Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168494.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_91, 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: 100055
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.42
File 3 of 3
Found at i:90617 original size:15 final size:16
Alignment explanation
Indices: 90599--90629 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
90589 TTAAATGGCC
90599 ATAATTAAT-ATTTTA
1 ATAATTAATAATTTTA
90614 ATAATTAATAATTTTA
1 ATAATTAATAATTTTA
90630 TTTAATTATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATAATTAATAATTTTA
Found at i:90952 original size:14 final size:15
Alignment explanation
Indices: 90935--90963 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
90925 TAATTATTAA
90935 TTTTTATTAT-ATAT
1 TTTTTATTATGATAT
90949 TTTTTATTATGATAT
1 TTTTTATTATGATAT
90964 ATGGTTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (15 bp):
TTTTTATTATGATAT
Found at i:91517 original size:15 final size:16
Alignment explanation
Indices: 91492--91522 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
91482 AATATATTTA
91492 TTAATATTTATTAATT
1 TTAATATTTATTAATT
91508 TTAA-ATTTATTAATT
1 TTAATATTTATTAATT
91523 AATTAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTAATATTTATTAATT
Found at i:91520 original size:9 final size:8
Alignment explanation
Indices: 91487--91539 Score: 54
Period size: 8 Copynumber: 6.4 Consensus size: 8
91477 GAATAAATAT
91487 ATTTATTAA
1 ATTTATT-A
91496 TATTTATTA
1 -ATTTATTA
*
91505 ATTT-TAA
1 ATTTATTA
91512 ATTTATTA
1 ATTTATTA
*
91520 ATTAATTA
1 ATTTATTA
91528 ATTTAATTA
1 ATTT-ATTA
91537 ATT
1 ATT
91540 ATATACAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
7 6 0.16
8 16 0.43
9 8 0.22
10 7 0.19
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (8 bp):
ATTTATTA
Found at i:91551 original size:19 final size:19
Alignment explanation
Indices: 91511--91566 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
91501 ATTAATTTTA
*
91511 AATTT-ATTAATTA-AT-T
1 AATTTAATTAATTATATAC
91527 AATTTAATTAATTATATAC
1 AATTTAATTAATTATATAC
* *
91546 AATTTAGTTATTTATATAC
1 AATTTAATTAATTATATAC
91565 AA
1 AA
91567 AATATAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
16 5 0.15
17 8 0.24
18 2 0.06
19 19 0.56
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.50
Consensus pattern (19 bp):
AATTTAATTAATTATATAC
Found at i:91809 original size:16 final size:16
Alignment explanation
Indices: 91798--91827 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
91788 TCATTAATAT
91798 AATA-TAAAATTAATG
1 AATATTAAAATTAATG
91813 AATATTAAAATTAAT
1 AATATTAAAATTAAT
91828 TATCGGTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (16 bp):
AATATTAAAATTAATG
Found at i:91858 original size:22 final size:20
Alignment explanation
Indices: 91833--91881 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 20
91823 TTAATTATCG
91833 GTAATAATAATATATCAATATT
1 GTAATAATAATA-AT-AATATT
*
91855 GTAATAATTATAATAATATT
1 GTAATAATAATAATAATATT
91875 -TAATAAT
1 GTAATAAT
91882 TTTAATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 7 0.27
20 6 0.23
