Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167992.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_249, 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: 43334
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Found at i:1321 original size:17 final size:17
Alignment explanation
Indices: 1301--1347 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
1291 TTTTGGAATG
1301 TTATTTTAAATTTATTT
1 TTATTTTAAATTTATTT
* * *
1318 TTATTTGAAACTAATTT
1 TTATTTTAAATTTATTT
1335 TT-TTTATAAATTT
1 TTATTT-TAAATTT
1348 TCTTTATGTA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
16 3 0.13
17 20 0.87
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (17 bp):
TTATTTTAAATTTATTT
Found at i:1876 original size:20 final size:19
Alignment explanation
Indices: 1827--1876 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
1817 GAGGTTTACA
*
1827 TTTTAAGGTTTAATTTAGG
1 TTTTAAGGTTTAATTAAGG
* * *
1846 GTTTGAGGTTTCACTTAAGG
1 TTTTAAGGTTT-AATTAAGG
1866 TTTTAAGGTTT
1 TTTTAAGGTTT
1877 GGGTTTCACT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.22, C:0.04, G:0.24, T:0.50
Consensus pattern (19 bp):
TTTTAAGGTTTAATTAAGG
Found at i:1887 original size:26 final size:27
Alignment explanation
Indices: 1840--1902 Score: 101
Period size: 26 Copynumber: 2.4 Consensus size: 27
1830 TAAGGTTTAA
*
1840 TTTAGGGTTTGAGGTTTCACTTAAGGT
1 TTTAAGGTTTGAGGTTTCACTTAAGGT
*
1867 TTTAAGGTTTG-GGTTTCACTTAGGGT
1 TTTAAGGTTTGAGGTTTCACTTAAGGT
1893 TTTAAGGTTT
1 TTTAAGGTTT
1903 CATTAGGATT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
26 24 0.71
27 10 0.29
ACGTcount: A:0.17, C:0.06, G:0.29, T:0.48
Consensus pattern (27 bp):
TTTAAGGTTTGAGGTTTCACTTAAGGT
Found at i:1903 original size:20 final size:20
Alignment explanation
Indices: 1827--1922 Score: 63
Period size: 26 Copynumber: 4.7 Consensus size: 20
1817 GAGGTTTACA
* *
1827 TTTTAAGGTTTAATTTAGGG
1 TTTTAAGGTTTCACTTAGGG
* *
1847 -TTTGAGGTTTCACTTAAGG
1 TTTTAAGGTTTCACTTAGGG
1866 TTTTAAGGTTTGGGTTTCACTTAGGG
1 TTTTAA------GGTTTCACTTAGGG
1892 TTTTAAGGTTTCA-TTA-GG
1 TTTTAAGGTTTCACTTAGGG
* *
1910 ATTTAGGGTTTCA
1 TTTTAAGGTTTCA
1923 TTAATTTACA
Statistics
Matches: 61, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
18 13 0.21
19 18 0.30
20 11 0.18
26 19 0.31
ACGTcount: A:0.21, C:0.06, G:0.26, T:0.47
Consensus pattern (20 bp):
TTTTAAGGTTTCACTTAGGG
Found at i:1919 original size:18 final size:19
Alignment explanation
Indices: 1877--1925 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
1867 TTTAAGGTTT
*
1877 GGGTTTCACTTAGGGTTTTA
1 GGGTTTCA-TTAGGGATTTA
*
1897 AGGTTTCATTA-GGATTTA
1 GGGTTTCATTAGGGATTTA
1915 GGGTTTCATTA
1 GGGTTTCATTA
1926 ATTTACAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 16 0.62
19 3 0.12
20 7 0.27
ACGTcount: A:0.20, C:0.08, G:0.27, T:0.45
Consensus pattern (19 bp):
GGGTTTCATTAGGGATTTA
