Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017772.1 Corchorus olitorius cultivar O-4 contig17805, 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: 90721
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:328 original size:21 final size:21
Alignment explanation
Indices: 272--328 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
262 TTTATAACAC
*
272 CTTGTTCCTGCCTCATCTCAT
1 CTTGTGCCTGCCTCATCTCAT
* ** * * *
293 CTTGCGAATGTCTCATTTCTT
1 CTTGTGCCTGCCTCATCTCAT
314 CTTGTGCCTGCCTCA
1 CTTGTGCCTGCCTCA
329 GATGTTGGAT
Statistics
Matches: 25, Mismatches: 11, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.11, C:0.33, G:0.14, T:0.42
Consensus pattern (21 bp):
CTTGTGCCTGCCTCATCTCAT
Found at i:4490 original size:28 final size:27
Alignment explanation
Indices: 4454--4517 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
4444 TAAAAAAAAG
* * *
4454 AATAAATAGGTATAGAGAATAATAGATA
1 AATAAATAGCTAAAAAGAATAATA-ATA
*
4482 AATAAATAGCTAAAAATAATAATAATA
1 AATAAATAGCTAAAAAGAATAATAATA
*
4509 ATTAAATAG
1 AATAAATAG
4518 ATAATAGCTA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
27 11 0.35
28 20 0.65
ACGTcount: A:0.61, C:0.02, G:0.11, T:0.27
Consensus pattern (27 bp):
AATAAATAGCTAAAAAGAATAATAATA
Found at i:4522 original size:46 final size:45
Alignment explanation
Indices: 4472--4716 Score: 206
Period size: 46 Copynumber: 5.5 Consensus size: 45
4462 GGTATAGAGA
* ** * *
4472 ATAATAGATAAATAAATAGCTAAAAATAATAATAATAATTAAATAG
1 ATAATAGATAAATTAATAAATAAAAAT-ATAATAGTAAATAAATAG
* * *
4518 ATAATAGCTAAATTAATAAATAAAAAGATAAATAGTAAATAGATAG
1 ATAATAGATAAATTAATAAATAAAAATAT-AATAGTAAATAAATAG
4564 ATAATA-ATTAAATTAATAAATGAAAAGATA-AATAGTAAATAAATAG
1 ATAATAGA-TAAATTAATAAAT-AAAA-ATATAATAGTAAATAAATAG
* ***
4610 ATAATAGTTAAA--AATAAA-AAAGGGATAATTAGTAAATAAATAG
1 ATAATAGATAAATTAATAAATAAAAATATAA-TAGTAAATAAATAG
* **
4653 ATAATAGTTAAA--AATAAA-AAGGGATA-AATAGTAAATAAATAG
1 ATAATAGATAAATTAATAAATAA-AAATATAATAGTAAATAAATAG
*
4695 ATAATAGTTAAA--AATAAATAAA
1 ATAATAGATAAATTAATAAATAAA
4717 TAGATAAATA
Statistics
Matches: 171, Mismatches: 19, Indels: 22
0.81 0.09 0.10
Matches are distributed among these distances:
41 1 0.01
42 37 0.22
43 38 0.22
44 8 0.05
45 2 0.01
46 79 0.46
47 4 0.02
48 2 0.01
ACGTcount: A:0.62, C:0.01, G:0.10, T:0.27
Consensus pattern (45 bp):
ATAATAGATAAATTAATAAATAAAAATATAATAGTAAATAAATAG
Found at i:4534 original size:27 final size:27
Alignment explanation
Indices: 4504--4613 Score: 78
Period size: 27 Copynumber: 4.4 Consensus size: 27
4494 AAAATAATAA
* *
4504 TAATAATTAAATAGAT-AATAGCTAAAT
1 TAATAAATAAAAAGATAAATAG-TAAAT
4531 TAATAAATAAAAAGATAAATAGTAAA-
1 TAATAAATAAAAAGATAAATAGTAAAT
*
4557 TAGATAGAT----A-AT-AAT--TAAAT
1 TA-ATAAATAAAAAGATAAATAGTAAAT
*
4577 TAATAAATGAAAAGATAAATAGTAAAT
1 TAATAAATAAAAAGATAAATAGTAAAT
* *
4604 AAATAGATAA
1 TAATAAATAA
4614 TAGTTAAAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 22
0.69 0.07 0.23
Matches are distributed among these distances:
19 9 0.14
20 2 0.03
21 3 0.05
22 2 0.03
23 2 0.03
24 2 0.03
25 3 0.05
26 2 0.03
27 35 0.54
28 5 0.08
ACGTcount: A:0.62, C:0.01, G:0.09, T:0.28
Consensus pattern (27 bp):
TAATAAATAAAAAGATAAATAGTAAAT
Found at i:4558 original size:42 final size:42
Alignment explanation
Indices: 4444--4726 Score: 156
Period size: 46 Copynumber: 6.4 Consensus size: 42
4434 AAAATAAGTT
* * *
4444 TAAA-AAAAAGAATAAATAGGTATAGAGAATAATAGATAAATAAA
1 TAAATAAAAAG-ATAAATA-GTAAATAG-ATAATAGATAAATTAA
** * * *
4488 TAGCTAAAAATAATAATAATAATTAAATAGATAATAGCTAAATTAA
1 TAAATAAAAA-GAT-A-AAT-AGTAAATAGATAATAGATAAATTAA
*
4534 TAAATAAAAAGATAAATAGTAAATAGATAGATAATAATTAAATTAA
1 TAAATAAAAAGATAAATAGTAAATAGATA-AT-A-GA-TAAATTAA
*
4580 TAAATGAAAAGATAAATAGTAAAT--A-AATAGATAATAGTTAA
1 TAAATAAAAAGATAAATAGTAAATAGATAATAGATAA-A-TTAA
*
4621 -AAATAAAAAAGGGATAATTAGTAAAT--A-AATAGATAATAGTTAA
1 TAAAT-AAAAA--GATAAATAGTAAATAGATAATAGATAA-A-TTAA
*
4664 -AAATAAAAAGGGATAAATAGTAAATAAATAGATAATAGTTAAA--AA
1 TAAATAAAAA--GATAAATAG----TAAATAGATAATAGATAAATTAA
*
4709 TAAATAAATAGATAAATA
1 TAAATAAAAAGATAAATA
4727 ATGAATAAAT
Statistics
Matches: 196, Mismatches: 21, Indels: 44
0.75 0.08 0.17
Matches are distributed among these distances:
39 3 0.02
40 6 0.03
41 9 0.05
42 28 0.14
43 40 0.20
44 13 0.07
45 11 0.06
46 67 0.34
47 8 0.04
48 3 0.02
49 8 0.04
ACGTcount: A:0.63, C:0.01, G:0.11, T:0.26
Consensus pattern (42 bp):
TAAATAAAAAGATAAATAGTAAATAGATAATAGATAAATTAA
Found at i:4564 original size:85 final size:83
Alignment explanation