21 2 0.08
22 11 0.42
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (20 bp):
GTAATAATAATAATAATATT
Found at i:91861 original size:19 final size:18
Alignment explanation
Indices: 91837--91916 Score: 58
Period size: 19 Copynumber: 4.2 Consensus size: 18
91827 TTATCGGTAA
91837 TAATAATAT-ATCAATATT
1 TAATAATATAAT-AATATT
91855 GTAATAATTATAATAATATT
1 -TAATAA-TATAATAATATT
* *
91875 TAATAATTTTAAT-TTAATT
1 TAATAA-TATAATAAT-ATT
91894 TAATTTAAT-TAATAATATT
1 TAA--TAATATAATAATATT
91913 TAAT
1 TAAT
91917 TTTCATTTAT
Statistics
Matches: 52, Mismatches: 3, Indels: 14
0.75 0.04 0.20
Matches are distributed among these distances:
17 1 0.02
18 1 0.02
19 34 0.65
20 11 0.21
21 5 0.10
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (18 bp):
TAATAATATAATAATATT
Found at i:91880 original size:10 final size:10
Alignment explanation
Indices: 91849--91916 Score: 54
Period size: 10 Copynumber: 7.0 Consensus size: 10
91839 ATAATATATC
91849 AATATTGTAAT
1 AATATT-TAAT
*
91860 AAT-TATAAT
1 AATATTTAAT
91869 AATATTTAAT
1 AATATTTAAT
91879 AAT-TTTAAT
1 AATATTTAAT
*
91888 -TTAATTTAAT
1 AAT-ATTTAAT
* *
91898 -TTAATTAAT
1 AATATTTAAT
91907 AATATTTAAT
1 AATATTTAAT
91917 TTTCATTTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
8 1 0.02
9 19 0.40
10 24 0.51
11 3 0.06
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (10 bp):
AATATTTAAT
Found at i:91891 original size:14 final size:14
Alignment explanation
Indices: 91872--91918 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 14
91862 TTATAATAAT
91872 ATTTAATAATTTTA
1 ATTTAATAATTTTA
91886 ATTTAATTTAA-TTTA
1 ATTTAA--TAATTTTA
91901 A-TTAATAATATTTA
1 ATTTAATAAT-TTTA
91915 ATTT
1 ATTT
91919 TCATTTATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
12 3 0.11
14 15 0.54
15 7 0.25
16 3 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTTAATAATTTTA
Found at i:91931 original size:24 final size:24
Alignment explanation
Indices: 91886--91931 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
91876 AATAATTTTA
*
91886 ATTTAATTTAATTTAATTAATAAT
1 ATTTAATTTAATTTAATAAATAAT
*
91910 ATTTAATTTTCATTT-ATAAATA
1 ATTTAA-TTTAATTTAATAAATA
91932 TAGTATAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (24 bp):
ATTTAATTTAATTTAATAAATAAT
Found at i:91998 original size:21 final size:21
Alignment explanation
Indices: 91959--91998 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
91949 ATTTATTAGT
* * *
91959 TAAATTAATTATAATAATATG
1 TAAATTAAATAAAAAAATATG
91980 TAAATTAAATAAAAAAATA
1 TAAATTAAATAAAAAAATA
91999 ATGTTCACAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (21 bp):
TAAATTAAATAAAAAAATATG
Found at i:92444 original size:9 final size:9
Alignment explanation
Indices: 92430--92458 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
92420 CTTGTTTGAT
92430 ATTATATTA
1 ATTATATTA
92439 ATTATATTA
1 ATTATATTA
92448 ATTAT-TTA
1 ATTATATTA
92456 ATT
1 ATT
92459 TTTAGTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 6 0.30
9 14 0.70
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
ATTATATTA
Found at i:92972 original size:182 final size:180
Alignment explanation
