Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168155.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_396, 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: 29033
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.38
Found at i:93 original size:7 final size:7
Alignment explanation
Indices: 79--144 Score: 59
Period size: 7 Copynumber: 9.6 Consensus size: 7
69 CCCCTTTTTG
79 TTTT-TA
1 TTTTGTA
85 TTTTGTA
1 TTTTGTA
92 TTTTGTA
1 TTTTGTA
99 -TTT-T-
1 TTTTGTA
*
103 TTTAGTA
1 TTTTGTA
*
110 TTTAGTA
1 TTTTGTA
117 TTTTGGTA
1 TTTT-GTA
125 TTTCTTGTA
1 -TT-TTGTA
134 TTTTGTA
1 TTTTGTA
141 TTTT
1 TTTT
145 TTGTATTCTA
Statistics
Matches: 51, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
5 3 0.06
6 8 0.16
7 28 0.55
8 5 0.10
9 5 0.10
10 2 0.04
ACGTcount: A:0.15, C:0.02, G:0.12, T:0.71
Consensus pattern (7 bp):
TTTTGTA
Found at i:97 original size:18 final size:18
Alignment explanation
Indices: 74--120 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
64 CATCCCCCCT
*
74 TTTTGT-TTTTATTTTGTA
1 TTTTGTATTTT-TTTAGTA
92 TTTTGTATTTTTTTAGTA
1 TTTTGTATTTTTTTAGTA
*
110 TTTAGTATTTT
1 TTTTGTATTTT
121 GGTATTTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 22 0.85
19 4 0.15
ACGTcount: A:0.15, C:0.00, G:0.11, T:0.74
Consensus pattern (18 bp):
TTTTGTATTTTTTTAGTA
Found at i:136 original size:9 final size:8
Alignment explanation
Indices: 85--151 Score: 57
Period size: 8 Copynumber: 8.1 Consensus size: 8
75 TTTGTTTTTA
85 TTTTGTA-
1 TTTTGTAT
92 TTTTGTAT
1 TTTTGTAT
*
100 TTTTTTAGT
1 TTTTGTA-T
*
109 ATTTAGTAT
1 -TTTTGTAT
*
118 TTTGGTAT
1 TTTTGTAT
126 TTCTTGTA-
1 TT-TTGTAT
134 TTTTGTATT
1 TTTTGTA-T
143 TTTTGTAT
1 TTTTGTAT
151 T
1 T
152 CTATATTTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
7 12 0.24
8 19 0.39
9 13 0.27
10 5 0.10
ACGTcount: A:0.15, C:0.01, G:0.13, T:0.70
Consensus pattern (8 bp):
TTTTGTAT
Found at i:153 original size:24 final size:24
Alignment explanation
Indices: 83--184 Score: 66
Period size: 25 Copynumber: 4.2 Consensus size: 24
73 TTTTTGTTTT
* * * *
83 TATTTTGTATTTTGTATTTTTTTAG
1 TATTTTGTATTTTTTGTATTCTT-G
* *
108 TATTTAGTA-TTTTGGTATTTCTTG
1 TATTTTGTATTTTTTGTA-TTCTTG
*
132 TATTTTGTATTTTTTGTATTC-TA
1 TATTTTGTATTTTTTGTATTCTTG
* *
155 TATTTT-TATTTAATTTTTATTATTG
1 TATTTTGTATTT--TTTGTATTCTTG
180 TATTT
1 TATTT
185 AATAATATTA
Statistics
Matches: 60, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
22 5 0.08
23 7 0.12
24 23 0.38
25 25 0.42
ACGTcount: A:0.19, C:0.02, G:0.10, T:0.70
Consensus pattern (24 bp):
TATTTTGTATTTTTTGTATTCTTG
Found at i:158 original size:16 final size:16
Alignment explanation