Indices: 4471--4726 Score: 259
Period size: 85 Copynumber: 3.0 Consensus size: 83
4461 AGGTATAGAG
* * * * *
4471 AATAATAGATAAA-TAAATAGCTAAAAATAAT-AATAATAATTAAATAGATAATAGCTAAATTAA
1 AATAATAGATAAATTAAATA-ATAAAAAAAATAAATAGTAAATAAATAGATAATAGTTAAA--AA
4534 TAAATAAAAAGATAAATAGTA
63 TAAATAAAAAGATAAATAGTA
4555 AATAGATAGATAATAATTAAATTAATAAATGAAAAGATAAATAGTAAATAAATAGATAATAGTTA
1 AATA-ATAGAT-A-AATTAAA-TAATAAA--AAAA-ATAAATAGTAAATAAATAGATAATAGTTA
** *
4620 AAAATAAA-AAAGGGATAATTAGTA
59 AAAATAAATAAAAAGATAAATAGTA
**
4644 AATAAATAGATAATAGTTAAA-AATAAAAAGGGATAAATAGTAAATAAATAGATAATAGTTAAAA
1 AAT-AATAGATAA-A-TTAAATAATAAAAA-AAATAAATAGTAAATAAATAGATAATAGTTAAAA
*
4708 ATAAATAAATAGATAAATA
62 ATAAATAAAAAGATAAATA
4727 ATGAATAAAT
Statistics
Matches: 145, Mismatches: 13, Indels: 26
0.79 0.07 0.14
Matches are distributed among these distances:
84 4 0.03
85 45 0.31
86 11 0.08
87 9 0.06
88 10 0.07
89 29 0.20
90 10 0.07
91 2 0.01
92 25 0.17
ACGTcount: A:0.62, C:0.01, G:0.10, T:0.27
Consensus pattern (83 bp):
AATAATAGATAAATTAAATAATAAAAAAAATAAATAGTAAATAAATAGATAATAGTTAAAAATAA
ATAAAAAGATAAATAGTA
Found at i:4643 original size:43 final size:43
Alignment explanation
Indices: 4544--4737 Score: 257
Period size: 42 Copynumber: 4.4 Consensus size: 43
4534 TAAATAAAAA
* * *
4544 GATAAATAGTAAATAGATAGATAATAATTAAATTAATAAATGAAA-A
1 GATAAATAGTAAATAAATAGATAATAGTTAAA--AATAAA--AAAGG
4590 GATAAATAGTAAATAAATAGATAATAGTTAAAAATAAAAAAGG
1 GATAAATAGTAAATAAATAGATAATAGTTAAAAATAAAAAAGG
*
4633 GATAATTAGTAAATAAATAGATAATAGTTAAAAAT-AAAAAGG
1 GATAAATAGTAAATAAATAGATAATAGTTAAAAATAAAAAAGG
**
4675 GATAAATAGTAAATAAATAGATAATAGTTAAAAATAAATAAATA
1 GATAAATAGTAAATAAATAGATAATAGTTAAAAATAAA-AAAGG
* *
4719 GATAAATAATGAATAAATA
1 GATAAATAGTAAATAAATA
4738 AAAAAAATCT
Statistics
Matches: 136, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
42 44 0.32
43 36 0.26
44 26 0.19
46 30 0.22
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.26
Consensus pattern (43 bp):
GATAAATAGTAAATAAATAGATAATAGTTAAAAATAAAAAAGG
Found at i:4735 original size:29 final size:25
Alignment explanation
Indices: 4675--4723 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
4665 AATAAAAAGG
*
4675 GATAAATAGTAAATAAATAGATAATA
1 GATAAA-AATAAATAAATAGATAATA
*
4701 GTTAAAAATAAATAAATAGATAA
1 GATAAAAATAAATAAATAGATAA
4724 ATAATGAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.63, C:0.00, G:0.10, T:0.27
Consensus pattern (25 bp):
GATAAAAATAAATAAATAGATAATA
Found at i:10381 original size:37 final size:37
Alignment explanation
Indices: 10314--10411 Score: 124
Period size: 37 Copynumber: 2.6 Consensus size: 37
10304 CCAGAACTAG
* * **
10314 TGGGATCTTTCCCTAAATTGAACGCTTTGAAAACCTAA
1 TGGGAACTTTCCC-AATTTGAAAACTTTGAAAACCTAA
* *
10352 TGGGAACTTTCCCAATTTGAAAACTTTGAAAACTTGA
1 TGGGAACTTTCCCAATTTGAAAACTTTGAAAACCTAA
*
10389 TGGGAACTTTCCCACTTTGAAAA
1 TGGGAACTTTCCCAATTTGAAAA
10412 GAGCTAAATT
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
37 41 0.77
38 12 0.23
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (37 bp):
TGGGAACTTTCCCAATTTGAAAACTTTGAAAACCTAA
Found at i:10406 original size:28 final size:28
Alignment explanation
Indices: 10374--10466 Score: 95
Period size: 28 Copynumber: 3.5 Consensus size: 28
10364 CAATTTGAAA
10374 ACTTTGAAAACTTGATGGGAACTTTCCC
1 ACTTTGAAAACTTGATGGGAACTTTCCC
** * ***
10402 ACTTTGAAAA---GA-GCTAAATTGAAC
1 ACTTTGAAAACTTGATGGGAACTTTCCC
*
10426 ATTTTGAAAACTTGATGGGAACTTTCCC
1 ACTTTGAAAACTTGATGGGAACTTTCCC
10454 ACTTTGAAAACTT
1 ACTTTGAAAACTT
10467 TGAAGAAAAC
Statistics
Matches: 47, Mismatches: 14, Indels: 8
0.68 0.20 0.12
Matches are distributed among these distances:
24 15 0.32
25 2 0.04
27 2 0.04
28 28 0.60
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Consensus pattern (28 bp):
ACTTTGAAAACTTGATGGGAACTTTCCC
Found at i:12160 original size:36 final size:35
Alignment explanation
Indices: 12082--12210 Score: 197
Period size: 36 Copynumber: 3.6 Consensus size: 35
12072 CGAAAATGAC
* *
12082 GGGAACTTTCCCTAAATTGAAAAC-TAAAACCTGAT
1 GGGAACTTTCCC-AATTTGAAAACTTAAAACTTGAT
12117 GGGAACTTTCCCAATTTGAAAACTTAAGAACTTGAT
1 GGGAACTTTCCCAATTTGAAAACTTAA-AACTTGAT
*
12153 GGGAACTTTCCCAATTTGAAAACTTAAAAATTTGAT
1 GGGAACTTTCCCAATTTGAAAACTT-AAAACTTGAT
12189 GGGAACTTTCCCAATTTGAAAA
1 GGGAACTTTCCCAATTTGAAAA
12211 GAGCTAAATT
Statistics
Matches: 88, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
34 10 0.11
35 15 0.17
36 61 0.69
37 2 0.02
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (35 bp):
GGGAACTTTCCCAATTTGAAAACTTAAAACTTGAT
