Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168222.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_456, 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: 26151
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:808 original size:21 final size:21
Alignment explanation
Indices: 766--820 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
756 GAATATTTTG
*
766 AATGAGAATTTTTGAAACTCA
1 AATGAGAATCTTTGAAACTCA
***
787 AATGAGAATCTTTGAGTTTCA
1 AATGAGAATCTTTGAAACTCA
*
808 AATGAAAATCTTT
1 AATGAGAATCTTT
821 TGAGGAGTGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (21 bp):
AATGAGAATCTTTGAAACTCA
Found at i:1459 original size:41 final size:40
Alignment explanation
Indices: 1394--1748 Score: 302
Period size: 41 Copynumber: 8.8 Consensus size: 40
1384 GGAGCAATTT
* ** *
1394 ATTTTTTTTCAAAGTTTTGTTGCCTCTGTTTAGAGGAGCA
1 ATTTATTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
* * * *
1434 ATTTACTTTTCAAAGTCATGGTGCCTCTGTTTATATGAGTA
1 ATTTA-TTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
* *
1475 ATTTATTTTTCAAAGTCGTGATGCCTCTGTTTAGAGGAGTA
1 ATTTA-TTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
* *
1516 ATTTATTTTCAAAGTCGTGGTTGCCTCTATTTAGATGAGCA
1 ATTTATTTTCAAAGTCGTGG-TGCCTCTGTTTAGAGGAGCA
* * *
1557 ATTTACTTTTCAAAGTTGTGGTGCCTCTGTTTATAGGTGC-
1 ATTTA-TTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
** * * * * * ***
1597 ATTTATTTTTGAAGTCATGGTACTTC-GACTTAGAAGATTT
1 ATTTATTTTCAAAGTCGTGGTGCCTCTG-TTTAGAGGAGCA
* * * * *
1637 ATTTA-TTTCAAAGTCGTTGAGCCTCTGATTAGATGAGCT
1 ATTTATTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
* * ** *
1676 ATTTATTTTTCAAAGTCGTTGAGCCTCTAATTAGAGGAGCC
1 ATTTA-TTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
* *
1717 ATTTATTTTCAAGGTCGTGGAGCCTCTGTTTA
1 ATTTATTTTCAAAGTCGTGGTGCCTCTGTTTA
1749 TAGAAGCTTT
Statistics
Matches: 256, Mismatches: 51, Indels: 16
0.79 0.16 0.05
Matches are distributed among these distances:
38 1 0.00
39 46 0.18
40 52 0.20
41 143 0.56
42 14 0.05
ACGTcount: A:0.23, C:0.14, G:0.20, T:0.43
Consensus pattern (40 bp):
ATTTATTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
Found at i:1794 original size:84 final size:80
Alignment explanation
Indices: 1637--1798 Score: 200
Period size: 84 Copynumber: 2.0 Consensus size: 80
1627 TAGAAGATTT
* * *
1637 ATTTATTTCAAAGTCGTTGAGCCTCTGATTAGATGAGCTATTTATTTTTCAAAGTCGTTGAGCCT
1 ATTTATTTCAAAGTCGTGGAGCCTCTGATTAGATGAGCTATTTATTTTTCAAAATCGTAGAGCCT
1702 CTAATTAGAGGAGCC
66 CTAATTAGAGGAGCC
* * *
1717 ATTTATTTTCAAGGTCGTGGAGCCTCTGTTTATA-GAAGCTTTATTTATTTTTTCAAAATCGTAG
1 ATTTA-TTTCAAAGTCGTGGAGCCTCTGATTAGATG-AGC--TATTTA-TTTTTCAAAATCGTAG
* *
1781 AGCTTCTATTTAGAGGAG
61 AGCCTCTAATTAGAGGAG
1799 TTTTGATAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
80 6 0.09
81 27 0.39
83 6 0.09
84 30 0.43
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.40
Consensus pattern (80 bp):
ATTTATTTCAAAGTCGTGGAGCCTCTGATTAGATGAGCTATTTATTTTTCAAAATCGTAGAGCCT
CTAATTAGAGGAGCC
Found at i:2060 original size:29 final size:30
Alignment explanation
Indices: 2026--2097 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
2016 TTTTTATTTT
*
2026 TATTTTTATTT-TTTGTCTATTTATTAATA
1 TATTTTTATTTATTTGTCTATCTATTAATA
* *
2055 TATTTTT-TTTATTTTTTTATCTATTAATA
1 TATTTTTATTTATTTGTCTATCTATTAATA
