Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168266.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_496, 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: 24935
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.35
Found at i:533 original size:9 final size:9
Alignment explanation
Indices: 509--551 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
499 TATTTTGATA
509 AAATAAAA-
1 AAATAAAAT
*
517 AAAGTAAAAC
1 AAA-TAAAAT
527 AAAT-AAAT
1 AAATAAAAT
535 AAATAAAAT
1 AAATAAAAT
544 AAATAAAA
1 AAATAAAA
552 AATACCAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
8 10 0.32
9 18 0.58
10 3 0.10
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.16
Consensus pattern (9 bp):
AAATAAAAT
Found at i:543 original size:13 final size:13
Alignment explanation
Indices: 509--550 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
499 TATTTTGATA
509 AAATAAAA-AAAGT
1 AAATAAAATAAA-T
522 AAA-ACAAATAAAT
1 AAATA-AAATAAAT
535 AAATAAAATAAAT
1 AAATAAAATAAAT
548 AAA
1 AAA
551 AAATACCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 1 0.04
13 21 0.81
14 4 0.15
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (13 bp):
AAATAAAATAAAT
Found at i:1020 original size:21 final size:22
Alignment explanation
Indices: 994--1034 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
984 AAGTTTTCCA
*
994 GAAAAAGAAC-TCCAAAAATTT
1 GAAAAAAAACTTCCAAAAATTT
*
1015 GAAAAAAAACTTCTAAAAAT
1 GAAAAAAAACTTCCAAAAAT
1035 CCTATACTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.61, C:0.12, G:0.07, T:0.20
Consensus pattern (22 bp):
GAAAAAAAACTTCCAAAAATTT
Found at i:1193 original size:13 final size:13
Alignment explanation
Indices: 1175--1200 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1165 CCTTCTGGGG
1175 TTTGAATTCAATC
1 TTTGAATTCAATC
1188 TTTGAATTCAATC
1 TTTGAATTCAATC
1201 CAAACTCTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (13 bp):
TTTGAATTCAATC
Found at i:1389 original size:23 final size:22
Alignment explanation
Indices: 1361--1459 Score: 87
Period size: 23 Copynumber: 4.5 Consensus size: 22
1351 AATAATTATA
1361 AAAAATAAAAGTAGATAAATAAT
1 AAAAATAAAA-TAGATAAATAAT
* *
1384 AAAAATATTAATAGATAAAAAAT
1 AAAAATA-AAATAGATAAATAAT
* *
1407 AAAAATAAAA-ATATATATTAAT
1 AAAAATAAAATAGATA-AATAAT
* *
1429 AAATAGACAAATA-ATAAA-AAT
1 AAAAATA-AAATAGATAAATAAT
1450 AAAAATAAAA
1 AAAAATAAAA
1460 ATAAAAGCCA
Statistics
Matches: 61, Mismatches: 11, Indels: 11
0.73 0.13 0.13
Matches are distributed among these distances:
20 3 0.05
21 12 0.20
22 12 0.20
23 31 0.51
24 3 0.05
ACGTcount: A:0.72, C:0.01, G:0.04, T:0.23
Consensus pattern (22 bp):
AAAAATAAAATAGATAAATAAT
Found at i:1390 original size:47 final size:52
Alignment explanation
Indices: 1284--1390 Score: 122
Period size: 47 Copynumber: 2.2 Consensus size: 52
1274 AATTAATCAA
*
1284 AATAAAAA-AGATAAATATATTAATAGATAACAAAAAATAATTAGATAAATT
1 AATAAAAATAGATAAATATATTAATAGATAACAAAAAATAAGTAGATAAATT
* *
1335 AA-AGAAATAGATAAATA-A-TAAT-TATAA-AAAATAA-AAGTAGATAAA-T
1 AATAAAAATAGATAAATATATTAATAGATAACAAAA-AATAAGTAGATAAATT
1381 AATAAAAATA
1 AATAAAAATA
1391 TTAATAGATA
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
46 3 0.06
47 20 0.41
48 6 0.12
49 4 0.08
50 5 0.10
51 11 0.22
ACGTcount: A:0.67, C:0.01, G:0.07, T:0.25
