Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168038.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_290, 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: 38551
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Found at i:1867 original size:23 final size:25
Alignment explanation
Indices: 1822--1868 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 25
1812 AAATAATAAT
*
1822 AAATATAAAAATATAAAAGGCAAAA
1 AAATATAAAAATATAAAACGCAAAA
*
1847 AAAT-TAAAAA-ATTAAACGCAAA
1 AAATATAAAAATATAAAACGCAAA
1869 TCTAAATCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 10 0.50
24 6 0.30
25 4 0.20
ACGTcount: A:0.70, C:0.06, G:0.06, T:0.17
Consensus pattern (25 bp):
AAATATAAAAATATAAAACGCAAAA
Found at i:1914 original size:43 final size:43
Alignment explanation
Indices: 1866--1950 Score: 143
Period size: 43 Copynumber: 2.0 Consensus size: 43
1856 AATTAAACGC
* * *
1866 AAATCTAAATCATCATAAAAAATTTTGGTCGTATTTTTCTTTT
1 AAATCTAAATCATCATAAAAAAATTTAGTCGCATTTTTCTTTT
1909 AAATCTAAATCATCATAAAAAAATTTAGTCGCATTTTTCTTT
1 AAATCTAAATCATCATAAAAAAATTTAGTCGCATTTTTCTTT
1951 CTCTTTTTCT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.38, C:0.13, G:0.06, T:0.44
Consensus pattern (43 bp):
AAATCTAAATCATCATAAAAAAATTTAGTCGCATTTTTCTTTT
Found at i:12250 original size:11 final size:11
Alignment explanation
Indices: 12216--12243 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
12206 TTTCTCTAAA
12216 TTTTTTGTAAT
1 TTTTTTGTAAT
12227 TTTTTTGTAAT
1 TTTTTTGTAAT
12238 TTTTTT
1 TTTTTT
12244 TTCATTTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (11 bp):
TTTTTTGTAAT
Found at i:13037 original size:30 final size:30
Alignment explanation
Indices: 12997--13070 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 30
12987 AAATCTTCTA
* *
12997 TTTCAATCAATTAAACCTTTACATATATTT
1 TTTCAATCAATTAAACCTTTACACATATGT
* * * *
13027 TTTCACTCAATTAAACTTTTATACATCTGT
1 TTTCAATCAATTAAACCTTTACACATATGT
*
13057 TTTCATTCAATTAA
1 TTTCAATCAATTAA
13071 GCTCTTTATT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.34, C:0.18, G:0.01, T:0.47
Consensus pattern (30 bp):
TTTCAATCAATTAAACCTTTACACATATGT
Found at i:15039 original size:25 final size:23
Alignment explanation
Indices: 14992--15107 Score: 66
Period size: 25 Copynumber: 5.2 Consensus size: 23
14982 TTTTCTTTCT
**
14992 TTTATATTTTATGTATTTTTATA
1 TTTATATTTTATGTATTAATATA
15015 TTTATTATTATTATGTATTAATATA
1 TTTA-TATT-TTATGTATTAATATA
* * *
15040 TGTATA---TATGTATTTATTTA
1 TTTATATTTTATGTATTAATATA
* * * *
15060 TTT-TTTTTTATTTA-GAATAGA
1 TTTATATTTTATGTATTAATATA
*
15081 TTTATA-TTTATATAGTT-ATATA
1 TTTATATTTTATGTA-TTAATATA
15103 TTTAT
1 TTTAT
15108 TATTATATTA
Statistics
Matches: 69, Mismatches: 16, Indels: 17
0.68 0.16 0.17
Matches are distributed among these distances:
19 1 0.01
20 14 0.20
21 13 0.19
22 15 0.22
23 4 0.06
24 6 0.09
25 16 0.23
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (23 bp):
TTTATATTTTATGTATTAATATA
Found at i:15116 original size:28 final size:26
Alignment explanation
Indices: 15082--15143 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 26
15072 TAGAATAGAT
15082 TTATATTTATATAGTTATATATTTATTA
1 TTATATTTATA-AGTTATATA-TTATTA
* *
15110 TTATA-TTATAATTTATGTATTATTA
1 TTATATTTATAAGTTATATATTATTA
15135 TTATTATTT
1 TTA-TATTT
15144 TTTTTTCTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
25 9 0.30
26 9 0.30
27 7 0.23
28 5 0.17
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (26 bp):
TTATATTTATAAGTTATATATTATTA
Found at i:15627 original size:31 final size:31