*
2084 TCTTTATTATTTAT
1 TATTT-TTATTTAT
2098 CTGCTTTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 3 0.08
29 26 0.72
30 2 0.06
31 5 0.14
ACGTcount: A:0.24, C:0.04, G:0.01, T:0.71
Consensus pattern (30 bp):
TATTTTTATTTATTTGTCTATCTATTAATA
Found at i:2079 original size:21 final size:21
Alignment explanation
Indices: 2016--2079 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
2006 GCCTAATTGG
*
2016 TTTTTATTTTTATT-TTTATTT
1 TTTTTATTTTT-TTATATATTT
* *
2037 TTTGTCTATTTATTAATATATTT
1 TTT-T-TATTTTTTTATATATTT
*
2060 TTTTTATTTTTTTATCTATT
1 TTTTTATTTTTTTATATATT
2080 AATATCTTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
21 16 0.47
22 3 0.09
23 15 0.44
ACGTcount: A:0.19, C:0.03, G:0.02, T:0.77
Consensus pattern (21 bp):
TTTTTATTTTTTTATATATTT
Found at i:2130 original size:14 final size:14
Alignment explanation
Indices: 2082--2130 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
2072 TATCTATTAA
2082 TATCT-TTATTATT
1 TATCTATTATTATT
*
2095 TATCTGCTT-TTATTT
1 TATCT-ATTATTA-TT
2110 TAT-TATTATTATT
1 TATCTATTATTATT
2123 TATCTATT
1 TATCTATT
2131 TCTTTTATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
13 12 0.40
14 11 0.37
15 7 0.23
ACGTcount: A:0.22, C:0.08, G:0.02, T:0.67
Consensus pattern (14 bp):
TATCTATTATTATT
Found at i:2138 original size:17 final size:17
Alignment explanation
Indices: 2112--2178 Score: 64
Period size: 17 Copynumber: 3.9 Consensus size: 17
2102 TTTTATTTTA
2112 TTATTATTATTTATCTAT
1 TTATT-TTATTTATCTAT
* *
2130 TTCTTTTATTTATCTAA
1 TTATTTTATTTATCTAT
*
2147 TTATTTTTTGTTATCTA-
1 TTATTTTAT-TTATCTAT
* *
2164 TTAATATATTTATCT
1 TTATTTTATTTATCT
2179 TTTTTTATTT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
16 6 0.15
17 24 0.59
18 11 0.27
ACGTcount: A:0.25, C:0.07, G:0.01, T:0.66
Consensus pattern (17 bp):
TTATTTTATTTATCTAT
Found at i:2180 original size:45 final size:43
Alignment explanation
Indices: 2066--2186 Score: 101
Period size: 43 Copynumber: 2.8 Consensus size: 43
2056 ATTTTTTTTA
* * * *
2066 TTTTTTTATCTATTAATATCTTTAT-TATTTATCT-GCTTTTAT
1 TTTTTTTATCTATTAATATATTTATCT-TTTATTTATCTATTAT
* *
2108 TTTATTATTAT-TATTTATCTA-TT-TCTTTTATTTATCTAATTAT
1 TTT-TT-TTATCTATTAATATATTTATCTTTTATTTATCT-ATTAT
2151 TTTTTGTTATCTATTAATATATTTATCTTTT-TTTAT
1 TTTTT-TTATCTATTAATATATTTATCTTTTATTTAT
2187 TTTGATTAAT
Statistics
Matches: 62, Mismatches: 9, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
41 7 0.11
42 14 0.23
43 24 0.39
44 11 0.18
45 6 0.10
ACGTcount: A:0.23, C:0.07, G:0.02, T:0.68
Consensus pattern (43 bp):
TTTTTTTATCTATTAATATATTTATCTTTTATTTATCTATTAT
Found at i:2916 original size:4 final size:4
Alignment explanation
Indices: 2907--2956 Score: 55
Period size: 4 Copynumber: 11.8 Consensus size: 4
2897 AGATTTTTGG
* *
2907 TATT TATT TATTT TATT TATT TATTT TAACT TATT TTTT TATT TATT TAT
1 TATT TATT TA-TT TATT TATT TA-TT T-ATT TATT TATT TATT TATT TAT
2957 CAAAATAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
4 29 0.74
5 9 0.23
6 1 0.03
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:2923 original size:13 final size:13
Alignment explanation
Indices: 2907--2956 Score: 75
Period size: 13 Copynumber: 3.8 Consensus size: 13
2897 AGATTTTTGG
2907 TATTTATTTATTT
1 TATTTATTTATTT
2920 TATTTATTTATTT
1 TATTTATTTATTT
*
2933 TAACTTATTT-TTT