Found at i:2062 original size:3 final size:3
Alignment explanation
Indices: 2054--2104 Score: 61
Period size: 3 Copynumber: 16.7 Consensus size: 3
2044 TCAATAAAAT
2054 TTA TTA TTA TTA TTA TTA TTGA -TA TTA TTA TTTA TTA TTTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA -TTA TTA -TTA TTA TTA
2100 TTA TT
1 TTA TT
2105 TTTTTATTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
2 3 0.07
3 33 0.77
4 7 0.16
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2105 original size:12 final size:13
Alignment explanation
Indices: 2054--2114 Score: 65
Period size: 12 Copynumber: 4.8 Consensus size: 13
2044 TCAATAAAAT
2054 TTATTA-TTATTA
1 TTATTATTTATTA
*
2066 TTATTATTGA-TA
1 TTATTATTTATTA
2078 TTATTATTTATTA
1 TTATTATTTATTA
2091 TTTATTATTTTATT-
1 -TTATTA-TTTATTA
*
2105 TTTTTATTTA
1 TTATTATTTA
2115 ATAATTCTCT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
12 21 0.50
13 9 0.21
14 6 0.14
15 6 0.14
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (13 bp):
TTATTATTTATTA
Found at i:3579 original size:120 final size:121
Alignment explanation
Indices: 3422--3664 Score: 425
Period size: 120 Copynumber: 2.0 Consensus size: 121
3412 CTTCTGGTCC
* * *
3422 TCCTCTTTTTCCTTTTTCGCGAATGCCTCTTTAACGAAAGCCTGCCTTTTTCTTCTTTCTGCTTG
1 TCCTCTTTTTCCTTTTTCGAGAATGCCTCTTTAACGAAAGCCTCCCTGTTTCTTCTTTCTGCTTG
*
3487 CTGCTCAGTTGTTCACATTCTTCATTTTTTCTAGTTCAGTTTTTTTGTTTTCTGCT
66 CTGCCCAGTTGTTCACATTCTTCATTTTTTCTAGTTCAGTTTTTTTGTTTTCTGCT
* *
3543 TCCTCTTTTTCCTTTTT-TAGAATGCCTCTTTCACGAAAGCCTCCCTGTTTCTTCTTTCTGCTTG
1 TCCTCTTTTTCCTTTTTCGAGAATGCCTCTTTAACGAAAGCCTCCCTGTTTCTTCTTTCTGCTTG
3607 CTGCCCAGTTGTTCACATTCTTCATTTTTTCTAGTTCAGTTTTTTTGTTTTCTGCT
66 CTGCCCAGTTGTTCACATTCTTCATTTTTTCTAGTTCAGTTTTTTTGTTTTCTGCT
3663 TC
1 TC
3665 ACCCCTCGTC
Statistics
Matches: 116, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
120 99 0.85
121 17 0.15
ACGTcount: A:0.11, C:0.26, G:0.12, T:0.52
Consensus pattern (121 bp):
TCCTCTTTTTCCTTTTTCGAGAATGCCTCTTTAACGAAAGCCTCCCTGTTTCTTCTTTCTGCTTG
CTGCCCAGTTGTTCACATTCTTCATTTTTTCTAGTTCAGTTTTTTTGTTTTCTGCT
Found at i:4213 original size:3 final size:3
Alignment explanation
Indices: 4205--4260 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
4195 TTTATAGCCT
4205 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
4253 TTA TTA TT
1 TTA TTA TT
4261 CGGCTTTATG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:6929 original size:14 final size:15
Alignment explanation
Indices: 6910--6948 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
6900 TCATAATATA
6910 AAATATAAAAA-AAG
1 AAATATAAAAAGAAG
*
6924 AAATATAAAAAGAAT
1 AAATATAAAAAGAAG
*
6939 AAAAATAAAA
1 AAATATAAAA
6949 TAAAAATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.15
Consensus pattern (15 bp):
AAATATAAAAAGAAG
Found at i:6947 original size:6 final size:6
Alignment explanation
Indices: 6907--7013 Score: 69
