGTTTGTA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
22 2 0.07
23 26 0.93
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.74
Consensus pattern (22 bp):
ATTTTTTATTTCTTGATCTTAT
Found at i:101025 original size:13 final size:12
Alignment explanation
Indices: 101001--101044 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 12
100991 TATTTTGTCA
*
101001 TTTTTCATTTTT
1 TTTTTTATTTTT
101013 TTGTTTTATTTTT
1 TT-TTTTATTTTT
101026 TTTTTTAATTTTT
1 TTTTTT-ATTTTT
101039 TCTTTT
1 T-TTTT
101045 GGCTTTTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 6 0.21
13 18 0.64
14 4 0.14
ACGTcount: A:0.09, C:0.05, G:0.02, T:0.84
Consensus pattern (12 bp):
TTTTTTATTTTT
Found at i:101537 original size:13 final size:15
Alignment explanation
Indices: 101519--101556 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
101509 TGATGTTGAC
101519 TTTTAT-TTT-ATTT
1 TTTTATCTTTGATTT
101532 TTTTATCTTTGATTT
1 TTTTATCTTTGATTT
*
101547 TTATATCTTT
1 TTTTATCTTT
101557 TTTCTATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 6 0.27
14 3 0.14
15 13 0.59
ACGTcount: A:0.16, C:0.05, G:0.03, T:0.76
Consensus pattern (15 bp):
TTTTATCTTTGATTT
Found at i:101646 original size:24 final size:25
Alignment explanation
Indices: 101599--101646 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
101589 CTTTGTATAT
*
101599 TTTAATACTAAAAGTTTTTTTTCTA
1 TTTAATACTAAAAGTTTTTATTCTA
* *
101624 TTTAATATTGAAA-TTTTTATTCT
1 TTTAATACTAAAAGTTTTTATTCT
101647 TTTGTCTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.58
Consensus pattern (25 bp):
TTTAATACTAAAAGTTTTTATTCTA
Found at i:101727 original size:27 final size:27
Alignment explanation
Indices: 101697--101760 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 27
101687 TTTTTACTTT
* *
101697 TTTTTCTTTTTTAGTATTTTATTTTAG
1 TTTTTCTTTTTTAATATTTTATCTTAG
* * *
101724 TTTTT-TTATATTAATATTTTCTCTTAT
1 TTTTTCTT-TTTTAATATTTTATCTTAG
101751 TTTTTCTTTT
1 TTTTTCTTTT
101761 ATATTTTTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
26 2 0.07
27 25 0.86
28 2 0.07
ACGTcount: A:0.16, C:0.06, G:0.03, T:0.75
Consensus pattern (27 bp):
TTTTTCTTTTTTAATATTTTATCTTAG
Found at i:102357 original size:19 final size:19
Alignment explanation
Indices: 102335--102373 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
102325 AGTTTTTTCA
*
102335 TTTTCTATTTTGTTTTTTG
1 TTTTCTATTTTATTTTTTG
* *
102354 TTTTTTTTTTTATTTTTTG
1 TTTTCTATTTTATTTTTTG
102373 T
1 T
102374 ACTTTATTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.05, C:0.03, G:0.08, T:0.85
Consensus pattern (19 bp):
TTTTCTATTTTATTTTTTG
Done.