Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168190.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_427, 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: 27173
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Found at i:1333 original size:22 final size:23
Alignment explanation
Indices: 1305--1349 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
1295 AAGGTTTTTG
*
1305 CTTTTCACCTAAAT-GAAAGCAT
1 CTTTTCACCTAAATAAAAAGCAT
1327 CTTTTCACCTAAATAAAAAGCAT
1 CTTTTCACCTAAATAAAAAGCAT
1350 TGATCTTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.40, C:0.22, G:0.07, T:0.31
Consensus pattern (23 bp):
CTTTTCACCTAAATAAAAAGCAT
Found at i:4430 original size:14 final size:14
Alignment explanation
Indices: 4407--4440 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
4397 ATGTCATAAT
*
4407 AGATATAATATTTA
1 AGATAAAATATTTA
*
4421 TGATAAAATATTTA
1 AGATAAAATATTTA
4435 AGATAA
1 AGATAA
4441 TTTTAACTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (14 bp):
AGATAAAATATTTA
Found at i:8581 original size:238 final size:236
Alignment explanation
Indices: 8068--8589 Score: 572
Period size: 238 Copynumber: 2.2 Consensus size: 236
8058 AAAACCAATG
* ** *
8068 TTTTTAACATAAAAACATTGTCTTTGTAAACAAACACTACATTTTTCAAACAAAAATCATTGTCA
1 TTTTTAACAT-AAAACATTGTCTTTGTAAACAAACATTGTATTTTTCAAACAAAAA-CATTATCA
* *
8133 TTATTAATTGACATGAAATTGACAAAGTTCAAACATAATTGACATAGACTATGTTTTAAACATAA
64 TTATTAATTGACATGAAATTGACAAAGTTCAAACATAACTCACATAGACTATGTTTTAAACATAA
* * * * * * *
8198 AAACGTCATGTTTGTAGACAAATATTATGTTTTTCAAACAAAAAATGTCATTACTATTAGATGAC
129 AAACGCCATGCTTCTAGACAAACAATATGTTTTTCAAACAAAAAATATCATCACTATTAGATGAC
** *
8263 AGAAATTAACAAAGTTCAAACATTAAACTAATATAGACTGCAT
194 AGAAATTAACAAAAATCAAACATTAAACTAACATAGACTGCAT
* *
8306 TTTTT-ACATAAAAAATGTTGTCTTTGTAGACAAACATTGTATTTTTCAAACAAAAA-ATGTCAT
1 TTTTTAACATAAAACA--TTGTCTTTGTAAACAAACATTGTATTTTTCAAACAAAAACAT-T-AT
* * * * *
8369 CATTGTTAGTTGATATGAAATTGATAAAGTTCAAACATTAAACTCACATAGA-T-TGCATTTTTA
62 CATTATTAATTGACATGAAATTGACAAAGTTCAAACA-T-AACTCACATAGACTATG--TTTTAA
* * * *
8432 ACATAAAAATGCCAT-CTTCTAGACAAACAATATGTTTTTCAAATAAAAAATATCATCATTGTTA
123 ACATAAAAACGCCATGCTTCTAGACAAACAATATGTTTTTCAAACAAAAAATATCATCACTATTA
* * * * *
8496 GTTGACATGAAATTGACAAAAATCAAACATT-AATTGACATAGATTGCAT
188 GATGACA-GAAATTAACAAAAATCAAACATTAAACTAACATAGACTGCAT
** *
8545 TTTTTAACATAGAAACATTGTCTTT-TATTCAAACATTGTGTTTTT
1 TTTTTAACATA-AAACATTGTCTTTGTAAACAAACATTGTATTTTT
8590 TAACCCAAAA
Statistics
Matches: 237, Mismatches: 36, Indels: 22
0.80 0.12 0.07
Matches are distributed among these distances:
236 7 0.03
237 5 0.02
238 93 0.39
239 75 0.32
240 53 0.22
241 4 0.02
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.36
Consensus pattern (236 bp):
TTTTTAACATAAAACATTGTCTTTGTAAACAAACATTGTATTTTTCAAACAAAAACATTATCATT
