Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014359.1 Corchorus olitorius cultivar O-4 contig14392, 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: 76900
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:3602 original size:30 final size:30
Alignment explanation
Indices: 3566--3628 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
3556 ATTAAAATGT
3566 CAACTCTATACTTAACAATGTGAATTAATC
1 CAACTCTATACTTAACAATGTGAATTAATC
3596 CAACTCTATACTTAACAATGTGAATTAATC
1 CAACTCTATACTTAACAATGTGAATTAATC
3626 CAA
1 CAA
3629 ATAATTGACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.41, C:0.21, G:0.06, T:0.32
Consensus pattern (30 bp):
CAACTCTATACTTAACAATGTGAATTAATC
Found at i:3887 original size:29 final size:29
Alignment explanation
Indices: 3850--3941 Score: 132
Period size: 29 Copynumber: 3.2 Consensus size: 29
3840 CCTGGAGTAC
* *
3850 AAATGACCAAAATACCCCTGAATGTGCAA
1 AAATGACCATAATGCCCCTGAATGTGCAA
*
3879 AAATGACCATAATGCCCCTGAATATGCAA
1 AAATGACCATAATGCCCCTGAATGTGCAA
*
3908 AAATGACCATAATGCCCCT-AGATGTGCGA
1 AAATGACCATAATGCCCCTGA-ATGTGCAA
3937 AAATG
1 AAATG
3942 CAAATTAAGC
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
28 1 0.02
29 56 0.98
ACGTcount: A:0.41, C:0.23, G:0.16, T:0.20
Consensus pattern (29 bp):
AAATGACCATAATGCCCCTGAATGTGCAA
Found at i:16799 original size:27 final size:27
Alignment explanation
Indices: 16722--16793 Score: 126
Period size: 27 Copynumber: 2.7 Consensus size: 27
16712 GGATCCTCGG
*
16722 GAGGATCGGATGGAGCAGATTCCTTGA
1 GAGGATCGGATGGAGCAGAATCCTTGA
16749 GAGGATCGGATGGAGCAGAATCCTTGA
1 GAGGATCGGATGGAGCAGAATCCTTGA
*
16776 GAGGTTCGGATGGAGCAG
1 GAGGATCGGATGGAGCAG
16794 CGTCCTCGAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.26, C:0.14, G:0.40, T:0.19
Consensus pattern (27 bp):
GAGGATCGGATGGAGCAGAATCCTTGA
Found at i:16804 original size:27 final size:27
Alignment explanation
Indices: 16714--16804 Score: 119
Period size: 27 Copynumber: 3.4 Consensus size: 27
16704 CAGAAAAGGG
*
16714 ATCCTCGGGAGGATCGGATGGAGCAGA
1 ATCCTCGAGAGGATCGGATGGAGCAGA
* *
16741 TTCCTTGAGAGGATCGGATGGAGCAGA
1 ATCCTCGAGAGGATCGGATGGAGCAGA
* * *
16768 ATCCTTGAGAGGTTCGGATGGAGCAGC
1 ATCCTCGAGAGGATCGGATGGAGCAGA
*
16795 GTCCTCGAGA
1 ATCCTCGAGA
16805 AAGGGGTTCG
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 56 1.00
ACGTcount: A:0.24, C:0.19, G:0.37, T:0.20
Consensus pattern (27 bp):
ATCCTCGAGAGGATCGGATGGAGCAGA
Found at i:25588 original size:3 final size:3
Alignment explanation
Indices: 25580--25620 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
25570 AAGTAGGAAA
25580 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
25621 AGGAACAGAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:39745 original size:33 final size:32
Alignment explanation
Indices: 39708--39874 Score: 120
Period size: 33 Copynumber: 5.4 Consensus size: 32
39698 GGTAATAATA
39708 ATTTGGTAATTAAAGTAAAAAGAGTAAATTGGT