Indices: 123--161 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
113 AGTATTTTGG
* * *
123 TATTTCTTGTATTTTG
1 TATTTTTTGTATTCTA
139 TATTTTTTGTATTCTA
1 TATTTTTTGTATTCTA
155 TATTTTT
1 TATTTTT
162 ATTTAATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.15, C:0.05, G:0.08, T:0.72
Consensus pattern (16 bp):
TATTTTTTGTATTCTA
Found at i:673 original size:51 final size:51
Alignment explanation
Indices: 450--1182 Score: 590
Period size: 50 Copynumber: 14.8 Consensus size: 51
440 AAAAAAAAGG
* * * * *
450 GGCTCATCTTAGCAAAGGTTCAACAACTTT-AAAA-TCTCATATTAGAAAAA
1 GGCTCATCTCAGTAGAGGCTCAACAACTTTAAAAATTCTCATCTT-GAAAAA
** * ** **
500 -GCTCATCTCAACAGAGGCTTAATGACTTT-AAAA-TCTCATC-TGGGAAA
1 GGCTCATCTCAGTAGAGGCTCAACAACTTTAAAAATTCTCATCTTGAAAAA
* * * * *
547 -GCTAATCTTAGTAGAGGCTCAATAACTTTCAAAATT-TTATCTTGAAAAA
1 GGCTCATCTCAGTAGAGGCTCAACAACTTTAAAAATTCTCATCTTGAAAAA
* ** *
596 TGCT-ATTCTCAGTAGAGGCTTGACAACTTTAAAAATTCTTATCTTGAAAAA
1 GGCTCA-TCTCAGTAGAGGCTCAACAACTTTAAAAATTCTCATCTTGAAAAA
* * * *
647 GGCTCATCTCGGCAAAAGCTCAACAACTTTAAAAATTCTCATCTTG-AAAA
1 GGCTCATCTCAGTAGAGGCTCAACAACTTTAAAAATTCTCATCTTGAAAAA
* * * * *
697 TGCTCCTCTCAGAAGAGGCTCGACAACTTTAAAAATTTTCATCTTGAAAAA
1 GGCTCATCTCAGTAGAGGCTCAACAACTTTAAAAATTCTCATCTTGAAAAA
* * *
748 GGTTTC-TCTCAGCAGAAGCTCAACAACTTTAAAAA-TC-C-TC-TGAAAAA
1 GG-CTCATCTCAGTAGAGGCTCAACAACTTTAAAAATTCTCATCTTGAAAAA
* * * **
795 AGCTCATCTCAGTAGAGGTTCAACAACTTT-AAAATTTTCATCTAAAAAAA
1 GGCTCATCTCAGTAGAGGCTCAACAACTTTAAAAATTCTCATCTTGAAAAA
** * * * *
845 AACTCTTCTTAATAGAGGCTCAACGACTTT-AAAA-TCTCATC-TGAAAAA
1 GGCTCATCTCAGTAGAGGCTCAACAACTTTAAAAATTCTCATCTTGAAAAA
* *
893 GCCTC-TC-CTAGTAGAGGCTCAACAACATTAAAAA-TCTCATCTTGAAAAA
1 GGCTCATCTC-AGTAGAGGCTCAACAACTTTAAAAATTCTCATCTTGAAAAA
* * * * * *
942 GGCTCATCTTAGCAGAAGCTCAATAACTTTAAAAA-TCTTTATCTTGAAAAT
1 GGCTCATCTCAGTAGAGGCTCAACAACTTTAAAAATTC-TCATCTTGAAAAA
* * * * *
993 GGCTCCTCTCAGTAGATGTTTAACAACTTTAAAAA-TCTCATTTTGAAAAA
1 GGCTCATCTCAGTAGAGGCTCAACAACTTTAAAAATTCTCATCTTGAAAAA
* *
1043 -ACTTC-TCTTAGTAGAGGCTCAACAACTTTAAAAATTCTCATCTTGAAAAA
1 GGC-TCATCTCAGTAGAGGCTCAACAACTTTAAAAATTCTCATCTTGAAAAA
* * * * *
1093 GGTTCCTCTTAGCAGAGGGCTCAACAATTTTAAAAA-TCTCA--TTGAAAAA
1 GGCTCATCTCAGTAGA-GGCTCAACAACTTTAAAAATTCTCATCTTGAAAAA
* * *
1142 -GCTCCTTTCAATAGAGGCTCAACAACTTTAAAAATTCTCAT
1 GGCTCATCTCAGTAGAGGCTCAACAACTTTAAAAATTCTCAT
1183 TTGTTCTTGA
Statistics
Matches: 553, Mismatches: 103, Indels: 55
0.78 0.14 0.08
Matches are distributed among these distances:
46 6 0.01
47 94 0.17
48 46 0.08
49 93 0.17
50 158 0.29
51 135 0.24
52 21 0.04
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (51 bp):
GGCTCATCTCAGTAGAGGCTCAACAACTTTAAAAATTCTCATCTTGAAAAA
Found at i:697 original size:101 final size:99