ATTAATTGACATGAAATTGACAAAGTTCAAACATAACTCACATAGACTATGTTTTAAACATAAAA
ACGCCATGCTTCTAGACAAACAATATGTTTTTCAAACAAAAAATATCATCACTATTAGATGACAG
AAATTAACAAAAATCAAACATTAAACTAACATAGACTGCAT
Found at i:8600 original size:119 final size:119
Alignment explanation
Indices: 8068--8589 Score: 483
Period size: 119 Copynumber: 4.4 Consensus size: 119
8058 AAAACCAATG
* * ** **
8068 TTTTTAACATAAAAACATTGTCTTTGTAAACAAACACTACATTTTTCAAAC-AAAAATCATTGTC
1 TTTTTAACAT-AAAACATTGTCTTT-TAGACAAACATTATGTTTTTCAAACAAAAAAT-ATCATC
* *
8132 ATTATTAATTGACATGAAATTGACAAAGTTCAAACA-T-AATTGACATAGACT--AT
63 ATTATTAGTTGACATGAAATTGACAAAGTTCAAACATTAAACTGACATAGACTGCAT
* * * * *
8185 GTTTTAAACATAAAAACGTCATGT-TTGTAGACAAATATTATGTTTTTCAAACAAAAAATGTCAT
1 -TTTTTAACAT-AAAACAT--TGTCTTTTAGACAAACATTATGTTTTTCAAACAAAAAATATCAT
* * * * * *
8249 TACTATTAGATGACA-GAAATTAACAAAGTTCAAACATTAAACTAATATAGACTGCAT
62 CATTATTAGTTGACATGAAATTGACAAAGTTCAAACATTAAACTGACATAGACTGCAT
* * * *
8306 TTTTT-ACATAAAAAATGTTGTCTTTGTAGACAAACATTGTATTTTTCAAACAAAAAATGTCATC
1 TTTTTAACATAAAACA--TTGTCTTT-TAGACAAACATTATGTTTTTCAAACAAAAAATATCATC
* * * * *
8370 ATTGTTAGTTGATATGAAATTGATAAAGTTCAAACATTAAACTCACATAGATTGCA-
63 ATTATTAGTTGACATGAAATTGACAAAGTTCAAACATTAAACTGACATAGACTGCAT
* * *
8426 TTTTTAACATAAAA-A-TGCCATCTTCTAGACAAACAATATGTTTTTCAAATAAAAAATATCATC
1 TTTTTAACATAAAACATTG---TCTTTTAGACAAACATTATGTTTTTCAAACAAAAAATATCATC
* ** * *
8489 ATTGTTAGTTGACATGAAATTGACAAAAATCAAACATT-AATTGACATAGATTGCAT
63 ATTATTAGTTGACATGAAATTGACAAAGTTCAAACATTAAACTGACATAGACTGCAT
** *
8545 TTTTTAACATAGAAACATTGTCTTTTATTCAAACATTGTGTTTTT
1 TTTTTAACATA-AAACATTGTCTTTTAGACAAACATTATGTTTTT
8590 TAACCCAAAA
Statistics
Matches: 331, Mismatches: 53, Indels: 39
0.78 0.13 0.09
Matches are distributed among these distances:
117 22 0.07
118 72 0.22
119 123 0.37
120 65 0.20
121 47 0.14
122 2 0.01
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.36
Consensus pattern (119 bp):
TTTTTAACATAAAACATTGTCTTTTAGACAAACATTATGTTTTTCAAACAAAAAATATCATCATT
ATTAGTTGACATGAAATTGACAAAGTTCAAACATTAAACTGACATAGACTGCAT
Found at i:13191 original size:16 final size:17
Alignment explanation
Indices: 13161--13195 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
13151 TTTGGAAATC
13161 AAGAAAATAAAAGTGCA
1 AAGAAAATAAAAGTGCA
13178 AAGAAAAT-AAAGTGCA
1 AAGAAAATAAAAGTGCA
13194 AA
1 AA
13196 AATTTAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.66, C:0.06, G:0.17, T:0.11
Consensus pattern (17 bp):
AAGAAAATAAAAGTGCA
Found at i:15527 original size:23 final size:23
Alignment explanation
Indices: 15484--15528 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
15474 TATTAGCAGA
15484 AACTTGACTGATCAATGAAAAAT
1 AACTTGACTGATCAATGAAAAAT
*
15507 AACTT-ACTGGTCAATGAAAAAT
1 AACTTGACTGATCAATGAAAAAT