Indices: 92716--93064 Score: 445
Period size: 182 Copynumber: 1.9 Consensus size: 180
92706 TAAGTTTACC
* * **
92716 AAGTTCCAAATAGCCATGACTATTTGAATAATTATCTATTTTAAATCATTGTACCATTTTGTTTA
1 AAGTTCCAAATAGCCATGACTATTTGAATAATTATCTATTTCAAAACATTCAACCATTTTGTTTA
* * * * *
92781 GTAATAAAACAATTGTTTCAATTCATGT-TAGGTTATTTGAAATAAAATAACACCAATTTATTAA
66 GTAATAAAACAATTGGTTCAATTCAT-TCAAGCTTATTTCAAATAAAATAACA-AAATTTATTAA
92845 TATTCCAAAAATTAAAAAGTAAGAGAATTTAAAAAATAAATATGTTTATCGAAT
129 TATTCCAAAAATTAAAAAGTAA-A-AATTTAAAAAATAAATATGTTTATCGAAT
**
92899 AAGTT-CAAATAGTTATGACTATCTT-AATAATTATCTATTTCAAAACATTACAACC-TTTTGTT
1 AAGTTCCAAATAGCCATGACTAT-TTGAATAATTATCTATTTCAAAACATT-CAACCATTTTGTT
* * * *
92961 TTGTCATAAAACAATTGGTTCTATTCATTCAAGCTTATTTCAAATAAAATAATAAAATTTATTAA
64 TAGTAATAAAACAATTGGTTCAATTCATTCAAGCTTATTTCAAATAAAATAACAAAATTTATTAA
* * * *
93026 TGTTTCAAAAATTAATAAGTAAAAATTTTAAAAATAAAT
129 TATTCCAAAAATTAAAAAGTAAAAATTTAAAAAATAAAT
93065 TTATTTAAAA
Statistics
Matches: 144, Mismatches: 19, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
179 15 0.10
180 1 0.01
181 30 0.21
182 88 0.61
183 10 0.07
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.39
Consensus pattern (180 bp):
AAGTTCCAAATAGCCATGACTATTTGAATAATTATCTATTTCAAAACATTCAACCATTTTGTTTA
GTAATAAAACAATTGGTTCAATTCATTCAAGCTTATTTCAAATAAAATAACAAAATTTATTAATA
TTCCAAAAATTAAAAAGTAAAAATTTAAAAAATAAATATGTTTATCGAAT
Found at i:94208 original size:179 final size:177
Alignment explanation
Indices: 93622--94210 Score: 459
Period size: 180 Copynumber: 3.3 Consensus size: 177
93612 ACATTAATTT
* *
93622 TAAATAAATTTATTTTTAAAAT-TTTT-CTTATTAAATTTTGGAACATTAAT-AAT-ATATATTA
1 TAAATAAATTTATTTTTTAAATCTTTTACTTATT-AATTTT---ATATTAATAAATCA-ATATTA
* ** * * * * **
93683 TTTTATTTGAAATATGCTTGAATGAATGGAACCAATTGTTTTATGTCAAAAC-AAAAGGTTGTAA
61 TTTTAATCCAAATAAGCTTGAATGAATGGAAACAATTGTTTTATGACAAAACAAAAAAGTCATAA
* *
93747 TGTTTTGAAATAGATAATTATTAAGATAGTC--AACTATTTGAACTTGTTCGA
126 -GATTTGAAATAGATAATTATTCAGATAGTCATAACTATTTGAACTTGTTCGA
* * * * * * * *
93798 TAAACAGATGTATTTTTTTAATTCTCTTACTTTTTAATTTTTGAAATATTAATAAATTAGTATTA
1 TAAATAAATTTA-TTTTTTAAATCTTTTACTTATTAA-TTTT---ATATTAATAAATCAATATTA
* * * * * * * *
93863 TTTTATTTCAAATAAGC-TAACATGAATTGAAGCAATTGTTTTATTACAAAACAAAATATTACA-
61 TTTTAATCCAAATAAGCTTGA-ATGAATGGAAACAATTGTTTTATGACAAAACAAAAAAGT-CAT
* * * * *
93926 ATGATTTGAAGTAGATAATTATTCAAATAGTAATGACTATTTGAACTTGTT---
124 AAGATTTGAAATAGATAATTATTCAGATAGTCATAACTATTTGAACTTGTTCGA
** * * * *
93977 T-GGTAAACTTATTTCTTAAAAAACTTTTATTTATTAATTGTTGAAATATTAATAAATCAATATT
1 TAAATAAATTTATTT-TT-TAAATCTTTTACTTATTAATT-TT---ATATTAATAAATCAATATT
* * *
94041 ATTTTAATCCGAATAAGCTTGTATGGATGGAAACAATTGTTTTATGACAAAACAAAAAAGTCATA
60 ATTTTAATCCAAATAAGCTTGAATGAATGGAAACAATTGTTTTATGACAAAACAAAAAAGTCATA
* * * *
94106 AGAATTTGAAATAAATAATTATTCAGATAATCATAACAATTTGAATTTGTTCGA
125 AG-ATTTGAAATAGATAATTATTCAGATAGTCATAACTATTTGAACTTGTTCGA
94160 TAAATAAATTTATTTTTTAAATCTTTTACTTATTAATTATCT-TATTAATAA
1 TAAATAAATTTATTTTTTAAATCTTTTACTTATTAATT-T-TATATTAATAA
94211 CTATTTGTAA
Statistics
Matches: 321, Mismatches: 70, Indels: 41
0.74 0.16 0.09