Found at i:12206 original size:20 final size:20
Alignment explanation
Indices: 12148--12207 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 20
12138 ACTTAAGAAC
12148 TTGATGGGAACTTTCCCAAT
1 TTGATGGGAACTTTCCCAAT
* ***
12168 TTGA---AAAC-TTAAAAAT
1 TTGATGGGAACTTTCCCAAT
12184 TTGATGGGAACTTTCCCAAT
1 TTGATGGGAACTTTCCCAAT
12204 TTGA
1 TTGA
12208 AAAGAGCTAA
Statistics
Matches: 28, Mismatches: 8, Indels: 8
0.64 0.18 0.18
Matches are distributed among these distances:
16 9 0.32
17 3 0.11
19 3 0.11
20 13 0.46
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (20 bp):
TTGATGGGAACTTTCCCAAT
Found at i:13322 original size:16 final size:16
Alignment explanation
Indices: 13303--13333 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
13293 AGAAAAGGGG
13303 ATTAAAACAATTAAAT
1 ATTAAAACAATTAAAT
*
13319 ATTAAAGCAATTAAA
1 ATTAAAACAATTAAA
13334 CTAAAAATAA
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:0.61, C:0.06, G:0.03, T:0.29
Consensus pattern (16 bp):
ATTAAAACAATTAAAT
Found at i:18418 original size:20 final size:20
Alignment explanation
Indices: 18393--18448 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
18383 TTCCAATCAA
18393 TCAAGAACCCTAATTTAAAC
1 TCAAGAACCCTAATTTAAAC
**
18413 TCAAGAACCCTAATTGGAAC
1 TCAAGAACCCTAATTTAAAC
*
18433 TCAAGAACCCTGATTT
1 TCAAGAACCCTAATTT
18449 GGAATTCAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.39, C:0.25, G:0.11, T:0.25
Consensus pattern (20 bp):
TCAAGAACCCTAATTTAAAC
Found at i:18452 original size:21 final size:20
Alignment explanation
Indices: 18393--18457 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
18383 TTCCAATCAA
*
18393 TCAAGAACCCTAATTT-AAAC
1 TCAAGAACCCT-ATTTGGAAC
*
18413 TCAAGAACCCTAATTGGAAC
1 TCAAGAACCCTATTTGGAAC
*
18433 TCAAGAACCCTGATTTGGAAT
1 TCAAGAACCCT-ATTTGGAAC
18454 TCAA
1 TCAA
18458 TGAGCTCCAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
19 3 0.08
20 25 0.64
21 11 0.28
ACGTcount: A:0.40, C:0.23, G:0.12, T:0.25
Consensus pattern (20 bp):
TCAAGAACCCTATTTGGAAC
Found at i:18617 original size:202 final size:202
Alignment explanation
Indices: 18391--18805 Score: 742
Period size: 202 Copynumber: 2.1 Consensus size: 202
18381 AATTCCAATC
**
18391 AATCAAGAACCCTAATTTAAACTCAAGAACCCTAATTGGAACTCAAGAACCCTGATTTGGAATTC
1 AATCAAGAACCCTAATTTAAACTCAAGAACCCTAATTAAAACTCAAGAACCCTGATTTGGAATTC
*
18456 AATGAGCTCCAAAATGAAATTCTTCAAATTGATTCTTCAATTGCAGCAAAAGCTTCCCAAAAACC
66 AATGAGCTCCAAAATGAAATTCTTCAAACTGATTCTTCAATTGCAGCAAAAGCTTCCCAAAAACC
* *
18521 TCAAACA-CACTTTCAATTCCAATCAATTTTCTCCAATTAGGGCTAATTGCAACAAATTAGATCA
131 TCAAA-AGCACATTCAATTCCAATCAATTTTCTCAAATTAGGGCTAATTGCAACAAATTAGATCA
18585 ATTGCACA
195 ATTGCACA
*
18593 AATTAAGAACCCTAATTTAAACTCAAGAACCCTAATTAAAACTCAAGAACCCTGATTTGGAATTC
1 AATCAAGAACCCTAATTTAAACTCAAGAACCCTAATTAAAACTCAAGAACCCTGATTTGGAATTC
* *
18658 AATGAGCTCCAAACTGAAATTCTTCAAACTGTTTCTTCAATTGCAGCAAAAGCTTCCCAAAAACC
66 AATGAGCTCCAAAATGAAATTCTTCAAACTGATTCTTCAATTGCAGCAAAAGCTTCCCAAAAACC
18723 TCAAAAGCACATTCAATTCCAATCAATTTTCTCAAATTAGGGCTAATTGCAACAAATTAGATCAA
131 TCAAAAGCACATTCAATTCCAATCAATTTTCTCAAATTAGGGCTAATTGCAACAAATTAGATCAA
18788 TTGCACA
196 TTGCACA
18795 AATCAAGAACC
1 AATCAAGAACC
18806 TTAACCCCCT
Statistics
Matches: 203, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
201 1 0.00
202 202 1.00
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.27
Consensus pattern (202 bp):
AATCAAGAACCCTAATTTAAACTCAAGAACCCTAATTAAAACTCAAGAACCCTGATTTGGAATTC
AATGAGCTCCAAAATGAAATTCTTCAAACTGATTCTTCAATTGCAGCAAAAGCTTCCCAAAAACC
TCAAAAGCACATTCAATTCCAATCAATTTTCTCAAATTAGGGCTAATTGCAACAAATTAGATCAA
TTGCACA
Found at i:18622 original size:20 final size:20
Alignment explanation
Indices: 18597--18650 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
18587 TGCACAAATT
18597 AAGAACCCTAATTTAAACTC
1 AAGAACCCTAATTTAAACTC
*
18617 AAGAACCCTAATTAAAACTC
1 AAGAACCCTAATTTAAACTC
*
18637 AAGAACCCTGATTT
1 AAGAACCCTAATTT
18651 GGAATTCAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.44, C:0.24, G:0.07, T:0.24
Consensus pattern (20 bp):
AAGAACCCTAATTTAAACTC
Found at i:28335 original size:11 final size:11
Alignment explanation
Indices: 28319--28344 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
28309 CTGGGAAAAA
28319 TTTTTTTATAT
1 TTTTTTTATAT
28330 TTTTTTTATAT
1 TTTTTTTATAT
28341 TTTT
1 TTTT
28345 CGATTAAACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTTATAT
Found at i:29301 original size:27 final size:27
Alignment explanation
Indices: 29254--29344 Score: 110