15529 GAGGTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.27
Consensus pattern (23 bp):
AACTTGACTGATCAATGAAAAAT
Found at i:16076 original size:41 final size:41
Alignment explanation
Indices: 16031--16113 Score: 123
Period size: 41 Copynumber: 2.0 Consensus size: 41
16021 TAGTATTACG
16031 TTTATTATTTTAATAATAAATAATAACAT-ATATAATAATAT
1 TTTATTATTTTAATAATAAATAATAA-ATAATATAATAATAT
* **
16072 TTTATTATTTTAATAATTAATGTTAAATAATATAATAATAT
1 TTTATTATTTTAATAATAAATAATAAATAATATAATAATAT
16113 T
1 T
16114 ATTTTCTTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 2 0.05
41 36 0.95
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (41 bp):
TTTATTATTTTAATAATAAATAATAAATAATATAATAATAT
Found at i:16077 original size:38 final size:40
Alignment explanation
Indices: 16031--16125 Score: 115
Period size: 41 Copynumber: 2.4 Consensus size: 40
16021 TAGTATTACG
16031 TTTATTATTTTAATAATAAATAATAACAT-ATATAATAATA
1 TTTATTATTTTAATAATAAATAATAA-ATAATATAATAATA
* **
16071 TTTTATTATTTTAATAATTAATGTTAAATAATATAATAATA
1 -TTTATTATTTTAATAATAAATAATAAATAATATAATAATA
16112 -TTATT-TTCTTAATA
1 TTTATTATT-TTAATA
16126 TGAATATTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
38 2 0.04
39 11 0.22
40 2 0.04
41 34 0.69
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (40 bp):
TTTATTATTTTAATAATAAATAATAAATAATATAATAATA
Found at i:17577 original size:14 final size:13
Alignment explanation
Indices: 17558--17598 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 13
17548 GGGTTTGAAG
17558 GATTTAGAGTTTAT
1 GATTTAG-GTTTAT
17572 GATTTAGGTTTTAT
1 GATTTAGG-TTTAT
17586 GATTTAGGGTTTA
1 GATTTA-GGTTTA
17599 GGGTTTCATG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.04
14 22 0.88
15 2 0.08
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (13 bp):
GATTTAGGTTTAT
Found at i:18156 original size:73 final size:73
Alignment explanation
Indices: 18037--18185 Score: 244
Period size: 73 Copynumber: 2.0 Consensus size: 73
18027 TTCATGGCAT
*
18037 TTCCATCACATAATCACCACTACATTCAAGAAAAATATGTATAAAACACCCATATAATCCAACTT
1 TTCCATCACATAATCACCACTACATTCAAGAAAAATATGTATAAAACACCCATATAATCCAACTG
*
18102 TGATATCA
66 CGATATCA
* * * *
18110 TTCCATCACATAATCACCATTTCATTCAAGCAAAATATGTATAAAACATCCATATAATCCAACTG
1 TTCCATCACATAATCACCACTACATTCAAGAAAAATATGTATAAAACACCCATATAATCCAACTG
18175 CGATATCA
66 CGATATCA
18183 TTC
1 TTC
18186 TAATCATGTA
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 70 1.00
ACGTcount: A:0.42, C:0.25, G:0.05, T:0.29
Consensus pattern (73 bp):
TTCCATCACATAATCACCACTACATTCAAGAAAAATATGTATAAAACACCCATATAATCCAACTG
CGATATCA
Found at i:19360 original size:149 final size:149
Alignment explanation
Indices: 19093--19361 Score: 346
Period size: 149 Copynumber: 1.8 Consensus size: 149
19083 TTCAACCCCA
* * * ***
19093 AAAAGGTCAAATTACAAAATTACCCTCAAGGGGTATTTTGGTAATTTTACACCTTTCAAGGTTTT