Alignment explanation
Indices: 450--1182 Score: 508
Period size: 101 Copynumber: 7.4 Consensus size: 99
440 AAAAAAAAGG
* * * * **
450 GGCTCATCTTAGCA-AAGGTTCAACAACTTT-AAAATCTCATATTAGAAAAAGCTCATCTCAACA
1 GGCTC-TCTTAGCAGAA-GCTCAACAACTTTAAAAATCTCATCTT-GAAAATGCTCCTCTCAGTA
** * **
513 GAGGCTTAATGACTTT-AAAA-TCTCATC-TGGGAAA
63 GAGGCTTAACAACTTTAAAAATTCTTATCTTGAAAAA
* * * * * * * **
547 -GCTAATCTTAGTAGAGGCTCAATAACTTTCAAAATTTTATCTTGAAAAATGCTATTCTCAGTAG
1 GGCT-CTCTTAGCAGAAGCTCAACAACTTTAAAAATCTCATCTTG-AAAATGCTCCTCTCAGTAG
*
611 AGGCTTGACAACTTTAAAAATTCTTATCTTGAAAAA
64 AGGCTTAACAACTTTAAAAATTCTTATCTTGAAAAA
** * *
647 GGCTCATCTCGGCAAAAGCTCAACAACTTTAAAAATTCTCATCTTGAAAATGCTCCTCTCAGAAG
1 GGCTC-TCTTAGCAGAAGCTCAACAACTTTAAAAA-TCTCATCTTGAAAATGCTCCTCTCAGTAG
**
712 AGGCTCGACAACTTTAAAAATT-TTCATCTTGAAAAA
64 AGGCTTAACAACTTTAAAAATTCTT-ATCTTGAAAAA
* * * *
748 GGTTTCTCTCAGCAGAAGCTCAACAACTTTAAAAATC-C-TC-TGAAAAAAGCTCATCTCAGTAG
1 GG-CTCTCTTAGCAGAAGCTCAACAACTTTAAAAATCTCATCTTG-AAAATGCTCCTCTCAGTAG
**
810 AGG-TTCAACAACTTT-AAAATT-TTCATCTAAAAAAA
64 AGGCTT-AACAACTTTAAAAATTCTT-ATCTTGAAAAA
** ** * * *
845 AACTCTTCTTAATAGAGGCTCAACGACTTT-AAAATCTCATC-TGAAAAAG--CCTCTCCTAGTA
1 GGCTC-TCTTAGCAGAAGCTCAACAACTTTAAAAATCTCATCTTGAAAATGCTCCTCT-C-AGTA
* * *
906 GAGGCTCAACAACATTAAAAA-TCTCATCTTGAAAAA
63 GAGGCTTAACAACTTTAAAAATTCTTATCTTGAAAAA
* *
942 GGCTCATCTTAGCAGAAGCTCAATAACTTTAAAAATCTTTATCTTGAAAATGGCTCCTCTCAGTA
1 GGCTC-TCTTAGCAGAAGCTCAACAACTTTAAAAATC-TCATCTTGAAAAT-GCTCCTCTCAGTA
* * * *
1007 GATGTTTAACAACTTTAAAAA-TCTCATTTTGAAAAA
63 GAGGCTTAACAACTTTAAAAATTCTTATCTTGAAAAA
* * * * * * *
1043 -ACTTCTCTTAGTAGAGGCTCAACAACTTTAAAAATTCTCATCTTGAAAAAGGTTCCTCTTAGCA
1 GGC-TCTCTTAGCAGAAGCTCAACAACTTTAAAAA-TCTCATCTTG-AAAATGCTCCTCTCAGTA
* * *
1107 GAGGGCTCAACAATTTTAAAAA-TCTCA--TTGAAAAA
63 GA-GGCTTAACAACTTTAAAAATTCTTATCTTGAAAAA
** *
1142 -GCTC-CTTTCAATAGAGGCTCAACAACTTTAAAAATTCTCAT
1 GGCTCTC-TT-AGCAGAAGCTCAACAACTTTAAAAA-TCTCAT
1183 TTGTTCTTGA
Statistics
Matches: 515, Mismatches: 87, Indels: 66
0.77 0.13 0.10
Matches are distributed among these distances:
95 4 0.01
96 31 0.06
97 133 0.26
98 53 0.10
99 51 0.10
100 61 0.12
101 166 0.32
102 11 0.02
103 5 0.01
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (99 bp):
GGCTCTCTTAGCAGAAGCTCAACAACTTTAAAAATCTCATCTTGAAAATGCTCCTCTCAGTAGAG
GCTTAACAACTTTAAAAATTCTTATCTTGAAAAA
Found at i:1117 original size:346 final size:344
Alignment explanation
Indices: 451--1174 Score: 864
Period size: 346 Copynumber: 2.1 Consensus size: 344
441 AAAAAAAGGG
* * * * * *
451 GCTCATCTTAGCAAAGGTTCAACAACTTTAAAATCTCATATTAGAAAAAGCTCATCTCAACAGAG
1 GCTCATCTCAGTAGAGGTTCAACAACTTTAAAATCTCATATAAAAAAAAACTCATCTCAACAGAG