Period size: 6 Copynumber: 17.2 Consensus size: 6
6897 TCATCATAAT
* * *
6907 ATAAAA TATAAAA A-AAGAA ATATAA A-AAGA ATAAAA ATAAAA TAAAAATA
1 ATAAAA -ATAAAA ATAA-AA ATAAAA ATAAAA ATAAAA ATAAAA -ATAAA-A
* *
6957 ATAAGAA ATAAAA TTAAAG A-AAAA ATCAAAAA ATAAAA AT-AAA ATGAAAA
1 ATAA-AA ATAAAA ATAAAA ATAAAA AT--AAAA ATAAAA ATAAAA AT-AAAA
7007 ATAAAA A
1 ATAAAA A
7014 CTTGATATCG
Statistics
Matches: 79, Mismatches: 10, Indels: 23
0.71 0.09 0.21
Matches are distributed among these distances:
5 14 0.18
6 33 0.42
7 24 0.30
8 8 0.10
ACGTcount: A:0.78, C:0.01, G:0.05, T:0.17
Consensus pattern (6 bp):
ATAAAA
Found at i:6948 original size:26 final size:26
Alignment explanation
Indices: 6911--7013 Score: 104
Period size: 26 Copynumber: 4.0 Consensus size: 26
6901 CATAATATAA
* *
6911 AATATAAA-AAAAGAAATATAAAAAG
1 AATAAAAATAAAAGAAAAATAAAAAG
* *
6936 AATAAAAATAAAATAAAAATAATAAG
1 AATAAAAATAAAAGAAAAATAAAAAG
* *
6962 AA-ATAAAATTAAAGAAAAAATCAAAA-
1 AATA-AAAATAAAAG-AAAAATAAAAAG
6988 AATAAAAATAAAATGAAAAATAAAAA
1 AATAAAAATAAAA-GAAAAATAAAAA
7014 CTTGATATCG
Statistics
Matches: 63, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
25 8 0.13
26 44 0.70
27 11 0.17
ACGTcount: A:0.78, C:0.01, G:0.05, T:0.17
Consensus pattern (26 bp):
AATAAAAATAAAAGAAAAATAAAAAG
Found at i:6958 original size:52 final size:53
Alignment explanation
Indices: 6902--7010 Score: 136
Period size: 52 Copynumber: 2.1 Consensus size: 53
6892 TTTTCTCATC
*
6902 ATAATATA-AAATATAAA-AAAAG-AAATATAAAAAGAATAAAAATAAAAT-AAAA
1 ATAATA-AGAAATA-AAATAAAAGAAAAAATAAAAA-AATAAAAATAAAATGAAAA
* *
6954 ATAATAAGAAATAAAATTAAAGAAAAAATCAAAAAATAAAAATAAAATGAAAA
1 ATAATAAGAAATAAAATAAAAGAAAAAATAAAAAAATAAAAATAAAATGAAAA
7007 ATAA
1 ATAA
7011 AAACTTGATA
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
51 4 0.08
52 29 0.58
53 17 0.34
ACGTcount: A:0.76, C:0.01, G:0.05, T:0.18
Consensus pattern (53 bp):
ATAATAAGAAATAAAATAAAAGAAAAAATAAAAAAATAAAAATAAAATGAAAA
Found at i:6965 original size:21 final size:20
Alignment explanation
Indices: 6902--6970 Score: 77
Period size: 21 Copynumber: 3.4 Consensus size: 20
6892 TTTTCTCATC
*
6902 ATAATATAAAATATAA-AAAA
1 ATAAAATAAAA-ATAATAAAA
* *
6922 AGAAATATAAAAAGAATAAAA
1 ATAAA-ATAAAAATAATAAAA
6943 ATAAAATAAAAATAATAAGAA
1 ATAAAATAAAAATAATAA-AA
6964 ATAAAAT
1 ATAAAAT
6971 TAAAGAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
20 18 0.44
21 23 0.56
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.20
Consensus pattern (20 bp):
ATAAAATAAAAATAATAAAA
Found at i:6993 original size:19 final size:18
Alignment explanation
Indices: 6907--7013 Score: 82
Period size: 17 Copynumber: 6.1 Consensus size: 18
6897 TCATCATAAT
6907 ATAAAATATAAAAA-AAGAA
1 ATAAAATA-AAAAATAA-AA
* *
6926 ATATAA-AAAGAATAAAA
1 ATAAAATAAAAAATAAAA
*
6943 ATAAAAT-AAAAATAATA
1 ATAAAATAAAAAATAAAA
* *
6960 A-GAAAT-AAAATTAAAGA