1 AAAAGGTCAAATTACAAAATTACCCTCAAGAGGTATTTTGGTAAGTTCACACCTTTCAAGGTACA
* * * *
19158 GCCAAGGTTTTCAATACACCAAAAATCATCAAATACTATAAAAACATGTTTTGGAATATAATGTT
66 ACCAAGGTTTTCAAAACACCAAAAATCATCAAATAATATAAAAACATGATTTGGAATATAATGTT
19223 TCATGAAAAACTAACCTTG
131 TCATGAAAAACTAACCTTG
* *
19242 AAAAGGTCAAATTACAAAATTACCCTTAAGAGGTAGTTTT-GTAAGTTCACACCTTTTAAGGTAC
1 AAAAGGTCAAATTACAAAATTACCCTCAAGAGGTA-TTTTGGTAAGTTCACACCTTTCAAGGTAC
* ** *
19306 AATCACA-GTTTTCAAAATTCCAAAAATCATCAAATAATATCAAATA-ATGATTTGGA
65 AACCA-AGGTTTTCAAAACACCAAAAATCATCAAATAATAT-AAAAACATGATTTGGA
19362 GTTTTTTTGA
Statistics
Matches: 101, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
149 92 0.91
150 9 0.09
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.32
Consensus pattern (149 bp):
AAAAGGTCAAATTACAAAATTACCCTCAAGAGGTATTTTGGTAAGTTCACACCTTTCAAGGTACA
ACCAAGGTTTTCAAAACACCAAAAATCATCAAATAATATAAAAACATGATTTGGAATATAATGTT
TCATGAAAAACTAACCTTG
Found at i:19744 original size:20 final size:20
Alignment explanation
Indices: 19702--19747 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
19692 TCTAATTGAT
* ***
19702 TTTGATCAATTTTGACTTTG
1 TTTGATCAAGTTTGACCGAG
19722 TTTGATCAAGTTTGACCGAG
1 TTTGATCAAGTTTGACCGAG
19742 TTTGAT
1 TTTGAT
19748 GTTAAGGCGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.22, C:0.11, G:0.20, T:0.48
Consensus pattern (20 bp):
TTTGATCAAGTTTGACCGAG
Found at i:20118 original size:49 final size:49
Alignment explanation
Indices: 20045--20238 Score: 223
Period size: 49 Copynumber: 4.0 Consensus size: 49
20035 TTAGGAAATG
* * * *
20045 GTGCTCCTATAATCATAGGTAAGTGACTTTAAAAATCT-TTATTTGAAAA
1 GTGCTTCTATAAACATAGGCAAGTGACTTTAAAAATCTCCT-TTTGAAAA
* * * *
20094 GTGCTTTTATAAACATAAGCAAGTGATTTTAAAAATCT-CTCTTTGAATA
1 GTGCTTCTATAAACATAGGCAAGTGACTTTAAAAATCTCCT-TTTGAAAA
* *
20143 TTG-TTCCTATAAACATTGGCAAGTGACTTTAAAAATCTCCTTTTGAAAA
1 GTGCTT-CTATAAACATAGGCAAGTGACTTTAAAAATCTCCTTTTGAAAA
* * *
20192 GTGCTTCTATGAACATAGGCTAGTGACTTTAAAAATCTCTTTTTGAA
1 GTGCTTCTATAAACATAGGCAAGTGACTTTAAAAATCTCCTTTTGAA
20239 TCATAGGATA
Statistics
Matches: 122, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
48 2 0.02
49 116 0.95
50 4 0.03
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.38
Consensus pattern (49 bp):
GTGCTTCTATAAACATAGGCAAGTGACTTTAAAAATCTCCTTTTGAAAA
Found at i:20223 original size:98 final size:98
Alignment explanation
Indices: 20049--20239 Score: 276
Period size: 98 Copynumber: 1.9 Consensus size: 98
20039 GAAATGGTGC
* * * *
20049 TCCTATAATCATAGGTAAGTGACTTTAAAAATCTTTATTTGAAAAGTGCTTTTATAAACATAAGC
1 TCCTATAAACATAGGCAAGTGACTTTAAAAATCTCTATTTGAAAAGTGCTTCTATAAACATAAGC
*
20114 AAGTGATTTTAAAAATCTCTCTTTGAATATTGT
66 AAGTGACTTTAAAAATCTCTCTTTGAATATTGT
* * *
20147 TCCTATAAACATTGGCAAGTGACTTTAAAAATCTCCT-TTTGAAAAGTGCTTCTATGAACATAGG