Period size: 27 Copynumber: 3.4 Consensus size: 27
29244 TTTACTTCTT
* * * *
29254 ATTTTGATCACTTGCATGTCCAGGGGA
1 ATTTTGGTCATTTGCACGTCCAGGGGC
*
29281 ATTTTGGTCATTTTCACGTCCAGGGGC
1 ATTTTGGTCATTTGCACGTCCAGGGGC
* * *
29308 ATTTTGGTTATTTGCGCATCCAGGGGC
1 ATTTTGGTCATTTGCACGTCCAGGGGC
29335 ATTTTGGTCA
1 ATTTTGGTCA
29345 CTTCAAGTAC
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 54 1.00
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.37
Consensus pattern (27 bp):
ATTTTGGTCATTTGCACGTCCAGGGGC
Found at i:40445 original size:129 final size:129
Alignment explanation
Indices: 40215--40460 Score: 431
Period size: 129 Copynumber: 1.9 Consensus size: 129
40205 AGGCTGATGC
* **
40215 ACTCTCAGGCGAAGTACTAAAGGTAACAGCACTAGGGGTAACTCCCCTCGTTACAGTCATAGTTG
1 ACTCTCAGACGAAGTACTAAAGGTAACAGCACTAGGGGTAACTCCCCTCGTTACAGTCATAGCAG
*
40280 AAGGCAGAATGGTGTCACCATGAGCAGTGACACTACAAGGCGTAACTCCCTCGTTACACTACAT
66 AAGGCAGAATGGTGTCACCATGAGCAGTGACACTACAAGGCGTAACTACCTCGTTACACTACAT
40344 ACTCTCAGACGAAGTACTAAAGGTAACAGCA-TCAGGGGTAACTCCCCTCGTTACAGTCATAGCA
1 ACTCTCAGACGAAGTACTAAAGGTAACAGCACT-AGGGGTAACTCCCCTCGTTACAGTCATAGCA
*
40408 GAAGGCAGAATGGTGTCACCATGAGCAGTGACACTACAAGGGGTAACTACCTC
65 GAAGGCAGAATGGTGTCACCATGAGCAGTGACACTACAAGGCGTAACTACCTC
40461 TGTCACAGTA
Statistics
Matches: 111, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
128 1 0.01
129 110 0.99
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.20
Consensus pattern (129 bp):
ACTCTCAGACGAAGTACTAAAGGTAACAGCACTAGGGGTAACTCCCCTCGTTACAGTCATAGCAG
AAGGCAGAATGGTGTCACCATGAGCAGTGACACTACAAGGCGTAACTACCTCGTTACACTACAT
Found at i:40726 original size:36 final size:36
Alignment explanation
Indices: 40686--40772 Score: 122
Period size: 36 Copynumber: 2.4 Consensus size: 36
40676 GCTGACTACG
* * *
40686 AGTCGTGCTAAAAGTGGTAT-GATGAGCAGAAGCAGC
1 AGTCGTGCCAAAAGTGGTATAG-TCAGAAGAAGCAGC
40722 AGTCGTGCCAAAAGTGGTATAGTCAGAAGAAGCAGC
1 AGTCGTGCCAAAAGTGGTATAGTCAGAAGAAGCAGC
*
40758 AGTCATGCCAAAAGT
1 AGTCGTGCCAAAAGT
40773 AGGACTGCCA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
36 45 0.98
37 1 0.02
ACGTcount: A:0.36, C:0.16, G:0.30, T:0.18
Consensus pattern (36 bp):
AGTCGTGCCAAAAGTGGTATAGTCAGAAGAAGCAGC
Found at i:45131 original size:2 final size:2
Alignment explanation
Indices: 45124--45149 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
45114 CTCACAAACA
45124 GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
45150 TTTTACCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:46753 original size:21 final size:21
Alignment explanation
Indices: 46727--46771 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
46717 GCTTTCTTGC
46727 TCAAATCATCTCCAAAT-GACT
1 TCAAATCATCTCC-AATGGACT
*
46748 TCAAATCTTCTCCAATGGACT
1 TCAAATCATCTCCAATGGACT
46769 TCA
1 TCA
46772 TCTCATCAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.33, C:0.29, G:0.07, T:0.31
Consensus pattern (21 bp):
TCAAATCATCTCCAATGGACT
Found at i:47989 original size:1 final size:1
Alignment explanation
Indices: 47983--48007 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
47973 TTGTTAATTT
47983 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
48008 CAGGAAAGCA
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:49493 original size:30 final size:30
Alignment explanation
Indices: 49393--49494 Score: 125
Period size: 30 Copynumber: 3.4 Consensus size: 30
49383 TTCAGATTCT
* *
49393 GAGGATGAATTTGACCCGGATGAGGATCCC
1 GAGGAGGATTTTGACCCGGATGAGGATCCC
* * * *
49423 GATGAGGATTTCGACCCGAACGAGGATCCC
1 GAGGAGGATTTTGACCCGGATGAGGATCCC
49453 G-GAGAGGATTTTGACCCGGATGAGGATCCC
1 GAG-GAGGATTTTGACCCGGATGAGGATCCC
*
49483 GAGGAAGATTTT
1 GAGGAGGATTTT
49495 AAGGTGTCAG
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
30 58 0.98
31 1 0.02
ACGTcount: A:0.26, C:0.20, G:0.33, T:0.21
Consensus pattern (30 bp):
GAGGAGGATTTTGACCCGGATGAGGATCCC
Found at i:57086 original size:177 final size:177
Alignment explanation
Indices: 56784--57121 Score: 649
Period size: 177 Copynumber: 1.9 Consensus size: 177
56774 AGTTAATTGC
*
56784 TAACAAAATGACTTCAATCATTTGTGATTGAAATAAAAAAAAAAAAGGAAATAGCAGAAGGTTTT
1 TAACAAAATGACTTCAATCATTTGTGATTGAAAAAAAAAAAAAAAAGGAAATAGCAGAAGGTTTT
*
56849 TTTATGAACCGAGTAAAAGCAAAAAGGAGAAAAAGACTTACACTATTGTTAAGCAACTCAAATCT
66 TTTACGAACCGAGTAAAAGCAAAAAGGAGAAAAAGACTTACACTATTGTTAAGCAACTCAAATCT
56914 AGAACTCTTTCTTGGATCGTACAAGTGAAGGAAATAGCAGAAGGAAA
131 AGAACTCTTTCTTGGATCGTACAAGTGAAGGAAATAGCAGAAGGAAA
56961 TAACAAAATGACTTCAATCATTTGTGATTGAAAAAAAAAAAAAAAAGGAAATAGCAGAAGGTTTT