1 ATAAAATAAAAAATAAA-A
6977 A-AAAATCAAAAAATAAAA
1 ATAAAAT-AAAAAATAAAA
*
6995 ATAAAATGAAAAATAAAA
1 ATAAAATAAAAAATAAAA
7013 A
1 A
7014 CTTGATATCG
Statistics
Matches: 71, Mismatches: 11, Indels: 13
0.75 0.12 0.14
Matches are distributed among these distances:
16 11 0.15
17 26 0.37
18 16 0.23
19 18 0.25
ACGTcount: A:0.78, C:0.01, G:0.05, T:0.17
Consensus pattern (18 bp):
ATAAAATAAAAAATAAAA
Found at i:15264 original size:6 final size:6
Alignment explanation
Indices: 15255--15289 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
15245 AAAATAACAT
*
15255 AAATTA AAATCA AAATTA AAATTA AAATTA AAATT
1 AAATTA AAATTA AAATTA AAATTA AAATTA AAATT
15290 TTTGGGCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (6 bp):
AAATTA
Found at i:15344 original size:18 final size:17
Alignment explanation
Indices: 15323--15361 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
15313 AAATTTCAAC
*
15323 TTTTGTATCAAGGTCCAA
1 TTTTGTATCAACGTCC-A
*
15341 TTTTTTATCAACGTCCA
1 TTTTGTATCAACGTCCA
15358 TTTT
1 TTTT
15362 AATCTTGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.23, C:0.18, G:0.10, T:0.49
Consensus pattern (17 bp):
TTTTGTATCAACGTCCA
Found at i:15572 original size:17 final size:18
Alignment explanation
Indices: 15540--15578 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
15530 TTGTATTTCT
15540 TTTTTATCATATTTATTA
1 TTTTTATCATATTTATTA
*
15558 TTTTTATCTTA-TTATTA
1 TTTTTATCATATTTATTA
15575 TTTT
1 TTTT
15579 ATATTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTTATCATATTTATTA
Found at i:16753 original size:18 final size:18
Alignment explanation
Indices: 16716--16753 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
16706 AGGATTTTTT
*
16716 TGTTTAAGGTTGTTTGAG
1 TGTTTAAGGTTGTTGGAG
16734 TGTTTAA-GTTGTTGGTAG
1 TGTTTAAGGTTGTTGG-AG
16752 TG
1 TG
16754 GGATTAAGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.16, C:0.00, G:0.34, T:0.50
Consensus pattern (18 bp):
TGTTTAAGGTTGTTGGAG
Found at i:20468 original size:19 final size:18
Alignment explanation
Indices: 20446--20489 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 18
20436 AATATAAAAT
20446 AAATAAAAATAAAATCAAA
1 AAATAAAAATAAAAT-AAA
20465 AAATAAAAATAAAATAAA
1 AAATAAAAATAAAATAAA
20483 AAA-AAAA
1 AAATAAAA
20490 CCTATGATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 4 0.16
18 6 0.24
19 15 0.60
ACGTcount: A:0.84, C:0.02, G:0.00, T:0.14
Consensus pattern (18 bp):
AAATAAAAATAAAATAAA
Found at i:20887 original size:25 final size:25
Alignment explanation
Indices: 20859--20909 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
20849 CAAAAAAGTG
20859 ATCTGGACTAAGCCAATATCAAAAT
1 ATCTGGACTAAGCCAATATCAAAAT
*
20884 ATCTGGACTGAGCCAATATCAAAAT
1 ATCTGGACTAAGCCAATATCAAAAT
20909 A
1 A
20910 GATGATCGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.24
Consensus pattern (25 bp):