1 TCCTATAAACATAGGCAAGTGACTTTAAAAATCT-CTATTTGAAAAGTGCTTCTATAAACATAAG
* *
20211 CTAGTGACTTTAAAAATCTCTTTTTGAAT
65 CAAGTGACTTTAAAAATCTCTCTTTGAAT
20240 CATAGGATAG
Statistics
Matches: 82, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
98 81 0.99
99 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (98 bp):
TCCTATAAACATAGGCAAGTGACTTTAAAAATCTCTATTTGAAAAGTGCTTCTATAAACATAAGC
AAGTGACTTTAAAAATCTCTCTTTGAATATTGT
Found at i:20251 original size:35 final size:34
Alignment explanation
Indices: 20201--20273 Score: 119
Period size: 35 Copynumber: 2.1 Consensus size: 34
20191 AGTGCTTCTA
* *
20201 TGAACATAGGCTAGTGACTTTAAAAATCTCTTTT
1 TGAACATAGGATAGTGACTTTAAAAATCTCCTTT
20235 TGAATCATAGGATAGTGACTTTAAAAATCTCCTTT
1 TGAA-CATAGGATAGTGACTTTAAAAATCTCCTTT
20270 TGAA
1 TGAA
20274 AAGTACTTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
34 4 0.11
35 32 0.89
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (34 bp):
TGAACATAGGATAGTGACTTTAAAAATCTCCTTT
Found at i:20320 original size:49 final size:48
Alignment explanation
Indices: 20252--20406 Score: 134
Period size: 49 Copynumber: 3.2 Consensus size: 48
20242 TAGGATAGTG
* * * * **
20252 ACTTTAAAAATCTCCTTTTGAAAA-GTACTTCTATGAAGATAGGCAATGA
1 ACTTTAAAATTTTCATTTTGAAAACG-AC-TCTATGAAAATAGGCAACAA
*
20301 ACTTTAAAATTTTCATTTTGAAAACGGCTCTATGAAAATAGGCAACAA
1 ACTTTAAAATTTTCATTTTGAAAACGACTCTATGAAAATAGGCAACAA
* * * * * * *
20349 ATTTTAATAATCTT-ATTTTGAAAAAGGCTCTTATGAAGATAAGTAACAA
1 ACTTTAA-AATTTTCATTTTGAAAACGACTC-TATGAAAATAGGCAACAA
20398 ACTTTAAAA
1 ACTTTAAAA
20407 AATCTCTTTG
Statistics
Matches: 89, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
48 40 0.45
49 48 0.54
50 1 0.01
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (48 bp):
ACTTTAAAATTTTCATTTTGAAAACGACTCTATGAAAATAGGCAACAA
Found at i:20320 original size:84 final size:84
Alignment explanation
Indices: 20164--20322 Score: 248
Period size: 84 Copynumber: 1.9 Consensus size: 84
20154 AACATTGGCA
* *
20164 AGTGACTTTAAAAATCTCCTTTTGAAAAGTGCTTCTATGAACATAGGCTAGTGACTTTAAAAATC
1 AGTGACTTTAAAAATCTCCTTTTGAAAAGTACTTCTATGAACATAGGCTAATGACTTTAAAAATC
*
20229 TCTTTTTGAATCATAGGAT
66 TCATTTTGAATCATAGGAT
* *
20248 AGTGACTTTAAAAATCTCCTTTTGAAAAGTACTTCTATGAAGATAGGC-AATGAACTTTAAAATT
1 AGTGACTTTAAAAATCTCCTTTTGAAAAGTACTTCTATGAACATAGGCTAATG-ACTTTAAAAAT
*
20312 TTCATTTTGAA
65 CTCATTTTGAA
20323 AACGGCTCTA
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
83 3 0.04
84 65 0.96
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.37
Consensus pattern (84 bp):
AGTGACTTTAAAAATCTCCTTTTGAAAAGTACTTCTATGAACATAGGCTAATGACTTTAAAAATC
TCATTTTGAATCATAGGAT
Found at i:20342 original size:48 final size:48
Alignment explanation
Indices: 20281--20404 Score: 142
Period size: 48 Copynumber: 2.6 Consensus size: 48