* * ** * * * *
516 GCTTAATGACTTTAAAATCTCATCTGGGAAAGCTAATCTTAGTAGAGGCTCAATAACTTTCAAAA
66 GCTCAACGACTTTAAAATCTCATCTGAAAAAGCTAATCCTAGTAGAGGCTCAACAACATTAAAAA
* * * * * **
581 TTTTATCTTGAAAAATGCTATTCTCAGTAGAGGCTTGACAACTTTAAAAATTCTTATCTTGAAAA
131 TCTCATCTTGAAAAAGGCTATTCTCAGCAGAAGCTCAACAACTTTAAAAATTCTTATCTTGAAAA
* **
646 AGGCTCATCTCGGCAAAAGCTCAACAACTTTAAAAATTCTCATCTTGAAAATGCTCCTCTCAGAA
196 AGGCTCATCTCAGCAAAAGCTCAACAACTTTAAAAATTCTCATCTTGAAAAAACTCCTCTCAGAA
* * *
711 GAGGCTCGACAACTTTAAAAATTTTCATCTTGAAAAAGGTTTCTCTCAGCAGAAGCTCAACAACT
261 GAGGCTCAACAACTTTAAAAATTCTCATCTTGAAAAAGGTTCCTCTCAGCAGAAGCTCAACAACT
776 TTAAAAATCCTC-TGAAAAAA
326 TTAAAAAT-CTCATG-AAAAA
* * * * *
796 GCTCATCTCAGTAGAGGTTCAACAACTTTAAAATTTTCATCTAAAAAAAAACTCTTCTTAATAGA
1 GCTCATCTCAGTAGAGGTTCAACAACTTTAAAA-TCTCATATAAAAAAAAACTCATCTCAACAGA
*
861 GGCTCAACGACTTTAAAATCTCATCTGAAAAAGCCT-CTCCTAGTAGAGGCTCAACAACATTAAA
65 GGCTCAACGACTTTAAAATCTCATCTGAAAAAG-CTAATCCTAGTAGAGGCTCAACAACATTAAA
* *
925 AATCTCATCTTGAAAAAGGCTCA-TCTTAGCAGAAGCTCAATAACTTTAAAAA-TCTTTATCTTG
129 AATCTCATCTTGAAAAAGGCT-ATTCTCAGCAGAAGCTCAACAACTTTAAAAATTC-TTATCTTG
* * * * * * * * * *
988 AAAATGGCTCCTCTCAGTAGATGTTTAACAACTTTAAAAA-TCTCATTTTGAAAAAACTTCTCTT
192 AAAAAGGCTCATCTCAGCAAAAGCTCAACAACTTTAAAAATTCTCATCTTGAAAAAACTCCTCTC
* * *
1052 AGTAGAGGCTCAACAACTTTAAAAATTCTCATCTTGAAAAAGGTTCCTCTTAGCAGAGGGCTCAA
257 AGAAGAGGCTCAACAACTTTAAAAATTCTCATCTTGAAAAAGGTTCCTCTCAGCAGA-AGCTCAA
*
1117 CAATTTTAAAAATCTCATTGAAAAA
321 CAACTTTAAAAATCTCA-TGAAAAA
* * * *
1142 GCTCCTTTCAATAGAGGCTCAACAACTTTAAAA
1 GCTCATCTCAGTAGAGGTTCAACAACTTTAAAA
1175 ATTCTCATTT
Statistics
Matches: 319, Mismatches: 53, Indels: 13
0.83 0.14 0.03
Matches are distributed among these distances:
345 106 0.33
346 208 0.65
347 5 0.02
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (344 bp):
GCTCATCTCAGTAGAGGTTCAACAACTTTAAAATCTCATATAAAAAAAAACTCATCTCAACAGAG
GCTCAACGACTTTAAAATCTCATCTGAAAAAGCTAATCCTAGTAGAGGCTCAACAACATTAAAAA
TCTCATCTTGAAAAAGGCTATTCTCAGCAGAAGCTCAACAACTTTAAAAATTCTTATCTTGAAAA
AGGCTCATCTCAGCAAAAGCTCAACAACTTTAAAAATTCTCATCTTGAAAAAACTCCTCTCAGAA
GAGGCTCAACAACTTTAAAAATTCTCATCTTGAAAAAGGTTCCTCTCAGCAGAAGCTCAACAACT
TTAAAAATCTCATGAAAAA
Found at i:14577 original size:16 final size:16
Alignment explanation
Indices: 14558--14625 Score: 57
Period size: 16 Copynumber: 4.1 Consensus size: 16
14548 TTTTGTTCTT
14558 TTTTTTGTATTTTATA
1 TTTTTTGTATTTTATA
*
14574 TTTTTTTGATATTTTGTA
1 -TTTTTTG-TATTTTATA
*
14592 -TTTTAGTATTTTTATA
1 TTTTTTGTA-TTTTATA
* * *
14608 TTTTATATTTTTTATA
1 TTTTTTGTATTTTATA
14624 TT
1 TT
14626 CCATATTTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
15 2 0.05