Consensus pattern (52 bp):
AATAAAAATAGATAAATATATTAATAGATAACAAAAAATAAGTAGATAAATT
Found at i:1416 original size:5 final size:6
Alignment explanation
Indices: 1401--1465 Score: 60
Period size: 6 Copynumber: 10.7 Consensus size: 6
1391 TTAATAGATA
* * * * *
1401 AAAAAT AAAAAT AAAAAT ATATATT AATAAAT AGACA- AATAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT A-AAAAT AA-AAAT AAAAAT AAAAAT AAAAAT
1450 AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAA
1466 GCCAATTGAG
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
5 2 0.04
6 37 0.80
7 7 0.15
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.22
Consensus pattern (6 bp):
AAAAAT
Found at i:1430 original size:29 final size:31
Alignment explanation
Indices: 1375--1450 Score: 95
Period size: 29 Copynumber: 2.5 Consensus size: 31
1365 ATAAAAGTAG
1375 ATAAATAATAAAAATATTAATAGATAAA-AA
1 ATAAATAATAAAAATATTAATAGATAAATAA
* *
1405 ATAAA-AATAAAAATATATATTA-ATAAATAG
1 ATAAATAATAAAAATAT-TAATAGATAAATAA
*
1435 ACAAATAATAAAAATA
1 ATAAATAATAAAAATA
1451 AAAATAAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
29 16 0.40
30 14 0.35
31 10 0.25
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.26
Consensus pattern (31 bp):
ATAAATAATAAAAATATTAATAGATAAATAA
Found at i:2366 original size:18 final size:19
Alignment explanation
Indices: 2345--2381 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
2335 ACCATTTCTT
2345 TAAAATAAT-AAAAATGAA
1 TAAAATAATAAAAAATGAA
2363 TAAAATAATAAAAAATGAA
1 TAAAATAATAAAAAATGAA
2382 AGAAAGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (19 bp):
TAAAATAATAAAAAATGAA
Found at i:6861 original size:2 final size:2
Alignment explanation
Indices: 6848--6883 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
6838 TTTATGGATG
*
6848 AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AGT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A
6884 ACTGTCATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:7156 original size:157 final size:161
Alignment explanation
Indices: 6862--7181 Score: 470
Period size: 157 Copynumber: 2.0 Consensus size: 161
6852 ATAAATATAT
*
6862 ATATATATATATATATAGTATAACTGTCATAAGAAAGGAGTTCAACTGTATATGTATATATATAT
1 ATATATAAATATATATAGTATAACTGTCAT---AAAGGAGTTCAACTGTATA-GTATATATATAT
** * * * * *
6927 ATATATATAGGTAAAATGGCGTTTTCTAAGTTTGAAATTTTACGATTTAAATGTGGCTTTCAGGC
62 ATATATATAGGTAAAATGGCAATTCCTAAGTTGGAAATTTTAAGATTTAAATATGGCTTTCAAGC
6992 TCAAGGACTTTGTCTTTTAAGCTTAAATATGGATG
127 TCAAGGACTTTGTCTTTTAAGCTTAAATATGGATG
*
7027 ATATATAAATATATA-ACGTATAACTGTCAT-AAGGAGTTCAA-T-TATA-TATGTATATATATA
1 ATATATAAATATATATA-GTATAACTGTCATAAAGGAGTTCAACTGTATAGTATATATATATATA
*
7087 TATATAGGTAAAATGGCAATTCCTAAGTTGGAAATTTTAAGATTTAAATATGGCTTTCAAGTTCA
65 TATATAGGTAAAATGGCAATTCCTAAGTTGGAAATTTTAAGATTTAAATATGGCTTTCAAGCTCA
7152 AGGACTTTGTCTTTTAAGCTTAAATATGGA
130 AGGACTTTGTCTTTTAAGCTTAAATATGGA
7182 GAGGTTGAAC
Statistics
Matches: 144, Mismatches: 10, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
157 100 0.69
159 4 0.03
160 1 0.01
161 11 0.08
164 1 0.01
165 27 0.19
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (161 bp):
ATATATAAATATATATAGTATAACTGTCATAAAGGAGTTCAACTGTATAGTATATATATATATAT
ATATAGGTAAAATGGCAATTCCTAAGTTGGAAATTTTAAGATTTAAATATGGCTTTCAAGCTCAA