1 TAACAAAATGACTTCAATCATTTGTGATTGAAAAAAAAAAAAAAAAGGAAATAGCAGAAGGTTTT
*
57026 TTTACGAACCGAGTAAAAGCAAAAAGGAGAAAAAGACTTACACTATTGTTAAGTAACTCAAATCT
66 TTTACGAACCGAGTAAAAGCAAAAAGGAGAAAAAGACTTACACTATTGTTAAGCAACTCAAATCT
57091 AGAACTCTTTCTTGGATCGTACAAGTGAAGG
131 AGAACTCTTTCTTGGATCGTACAAGTGAAGG
57122 TTTCGATCCT
Statistics
Matches: 158, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
177 158 1.00
ACGTcount: A:0.46, C:0.12, G:0.18, T:0.24
Consensus pattern (177 bp):
TAACAAAATGACTTCAATCATTTGTGATTGAAAAAAAAAAAAAAAAGGAAATAGCAGAAGGTTTT
TTTACGAACCGAGTAAAAGCAAAAAGGAGAAAAAGACTTACACTATTGTTAAGCAACTCAAATCT
AGAACTCTTTCTTGGATCGTACAAGTGAAGGAAATAGCAGAAGGAAA
Found at i:57493 original size:31 final size:31
Alignment explanation
Indices: 57455--57528 Score: 139
Period size: 31 Copynumber: 2.4 Consensus size: 31
57445 GCAGACACCC
57455 TGTTACAGGTAATACCTCACGTGGTTACACA
1 TGTTACAGGTAATACCTCACGTGGTTACACA
*
57486 TGTTACAGGTAATACCTCACTTGGTTACACA
1 TGTTACAGGTAATACCTCACGTGGTTACACA
57517 TGTTACAGGTAA
1 TGTTACAGGTAA
57529 CACCATGTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (31 bp):
TGTTACAGGTAATACCTCACGTGGTTACACA
Found at i:57545 original size:17 final size:17
Alignment explanation
Indices: 57525--57578 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
57515 CATGTTACAG
57525 GTAACACCATGTAACTA
1 GTAACACCATGTAACTA
* *** *
57542 GTAATA-CATGTTGTTG
1 GTAACACCATGTAACTA
57558 GTAACACCATGTAACTA
1 GTAACACCATGTAACTA
57575 GTAA
1 GTAA
57579 TACATGTTGT
Statistics
Matches: 26, Mismatches: 10, Indels: 2
0.68 0.26 0.05
Matches are distributed among these distances:
16 11 0.42
17 15 0.58
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.30
Consensus pattern (17 bp):
GTAACACCATGTAACTA
Found at i:57561 original size:16 final size:16
Alignment explanation
Indices: 57542--57630 Score: 88
Period size: 16 Copynumber: 5.4 Consensus size: 16
57532 CATGTAACTA
57542 GTAATACATGTTGTTG
1 GTAATACATGTTGTTG
* *** *
57558 GTAACACCATGTAACTA
1 GTAATA-CATGTTGTTG
57575 GTAATACATGTTGTTG
1 GTAATACATGTTGTTG
* **
57591 GTAATACCTTGTTACTG
1 GTAATA-CATGTTGTTG
57608 GTAATACATGTTGTTG
1 GTAATACATGTTGTTG
57624 GTAATAC
1 GTAATAC
57631 CCTGTGAATT
Statistics
Matches: 55, Mismatches: 16, Indels: 4
0.73 0.21 0.05
Matches are distributed among these distances:
16 31 0.56
17 24 0.44
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.38
Consensus pattern (16 bp):
GTAATACATGTTGTTG
Found at i:57631 original size:33 final size:33
Alignment explanation
Indices: 57524--57627 Score: 172
Period size: 33 Copynumber: 3.2 Consensus size: 33
57514 ACATGTTACA
57524 GGTAACACCATGTAACTAGTAATACATGTTGTT
1 GGTAACACCATGTAACTAGTAATACATGTTGTT
57557 GGTAACACCATGTAACTAGTAATACATGTTGTT
1 GGTAACACCATGTAACTAGTAATACATGTTGTT
* * * *
57590 GGTAATACCTTGTTACTGGTAATACATGTTGTT
1 GGTAACACCATGTAACTAGTAATACATGTTGTT
57623 GGTAA
1 GGTAA
57628 TACCCTGTGA
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 67 1.00
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (33 bp):
GGTAACACCATGTAACTAGTAATACATGTTGTT
Found at i:57900 original size:3 final size:3
Alignment explanation
Indices: 57892--57955 Score: 119
Period size: 3 Copynumber: 21.0 Consensus size: 3
57882 ATATCTTGCA
57892 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
57940 TAT TATT TAT TAT TAT
1 TAT TA-T TAT TAT TAT
57956 GCATAAGAAT
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 57 0.95
4 3 0.05
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:58628 original size:13 final size:13
Alignment explanation
Indices: 58610--58645 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
58600 AAAGGGCAAA
58610 AGAGTGAGAACTC
1 AGAGTGAGAACTC
58623 AGAGTGAGAACTC
1 AGAGTGAGAACTC
58636 AGAGTGAGAA
1 AGAGTGAGAA
58646 GAAATACTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.42, C:0.11, G:0.33, T:0.14
Consensus pattern (13 bp):
AGAGTGAGAACTC
Found at i:59115 original size:24 final size:23
Alignment explanation
Indices: 59087--59169 Score: 62
Period size: 24 Copynumber: 3.3 Consensus size: 23
59077 TTATCCATAA
59087 ATATATTAGAGATAATTATGATG
1 ATATATTAGAGATAATTATGATG
*
59110 ACTATATTATTAGCCATATTATTCAT-AT-
1 A-TATATTA-GAG--ATA--ATT-ATGATG
*
59138 ATATATTAGAGATAATTATGGTG
1 ATATATTAGAGATAATTATGATG
59161 ATTATATTA
1 A-TATATTA
59170 TTAACCATAT
Statistics
Matches: 47, Mismatches: 3, Indels: 19
0.68 0.04 0.28
Matches are distributed among these distances:
21 2 0.04
22 4 0.09
23 2 0.04
24 17 0.36
25 2 0.04
26 2 0.04
27 10 0.21
28 1 0.02