Matches are distributed among these distances:
176 9 0.03
177 11 0.03
178 15 0.05
179 115 0.36
180 116 0.36
181 6 0.02
182 35 0.11
183 4 0.01
184 10 0.03
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (177 bp):
TAAATAAATTTATTTTTTAAATCTTTTACTTATTAATTTTATATTAATAAATCAATATTATTTTA
ATCCAAATAAGCTTGAATGAATGGAAACAATTGTTTTATGACAAAACAAAAAAGTCATAAGATTT
GAAATAGATAATTATTCAGATAGTCATAACTATTTGAACTTGTTCGA
Found at i:94452 original size:16 final size:16
Alignment explanation
Indices: 94431--94492 Score: 58
Period size: 16 Copynumber: 3.9 Consensus size: 16
94421 TCCTTTTGTA
94431 ATATTATAATTATAAT
1 ATATTATAATTATAAT
* *
94447 ATATTAGAATAAT-AT
1 ATATTATAATTATAAT
94462 AGTATTA-AATTAGTAAT
1 A-TATTATAATTA-TAAT
94479 AT-TTGATAATTATA
1 ATATT-ATAATTATA
94493 TTATCAAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
15 9 0.24
16 21 0.55
17 8 0.21
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (16 bp):
ATATTATAATTATAAT
Found at i:94656 original size:19 final size:19
Alignment explanation
Indices: 94629--94669 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
94619 ATAATTGTTG
* *
94629 TTTATAATAGTAAATATTA
1 TTTAAAATAGTAAATAATA
*
94648 TTTAAAATAGTTAATAATA
1 TTTAAAATAGTAAATAATA
94667 TTT
1 TTT
94670 TGAAAATTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (19 bp):
TTTAAAATAGTAAATAATA
Found at i:94782 original size:19 final size:19
Alignment explanation
Indices: 94758--94797 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
94748 ATAAATGAAG
*
94758 ATTAAA-TATTATTAATTAA
1 ATTAAATTAATATT-ATTAA
94777 ATTAAATTAATATTATTAA
1 ATTAAATTAATATTATTAA
94796 AT
1 AT
94798 ATTATTGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTAAATTAATATTATTAA
Found at i:94827 original size:19 final size:18
Alignment explanation
Indices: 94782--94849 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 18
94772 ATTAAATTAA
94782 ATTA-ATATTATTA-AAT
1 ATTATATATTATTATAAT
*
94798 ATTAT-TGTTATTAT-AT
1 ATTATATATTATTATAAT
*
94814 ATTATTATAATTATTGTAAT
1 ATTA-TAT-ATTATTATAAT
94834 ATTGATATATTATTAT
1 ATT-ATATATTATTAT
94850 TACCCATAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
16 17 0.41
17 1 0.02
18 1 0.02
19 13 0.32
20 8 0.20
21 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (18 bp):
ATTATATATTATTATAAT
Found at i:95176 original size:10 final size:10
Alignment explanation
Indices: 95147--95178 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
95137 AAATTAATTA
*
95147 ATTAATAAAA
1 ATTAATAAAT
95157 ATTAATAAAT
1 ATTAATAAAT
95167 ATTAATAAAT
1 ATTAATAAAT
95177 AT
1 AT
95179 ATTTATTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
ATTAATAAAT
Found at i:95782 original size:13 final size:13
Alignment explanation
Indices: 95755--95798 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
95745 AATTATTATT
95755 TAAATTATTAA-TA
1 TAAA-TATTAATTA
95768 TAAATATTAATTA
1 TAAATATTAATTA
* *
95781 TATATATTTATTA
1 TAAATATTAATTA
95794 TAAAT
1 TAAAT
95799 TAGAAATAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
12 6 0.22
13 21 0.78
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TAAATATTAATTA