16 20 0.49
17 11 0.27
18 8 0.20
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.74
Consensus pattern (16 bp):
TTTTTTGTATTTTATA
Found at i:14577 original size:18 final size:19
Alignment explanation
Indices: 14556--14620 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 19
14546 TTTTTTGTTC
14556 TTTTTTTTG-TATTTTATA
1 TTTTTTTTGATATTTTATA
*
14574 -TTTTTTTGATATTTTGTA
1 TTTTTTTTGATATTTTATA
*
14592 TTTTAGTATTTTTATATTTTATA
1 -TTT--T-TTTTGATATTTTATA
14615 TTTTTT
1 TTTTTT
14621 ATATTCCATA
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
17 8 0.21
18 8 0.21
19 2 0.05
20 3 0.08
22 4 0.11
23 13 0.34
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.75
Consensus pattern (19 bp):
TTTTTTTTGATATTTTATA
Found at i:14605 original size:9 final size:8
Alignment explanation
Indices: 14567--14625 Score: 50
Period size: 9 Copynumber: 7.1 Consensus size: 8
14557 TTTTTTTGTA
14567 TTTTATAT
1 TTTTATAT
*
14575 TTTTTTGAT
1 TTTTAT-AT
*
14584 ATTTTGTA-
1 -TTTTATAT
14592 TTTTAGTAT
1 TTTTA-TAT
14601 TTTTATA-
1 TTTTATAT
14608 TTTTATATT
1 TTTTATA-T
14617 TTTTATAT
1 TTTTATAT
14625 T
1 T
14626 CCATATTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
7 11 0.26
8 11 0.26
9 15 0.36
10 5 0.12
ACGTcount: A:0.22, C:0.00, G:0.05, T:0.73
Consensus pattern (8 bp):
TTTTATAT
Found at i:14631 original size:16 final size:16
Alignment explanation
Indices: 14600--14635 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
14590 TATTTTAGTA
**
14600 TTTTTATATTTTATAT
1 TTTTTATATTCCATAT
14616 TTTTTATATTCCATAT
1 TTTTTATATTCCATAT
14632 TTTT
1 TTTT
14636 GTTTAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTTATATTCCATAT
Found at i:14860 original size:65 final size:64
Alignment explanation
Indices: 14773--14951 Score: 234
Period size: 65 Copynumber: 2.8 Consensus size: 64
14763 TCAAAATTTC
* * * *
14773 ATCCAACTCTCAAAATTGAATAGTAGTAGTTGCAAAGGACAATTATTGAATTGGACGAATTAAT
1 ATCCAACCCTCAAATTTTAATAGTAGTAGTTGCAAAGGACAATTATTGAAATGGACGAATTAAT
* * * *
14837 ATCCCAACCTTCAAATTTTAATAGTAGTAGTTGCCAAGAACAATTATTGAAATGGATGAATTAAT
1 AT-CCAACCCTCAAATTTTAATAGTAGTAGTTGCAAAGGACAATTATTGAAATGGACGAATTAAT
* * *
14902 ATCCAACCCACAAAATTTT-ATAGTAGTAGTTGCAAAAGATAATTATTGAA
1 ATCCAACCCTC-AAATTTTAATAGTAGTAGTTGCAAAGGACAATTATTGAA
14952 GTCTCAAAAG
Statistics
Matches: 99, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
64 36 0.36
65 63 0.64
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (64 bp):
ATCCAACCCTCAAATTTTAATAGTAGTAGTTGCAAAGGACAATTATTGAAATGGACGAATTAAT
Found at i:16011 original size:2 final size:2
Alignment explanation
Indices: 16004--16037 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
15994 TAGATAAATC