ATCTGGACTAAGCCAATATCAAAAT
Found at i:21190 original size:55 final size:57
Alignment explanation
Indices: 21093--21214 Score: 130
Period size: 55 Copynumber: 2.2 Consensus size: 57
21083 AATGAATGAC
* *
21093 GGGATGAAACTGTGAGTCAGGAAAAATGATCTGAATTAAGCCA-ATATC-AAATGA-TA
1 GGGATGAAACTGTGAGTCAGGAAAAATGATCTAAACTAAGCCATA-ATCGAAA-GATTA
* * *
21149 GGGATGAAACTGTGATTTTA-G-AAAATGATCTAAACTGAGCCATAATCGAAAGATTA
1 GGGATGAAACTGTGA-GTCAGGAAAAATGATCTAAACTAAGCCATAATCGAAAGATTA
21205 -GGATGAAACT
1 GGGATGAAACT
21215 ACAAGTCTAA
Statistics
Matches: 57, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
55 33 0.58
56 22 0.39
57 2 0.04
ACGTcount: A:0.42, C:0.11, G:0.23, T:0.25
Consensus pattern (57 bp):
GGGATGAAACTGTGAGTCAGGAAAAATGATCTAAACTAAGCCATAATCGAAAGATTA
Found at i:21324 original size:66 final size:66
Alignment explanation
Indices: 21204--21361 Score: 194
Period size: 66 Copynumber: 2.4 Consensus size: 66
21194 TCGAAAGATT
* * * ** * *
21204 AGGATGAAACTACAAGTCTAAAAGATAAAGTGACCAAGACTGAGTCAATGTAAAAAATGAATGAC
1 AGGATAAAACCACAAGTCTAAAAAATAAAGCAACCAAAACTAAGTCAATGTAAAAAATGAATGAC
21269 C
66 C
21270 -GAGATAAAACCACAAGTCTAAAAAATAAAGCAACCAAAACTAAGTCAA-GATAAAAAATGAATG
1 AG-GATAAAACCACAAGTCTAAAAAATAAAGCAACCAAAACTAAGTCAATG-TAAAAAATGAATG
*
21333 ATC
64 ACC
* *
21336 AGGATAAAACCACGAGTCAAAAAAAT
1 AGGATAAAACCACAAGTCTAAAAAAT
21362 GATTTGGACT
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
65 2 0.03
66 76 0.96
67 1 0.01
ACGTcount: A:0.54, C:0.15, G:0.16, T:0.16
Consensus pattern (66 bp):
AGGATAAAACCACAAGTCTAAAAAATAAAGCAACCAAAACTAAGTCAATGTAAAAAATGAATGAC
C
Found at i:21501 original size:120 final size:120
Alignment explanation
Indices: 21261--21629 Score: 397
Period size: 121 Copynumber: 3.1 Consensus size: 120
21251 ATGTAAAAAA
* * * * * *
21261 TGAATGACC-GAGATAAAACCACAAGTCTAAAAAATAAAGCAACCAAAACTAAGTCAAGATAAAA
1 TGAATGACCAG-GATAAAATCACAAGTCTAAAAGATAAAGCAACCAGAAC-GAGTCAAGGTCAAA
* * * *
21325 AATGAATGATCAGGATAAAACCACGAGTCAAAAAAATGATTTGGACTAAGCTAAGAT
64 AATGAATGATTAGGATGAAACCACGAGTCAAAAAAATGATCTGGACTAAGCCAAGAT
* * *
21382 TGAATGACCAGGATGAAATCACAAGTCTAAAAGATAAAGCAACTAGGAACGAGTC-GGGTCAAAA
1 TGAATGACCAGGATAAAATCACAAGTCTAAAAGATAAAGCAACCA-GAACGAGTCAAGGTCAAAA
* * * *
21446 ATGAATGATTAGGATGAAACCATGAGTTAGAAAGATGATCTGGAC-AGAGCCAAGAT
65 ATGAATGATTAGGATGAAACCACGAGTCAAAAAAATGATCTGGACTA-AGCCAAGAT
* ** * *
21502 CGAATGATAAGGATAAAACTGCA-AA-TCTAAAAGATAAAGTAGCCAGAATCGAGTCAAGGTCAA
1 TGAATGACCAGGATAAAA-T-CACAAGTCTAAAAGATAAAGCAACCAGAA-CGAGTCAAGGTCAA
* * * * *
21565 AAATGAATCACTGGGATGAAATCGCGAGTCAAAAAAATGATCTGGACTAAGCCAAGAT
63 AAATGAATGATTAGGATGAAACCACGAGTCAAAAAAATGATCTGGACTAAGCCAAGAT
21623 TGAATGA
1 TGAATGA
21630 GTAATAGGTG
Statistics
Matches: 205, Mismatches: 35, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
119 4 0.02
120 89 0.43
121 105 0.51
122 7 0.03
ACGTcount: A:0.47, C:0.14, G:0.21, T:0.18