Found at i:95943 original size:14 final size:15
Alignment explanation
Indices: 95924--95952 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
95914 TTACTTAAAT
95924 CAATTATT-TATTAA
1 CAATTATTATATTAA
95938 CAATTATTATATTAA
1 CAATTATTATATTAA
95953 AAAATAAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (15 bp):
CAATTATTATATTAA
Found at i:96349 original size:31 final size:30
Alignment explanation
Indices: 96289--96374 Score: 77
Period size: 31 Copynumber: 2.7 Consensus size: 30
96279 ATAAGTTTAT
*
96289 TAATATAATTAATTAATTATATTAAATGATACAA
1 TAATATAAATAATT-ATTA-ATT-AATGATA-AA
96323 TCAATATAAATAATTATTAATT-ATGATAAA
1 T-AATATAAATAATTATTAATTAATGATAAA
96353 TAAT-TAATATTAAATTATTAAT
1 TAATATAA-A-T-AATTATTAAT
96375 ATATTATTTG
Statistics
Matches: 47, Mismatches: 1, Indels: 11
0.80 0.02 0.19
Matches are distributed among these distances:
28 3 0.06
29 4 0.09
30 4 0.09
31 16 0.34
33 3 0.06
34 5 0.11
35 12 0.26
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (30 bp):
TAATATAAATAATTATTAATTAATGATAAA
Found at i:96372 original size:14 final size:15
Alignment explanation
Indices: 96334--96378 Score: 56
Period size: 14 Copynumber: 2.9 Consensus size: 15
96324 CAATATAAAT
96334 AATTATTAATTATGATA
1 AATTATTAA-TAT-ATA
*
96351 AATAATTAATAT-TA
1 AATTATTAATATATA
96365 AATTATTAATATAT
1 AATTATTAATATAT
96379 TATTTGAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 13 0.52
15 1 0.04
16 3 0.12
17 8 0.32
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (15 bp):
AATTATTAATATATA
Found at i:96601 original size:19 final size:19
Alignment explanation
Indices: 96579--96624 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
96569 ATTAAAAGGA
*
96579 TAATATTATAT-TACTTAAT
1 TAATATAATATATA-TTAAT
96598 TAATATAATATATATTAAT
1 TAATATAATATATATTAAT
*
96617 TAACATAA
1 TAATATAA
96625 CAATTAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 22 0.92
20 2 0.08
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (19 bp):
TAATATAATATATATTAAT
Found at i:96672 original size:24 final size:25
Alignment explanation
Indices: 96632--96682 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
96622 TAACAATTAA
*
96632 TAATTTAACTTATTATAAATTATAT
1 TAATATAACTTATTATAAATTATAT
* *
96657 TAATATAA-TTATTATATATTTTAT
1 TAATATAACTTATTATAAATTATAT
96681 TA
1 TA
96683 TTGTTTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (25 bp):
TAATATAACTTATTATAAATTATAT
Found at i:96854 original size:25 final size:24
Alignment explanation
Indices: 96826--96897 Score: 67
Period size: 25 Copynumber: 2.9 Consensus size: 24
96816 TATTATTAAT
*
96826 TAAATGAATAATATAATTATATATA
1 TAAAT-AATAATATAATTATATAGA
*
96851 TAAATAAATAATTATAATATATTTAGA
1 TAAAT-AATAA-TATAAT-TATATAGA
96878 TAAAT-ATCAATAT-ATTATAT
1 TAAATAAT-AATATAATTATAT
96898 TTAAGTATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
23 4 0.10
24 2 0.05
25 15 0.38
26 8 0.20
27 11 0.28
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (24 bp):
TAAATAATAATATAATTATATAGA
Found at i:96883 original size:23 final size:20
Alignment explanation
Indices: 96832--96871 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