GGACTTTGTCTTTTAAGCTTAAATATGGATG
Found at i:8822 original size:21 final size:20
Alignment explanation
Indices: 8797--8862 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 20
8787 ATATATTTTC
8797 TTTTTATTCATTTTTACTTAT
1 TTTTTATTCATTTTTA-TTAT
8818 TTTTTATGT-ATTTTTA-TAT
1 TTTTTAT-TCATTTTTATTAT
*
8837 TTTTTATTCCTATTTTTATGAT
1 TTTTTATT-C-ATTTTTATTAT
8859 TTTT
1 TTTT
8863 ATTGTATTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
18 1 0.03
19 10 0.26
21 21 0.54
22 7 0.18
ACGTcount: A:0.18, C:0.06, G:0.03, T:0.73
Consensus pattern (20 bp):
TTTTTATTCATTTTTATTAT
Found at i:9102 original size:17 final size:17
Alignment explanation
Indices: 9080--9117 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
9070 GAAAATGTTG
9080 AAATATCAAAATTTCCT
1 AAATATCAAAATTTCCT
* *
9097 AAATATCAACATTTTCT
1 AAATATCAAAATTTCCT
9114 AAAT
1 AAAT
9118 TCTTTAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (17 bp):
AAATATCAAAATTTCCT
Found at i:10432 original size:15 final size:15
Alignment explanation
Indices: 10412--10442 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
10402 TTTTTATTTC
*
10412 AATAAAATCAATAAA
1 AATAAAAACAATAAA
10427 AATAAAAACAATAAA
1 AATAAAAACAATAAA
10442 A
1 A
10443 TTACATCGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.16
Consensus pattern (15 bp):
AATAAAAACAATAAA
Found at i:13403 original size:6 final size:6
Alignment explanation
Indices: 13392--13427 Score: 54
Period size: 6 Copynumber: 5.7 Consensus size: 6
13382 ATAAGAAAAA
13392 CATTTG CATTTG CATAATTG CATTTG CATTTG CATT
1 CATTTG CATTTG CAT--TTG CATTTG CATTTG CATT
13428 AGAGAAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 22 0.79
8 6 0.21
ACGTcount: A:0.22, C:0.17, G:0.14, T:0.47
Consensus pattern (6 bp):
CATTTG
Found at i:14257 original size:20 final size:21
Alignment explanation
Indices: 14183--14262 Score: 63
Period size: 22 Copynumber: 3.8 Consensus size: 21
14173 AAATTTTGAA
*
14183 CCTTTGATTTGAATCTCGAAG
1 CCTTTGATGTGAATCTCGAAG
* ** *
14204 ACTTTCGATGCAAATCTCGAAAT
1 CCTTT-GATGTGAATCTCG-AAG
** *
14227 TTTTTGGTGTGAATCTCGAA-
1 CCTTTGATGTGAATCTCGAAG
14247 CCTTTGATGTGAATCT
1 CCTTTGATGTGAATCT
14263 AGATAACTTT
Statistics
Matches: 44, Mismatches: 13, Indels: 5
0.71 0.21 0.08
Matches are distributed among these distances:
20 13 0.30
21 6 0.14
22 20 0.45
23 5 0.11
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.39
Consensus pattern (21 bp):
CCTTTGATGTGAATCTCGAAG
Found at i:14284 original size:64 final size:65
Alignment explanation
Indices: 14180--14312 Score: 144
Period size: 64 Copynumber: 2.1 Consensus size: 65
14170 TGCAAATTTT
* * ** * *
14180 GAACCTTTGATTTGAATCTCGAAGACTTTCGATGCAAATC-TCGAAATTTTTTGGTGTGAATCTC
1 GAACCTTTGATGTGAATCTAGAAGACTTTCGATGCAAATCTTAAAAACTTTTTAGTGTGAATCTC
** **
14244 GAACCTTTGATGTGAATCTAGATA-ACTTTTTATGTGAATCTTAAAAACTTTTTAGTGTGAATCT
1 GAACCTTTGATGTGAATCTAGA-AGACTTTCGATGCAAATCTTAAAAACTTTTTAGTGTGAATCT
*
14308 T
65 C
14309 GAAC
1 GAAC
14313 TTCAGTGAGA
Statistics
Matches: 56, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
64 32 0.57
65 24 0.43
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.39
Consensus pattern (65 bp):
GAACCTTTGATGTGAATCTAGAAGACTTTCGATGCAAATCTTAAAAACTTTTTAGTGTGAATCTC