Alignment explanation
Indices: 15560--15632 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
15550 AATTTCCAGA
* * *
15560 TTCCGACGAAAATTCCGGCGACTTTTGAATT
1 TTCCGGCGACAATTCCGGCGACTTTTGAAGT
15591 TTCCGGCGACAATTCCGGCGAAC-TTTGAAGT
1 TTCCGGCGACAATTCCGGCG-ACTTTTGAAGT
15622 TTCCGGCGACA
1 TTCCGGCGACA
15633 GACCCAGTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
31 36 0.95
32 2 0.05
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.27
Consensus pattern (31 bp):
TTCCGGCGACAATTCCGGCGACTTTTGAAGT
Found at i:15721 original size:19 final size:20
Alignment explanation
Indices: 15692--15731 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
15682 CTTCCGGCCA
15692 ATTTCCGGCGAAATTCCCAG
1 ATTTCCGGCGAAATTCCCAG
*
15712 ATTT-CGGCGAAATTTCCAG
1 ATTTCCGGCGAAATTCCCAG
15731 A
1 A
15732 ATCCGGCACC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.28
Consensus pattern (20 bp):
ATTTCCGGCGAAATTCCCAG
Found at i:15738 original size:19 final size:19
Alignment explanation
Indices: 15695--15738 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
15685 CCGGCCAATT
*
15695 TCCGGCGAAATTCCCAGAT
1 TCCGGCGAAATTCCCAGAA
* *
15714 TTCGGCGAAATTTCCAGAA
1 TCCGGCGAAATTCCCAGAA
15733 TCCGGC
1 TCCGGC
15739 ACCGGCGTTC
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:0.25, C:0.30, G:0.23, T:0.23
Consensus pattern (19 bp):
TCCGGCGAAATTCCCAGAA
Found at i:15966 original size:5 final size:5
Alignment explanation
Indices: 15956--15998 Score: 68
Period size: 5 Copynumber: 8.6 Consensus size: 5
15946 TTCAGCCCCT
* *
15956 CCGAG CCGAG CCGAG CCGAG CCGAG CCGAA CCAAG CCGAG CCG
1 CCGAG CCGAG CCGAG CCGAG CCGAG CCGAG CCGAG CCGAG CCG
15999 CGATCCGAGC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.23, C:0.42, G:0.35, T:0.00
Consensus pattern (5 bp):
CCGAG
Found at i:16047 original size:15 final size:14
Alignment explanation
Indices: 16018--16085 Score: 50
Period size: 15 Copynumber: 4.6 Consensus size: 14
16008 CCGCTCCAGG
16018 TTTTTTTTTTT--T
1 TTTTTTTTTTTGAT
16030 TTTTTTTTTTTGAAT
1 TTTTTTTTTTTG-AT
*
16045 TTTTTTTATTTGACT
1 TTTTTTTTTTTGA-T
* *
16060 TTGATTTTGATCTTGAT
1 TT--TTTT-TTTTTGAT
16077 TTTTTTTTT
1 TTTTTTTTT
16086 CTTTTTTTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
12 11 0.26
14 2 0.05
15 19 0.44
17 7 0.16
18 4 0.09
ACGTcount: A:0.10, C:0.03, G:0.07, T:0.79
Consensus pattern (14 bp):
TTTTTTTTTTTGAT
Found at i:16092 original size:11 final size:11
Alignment explanation
Indices: 16076--16100 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
16066 TTGATCTTGA
16076 TTTTTTTTTTC
1 TTTTTTTTTTC
16087 TTTTTTTTTTC
1 TTTTTTTTTTC
16098 TTT
1 TTT
16101 AATTAATCCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:16600 original size:154 final size:153
Alignment explanation
Indices: 16090--16699 Score: 913
Period size: 155 Copynumber: 3.9 Consensus size: 153
16080 TTTTTTCTTT
* * *
16090 TTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTACAAGTAAAAATAGTAGTTTTTCTTGCATA
1 TTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGT-GAAACAGTAGTTTTTCTTGCATA
16155 CTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTT
65 CTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTT
* * *
16220 CTGATAATTAATTACTTGGCTGATTTTG
130 C---CAA-TAATTAATTGGATGATTTTG
*
16248 ATTTTTTTTCTTTAATTAATCCGACGATGGA-CCTCTGCAAGTGAAACAGTAGTTTTTTCTTGCA
1 --TTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAG-TTTTTCTTGCA
* *
16312 TACTCTTGAGGTGAGGGAA-TTTCTCAAATTTTCTGCTAAAAGTATTAGAGTTAATTGAGAATAA