96822 TAATTAAATG
96832 AATAATATAATTATATATATA
1 AATAA-ATAATTATATATATA
96853 AATAAATAATTATA-ATATA
1 AATAAATAATTATATATATA
96872 TTTAGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.26
20 9 0.47
21 5 0.26
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AATAAATAATTATATATATA
Found at i:97237 original size:21 final size:20
Alignment explanation
Indices: 97202--97240 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
97192 TTTAATGTTA
97202 TAATTAAATATATATTATAT
1 TAATTAAATATATATTATAT
*
97222 TAATTAAGTAATATATTAT
1 TAATTAAAT-ATATATTAT
97241 TACTATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TAATTAAATATATATTATAT
Found at i:97276 original size:25 final size:24
Alignment explanation
Indices: 97217--97292 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 24
97207 AAATATATAT
*
97217 TATATTAATTAAGTAATATATTATTAC
1 TATATT-ATTAA-TAATAT-TTAATAC
*
97244 TATTTTATTAATAATATTTAATAC
1 TATATTATTAATAATATTTAATAC
97268 TATAATTATATAA-AATATTTGAATA
1 TAT-ATTAT-TAATAATATTT-AATA
97293 AATTCATATA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
24 9 0.21
25 17 0.40
26 12 0.28
27 5 0.12
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (24 bp):
TATATTATTAATAATATTTAATAC
Found at i:97353 original size:20 final size:20
Alignment explanation
Indices: 97316--97354 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
97306 ACAAAATTTA
*
97316 TAATTTATTATTTGTAATTG
1 TAATTTATTATATGTAATTG
97336 TAATTTATATATAT-TAATT
1 TAATTTAT-TATATGTAATT
97355 AATTAATAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (20 bp):
TAATTTATTATATGTAATTG
Found at i:98074 original size:23 final size:23
Alignment explanation
Indices: 98016--98075 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 23
98006 ATATTTAATT
*
98016 AATAATTAAGTTATTATAAATATC
1 AATAATTAA-TAATTATAAATATC
*
98040 AATTATTAATAATTATAAATATC
1 AATAATTAATAATTATAAATATC
98063 AATAAATT-ATAAT
1 AAT-AATTAATAAT
98076 ATTTTATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 21 0.66
24 11 0.34
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (23 bp):
AATAATTAATAATTATAAATATC
Found at i:98515 original size:40 final size:40
Alignment explanation
Indices: 98471--98546 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
98461 AAATTAACTA
*
98471 TTTTTAATT-TATTTA-AATTAATAATTAATAATTATTTTGT
1 TTTTTAATTATA-TTACAATTAATAACT-ATAATTATTTTGT
*
98511 TTTTTAATTATATTACTATTAATAACTATAATTATT
1 TTTTTAATTATATTACAATTAATAACTATAATTATT
98547 ATATTAATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
40 21 0.66
41 11 0.34
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (40 bp):
TTTTTAATTATATTACAATTAATAACTATAATTATTTTGT
Found at i:98611 original size:34 final size:36
Alignment explanation
Indices: 98558--98625 Score: 97
Period size: 34 Copynumber: 1.9 Consensus size: 36
98548 TATTAATCAA
98558 AATAAGTTATTTAATATTAATATT-AAATTTATTATT
1 AATAAGTTATTTAATATTAAT-TTCAAATTTATTATT
*
98594 AATAA-TTA-TTAATATTAATTTCAATTTTATTA
1 AATAAGTTATTTAATATTAATTTCAAATTTATTA
98626 ACAAAAACAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 2 0.07
34 20 0.67
35 3 0.10