Consensus pattern (120 bp):
TGAATGACCAGGATAAAATCACAAGTCTAAAAGATAAAGCAACCAGAACGAGTCAAGGTCAAAAA
TGAATGATTAGGATGAAACCACGAGTCAAAAAAATGATCTGGACTAAGCCAAGAT
Found at i:28009 original size:3 final size:3
Alignment explanation
Indices: 27994--28157 Score: 88
Period size: 3 Copynumber: 56.3 Consensus size: 3
27984 AAATTAAAAA
* * * * * * * *
27994 AAT AAA AAT -AT AAT AAT AAT AAT AAC AAC AAC AAC AAC AAC AAT ACT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * ** * * *
28041 AAT AAC AAT AGT AGC AGT AAT AGT AAT AAT AAT AAT AAT AAT AAT ATT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
** * *
28089 AAT AAT AAT AAT GGT AAT -AT AAT ATAT GAT AAT AAT -AC AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT
* *
28132 AAT AGT AAT -GT AAT AAT AAT -AT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
28158 TAGTATAGTC
Statistics
Matches: 126, Mismatches: 28, Indels: 14
0.75 0.17 0.08
Matches are distributed among these distances:
2 10 0.08
3 114 0.90
4 2 0.02
ACGTcount: A:0.59, C:0.06, G:0.05, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:28166 original size:29 final size:27
Alignment explanation
Indices: 28056--28175 Score: 90
Period size: 27 Copynumber: 4.4 Consensus size: 27
28046 CAATAGTAGC
*
28056 AGTAATAGTAATAATAATAATAATAATAAT
1 AGTAAT-GTAATAATAAT-ACAAT-ATAAT
* **
28086 ATTAA--TAATAATAATGGTAATATAAT
1 AGTAATGTAATAATAAT-ACAATATAAT
28112 A-T-ATG--ATAATAATACAATATAAT
1 AGTAATGTAATAATAATACAATATAAT
*
28135 AGTAATGTAATAATAATATAATATAGTAT
1 AGTAATGTAATAATAATACAATATA--AT
*
28164 AGTCATGTAATA
1 AGTAATGTAATA
28176 TAACAAAAAT
Statistics
Matches: 75, Mismatches: 7, Indels: 17
0.76 0.07 0.17
Matches are distributed among these distances:
23 9 0.12
24 10 0.13
25 4 0.05
26 6 0.08
27 29 0.39
29 13 0.17
30 4 0.05
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.36
Consensus pattern (27 bp):
AGTAATGTAATAATAATACAATATAAT
Found at i:31893 original size:18 final size:17
Alignment explanation
Indices: 31872--31922 Score: 59
Period size: 16 Copynumber: 2.9 Consensus size: 17
31862 TATTTGCAAT
31872 AATTCAAATATTCATAAG
1 AATTCAAA-ATTCATAAG
*
31890 AATTC-AAATTCATGAG
1 AATTCAAAATTCATAAG
*
31906 AATTTAAAGATTCATAA
1 AATTCAAA-ATTCATAA
31923 AGCTTTCATA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 12 0.43
17 4 0.14
18 12 0.43
ACGTcount: A:0.49, C:0.10, G:0.08, T:0.33
Consensus pattern (17 bp):
AATTCAAAATTCATAAG
Found at i:32259 original size:46 final size:46
Alignment explanation
Indices: 32157--32328 Score: 194
Period size: 46 Copynumber: 3.8 Consensus size: 46
32147 TTCTCATTCA
* * *
32157 AAAATTTTAGAGATTTTTATTTGAAAAAC-TTAGT-TATTCACAT-C
1 AAAATTTTAAAGATTCTCATTTGAAAAACTTTAGTGT-TTCACATCC
* *
32201 AAAATTTTAAAGATTCACATTTGAAAAACTTTAGTGTTTTACATCC
1 AAAATTTTAAAGATTCTCATTTGAAAAACTTTAGTGTTTCACATCC
32247 AAAATTTTAAAGATT-T-ATTGTCGAAAAACTTTA-TGGTTTCACATCC