63 TACTCCTGAGGTGAGGGAATTTTCTC-AATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAA
*
16376 TTTCCCATACATTAATTGGATGATTTTG
127 TTTCCAATA-ATTAATTGGATGATTTTG
*
16404 -ATTTTTCTTTAATTAATCCGACGACAGGAGCCTCTGCAAGTGAAACAGTAGTTTTTTCTTGCAT
1 TTTTTTTCTTTAATTAATCCGACGAC-GGAGCCTCTGCAAGTGAAACAGTAG-TTTTTCTTGCAT
* *
16468 ACTCTTGAGGTGA-GGAATTTTCTCAATTTTCTGCTAAAAAGTATTAGAGTTAATTGAGAATAAT
64 ACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCT-AAAAGTATTAGAGTCAATTGAGAATAAT
16532 TTCCAATAATTAATTGGATGATTTTG
128 TTCCAATAATTAATTGGATGATTTTG
* *
16558 TTTTTTTCTTTAATAAATCCGACGACGGAGCCCCTGCAAGTGAAACAGTAGTTTTTCTTGCATAC
1 TTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGCATAC
*
16623 TCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATCATTTC
66 TCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTC
* *
16688 CAACAACTAATT
131 CAATAATTAATT
16700 ACTTGGTAAA
Statistics
Matches: 420, Mismatches: 21, Indels: 25
0.90 0.05 0.05
Matches are distributed among these distances:
153 86 0.20
154 82 0.20
155 113 0.27
156 17 0.04
158 14 0.03
159 80 0.19
160 28 0.07
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.39
Consensus pattern (153 bp):
TTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGCATAC
TCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTC
CAATAATTAATTGGATGATTTTG
Found at i:20367 original size:8 final size:8
Alignment explanation
Indices: 20354--20400 Score: 51
Period size: 8 Copynumber: 5.9 Consensus size: 8
20344 GATGATGGAA
20354 AAAAAAAG
1 AAAAAAAG
20362 AAAAAAAG
1 AAAAAAAG
20370 -AAAAAAG
1 AAAAAAAG
*
20377 AAAGAAATG
1 AAA-AAAAG
* *
20386 AGAAAATG
1 AAAAAAAG
20394 AAAAAAA
1 AAAAAAA
20401 AGAGATTCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
7 7 0.21
8 20 0.61
9 6 0.18
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (8 bp):
AAAAAAAG
Found at i:21776 original size:42 final size:41
Alignment explanation
Indices: 21626--22162 Score: 773
Period size: 42 Copynumber: 13.0 Consensus size: 41
21616 GTCAAGGAGT
* *
21626 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTCCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCA
* *
21667 ATTTAATTTCCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTCCAAAG-TCGTGGTGCCTCTGTTGAGAGGAGCA
*
21707 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCA
1 ATTTACTTTCCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCA
*
21748 ATTTATCTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTA-CTTTCCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCA
*
21790 ATTTATTTTTCCAAAGTCGTGGTG-CTCTGTTGAGAGGAGCA
1 ATTTA-CTTTCCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCA
*
21831 ATTTATTTTTTCCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCA
1 ATTTA--CTTTCCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCA
*
21874 ATTTATTTTTTCCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCA
1 ATTTA--CTTTCCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCA
* *
21917 ATTTATTTTTTCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCA
1 ATTTA-CTTTCCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCA
*
21959 ATTTACTTTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGCA
1 ATTTAC-TTTCCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCA
*
22001 ATTTACTTTCCAAAGTCCGT--TGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTCCAAAGT-CGTGGTGCCTCTGTTGAGAGGAGCA
22041 ATTTACTTTCCAAAGTCCGT--TGCCTCTGTTGAGAGGAGCA
1 ATTTACTTTCCAAAGT-CGTGGTGCCTCTGTTGAGAGGAGCA
*
22081 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCA
1 ATTTACTTTCCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCA
* *
22122 ATTTATCTTTCCAAAGTCGTGTTGCCTCTGTTTAGAGGAGC
1 ATTTA-CTTTCCAAAGTCGTGGTGCCTCTGTTGAGAGGAGC
22163 TTCGGCAAAA
Statistics
Matches: 465, Mismatches: 20, Indels: 21
0.92 0.04 0.04
Matches are distributed among these distances:
39 7 0.02
40 105 0.23
41 93 0.20
42 195 0.42
43 65 0.14
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (41 bp):
ATTTACTTTCCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCA
Found at i:22186 original size:9 final size:9
Alignment explanation
Indices: 22169--22242 Score: 107
Period size: 9 Copynumber: 8.2 Consensus size: 9
22159 GAGCTTCGGC
22169 AAAAA-AAA
1 AAAAACAAA
22177 AAAAACAAA
1 AAAAACAAA
22186 AAAAACAAA
1 AAAAACAAA
22195 AAACAA-AAA
1 AAA-AACAAA
*
22204 AAAACAAAAA
1 AAAA-ACAAA
22214 AAAAACAAA
1 AAAAACAAA
22223 AAAAACAAA
1 AAAAACAAA
22232 AAAAACAAA
1 AAAAACAAA
22241 AA
1 AA
22243 TTTTTAAAAA
Statistics
Matches: 61, Mismatches: 1, Indels: 7
0.88 0.01 0.10
Matches are distributed among these distances:
8 6 0.10
9 46 0.75
10 9 0.15
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAACAAA
Found at i:22255 original size:37 final size:37
Alignment explanation
Indices: 22172--22242 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
22162 CTTCGGCAAA
22172 AAAAAAAAAACAAAAAAAACAAAAAACAAAAAAAAAC
1 AAAAAAAAAACAAAAAAAACAAAAAACAAAAAAAAAC
*
22209 AAAAAAAAAACAAAAAAAACAAAAAA-AACAAAAA
1 AAAAAAAAAACAAAAAAAACAAAAAACAAAAAAAA
22243 TTTTTAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 7 0.21
37 26 0.79
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (37 bp):
AAAAAAAAAACAAAAAAAACAAAAAACAAAAAAAAAC
Found at i:22257 original size:1 final size:1
Alignment explanation
Indices: 22169--22242 Score: 85
Period size: 1 Copynumber: 74.0 Consensus size: 1
22159 GAGCTTCGGC
* * * * * *
22169 AAAAAAAAAAAAACAAAAAAAACAAAAAACAAAAAAAAACAAAAAAAAAACAAAAAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
22234 AAACAAAAA
1 AAAAAAAAA
22243 TTTTTAAAAA
Statistics
Matches: 59, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 59 1.00
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:22592 original size:3 final size:3
Alignment explanation
Indices: 22579--22609 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
22569 TGGGTTTATC
22579 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
22610 TTTAATTATC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:23106 original size:31 final size:31
Alignment explanation
Indices: 23035--23107 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
23025 AATTTCCAGA
* *
23035 TTCCGGCGAAAATTCCGGCGACTTTTGAATT
1 TTCCGGCGACAATTCCGGCGACTTTTGAAGT
*
23066 TTTCGGCGACAATTCCGGCGAAC-TTTGAAGT
1 TTCCGGCGACAATTCCGGCG-ACTTTTGAAGT
23097 TTCCGGCGACA
1 TTCCGGCGACA
23108 GACCCAGTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
31 35 0.95
32 2 0.05
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.29
Consensus pattern (31 bp):
TTCCGGCGACAATTCCGGCGACTTTTGAAGT
Found at i:23195 original size:19 final size:19
Alignment explanation
Indices: 23171--23212 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
23161 CGGCCAATTT
*
23171 CGGCGAAATTCCCAGATTC
1 CGGCGAAATTCCCAGAATC
*
23190 CGGCGAAATTTCCAGAATC
1 CGGCGAAATTCCCAGAATC
23209 CGGC
1 CGGC
23213 ACCGGCGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.26, C:0.31, G:0.24, T:0.19
Consensus pattern (19 bp):
CGGCGAAATTCCCAGAATC
Found at i:23442 original size:5 final size:5
Alignment explanation
Indices: 23432--23474 Score: 68
Period size: 5 Copynumber: 8.6 Consensus size: 5