Found at i:14302 original size:23 final size:23
Alignment explanation
Indices: 14253--14308 Score: 80
Period size: 22 Copynumber: 2.5 Consensus size: 23
14243 CGAACCTTTG
*
14253 ATGTGAATC-TAGATAACTTTTT
1 ATGTGAATCTTAGAAAACTTTTT
14275 ATGTGAATCTTA-AAAACTTTTT
1 ATGTGAATCTTAGAAAACTTTTT
14297 AGTGTGAATCTT
1 A-TGTGAATCTT
14309 GAACTTCAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
22 19 0.61
23 12 0.39
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.45
Consensus pattern (23 bp):
ATGTGAATCTTAGAAAACTTTTT
Found at i:14407 original size:23 final size:23
Alignment explanation
Indices: 14340--14410 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
14330 ACCCTTACTA
*
14340 TGAATTTCAAGGACCTTTTGGTG
1 TGAATTTCAAGGACCTTTTAGTG
* ** * *
14363 AGAATCCCAA--ACC-CTTATTG
1 TGAATTTCAAGGACCTTTTAGTG
14383 TGAATTTCAAGGACCTTTTAGTG
1 TGAATTTCAAGGACCTTTTAGTG
14406 TGAAT
1 TGAAT
14411 CCCTAACCTT
Statistics
Matches: 34, Mismatches: 11, Indels: 6
0.67 0.22 0.12
Matches are distributed among these distances:
20 11 0.32
21 3 0.09
22 3 0.09
23 17 0.50
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (23 bp):
TGAATTTCAAGGACCTTTTAGTG
Found at i:14428 original size:43 final size:43
Alignment explanation
Indices: 14316--14430 Score: 167
Period size: 43 Copynumber: 2.7 Consensus size: 43
14306 CTTGAACTTC
* *
14316 AGTGAGAATCCCAAACCCTTACTATGAATTTCAAGGACCTTTT
1 AGTGAGAATCCCAAACCCTTAATGTGAATTTCAAGGACCTTTT
* *
14359 GGTGAGAATCCCAAACCCTTATTGTGAATTTCAAGGACCTTTT
1 AGTGAGAATCCCAAACCCTTAATGTGAATTTCAAGGACCTTTT
* * *
14402 AGTGTGAATCCCTAACCTTTAATGTGAAT
1 AGTGAGAATCCCAAACCCTTAATGTGAAT
14431 CTCCAGAACT
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 64 1.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (43 bp):
AGTGAGAATCCCAAACCCTTAATGTGAATTTCAAGGACCTTTT
Found at i:14562 original size:20 final size:21
Alignment explanation
Indices: 14523--14564 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
14513 AATTTTGAGG
14523 ACTTTTCGATATGAAGATCAA
1 ACTTTTCGATATGAAGATCAA
* *
14544 ACTTTT-GATGTGAATATCAA
1 ACTTTTCGATATGAAGATCAA
14564 A
1 A
14565 GACCTTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (21 bp):
ACTTTTCGATATGAAGATCAA
Found at i:14827 original size:43 final size:43
Alignment explanation
Indices: 14780--14862 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
14770 GAATCTTAAA
*
14780 CTTTTAATGTAAATCTCGAACCCTCGATGTGAATCTCAAAAAC
1 CTTTTAATGTAAATCTCGAACCCTCGATGAGAATCTCAAAAAC
* * * **
14823 CTTTTAGTGTGAATCTCGAGCTTTCGATGAGAATCTCAAA
1 CTTTTAATGTAAATCTCGAACCCTCGATGAGAATCTCAAA
14863 GATGAAAACT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (43 bp):
CTTTTAATGTAAATCTCGAACCCTCGATGAGAATCTCAAAAAC
Found at i:15001 original size:31 final size:31
Alignment explanation
Indices: 14951--15038 Score: 108
Period size: 31 Copynumber: 2.9 Consensus size: 31
14941 TAAGTTTTTA
*
14951 TTTTTT-AGTGTCATAGCCTCTAGTTAAGAG
1 TTTTTTAAGTTTCATAGCCTCTAGTTAAGAG
* * *
14981 TTTTTTAAGTTTCATTGCCTCTGGTTAGGAG
1 TTTTTTAAGTTTCATAGCCTCTAGTTAAGAG
* *
15012 TTTTTTAAGTTTAAGAG-CTCTAGTTAA
1 TTTTTTAAGTTTCATAGCCTCTAGTTAA
15039 AAGACTATTT
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
30 14 0.29
31 34 0.71
ACGTcount: A:0.23, C:0.11, G:0.19, T:0.47