1 AAAATTTTAAAGATTCTCATT-T-GAAAAACTTTAGT-GTTTCACATCC
* **
32293 AAAATTTCAAAGATTCTCATTCAAAAAACTTTAGTG
1 AAAATTTTAAAGATTCTCATTTGAAAAACTTTAGTG
32329 GTTATGTCCG
Statistics
Matches: 109, Mismatches: 10, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
44 28 0.26
45 13 0.12
46 63 0.58
47 2 0.02
48 3 0.03
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.39
Consensus pattern (46 bp):
AAAATTTTAAAGATTCTCATTTGAAAAACTTTAGTGTTTCACATCC
Found at i:38229 original size:14 final size:14
Alignment explanation
Indices: 38210--38239 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
38200 TTTGGTATGA
38210 TTGAAAAACATTTT
1 TTGAAAAACATTTT
*
38224 TTGAAAAACCTTTT
1 TTGAAAAACATTTT
38238 TT
1 TT
38240 TATTTAAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.47
Consensus pattern (14 bp):
TTGAAAAACATTTT
Found at i:38346 original size:26 final size:29
Alignment explanation
Indices: 38311--38373 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
38301 AATAATAGTA
38311 CAATATATCATGC-AATAAA-AT-ATCATG
1 CAAT-TATCATGCTAATAAATATAATCATG
*
38338 CAATTATCATGCTATTAAATATAATCATG
1 CAATTATCATGCTAATAAATATAATCATG
38367 CAATTAT
1 CAATTAT
38374 GCAAAATATA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 8 0.25
27 9 0.28
28 2 0.06
29 13 0.41
ACGTcount: A:0.44, C:0.14, G:0.06, T:0.35
Consensus pattern (29 bp):
CAATTATCATGCTAATAAATATAATCATG
Found at i:39091 original size:19 final size:19
Alignment explanation
Indices: 39069--39105 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
39059 GTTCATAAAA
*
39069 AAACCAAAAAATTTAAACT
1 AAACCAAAAAATTCAAACT
*
39088 AAACCCAAAAATTCAAAC
1 AAACCAAAAAATTCAAAC
39106 AGGTTCCCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.62, C:0.22, G:0.00, T:0.16
Consensus pattern (19 bp):
AAACCAAAAAATTCAAACT
Found at i:39709 original size:6 final size:6
Alignment explanation
Indices: 39694--39733 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
39684 GATGAAAAAC
*
39694 AAAATT -AAATC AAAATT -AAATT AAAATT AAAATT AAAATT
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT
39734 TTGGGCTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 9 0.30
6 21 0.70
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (6 bp):
AAAATT
Found at i:39728 original size:12 final size:11
Alignment explanation
Indices: 39694--39733 Score: 62
Period size: 11 Copynumber: 3.5 Consensus size: 11
39684 GATGAAAAAC
*
39694 AAAATTAAATC
1 AAAATTAAATT
39705 AAAATTAAATT
1 AAAATTAAATT
39716 AAAATTAAAATT
1 AAAATT-AAATT
39728 AAAATT
1 AAAATT
39734 TTGGGCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (11 bp):
AAAATTAAATT
Found at i:41032 original size:29 final size:29
Alignment explanation
Indices: 40999--41084 Score: 172
Period size: 29 Copynumber: 3.0 Consensus size: 29
40989 TAAGAAGATG
40999 AACAACCATGTTTCTCTTAAATCTTTTTA