23422 TTCAGCCCCT
* *
23432 CCGAG CCGAG CCGAG CCGAG CCGAG CCGAA CCAAG CCGAG CCG
1 CCGAG CCGAG CCGAG CCGAG CCGAG CCGAG CCGAG CCGAG CCG
23475 CGATCCGAGC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.23, C:0.42, G:0.35, T:0.00
Consensus pattern (5 bp):
CCGAG
Found at i:23824 original size:160 final size:154
Alignment explanation
Indices: 23556--24019 Score: 743
Period size: 160 Copynumber: 3.0 Consensus size: 154
23546 CTTGATTTTT
* *
23556 TTTTCTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTACAAGTGAAACAGTAGTTTTTCTTGC
1 TTTTGTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGC
23621 ATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAA
66 ATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAA
* *
23686 TTTTCGATAATTAATTACTTGGCTGA
131 TTTTC-ACAA-TAATTACTTGGATGA
23712 TTTTGATTTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTTC
1 TTTTG---TTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAG-TTTTTC
*
23777 TTGCATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTTAATTGAGA
62 TTGCATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGA
*
23842 ATAA-TTTC-CAATAATTAATTGGATGA
127 ATAATTTTCACAATAATTACTTGGATGA
* *
23868 TTTTGTTTTTTCTTTAATAAATCCGACGACGGAGCCCCTGCAAGTGAAACAGTAGTTTTTCTTGC
1 TTTTGTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGC
* *
23933 ATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATCA
66 ATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAA
*
23998 TTTCCAACAACTAATTACTTGG
131 TTTTC-ACAA-TAATTACTTGG
24020 TAAAATTTTA
Statistics
Matches: 287, Mismatches: 13, Indels: 16
0.91 0.04 0.05
Matches are distributed among these distances:
152 72 0.25
153 51 0.18
155 3 0.01
156 32 0.11
157 2 0.01
159 53 0.18
160 74 0.26
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (154 bp):
TTTTGTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGC
ATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAA
TTTTCACAATAATTACTTGGATGA
Found at i:23992 original size:152 final size:152
Alignment explanation
Indices: 23556--24013 Score: 736
Period size: 152 Copynumber: 3.0 Consensus size: 152
23546 CTTGATTTTT
* *
23556 TTTTCTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTACAAGTGAAACAGTAGTTTTTCTTGC
1 TTTTGTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGC
23621 ATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAA
66 ATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAA
* * *
23686 TTTTCGATAATTAATTACTTGGCTGA
131 -TTTC--CAA-TAATTAATTGGATGA
23712 TTTTGATTTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTTC
1 TTTTG---TTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAG-TTTTTC
*
23777 TTGCATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTTAATTGAGA
62 TTGCATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGA
23842 ATAATTTCCAATAATTAATTGGATGA
127 ATAATTTCCAATAATTAATTGGATGA
* *
23868 TTTTGTTTTTTCTTTAATAAATCCGACGACGGAGCCCCTGCAAGTGAAACAGTAGTTTTTCTTGC
1 TTTTGTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGC
* *
23933 ATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATCA
66 ATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAA
* *
23998 TTTCCAACAACTAATT
131 TTTCCAATAATTAATT
24014 ACTTGGTAAA
Statistics
Matches: 285, Mismatches: 13, Indels: 12
0.92 0.04 0.04
Matches are distributed among these distances:
152 86 0.30
153 48 0.17
156 22 0.08
157 2 0.01
159 53 0.19
160 74 0.26
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39
Consensus pattern (152 bp):
TTTTGTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGC
ATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAA
TTTCCAATAATTAATTGGATGA
Found at i:29174 original size:20 final size:20
Alignment explanation
Indices: 29137--29175 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
29127 TTTTTGTAGT
* *
29137 TTTTTTTTTCTATATTTTCA
1 TTTTTATTTATATATTTTCA
*
29157 TTTTTATTTATATTTTTTC
1 TTTTTATTTATATATTTTC
29176 TCTTTTCTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTTATTTATATATTTTCA
Found at i:33198 original size:170 final size:170
Alignment explanation
Indices: 32916--33262 Score: 563
Period size: 170 Copynumber: 2.0 Consensus size: 170
32906 AAAGTTCTTA
* *
32916 AAATGTTTATAATTTAAAATAAATTGAAAAAACGTCATAGATTTGATCAAATCATTTATAAATTT
1 AAATGTTCATAATTTAAAATAAATTGAAAAAACGTCATAGATTTGATCAAATCATTTAAAAATTT
*
32981 AAAAATAAAAAATAAAAGTTCACATCATCGCACAAAAAAAACCAACAACAAAAACGTAATCATAA
66 AAAAATAAAAAATAAAAGTTCACATCATAGCACAAAAAAAACCAACAACAAAAACGTAATCATAA
* *
33046 TATATTAATTATTTTTAGTTTTGATGTATTTATAAGATTC
131 TATATTAATTATTTTTAATTTTGATATATTTATAAGATTC
*
33086 AAATGTTCATAATTTAAAATAAATTGAAAAAAGGTCATAGATTTGATCAAAT-AGTTTAAAAATT
1 AAATGTTCATAATTTAAAATAAATTGAAAAAACGTCATAGATTTGATCAAATCA-TTTAAAAATT
* * *
33150 TTAAAATAAAAAATGAAAGTTCACTTCATAGCA-AAAAACAAACCAACAACAAAAACGTAATCAT
65 TAAAAATAAAAAATAAAAGTTCACATCATAGCACAAAAA-AAACCAACAACAAAAACGTAATCAT
*
33214 AGTATATTAATTATTTTTAATTTTGATATATTTATAAGATTC
129 AATATATTAATTATTTTTAATTTTGATATATTTATAAGATTC
33256 AACATGT
1 AA-ATGT
33263 GAGTATTTTT
Statistics
Matches: 164, Mismatches: 10, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
169 6 0.04
170 154 0.94
171 4 0.02
ACGTcount: A:0.49, C:0.10, G:0.08, T:0.33
Consensus pattern (170 bp):
AAATGTTCATAATTTAAAATAAATTGAAAAAACGTCATAGATTTGATCAAATCATTTAAAAATTT
AAAAATAAAAAATAAAAGTTCACATCATAGCACAAAAAAAACCAACAACAAAAACGTAATCATAA
TATATTAATTATTTTTAATTTTGATATATTTATAAGATTC
Found at i:33318 original size:21 final size:21
Alignment explanation
Indices: 33278--33319 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
33268 TTTTTTTTTG
* * *
33278 TATTAAAAATAATTATAAATA
1 TATTAAAAACAATGAAAAATA
33299 TATTAAAAACAATGAAAAATA
1 TATTAAAAACAATGAAAAATA
33320 ACTTATCCTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (21 bp):
TATTAAAAACAATGAAAAATA
Found at i:33859 original size:32 final size:34
Alignment explanation
Indices: 33807--33890 Score: 104
Period size: 32 Copynumber: 2.5 Consensus size: 34
33797 TTTTTATAAA
*
33807 ATAAA-AATAATAATTGTATATGAAAAT-ATAT-T
1 ATAAATAATAA-AATTTTATATGAAAATAATATAT
33839 -TAAATATATAAAATTTTATATGAAAATAATATAT
1 ATAAATA-ATAAAATTTTATATGAAAATAATATAT
*
33873 ATAAATAATTAAATTTTA
1 ATAAATAATAAAATTTTA
33891 AAAATTGATA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
31 4 0.09
32 16 0.36
33 8 0.18
34 11 0.24
35 6 0.13
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (34 bp):
ATAAATAATAAAATTTTATATGAAAATAATATAT
Found at i:37887 original size:52 final size:52
Alignment explanation
Indices: 37814--37918 Score: 158
Period size: 52 Copynumber: 2.0 Consensus size: 52
37804 TATAAGTATA
*
37814 CAAACTTGCCTATTAGAAATCCCTTTCCTCTTAGAATTCTTCTTCTACAAGT
1 CAAACTTGCCTATTAGAAATCCATTTCCTCTTAGAATTCTTCTTCTACAAGT
* * *
37866 CAAACTTGCCTATTA-ATAATCCATTTTCTCTTAGAATTCTTCTTTTGCAAGT
1 CAAACTTGCCTATTAGA-AATCCATTTCCTCTTAGAATTCTTCTTCTACAAGT
37918 C
1 C
37919 TTCTTGTCCA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
51 1 0.02
52 47 0.98
ACGTcount: A:0.27, C:0.25, G:0.08, T:0.41
Consensus pattern (52 bp):
CAAACTTGCCTATTAGAAATCCATTTCCTCTTAGAATTCTTCTTCTACAAGT
Done.