20271 GAAAAGTACT
* ** * *
20281 TCTATGAAGATAGGCAATGAACTTTAA-AATTTTCATTTTGAAAACGGC
1 TCTATGAAAATAGGCAACAAACTTTAATAATCTT-ATTTTGAAAAAGGC
*
20329 TCTATGAAAATAGGCAACAAATTTTAATAATCTTATTTTGAAAAAGGC
1 TCTATGAAAATAGGCAACAAACTTTAATAATCTTATTTTGAAAAAGGC
* * *
20377 TCTTATGAAGATAAGTAACAAACTTTAA
1 TC-TATGAAAATAGGCAACAAACTTTAA
20405 AAAATCTCTT
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
48 38 0.59
49 26 0.41
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (48 bp):
TCTATGAAAATAGGCAACAAACTTTAATAATCTTATTTTGAAAAAGGC
Found at i:20453 original size:25 final size:27
Alignment explanation
Indices: 20413--20474 Score: 83
Period size: 26 Copynumber: 2.3 Consensus size: 27
20403 AAAAAATCTC
*
20413 TTTGGCAAAAGGTTTTGA-AAGTCTTAT
1 TTTGG-AAAAGGTTTTGACAAGTCTCAT
20440 TTTGGAAAA-GTTTTGACAAGTCTCAT
1 TTTGGAAAAGGTTTTGACAAGTCTCAT
*
20466 TTTGAAAAA
1 TTTGGAAAA
20475 TTAGGTTACA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
25 7 0.22
26 20 0.62
27 5 0.16
ACGTcount: A:0.34, C:0.08, G:0.19, T:0.39
Consensus pattern (27 bp):
TTTGGAAAAGGTTTTGACAAGTCTCAT
Found at i:21150 original size:17 final size:16
Alignment explanation
Indices: 21108--21159 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 16
21098 TTCATTCCAA
*
21108 TTCATTCATTTGTTTT
1 TTCATTCATTTATTTT
21124 CATTCA-TCATTTATTTT
1 --TTCATTCATTTATTTT
*
21141 TGTCATTCATTCATTTT
1 T-TCATTCATTTATTTT
21158 TT
1 TT
21160 TCTTTTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
15 1 0.03
16 4 0.13
17 21 0.70
18 4 0.13
ACGTcount: A:0.17, C:0.15, G:0.04, T:0.63
Consensus pattern (16 bp):
TTCATTCATTTATTTT
Found at i:24404 original size:55 final size:55
Alignment explanation
Indices: 24320--24428 Score: 184
Period size: 55 Copynumber: 2.0 Consensus size: 55
24310 TCACATTTTA
*
24320 AGGATTTTACAATCAAATCATCCACATAAACCAT-TATCCCTTTATGCATCATATT
1 AGGATTTTACAATCAAATCATCCACATAAACC-TCTATCCCATTATGCATCATATT
*
24375 AGGATTTTACAATCAAATCATCCACATAAACCTCTATCTCATTATGCATCATAT
1 AGGATTTTACAATCAAATCATCCACATAAACCTCTATCCCATTATGCATCATAT
24429 CATGGAAAAG
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
54 1 0.02
55 50 0.98
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.34
Consensus pattern (55 bp):
AGGATTTTACAATCAAATCATCCACATAAACCTCTATCCCATTATGCATCATATT
Found at i:26060 original size:21 final size:22
Alignment explanation
Indices: 26014--26061 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
26004 TAGTGAATTT
* *
26014 TTTCTCTATCAACATAGACTTG
1 TTTCTCTATCAACACAGACTTC
26036 TTTC-CTATCAACACA-ACTTAC
1 TTTCTCTATCAACACAGACTT-C
26057 TTTCT
1 TTTCT
26062 GATGCAAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 4 0.18
21 14 0.64
22 4 0.18
ACGTcount: A:0.27, C:0.27, G:0.04, T:0.42
Consensus pattern (22 bp):
TTTCTCTATCAACACAGACTTC
Done.