1 AACAACCATGTTTCTCTTAAATCTTTTTA
41028 AACAACCATGTTTCTCTTAAATCTTTTTA
1 AACAACCATGTTTCTCTTAAATCTTTTTA
41057 AACAACCATGTTTCTCTTAAATCTTTTT
1 AACAACCATGTTTCTCTTAAATCTTTTT
41085 TCTTTTTTTT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 57 1.00
ACGTcount: A:0.30, C:0.21, G:0.03, T:0.45
Consensus pattern (29 bp):
AACAACCATGTTTCTCTTAAATCTTTTTA
Found at i:42289 original size:10 final size:9
Alignment explanation
Indices: 42247--42344 Score: 74
Period size: 9 Copynumber: 10.4 Consensus size: 9
42237 AAAAAATTTA
*
42247 TTTTATAAT
1 TTTTAGAAT
42256 TTTTAGAAT
1 TTTTAGAAT
*
42265 TTTTGAAAAAT
1 TTTT--AGAAT
42276 TTTTAGAAT
1 TTTTAGAAT
42285 CTTTTAGAAAT
1 -TTTTAG-AAT
42296 TTTT--AAT
1 TTTTAGAAT
*
42303 TTTTATAAT
1 TTTTAGAAT
*
42312 TTTTAACAAT
1 TTTT-AGAAT
* *
42322 TTCTACAAGT
1 TTTTAGAA-T
42332 TTTTAGAAT
1 TTTTAGAAT
42341 TTTT
1 TTTT
42345 TAAAACTTTT
Statistics
Matches: 74, Mismatches: 7, Indels: 16
0.76 0.07 0.16
Matches are distributed among these distances:
7 7 0.09
9 32 0.43
10 24 0.32
11 11 0.15
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.56
Consensus pattern (9 bp):
TTTTAGAAT
Found at i:42335 original size:56 final size:56
Alignment explanation
Indices: 42247--42355 Score: 141
Period size: 56 Copynumber: 1.9 Consensus size: 56
42237 AAAAAATTTA
* *
42247 TTTTATAATTTTTAGAATTTTTGAAAAATTTTTAGAATCTTTTAGAAA-TTTTTAAT
1 TTTTATAATTTTTACAATTTCTGAAAAATTTTTAGAATCTTTTA-AAACTTTTTAAT
* * *
42303 TTTTATAATTTTTAACAATTTCT-ACAAGTTTTTAGAATTTTTTAAAACTTTTT
1 TTTTATAATTTTT-ACAATTTCTGAAAAATTTTTAGAATCTTTTAAAACTTTTT
42356 TGAAATTTTC
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
55 3 0.07
56 36 0.78
57 7 0.15
ACGTcount: A:0.34, C:0.05, G:0.06, T:0.56
Consensus pattern (56 bp):
TTTTATAATTTTTACAATTTCTGAAAAATTTTTAGAATCTTTTAAAACTTTTTAAT
Found at i:42364 original size:10 final size:10
Alignment explanation
Indices: 42189--42364 Score: 62
Period size: 10 Copynumber: 17.8 Consensus size: 10
42179 TAGAATTTAA
*
42189 AAAATATTTT
1 AAAATTTTTT
*
42199 AAAATATTTT
1 AAAATTTTTT
*
42209 AAATTTTTTT
1 AAAATTTTTT
**
42219 TTAATTTTCTT
1 AAAATTTT-TT
***
42230 -AAATTTAAA
1 AAAATTTTTT
42239 AAAATTTATTTT
1 AAAA-TT-TTTT
*
42251 ATAA-TTTTT
1 AAAATTTTTT
* *
42260 AGAATTTTTG
1 AAAATTTTTT
*
42270 AAAAATTTTT
1 AAAATTTTTT
* *
42280 AGAATCTTTT
1 AAAATTTTTT
42290 AGAAA-TTTTT
1 A-AAATTTTTT
42300 --AA-TTTTT
1 AAAATTTTTT
*
42307 ATAA-TTTTT
1 AAAATTTTTT
*
42316 AACAA-TTTCT
1 AA-AATTTTTT
* *
42326 ACAAGTTTTT
1 AAAATTTTTT
*
42336 AGAATTTTTT
1 AAAATTTTTT
42346 AAAACTTTTTT
1 AAAA-TTTTTT
*
42357 GAAATTTT
1 AAAATTTT
42365 CTTTTAATGA
Statistics
Matches: 124, Mismatches: 31, Indels: 22
0.70 0.18 0.12
Matches are distributed among these distances:
7 7 0.06
9 17 0.14
10 81 0.65
11 15 0.12
12 4 0.03
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.55
Consensus pattern (10 bp):
AAAATTTTTT
Done.