16004 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16038 TTTTATTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16141 original size:22 final size:21
Alignment explanation
Indices: 16114--16179 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 21
16104 TTTGTTTAAG
16114 ATATTAACTTAATAAAAATATT
1 ATATTAA-TTAATAAAAATATT
* *
16136 ATATTAATATAATTAAAATATA
1 ATATTAAT-TAATAAAAATATT
16158 AT-TTATATTAA-AAAAAT-TT
1 ATATTA-ATTAATAAAAATATT
16177 ATA
1 ATA
16180 AATATTATAC
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
19 3 0.08
20 5 0.14
21 7 0.19
22 22 0.59
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
ATATTAATTAATAAAAATATT
Found at i:16177 original size:15 final size:17
Alignment explanation
Indices: 16147--16179 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
16137 TATTAATATA
16147 ATTAAAATATAATTTAT
1 ATTAAAATATAATTTAT
16164 ATTAAAA-A-AATTTAT
1 ATTAAAATATAATTTAT
16179 A
1 A
16180 AATATTATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 1 0.06
17 7 0.44
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATTAAAATATAATTTAT
Found at i:16815 original size:1 final size:1
Alignment explanation
Indices: 16804--16833 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
16794 AAGACTCAAT
*
16804 AAAACAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
16834 CAAGACAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.97, C:0.03, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:21421 original size:91 final size:90
Alignment explanation
Indices: 21267--21449 Score: 339
Period size: 91 Copynumber: 2.0 Consensus size: 90
21257 GACAAGACGA
**
21267 TTGTGCTCCAGTCGTTGGTCAAAGGCCTTTTTTTTTCCACCGTTTGTTTTAATCTGCGTCGTTAT
1 TTGTGCTCCAGTCGTTGGTCAAACCCCTTTTTTTTTCCACCGTTTGTTTTAATCTGCGTCGTTAT
21332 CTGTACACATCGTTACGACGTGTCC
66 CTGTACACATCGTTACGACGTGTCC
21357 TTGTGCTCCAGTCGTTGGTCAAACCCCTTTTTTTTTTCCACCGTTTGTTTTAATCTGCGTCGTTA
1 TTGTGCTCCAGTCGTTGGTCAAACCCC-TTTTTTTTTCCACCGTTTGTTTTAATCTGCGTCGTTA
21422 TCTGTACACATCGTTACGACGTGTCC
65 TCTGTACACATCGTTACGACGTGTCC
21448 TT
1 TT
21450 TTCCAGTGTC
Statistics
Matches: 90, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
90 25 0.28
91 65 0.72
ACGTcount: A:0.14, C:0.25, G:0.19, T:0.42
Consensus pattern (90 bp):
TTGTGCTCCAGTCGTTGGTCAAACCCCTTTTTTTTTCCACCGTTTGTTTTAATCTGCGTCGTTAT
CTGTACACATCGTTACGACGTGTCC
Found at i:21608 original size:24 final size:24
Alignment explanation
Indices: 21581--21637 Score: 69
Period size: 28 Copynumber: 2.2 Consensus size: 24
21571 TGATTATACA
21581 AATTTATTCAATAAATTAATTTTT
1 AATTTATTCAATAAATTAATTTTT
*
21605 AATTTATATATTCAATAAATTTATTTTT
1 AA--T-T-TATTCAATAAATTAATTTTT