Consensus pattern (31 bp):
TTTTTTAAGTTTCATAGCCTCTAGTTAAGAG
Found at i:15335 original size:67 final size:68
Alignment explanation
Indices: 15223--15351 Score: 165
Period size: 67 Copynumber: 1.9 Consensus size: 68
15213 TTTAATATCA
* * *
15223 TAGCTTCTGGTTAAAGGAGTTTTTAAAAGTATTATTACCTTTAGTTATAGGAGTTTTTTAAAATA
1 TAGCTTCTGGTTAAAGGAGTTTTTAAAAGTATTATTACCTCTAGTTAGAGGAGCTTTTTAAAATA
15288 CTG
66 CTG
* **
15291 TAGCTTCTGGTTTGAA-GA-TTTTTTCAAGTATTA-TAGCCTCTAGTTAGAGGAGCTTTTTAAA
1 TAGCTTCTGG-TTAAAGGAGTTTTTAAAAGTATTATTA-CCTCTAGTTAGAGGAGCTTTTTAAA
15352 GTTTAATTAC
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
66 2 0.04
67 35 0.66
68 12 0.23
69 4 0.08
ACGTcount: A:0.29, C:0.09, G:0.19, T:0.43
Consensus pattern (68 bp):
TAGCTTCTGGTTAAAGGAGTTTTTAAAAGTATTATTACCTCTAGTTAGAGGAGCTTTTTAAAATA
CTG
Found at i:16219 original size:20 final size:19
Alignment explanation
Indices: 16194--16231 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
16184 TGGTAGCTCT
16194 ACAAAAAAAAAAGCCTATAA
1 ACAAAAAAAAAA-CCTATAA
16214 ACAAAAAAAAAACCTATA
1 ACAAAAAAAAAACCTATA
16232 GACCCGAGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.71, C:0.16, G:0.03, T:0.11
Consensus pattern (19 bp):
ACAAAAAAAAAACCTATAA
Found at i:17112 original size:21 final size:23
Alignment explanation
Indices: 17066--17116 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
17056 TTTTTTGTTG
*
17066 TATTTTT-TATATTCTTTATTAC
1 TATTTTTGTATATTCTCTATTAC
*
17088 TATTTTTGTA-ATTCTCTATT-T
1 TATTTTTGTATATTCTCTATTAC
17109 TATTTTTG
1 TATTTTTG
17117 GGTGAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 8 0.31
22 16 0.62
23 2 0.08
ACGTcount: A:0.20, C:0.08, G:0.04, T:0.69
Consensus pattern (23 bp):
TATTTTTGTATATTCTCTATTAC
Found at i:17229 original size:21 final size:22
Alignment explanation
Indices: 17190--17231 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
17180 ACTTAAATTT
*
17190 TATTTAAGATAAATGTTGAAAA
1 TATTTAAGATAAATATTGAAAA
17212 TATTTAAGA-AAATATTGAAA
1 TATTTAAGATAAATATTGAAA
17232 TATCAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.36
Consensus pattern (22 bp):
TATTTAAGATAAATATTGAAAA
Found at i:17500 original size:14 final size:14
Alignment explanation
Indices: 17477--17520 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
17467 AAATATCAAT
* *
17477 TTTTTTAGAATAAA
1 TTTTTAAGAAAAAA
17491 TTTTTAAGAAAAAA
1 TTTTTAAGAAAAAA
*
17505 TATTTAAGAAAAAA
1 TTTTTAAGAAAAAA
17519 TT
1 TT
17521 GAAATATCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (14 bp):
TTTTTAAGAAAAAA
Found at i:22022 original size:27 final size:27
Alignment explanation
Indices: 21984--22035 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
21974 TTATGAATTT
21984 TCTTTTTCATTGATATGATAAAATGAC
1 TCTTTTTCATTGATATGATAAAATGAC
*
22011 TCTTTTTCATTGATGTGATAAAATG
1 TCTTTTTCATTGATATGATAAAATG
22036 GATCATCATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.46
Consensus pattern (27 bp):
TCTTTTTCATTGATATGATAAAATGAC
Found at i:24075 original size:2 final size:2
Alignment explanation
Indices: 24068--24092 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
24058 CCTCTTATTA
24068 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
24093 GTAGATTGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.