36 5 0.17
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (36 bp):
AATAAGTTATTTAATATTAATTTCAAATTTATTATT
Found at i:98820 original size:19 final size:19
Alignment explanation
Indices: 98757--98827 Score: 52
Period size: 19 Copynumber: 3.5 Consensus size: 19
98747 TTATAGTTAC
* *
98757 ATTAATTTAATTAATATTT
1 ATTAATTTAATTAAAATTA
* * *
98776 ATTAATTAAAGATAATGAATAGA
1 ATTAATTTAA-TTAA--AAT-TA
98799 ATTAATTTAATTAAAATTA
1 ATTAATTTAATTAAAATTA
*
98818 ATTAAATTAA
1 ATTAATTTAA
98828 ATGTATTGAA
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
19 19 0.49
20 6 0.15
22 5 0.13
23 9 0.23
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (19 bp):
ATTAATTTAATTAAAATTA
Found at i:98944 original size:21 final size:20
Alignment explanation
Indices: 98920--98981 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 20
98910 CATGTTAAAA
98920 TTATTATAATTTAATATATGT
1 TTATTATAATTTAATATAT-T
*
98941 TTATAATAA-TTAACTATA-T
1 TTATTATAATTTAA-TATATT
*
98960 TTATTAAAACTTATAATATATT
1 TTATTATAA-TT-TAATATATT
98982 AAATTATATA
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
19 8 0.24
20 4 0.12
21 17 0.52
22 4 0.12
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.52
Consensus pattern (20 bp):
TTATTATAATTTAATATATT
Found at i:99018 original size:16 final size:15
Alignment explanation
Indices: 98970--99019 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
98960 TTATTAAAAC
*
98970 TTATAATATATTAAA
1 TTATAATATATTTAA
98985 TTAT-ATAT-TCATTAA
1 TTATAATATAT--TTAA
99000 TTATAATATATTTATA
1 TTATAATATATTTA-A
99016 TTAT
1 TTAT
99020 TAATTTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
13 1 0.03
14 4 0.14
15 14 0.48
16 9 0.31
17 1 0.03
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (15 bp):
TTATAATATATTTAA
Found at i:99185 original size:32 final size:35
Alignment explanation
Indices: 99144--99218 Score: 95
Period size: 35 Copynumber: 2.2 Consensus size: 35
99134 GAATTTGTTT
99144 TATATATAAT-TAATAAATA-A-ATT-ATTTAATTA
1 TATATATAATATAATAAATATATATTCA-TTAATTA
*
99176 TATATATAATATATTAAATATATATTCATTAATTA
1 TATATATAATATAATAAATATATATTCATTAATTA
99211 TAATATAT
1 T-ATATAT
99219 TTATATTATT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
32 10 0.27
33 8 0.22
34 1 0.03
35 11 0.30
36 7 0.19
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (35 bp):
TATATATAATATAATAAATATATATTCATTAATTA
Found at i:99215 original size:20 final size:19
Alignment explanation
Indices: 99169--99218 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 19
99159 AATAAATTAT
99169 TTAATTAT-ATATATAATA
1 TTAATTATAATATATAATA
*
99187 -T-ATTA-AATATATATTCA
1 TTAATTATAATATATAAT-A
99204 TTAATTATAATATAT
1 TTAATTATAATATAT
99219 TTATATTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
16 12 0.46
17 2 0.08
18 1 0.04
19 4 0.15
20 7 0.27
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
TTAATTATAATATATAATA
Found at i:99226 original size:20 final size:20
Alignment explanation
Indices: 99142--99226 Score: 51
Period size: 20 Copynumber: 4.5 Consensus size: 20
99132 ATGAATTTGT
99142 TTTATATATAATTAATAA-ATAA
1 TTTATAT-TAATT-ATAATAT-A