29 5 0.11
30 2 0.04
ACGTcount: A:0.40, C:0.05, G:0.12, T:0.43
Consensus pattern (23 bp):
ATATATTAGAGATAATTATGATG
Found at i:59142 original size:51 final size:51
Alignment explanation
Indices: 59065--59187 Score: 201
Period size: 51 Copynumber: 2.4 Consensus size: 51
59055 ACAGTTACCT
59065 TTATTAACCATATTATCCATAAATATATTAGAGATAATTATGATGACTATA
1 TTATTAACCATATTATCCATAAATATATTAGAGATAATTATGATGACTATA
* * * * *
59116 TTATTAGCCATATTATTCATATATATATTAGAGATAATTATGGTGATTATA
1 TTATTAACCATATTATCCATAAATATATTAGAGATAATTATGATGACTATA
59167 TTATTAACCATATTATCCATA
1 TTATTAACCATATTATCCATA
59188 CAAGGTATGA
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 65 1.00
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (51 bp):
TTATTAACCATATTATCCATAAATATATTAGAGATAATTATGATGACTATA
Found at i:59171 original size:27 final size:25
Alignment explanation
Indices: 59090--59172 Score: 80
Period size: 27 Copynumber: 3.2 Consensus size: 25
59080 TCCATAAATA
59090 TATTAGAGATAATTATGATGACTATAT
1 TATTAGAGATAATTATG-TGA-TATAT
** *
59117 TATTAGCCAT-ATTAT-TCATATAT
1 TATTAGAGATAATTATGTGATATAT
59140 ATATTAGAGATAATTATGGTGATTATAT
1 -TATTAGAGATAATTAT-GTGA-TATAT
59168 TATTA
1 TATTA
59173 ACCATATTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
23 5 0.11
24 10 0.22
25 5 0.11
26 5 0.11
27 15 0.33
28 5 0.11
ACGTcount: A:0.39, C:0.05, G:0.12, T:0.45
Consensus pattern (25 bp):
TATTAGAGATAATTATGTGATATAT
Found at i:61645 original size:1 final size:1
Alignment explanation
Indices: 61639--61663 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
61629 AGAAAAGAAG
61639 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
61664 CCAAAGGCAA
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:62005 original size:28 final size:27
Alignment explanation
Indices: 61954--62007 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 27
61944 AGAGAGCCAT
61954 GAAAGAAAAAAAAAAAAAGGAAAGTACA
1 GAAAGAAAAAAAAAAAAA-GAAAGTACA
61982 GAAAGAAAAATAAAAAAGAA-AAAGTA
1 GAAAGAAAAA-AAAAAA-AAGAAAGTA
62008 GAAGAGAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 16 0.67
29 6 0.25
30 2 0.08
ACGTcount: A:0.76, C:0.02, G:0.17, T:0.06
Consensus pattern (27 bp):
GAAAGAAAAAAAAAAAAAGAAAGTACA
Found at i:63779 original size:27 final size:28
Alignment explanation
Indices: 63729--63781 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
63719 AAATCAATTA
*
63729 GAAATCATAAAAACATAAAGATAAATCT
1 GAAATCATAAAAACACAAAGATAAATCT
63757 GAAATCATAAAATAC-CAAA-ATAAAT
1 GAAATCATAAAA-ACACAAAGATAAAT
63782 AATCAGATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 6 0.26
28 15 0.65
29 2 0.09
ACGTcount: A:0.62, C:0.11, G:0.06, T:0.21
Consensus pattern (28 bp):
GAAATCATAAAAACACAAAGATAAATCT
Found at i:64244 original size:22 final size:22
Alignment explanation
Indices: 64219--64260 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
64209 GCGTTCCTGA
64219 GGGTACCCGGGGCCGGGTAGGG
1 GGGTACCCGGGGCCGGGTAGGG
64241 GGGTACCCGGGGCCGGGTAG
1 GGGTACCCGGGGCCGGGTAG
64261 CCTCAGAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.10, C:0.24, G:0.57, T:0.10
Consensus pattern (22 bp):
GGGTACCCGGGGCCGGGTAGGG
Found at i:65713 original size:9 final size:9
Alignment explanation
Indices: 65699--65732 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
65689 CTATAATTAA
65699 ATATATATT
1 ATATATATT
*
65708 ATATATATA
1 ATATATATT
65717 ATA-ATATT
1 ATATATATT
65725 ATATATAT
1 ATATATAT
65733 AATTATATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (9 bp):
ATATATATT
Found at i:65723 original size:19 final size:18
Alignment explanation
Indices: 65698--65762 Score: 80
Period size: 17 Copynumber: 3.6 Consensus size: 18
65688 TCTATAATTA
65698 AATATATATTATATATAT
1 AATATATATTATATATAT
65716 AATA-ATATTATATATAT
1 AATATATATTATATATAT
*
65733 AATTATATACTCCATATA-AT
1 AA-TATATA-T-TATATATAT
65753 AATATATATT
1 AATATATATT
65763 TATTAAACGG
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
17 15 0.37
18 7 0.17
19 9 0.22
20 5 0.12
21 5 0.12
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (18 bp):
AATATATATTATATATAT
Found at i:66241 original size:118 final size:118
Alignment explanation
Indices: 66033--66254 Score: 408
Period size: 118 Copynumber: 1.9 Consensus size: 118
66023 AATATTGAAA
*
66033 ATCTATACCTTACTATTAAAGTTATCCTCAAGCTATTGTATGCTCAGTATTTGTTTCTTCTCATG
1 ATCTATACCTTACTATTAAAGTTATCCTCAAGCTATTGTATGCTCAGTATTTGGTTCTTCTCATG
*
66098 CTGGCATTTGTCCAAAGGTGATTGGTTGGGAAAAAACCAATATATATTATTAT
66 CTGACATTTGTCCAAAGGTGATTGGTTGGGAAAAAACCAATATATATTATTAT