1 T-ATTTATTTATTT
2946 TATTTATTTAT
1 TATTTATTTAT
2957 CAAAATAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
12 7 0.21
13 19 0.58
14 7 0.21
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (13 bp):
TATTTATTTATTT
Found at i:4743 original size:28 final size:28
Alignment explanation
Indices: 4711--4764 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
4701 GCTGAATGAT
* *
4711 TTGCTGAACCTTGTTGTATGATATTGTA
1 TTGCTGAACCGTATTGTATGATATTGTA
**
4739 TTGCTGAATGGTATTGTATGATATTG
1 TTGCTGAACCGTATTGTATGATATTG
4765 GAGAGCTGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.22, C:0.07, G:0.24, T:0.46
Consensus pattern (28 bp):
TTGCTGAACCGTATTGTATGATATTGTA
Found at i:4754 original size:80 final size:79
Alignment explanation
Indices: 4627--4874 Score: 336
Period size: 80 Copynumber: 3.1 Consensus size: 79
4617 CTTAAATATT
* * * *
4627 ATGATTTGCTAAACCTTATTGTTTGAT-TTTTTTTGCTGAATGGTATTGTATGATATTGGGAGGT
1 ATGATTTGCTGAACCTTATTGTATGATATTATTTTGCTGAATGGTATTGTATGATATT-GGAGGC
4691 TGAATCGTATGCTGA
65 TGAATCGTATGCTGA
* * *
4706 ATGATTTGCTGAACCTTGTTGTATGATATTGTATTGCTGAATGGTATTGTATGATATTGGAGAGC
1 ATGATTTGCTGAACCTTATTGTATGATATTATTTTGCTGAATGGTATTGTATGATATTGGAG-GC
*
4771 TGAATCATATGCTGA
65 TGAATCGTATGCTGA
* * * * * *
4786 ATGGTTTGTTGAACCTTATTATCTGATATTATTTTGCTGAATGGTTTTGTATGATATTGGAGCCT
1 ATGATTTGCTGAACCTTATTGTATGATATTATTTTGCTGAATGGTATTGTATGATATTGGAGGCT
4851 GAATCGTATGCTGA
66 GAATCGTATGCTGA
*
4865 ATGGTTTGCT
1 ATGATTTGCT
4875 AAATGGTGTT
Statistics
Matches: 149, Mismatches: 18, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
79 52 0.35
80 97 0.65
ACGTcount: A:0.23, C:0.09, G:0.24, T:0.44
Consensus pattern (79 bp):
ATGATTTGCTGAACCTTATTGTATGATATTATTTTGCTGAATGGTATTGTATGATATTGGAGGCT
GAATCGTATGCTGA
Found at i:9409 original size:159 final size:159
Alignment explanation
Indices: 9035--9655 Score: 1052
Period size: 159 Copynumber: 3.9 Consensus size: 159
9025 GTTAGTTGTT
*
9035 GAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAAG
1 GAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAGG
*
9100 AGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTATTTAAAG---AAA
66 AGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGAAAAAA
* *
9162 AATCAAGATCAACCAATTAATTAATTATC
131 AAACAAAATCAACCAATTAATTAATTATC
9191 GAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAGG
1 GAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAGG
9256 AGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGAAAAAA
66 AGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGAAAAAA
*
9321 AAACAAGATCAACCAATTAATTAATTATC
131 AAACAAAATCAACCAATTAATTAATTATC
*
9350 AAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAGG
1 GAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAGG
*
9415 AGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGAATTAATTAAAGAAAAAA
66 AGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAG-AAAAA
* *
9480 AAAATCAAAATCAGCCAAGTAATTAATTATC
130 AAAA-CAAAATCAACCAATTAATTAATTATC
*
9511 GGAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAAATTCCCTCACCTCAG
1 GAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAG-AAAATTCCCTCACCTCAG
* *
9576 GAGTATGCAAGAAAAACTACTGTTTTTACTTGTAGAGGCTCCGTCGTCGGATTAATTAAAGAATA
65 GAGTATGCAAGAAAAACTACTG-TTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGAA-A