21633 AATTT
1 AATTT
21638 TTAAAATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
24 3 0.11
25 1 0.04
26 2 0.07
27 1 0.04
28 21 0.75
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (24 bp):
AATTTATTCAATAAATTAATTTTT
Found at i:21672 original size:21 final size:21
Alignment explanation
Indices: 21606--21674 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
21596 TTAATTTTTA
*
21606 ATTTATATATTCAATAAATTT
1 ATTTATATATTAAATAAATTT
* * **
21627 ATTTTTAATTTTTAAA-ATTTTT
1 ATTTAT-A-TATTAAATAAATTT
21649 ATTTATATATTAAATAAATTT
1 ATTTATATATTAAATAAATTT
21670 ATTTA
1 ATTTA
21675 AACAAAAAAT
Statistics
Matches: 36, Mismatches: 9, Indels: 6
0.71 0.18 0.12
Matches are distributed among these distances:
20 6 0.17
21 15 0.42
22 10 0.28
23 5 0.14
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (21 bp):
ATTTATATATTAAATAAATTT
Found at i:26815 original size:9 final size:9
Alignment explanation
Indices: 26797--26867 Score: 51
Period size: 9 Copynumber: 7.9 Consensus size: 9
26787 TCTGTTCATT
26797 TTTTTATATA
1 TTTTT-TATA
26807 TTTTTTATA
1 TTTTTTATA
*
26816 TTTTGTATTA
1 TTTTTTA-TA
*
26826 TTTTTAATA
1 TTTTTTATA
26835 -TTTTTAT-
1 TTTTTTATA
*
26842 TGTATTTCATA
1 T-T-TTTTATA
26853 --TTTTATA
1 TTTTTTATA
26860 TTTTTTAT
1 TTTTTTAT
26868 TACAGTATTT
Statistics
Matches: 48, Mismatches: 6, Indels: 15
0.70 0.09 0.22
Matches are distributed among these distances:
7 6 0.12
8 6 0.12
9 19 0.40
10 17 0.35
ACGTcount: A:0.24, C:0.01, G:0.03, T:0.72
Consensus pattern (9 bp):
TTTTTTATA
Found at i:26819 original size:18 final size:17
Alignment explanation
Indices: 26803--26866 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 17
26793 CATTTTTTTA
26803 TATATTTTTT-ATATTT
1 TATATTTTTTAATATTT
*
26819 TGTATTATTTTTAATATTT
1 TATA-T-TTTTTAATATTT
*
26838 T-TATTGTATTTCATATTT
1 TATATT-T-TTTAATATTT
26856 TATATTTTTTA
1 TATATTTTTTA
26867 TTACAGTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
16 4 0.10
17 6 0.15
18 18 0.46
19 11 0.28
ACGTcount: A:0.25, C:0.02, G:0.03, T:0.70
Consensus pattern (17 bp):
TATATTTTTTAATATTT
Found at i:26819 original size:19 final size:18
Alignment explanation
Indices: 26797--26864 Score: 68
Period size: 19 Copynumber: 3.8 Consensus size: 18
26787 TCTGTTCATT
*
26797 TTTTTATATATTTTTTATA
1 TTTTTAT-TATTTTTAATA
26816 TTTTGTATTATTTTTAATA
1 TTTT-TATTATTTTTAATA
* * *
26835 TTTTTATTGTATTTCATA
1 TTTTTATTATTTTTAATA
26853 -TTTTA-TATTTTT
1 TTTTTATTATTTTT
26865 TATTACAGTA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
16 5 0.12
17 5 0.12
18 11 0.26
19 18 0.43
20 3 0.07
ACGTcount: A:0.24, C:0.01, G:0.03, T:0.72
Consensus pattern (18 bp):
TTTTTATTATTTTTAATA
Done.