**
66151 ATCTATACCTTGTTATTAAAGTTATCCTCAAGCTATTGTATGCTCAGTATTTGGTTCTTCTCATG
1 ATCTATACCTTACTATTAAAGTTATCCTCAAGCTATTGTATGCTCAGTATTTGGTTCTTCTCATG
66216 CTGACATTTGTCCAAAGGTGATTGGTTGGGAAAAAACCA
66 CTGACATTTGTCCAAAGGTGATTGGTTGGGAAAAAACCA
66255 TATTTGAAAT
Statistics
Matches: 100, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
118 100 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.39
Consensus pattern (118 bp):
ATCTATACCTTACTATTAAAGTTATCCTCAAGCTATTGTATGCTCAGTATTTGGTTCTTCTCATG
CTGACATTTGTCCAAAGGTGATTGGTTGGGAAAAAACCAATATATATTATTAT
Found at i:68669 original size:2 final size:2
Alignment explanation
Indices: 68658--68687 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
68648 TTGATTAATC
68658 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
68688 TAAAGGCTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:71442 original size:439 final size:433
Alignment explanation
Indices: 70497--71569 Score: 1305
Period size: 439 Copynumber: 2.5 Consensus size: 433
70487 AATTTTTGTT
* * * * *
70497 AATCGGACATTTGGATCAAAAATAATATGATATTAAATAGATTGTCAATCGAAATCACAAAATTT
1 AATCGGACATGTGGATCAAAAATTATATGATATTAAATAGACTGACAATCGAAACCA-AAAATTT
** * *
70562 CAAAAGCATTTTTTAGAATTGAAATATAAAAATTAGCTTTTGAGTCTTTAATGAAAGTTGTAGAT
65 CGGAAGCATTTTTTAGAATTGAAACATAAAAATTTGC-TTTGAGTCTTTAATGAAAGTTGTAGAT
* * * * * *
70627 CGTAAAATTACCTGTTAATAGACACCTGAATTACCTTAATTGGACAAATAGAACAAAGAA-AAAA
129 CATGAAATTACCTCTTAATAGACACATGAATCACCTTAATCGGACAAATAGAACAAAGAATAAAA
* * *
70691 AAATGAAGTGTTAAATCAAGTAAGATAAAATTTGGAAAGGACTAAATAGCATAAAATAGAAAAGT
194 AAATAAAGTGTCAAATCAAGTAAGATAAAATTTGGAAAGGACTAAATAGAATAAAATAGAAAAGT
* * **
70756 ATGACGGTGATTTGATAACTAATTTAAATAAGAAAATATTTGTTAAGGGAGATCTTGAAACATAA
259 ATGACGGTCATTTGATAAATAATCCAAATAAGAAAATATTTGTTAAGGGAGATCTTGAAACATAA
* * *
70821 AAATTCCCTTTTGAACCCTTCATGAAACTCGTAGATCAAATTAACTTTCGGGTTCTTCATGAAAG
324 AAATTCCCTTTTGAACCCGTCACGAAACTCGTAGATCAAATTAACTTTCGGGTCCTTCATGAAAG
* * * * *
70886 TCGTAGATTATACAGTAACCTTTTAACCGACACTTGAATAACTTT
389 TCGTAAATCATACAATAACCTTTTAACCGACACTTCAATAACTTC
* * * ** *
70931 AATTGGACATGTGGATCGAAAATTATATGGTATTAAATAGACCAACAATCGAAACGAACAAATTT
1 AATCGGACATGTGGATCAAAAATTATATGATATTAAATAGACTGACAATCGAAACCAA-AAATTT
* * * * *
70996 AGGAAGCATTTTTTTGAATTGAAACATAAAAATTTGCTTTGAGTCCTTCATGAAAGTTGCAGATC
65 CGGAAGCATTTTTTAGAATTGAAACATAAAAATTTGCTTTGAGTCTTTAATGAAAGTTGTAGATC
* *
71061 ATGAAATTACCTTTTAATAGACACATGAATCAACTTAATCGGACAAATAGAACAAAGAATAAAAA
130 ATGAAATTACCTCTTAATAGACACATGAATCACCTTAATCGGACAAATAGAACAAAGAATAAAAA
* * * * * * *
71126 AATAAAGCT-TCAACGTTAGATTAAGATAGAATTTGTAATGGACTAAGTAGAATAAAGTAGTAGA
195 AATAAAG-TGTCAA-ATCA-AGTAAGATAAAATTTGGAAAGGACTAAATAGAATAAA--A-TAGA
* *
71190 AAAGTATGAGGGTCATTTGATAAATAATCCAAATAAGAAAATATTTGTTAATGGAGATCTTGAAA
254 AAAGTATGACGGTCATTTGATAAATAATCCAAATAAGAAAATATTTGTTAAGGGAGATCTTGAAA
* *
71255 CATAAAAATTTCCTTTTGAACCCGTCACGAAACTCGTAGATCAAATTTAGCTTTCGGGTCCTTCA
319 CATAAAAATTCCCTTTTGAACCCGTCACGAAACTCGTAGATCAAA-TTAACTTTCGGGTCCTTCA
* **
71320 TGAAAGTCGTAAATCATGCAATAACCTTTTATTCGACACTTCAATAACTTC
383 TGAAAGTCGTAAATCATACAATAACCTTTTAACCGACACTTCAATAACTTC
* * * *
71371 AATCGGACATGTGGA-CAAAAAATTATACGATATTAAATTA-ACTGGCAATCAAAACCAAAAAAT
1 AATCGGACATGTGGATC-AAAAATTATATGATATTAAA-TAGACTGACAATCGAAACCAAAAATT
* * * *
71434 TCGGAAGCATTTTTTAGAA-T-CAACATATTAAAA-TTGAATTTTTGAGTTTTTAATGAAAATTG
64 TCGGAAGCATTTTTTAGAATTGAAACATA--AAAATTTG---CTTTGAGTCTTTAATGAAAGTTG
* * * * *
71496 TAAATCATGAAATTACCTCTTAATACACACTTGAATCACCTTAATCGGACAAATAGAAAAAAAAA
124 TAGATCATGAAATTACCTCTTAATAGACACATGAATCACCTTAATCGGACAAATAGAACAAAGAA
71561 TACAAAAAA
189 TA-AAAAAA
71570 AAGGCAACAC
Statistics
Matches: 540, Mismatches: 82, Indels: 26
0.83 0.13 0.04
Matches are distributed among these distances:
433 78 0.14
434 97 0.18
435 3 0.01
436 31 0.06
437 6 0.01
438 5 0.01
439 131 0.24
440 104 0.19
441 79 0.15
442 6 0.01
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.30
Consensus pattern (433 bp):
AATCGGACATGTGGATCAAAAATTATATGATATTAAATAGACTGACAATCGAAACCAAAAATTTC
GGAAGCATTTTTTAGAATTGAAACATAAAAATTTGCTTTGAGTCTTTAATGAAAGTTGTAGATCA
TGAAATTACCTCTTAATAGACACATGAATCACCTTAATCGGACAAATAGAACAAAGAATAAAAAA
ATAAAGTGTCAAATCAAGTAAGATAAAATTTGGAAAGGACTAAATAGAATAAAATAGAAAAGTAT
GACGGTCATTTGATAAATAATCCAAATAAGAAAATATTTGTTAAGGGAGATCTTGAAACATAAAA
ATTCCCTTTTGAACCCGTCACGAAACTCGTAGATCAAATTAACTTTCGGGTCCTTCATGAAAGTC
GTAAATCATACAATAACCTTTTAACCGACACTTCAATAACTTC
Found at i:72227 original size:2 final size:2
Alignment explanation
Indices: 72220--72276 Score: 58