9641 AAGAAAA-AAAATCAA
128 AA-AAAACAAAATCAA
9656 GATCAAAATC
Statistics
Matches: 442, Mismatches: 14, Indels: 12
0.94 0.03 0.03
Matches are distributed among these distances:
156 122 0.28
159 153 0.35
160 9 0.02
161 67 0.15
162 49 0.11
163 38 0.09
164 4 0.01
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (159 bp):
GAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAGG
AGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGAAAAAA
AAACAAAATCAACCAATTAATTAATTATC
Found at i:10026 original size:19 final size:19
Alignment explanation
Indices: 9985--10028 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
9975 AACGCCGGTG
* *
9985 CCGGATTCTGGAAAATTCG
1 CCGGAATCTGGAAAATTCA
* *
10004 CCGGAATCTGGGAATTTCA
1 CCGGAATCTGGAAAATTCA
10023 CCGGAA
1 CCGGAA
10029 ATTGGCCGGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (19 bp):
CCGGAATCTGGAAAATTCA
Found at i:10484 original size:12 final size:12
Alignment explanation
Indices: 10467--10499 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
10457 CTAGCCCTCC
10467 AAAATAAAAATT
1 AAAATAAAAATT
10479 AAAAT-AAAATT
1 AAAATAAAAATT
10490 AAAA-AAAAAT
1 AAAATAAAAAT
10500 CTAGATAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 15 0.75
12 5 0.25
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (12 bp):
AAAATAAAAATT
Found at i:10738 original size:16 final size:16
Alignment explanation
Indices: 10719--10749 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
10709 TACACAAGAG
10719 AAAAAAAAAATAAAAT
1 AAAAAAAAAATAAAAT
*
10735 AAAATAAAAATAAAA
1 AAAAAAAAAATAAAA
10750 AATAAAGAAT
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:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (16 bp):
AAAAAAAAAATAAAAT
Found at i:10852 original size:20 final size:20
Alignment explanation
Indices: 10797--10855 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
10787 CCATTTGGGG
* *
10797 CAGGCCCAAATGATCTGGGT
1 CAGGCCCAATTGATCCGGGT
10817 CAGGCCCAATTGATCCGGGT
1 CAGGCCCAATTGATCCGGGT
10837 CAGGCCCAATTGATCCGGG
1 CAGGCCCAATTGATCCGGG
10856 CCCGGACCTG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.22, C:0.29, G:0.31, T:0.19
Consensus pattern (20 bp):
CAGGCCCAATTGATCCGGGT
Found at i:11051 original size:41 final size:40
Alignment explanation
Indices: 10994--11640 Score: 808
Period size: 41 Copynumber: 15.7 Consensus size: 40
10984 AGCTCTTCTG
*
10994 ACAGAGGCTCTACGACTTTGAAAAATAAATTGCTCCTCTAA
1 ACAGAGGCAC-ACGACTTTGAAAAATAAATTGCTCCTCTAA
*
11035 ACAGAGGCACCACGACTTTGAAAGATAAATTGCTCCTCTAA
1 ACAGAGGCA-CACGACTTTGAAAAATAAATTGCTCCTCTAA
*
11076 ACAGAGG-ACCACGACTTTGAAAAAATAAATTGCTCCTCTCA
1 ACAGAGGCA-CACGACTTTG-AAAAATAAATTGCTCCTCTAA
*
11117 ACAGAGGTACCACGACTTTGGAAAAATAAATTTGCTCCTCTAA
1 ACAGAGGCA-CACGACTTT-GAAAAATAAA-TTGCTCCTCTAA
* * * *
11160 ACCGAGGTACCACGACTTTGGAAAAGTAAATTGCTCCTCTCA
1 ACAGAGGCA-CACGACTTT-GAAAAATAAATTGCTCCTCTAA
*
11202 ACAGAGGCACCACGACTTTGGAAAAAT-AATTGCTCCTCTCA
1 ACAGAGGCA-CACGACTTT-GAAAAATAAATTGCTCCTCTAA
*
11243 ACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAA
1 ACAGAGGCA-CACGACTTTGAAAAATAAATTGCTCCTCTAA
*
11284 ACAGAGGCA-ACGAACTTTGAAAAGTAAATTGCTCCTCTAA
1 ACAGAGGCACACG-ACTTTGAAAAATAAATTGCTCCTCTAA
* *
11324 ACAGAGGCACTACGACTTTGGAAAGTAAATTGCTCCTCTAA
1 ACAGAGGCAC-ACGACTTTGAAAAATAAATTGCTCCTCTAA