*
99164 ATTAT-TTAATTAT-ATATA
1 TTTATATTAATTATAATATA
*
99182 -TAATA-T-ATTA-AATATA
1 TTTATATTAATTATAATATA
*
99198 TATT-CATTAATTATAATATA
1 T-TTATATTAATTATAATATA
99218 TTTATATTA
1 TTTATATTA
99227 TTAATTTTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 20
0.66 0.07 0.27
Matches are distributed among these distances:
16 9 0.18
17 5 0.10
18 4 0.08
19 10 0.20
20 16 0.33
21 1 0.02
22 4 0.08
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTATATTAATTATAATATA
Found at i:99238 original size:27 final size:29
Alignment explanation
Indices: 99161--99232 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
99151 AATTAATAAA
99161 TAAAT-TAT-TTAATTATATATATAATATAT
1 TAAATATATATTAATTA-AT-TATAATATAT
*
99190 TAAATATATATTCATTAATTATAATATAT
1 TAAATATATATTAATTAATTATAATATAT
*
99219 T-TATAT-TATTAATT
1 TAAATATATATTAATT
99233 TTTTATTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
27 7 0.18
28 4 0.11
29 16 0.42
30 5 0.13
31 6 0.16
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (29 bp):
TAAATATATATTAATTAATTATAATATAT
Found at i:99342 original size:207 final size:209
Alignment explanation
Indices: 98971--99384 Score: 805
Period size: 207 Copynumber: 2.0 Consensus size: 209
98961 TATTAAAACT
98971 TATAATATATTAAATTATATATTCATTAATTATAATATATTTATATTATTAATTTTTTTATTAAA
1 TATAATATATTAAATTATATATTCATTAATTATAATATATTTATATTATTAATTTTTTTATTAAA
99036 TACTAATTATTAATAAATAGTATATATTTAGTATAGAATATAATTATTATTTATAAGTAAAATAT
66 TACTAATTATTAATAAATAGTATATATTTAGTATAGAATATAATTATTATTTATAAGTAAAATAT
99101 TTACTTTAATTTATAATAGTTATAACAATTAATGAATTTGTTTTATATATAATTAATAAATAAAT
131 TTACTTTAATTTATAATAGTTATAACAATTAATGAATTTGTTTTATATATAATTAATAAATAAAT
*
99166 TATTTAATTATATA
196 TATTTAACTATATA
99180 TATAATATATTAAA-TATATATTCATTAATTATAATATATTTATATTATTAA-TTTTTTATTAAA
1 TATAATATATTAAATTATATATTCATTAATTATAATATATTTATATTATTAATTTTTTTATTAAA
99243 TACTAATTATTAATAAATAGTATATATTTAGTATAGAATATAATTATTATTTATAAGTAAAATAT
66 TACTAATTATTAATAAATAGTATATATTTAGTATAGAATATAATTATTATTTATAAGTAAAATAT
99308 TTACTTTAATTTATAATAGTTATAACAATTAATGAATTTGTTTTATATATAATTAATAAATAAAT
131 TTACTTTAATTTATAATAGTTATAACAATTAATGAATTTGTTTTATATATAATTAATAAATAAAT
99373 TATTTAACTATA
196 TATTTAACTATA
99385 ATTATCTATT
Statistics
Matches: 204, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
207 153 0.75
208 37 0.18
209 14 0.07
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.49
Consensus pattern (209 bp):
TATAATATATTAAATTATATATTCATTAATTATAATATATTTATATTATTAATTTTTTTATTAAA
TACTAATTATTAATAAATAGTATATATTTAGTATAGAATATAATTATTATTTATAAGTAAAATAT
TTACTTTAATTTATAATAGTTATAACAATTAATGAATTTGTTTTATATATAATTAATAAATAAAT
TATTTAACTATATA
Found at i:99796 original size:14 final size:14
Alignment explanation
Indices: 99772--99816 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
99762 ATACTACTAC
*
99772 TAATCATATATTATT
1 TAAT-ATATATTAAT
*
99787 TAATATATATAAAT
1 TAATATATATTAAT
*
99801 AAATATATATTAAT
1 TAATATATATTAAT
99815 TA
1 TA
99817 CACAATATCT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 21 0.84
15 4 0.16
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (14 bp):
TAATATATATTAAT
Done.