Period size: 2 Copynumber: 32.5 Consensus size: 2
72210 CCGAATATTA
72220 AT AT AT AT -T AT AT AT A- AT A- AT AT -T AT AT AT AT A- AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
72256 AT AT AT AT A- AT AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
72277 ATTATTAAAC
Statistics
Matches: 47, Mismatches: 0, Indels: 16
0.75 0.00 0.25
Matches are distributed among these distances:
1 8 0.17
2 39 0.83
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:72242 original size:17 final size:16
Alignment explanation
Indices: 72214--72278 Score: 74
Period size: 14 Copynumber: 4.6 Consensus size: 16
72204 AACCGACCGA
72214 ATAT-TAATATATATT
1 ATATATAATATATATT
72229 ATATATAATA-ATA-T
1 ATATATAATATATATT
72243 -TATAT-ATATA-ATT
1 ATATATAATATATATT
72256 ATATAT-ATA-ATATT
1 ATATATAATATATATT
72270 ATATATAAT
1 ATATATAAT
72279 TATTAAACGG
Statistics
Matches: 44, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
12 4 0.09
13 8 0.18
14 18 0.41
15 9 0.20
16 5 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATATATAATATATATT
Found at i:72258 original size:12 final size:12
Alignment explanation
Indices: 72216--72281 Score: 75
Period size: 12 Copynumber: 5.4 Consensus size: 12
72206 CCGACCGAAT
72216 ATTA-ATATAT-
1 ATTATATATATA
72226 ATTATATATAATAA
1 ATTATATAT-AT-A
72240 TATTATATATATA
1 -ATTATATATATA
72253 ATTATATATATA
1 ATTATATATATA
72265 A-TATTATATATA
1 ATTA-TATATATA
72277 ATTAT
1 ATTAT
72282 TAAACGGTCT
Statistics
Matches: 49, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
10 4 0.08
11 6 0.12
12 25 0.51
13 3 0.06
14 2 0.04
15 9 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
ATTATATATATA
Found at i:72265 original size:26 final size:26
Alignment explanation
Indices: 72213--72281 Score: 108
Period size: 26 Copynumber: 2.7 Consensus size: 26
72203 AAACCGACCG
72213 AATATTA-ATATATATTATATATAAT
1 AATATTATATATATATTATATATAAT
72238 AATATTATATATATAATTATATAT-AT
1 AATATTATATATAT-ATTATATATAAT
72264 AATATTATATATA-ATTAT
1 AATATTATATATATATTAT
72282 TAAACGGTCT
Statistics
Matches: 42, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
24 5 0.12
25 7 0.17
26 21 0.50
27 9 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
AATATTATATATATATTATATATAAT
Found at i:72272 original size:24 final size:25
Alignment explanation
Indices: 72213--72281 Score: 97
Period size: 24 Copynumber: 2.7 Consensus size: 25
72203 AAACCGACCG
72213 AATATTA-ATATATATTATATATAAT
1 AATATTATATATA-ATTATATATAAT
72238 AATATTATATATATAATTATATAT-AT
1 AATA-T-TATATATAATTATATATAAT
72264 AATATTATATATAATTAT
1 AATATTATATATAATTAT
72282 TAAACGGTCT
Statistics
Matches: 41, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
24 13 0.32
25 5 0.12
26 7 0.17
27 11 0.27
28 5 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
AATATTATATATAATTATATATAAT
Found at i:77436 original size:6 final size:6
Alignment explanation
Indices: 77427--77454 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
77417 TAGTACTAGT
77427 ATTTTC ATTTTC ATTTTC ATTTTC ATTT
1 ATTTTC ATTTTC ATTTTC ATTTTC ATTT
77455 AAAAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.14, G:0.00, T:0.68
Consensus pattern (6 bp):
ATTTTC
Found at i:79345 original size:11 final size:12
Alignment explanation
Indices: 79328--79357 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
79318 TGGTTTTTGC
79328 TATTTTTTTTTT
1 TATTTTTTTTTT
79340 TATTTTTTTTTT
1 TATTTTTTTTTT
79352 TATTTT
1 TATTTT
79358 AAGTGTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (12 bp):
TATTTTTTTTTT
Found at i:86045 original size:25 final size:25
Alignment explanation
Indices: 86011--86059 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
86001 CTCTTTGAGT
86011 GATCAAAGTTCGAAATGGCCTGAAA
1 GATCAAAGTTCGAAATGGCCTGAAA
86036 GATCAAAGTTCGAAATGGCCTGAA
1 GATCAAAGTTCGAAATGGCCTGAA
86060 TAGTGACTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.20
Consensus pattern (25 bp):
GATCAAAGTTCGAAATGGCCTGAAA
Found at i:86483 original size:32 final size:34
Alignment explanation
Indices: 86433--86495 Score: 103
Period size: 32 Copynumber: 1.9 Consensus size: 34
86423 AAAACTAAGA
*
86433 TAATAAAACTATATAGCATGAGGTTAACATCAGG
1 TAATAAAACTATATAGCATGAGGTGAACATCAGG
86467 TAATAAAA-T-TATAGCATGAGGTGAACATC
1 TAATAAAACTATATAGCATGAGGTGAACATC
86496 TGGGGAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 19 0.68
33 1 0.04
34 8 0.29
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.27
Consensus pattern (34 bp):
TAATAAAACTATATAGCATGAGGTGAACATCAGG
Done.