* * *
11365 ACAGAGGCA-ACGAACTTTGGAAAGTAAATTGCTCCTCTCA
1 ACAGAGGCACACG-ACTTTGAAAAATAAATTGCTCCTCTAA
11405 ACAGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTAA
1 ACAGAGGCA-CACGACTTT-GAAAAATAAATTGCTCCTCTAA
* *
11447 ACAGAGGCA-ACGAACTTGGAAAAGTAAATTGCTCCTCTAA
1 ACAGAGGCACACG-ACTTTGAAAAATAAATTGCTCCTCTAA
11487 ACAGAGGCA-ACGAACTTTGAAAAAAGTAAATTGCTCCTCTAA
1 ACAGAGGCACACG-ACTTTG-AAAAA-TAAATTGCTCCTCTAA
*
11529 ATAGAGGCA-ACGAACTTTGAAAAAAATAAATTGCTCCTCTAA
1 ACAGAGGCACACG-ACTTTG--AAAAATAAATTGCTCCTCTAA
11571 ACAGAGGCA-ACGGAACTTTGAAAAATAAATTGCTCCTCTAA
1 ACAGAGGCACAC-G-ACTTTGAAAAATAAATTGCTCCTCTAA
*
11612 ACAGAGGCA-ACGAACTTTGAAAAGTAAAT
1 ACAGAGGCACACG-ACTTTGAAAAATAAAT
11641 ACTCCTAGAC
Statistics
Matches: 563, Mismatches: 25, Indels: 37
0.90 0.04 0.06
Matches are distributed among these distances:
39 6 0.01
40 148 0.26
41 205 0.36
42 150 0.27
43 54 0.10
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23
Consensus pattern (40 bp):
ACAGAGGCACACGACTTTGAAAAATAAATTGCTCCTCTAA
Found at i:12849 original size:7 final size:7
Alignment explanation
Indices: 12831--12865 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
12821 TCGGATCTCT
12831 TTTTTCA
1 TTTTTCA
12838 TTTTTTCA
1 -TTTTTCA
12846 TTTTTCA
1 TTTTTCA
*
12853 TTTCTCA
1 TTTTTCA
12860 TTTTTC
1 TTTTTC
12866 TTCTTTCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.11, C:0.17, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTTTCA
Found at i:12851 original size:15 final size:14
Alignment explanation
Indices: 12826--12865 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
12816 TCAATTCGGA
*
12826 TCTCTTTTTTCATTT
1 TCTCATTTTTCA-TT
*
12841 TTTCATTTTTCATT
1 TCTCATTTTTCATT
12855 TCTCATTTTTC
1 TCTCATTTTTC
12866 TTCTTTCTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.10, C:0.20, G:0.00, T:0.70
Consensus pattern (14 bp):
TCTCATTTTTCATT
Found at i:12865 original size:21 final size:20
Alignment explanation
Indices: 12839--12877 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
12829 CTTTTTTCAT
12839 TTTTTCATT-TTTCATTTCTCA
1 TTTTTC-TTCTTTC-TTTCTCA
12860 TTTTTCTTCTTTCTTTCT
1 TTTTTCTTCTTTCTTTCT
12878 TTTTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.08, C:0.21, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTTCTTCTTTCTTTCTCA
Found at i:17139 original size:17 final size:16
Alignment explanation
Indices: 17092--17162 Score: 60
Period size: 16 Copynumber: 4.5 Consensus size: 16
17082 AAAGAAAAAG
17092 AAAAAAAAATCAAGATCA
1 AAAAAAAAATCAA-AT-A
** *
17110 AAATCAAAGTCAAATA
1 AAAAAAAAATCAAATA
17126 AAAAAAAAATTCAAA-A
1 AAAAAAAAA-TCAAATA
17142 AAAAAAAAA--AAA-A
1 AAAAAAAAATCAAATA
17155 AAAAAAAA
1 AAAAAAAA
17163 CCTGGAGCGG
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
13 12 0.26
16 17 0.37
17 7 0.15
18 10 0.22
ACGTcount: A:0.80, C:0.07, G:0.03, T:0.10
Consensus pattern (16 bp):
AAAAAAAAATCAAATA
Found at i:17142 original size:1 final size:1
Alignment explanation
Indices: 17138--17162 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
17128 AAAAAAATTC
17138 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
17163 CCTGGAGCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:17445 original size:19 final size:19
Alignment explanation
Indices: 17421--17465 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
17411 GAACGCCGGT
17421 GCCGGATTCTGGAAATTTC
1 GCCGGATTCTGGAAATTTC
* *
17440 GCCGGAATCTGGGAATTTC
1 GCCGGATTCTGGAAATTTC
17459 GCCGGAT
1 GCCGGAT
17466 GGTCGCCGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.20, C:0.22, G:0.31, T:0.27
Consensus pattern (19 bp):
GCCGGATTCTGGAAATTTC
Found at i:17551 original size:29 final size:30
Alignment explanation
Indices: 17509--17565 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
17499 TGGGTCTGTC
*
17509 GCCGGAAACTTC-AAAGTTCG-CGGAATTGT
1 GCCGGAAAATTCAAAAG-TCGCCGGAATTGT
17538 GCCGGAAAATTCAAAAGTCGCCGGAATT
1 GCCGGAAAATTCAAAAGTCGCCGGAATT
17566 TCCGCCGGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.21
Consensus pattern (30 bp):
GCCGGAAAATTCAAAAGTCGCCGGAATTGT
Found at i:17953 original size:35 final size:35
Alignment explanation
Indices: 17890--17959 Score: 88
Period size: 36 Copynumber: 2.0 Consensus size: 35
17880 TTAGCCCTCC
* *
17890 AAATCAAAAATAAAAAAATACTAGATAATAATCAGA
1 AAATCAAAAATAAAAAAATACAAAATAAT-ATCAGA
* *
17926 AAATCAAAAATTAAAAATTA-AAAATAATATCAGA
1 AAATCAAAAATAAAAAAATACAAAATAATATCAGA
17960 TAATTCGGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 6 0.20
35 6 0.20
36 18 0.60
ACGTcount: A:0.67, C:0.07, G:0.04, T:0.21
Consensus pattern (35 bp):
AAATCAAAAATAAAAAAATACAAAATAATATCAGA
Found at i:20981 original size:26 final size:25
Alignment explanation
Indices: 20930--20992 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 25
20920 AAATTTACCC
*
20930 ATTTTATTAATGATATCATCTTATTT
1 ATTTTATTAATAATATCATC-TATTT
20956 ATTTTATTAATAATATGACATC-ATTT
1 ATTTTATTAATAATAT--CATCTATTT
*
20982 AATTT-TTAATA
1 ATTTTATTAATA
20993 TAATATAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
25 6 0.18
26 23 0.70
28 4 0.12
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.54
Consensus pattern (25 bp):
ATTTTATTAATAATATCATCTATTT
Found at i:21168 original size:18 final size:16
Alignment explanation
Indices: 21128--21173 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 16
21118 ATATATTAAT
21128 AGAAAATAAATTAAATG
1 AGAAAA-AAATTAAATG
21145 AGAAAAAAATATAAATG
1 AGAAAAAAAT-TAAATG
21162 AGCAAAAAAATT
1 AG-AAAAAAATT
21174 GTCATGTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 4 0.15
17 15 0.56
18 8 0.30
ACGTcount: A:0.67, C:0.02, G:0.11, T:0.20
Consensus pattern (16 bp):
AGAAAAAAATTAAATG
Found at i:22055 original size:21 final size:21
Alignment explanation
Indices: 22020--22081 Score: 81
Period size: 21 Copynumber: 2.9 Consensus size: 21
22010 ATAATTTTTT
*
22020 TTATGAATTTTTTTAATTATAA
1 TTAT-AATATTTTTAATTATAA
*
22042 TTATAATATTTTTAACTATAA
1 TTATAATATTTTTAATTATAA
22063 TTATAATAATTTTT-ATTAT
1 TTATAAT-ATTTTTAATTAT
22082 TTTTTTAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
21 26 0.72
22 10 0.28
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (21 bp):
TTATAATATTTTTAATTATAA
Found at i:25874 original size:22 final size:22
Alignment explanation
Indices: 25846--25889 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
25836 ATCAAAACCT
25846 TGTTTGGAATTTTGAGCCAGTA
1 TGTTTGGAATTTTGAGCCAGTA
25868 TGTTTGGAATTTTGAGCCAGTA
1 TGTTTGGAATTTTGAGCCAGTA
25890 CTAACTCATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.09, G:0.27, T:0.41
Consensus pattern (22 bp):
TGTTTGGAATTTTGAGCCAGTA
Done.