1 ATTTGGTAATTAAAGTAAAAAGA-TAAATTGGT
* **
39741 ATTTGGTAATCAAAGTAAAAAGA-AAATATGAA
1 ATTTGGTAATTAAAGTAAAAAGATAAAT-TGGT
* **
39773 ATTGGGTAGCTAAAGT-------TAAA-TGGT
1 ATTTGGTAATTAAAGTAAAAAGATAAATTGGT
* *
39797 ATTTGGTAATTAAAGTTAAAAGAGTAAAGTGGT
1 ATTTGGTAATTAAAGTAAAAAGA-TAAATTGGT
* ** *
39830 ATTTGGTAATCAAAGTAAAAAGA-AAAAAGGG
1 ATTTGGTAATTAAAGTAAAAAGATAAATTGGT
*
39861 AATTGGTAATTAAA
1 ATTTGGTAATTAAA
39875 AGAGTAAAAA
Statistics
Matches: 104, Mismatches: 19, Indels: 24
0.71 0.13 0.16
Matches are distributed among these distances:
24 15 0.14
26 3 0.03
31 21 0.20
32 18 0.17
33 47 0.45
ACGTcount: A:0.47, C:0.02, G:0.22, T:0.29
Consensus pattern (32 bp):
ATTTGGTAATTAAAGTAAAAAGATAAATTGGT
Found at i:39907 original size:19 final size:19
Alignment explanation
Indices: 39885--39956 Score: 128
Period size: 19 Copynumber: 3.8 Consensus size: 19
39875 AGAGTAAAAA
39885 AAAAAGAATTTGGTAAAGT
1 AAAAAGAATTTGGTAAAGT
*
39904 AAAAAGAATTTGGT-AATT
1 AAAAAGAATTTGGTAAAGT
39922 AAAAAGAATTTGGTAAAGT
1 AAAAAGAATTTGGTAAAGT
39941 AAAAAGAATTTGGTAA
1 AAAAAGAATTTGGTAA
39957 TTAAAGAGTA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
18 17 0.34
19 33 0.66
ACGTcount: A:0.53, C:0.00, G:0.19, T:0.28
Consensus pattern (19 bp):
AAAAAGAATTTGGTAAAGT
Found at i:39924 original size:18 final size:18
Alignment explanation
Indices: 39885--40082 Score: 141
Period size: 18 Copynumber: 10.4 Consensus size: 18
39875 AGAGTAAAAA
*
39885 AAAAAGAATTTGGTAAAGT
1 AAAAAGAATTTGGT-AATT
39904 AAAAAGAATTTGGTAATT
1 AAAAAGAATTTGGTAATT
*
39922 AAAAAGAATTTGGTAAAGT
1 AAAAAGAATTTGGT-AATT
39941 AAAAAGAATTTGGTAATT
1 AAAAAGAATTTGGTAATT
* *
39959 AAAGAGTAAAAGTAAGATTGGTAAGTAA
1 ----A--AAAAG-AA-TTTGGTAA-T-T
39987 AAAAAGAATTTGGTAATT
1 AAAAAGAATTTGGTAATT
40005 AAAAAGAATTTGGTAATT
1 AAAAAGAATTTGGTAATT
* ***
40023 AAAGAGAA-AAAGTAAATT
1 AAAAAGAATTTGGT-AATT
****
40041 --GGTTAATTTGGTAATT
1 AAAAAGAATTTGGTAATT
40057 AAAAAGAATTTGGTAATT
1 AAAAAGAATTTGGTAATT
*
40075 AAAGAGAA
1 AAAAAGAA
40083 AAAGTAAATT
Statistics
Matches: 142, Mismatches: 22, Indels: 31
0.73 0.11 0.16
Matches are distributed among these distances:
16 7 0.05
17 4 0.03
18 68 0.48
19 32 0.23
20 7 0.05
21 2 0.01
22 6 0.04
24 6 0.04
25 2 0.01
26 7 0.05
27 1 0.01
ACGTcount: A:0.52, C:0.00, G:0.20, T:0.29
Consensus pattern (18 bp):
AAAAAGAATTTGGTAATT
Found at i:39931 original size:37 final size:37
Alignment explanation
Indices: 39885--40020 Score: 166
Period size: 37 Copynumber: 3.4 Consensus size: 37
39875 AGAGTAAAAA
39885 AAAAAGAATTTGGTAAAGTAAAAAGAATTTGGTAATT
1 AAAAAGAATTTGGTAAAGTAAAAAGAATTTGGTAATT
39922 AAAAAGAATTTGGTAAAGTAAAAAGAATTTGGTAATT
1 AAAAAGAATTTGGTAAAGTAAAAAGAATTTGGTAATT
*
39959 AAAGAGTAAAAGTAAGATTGGT-AAGTAAAAAAAGAATTTGGTAATT
1 ----A--AAAAG-AA-TTTGGTAAAGT--AAAAAGAATTTGGTAATT
40005 AAAAAGAATTTGGTAA
1 AAAAAGAATTTGGTAA
40021 TTAAAGAGAA
Statistics
Matches: 86, Mismatches: 2, Indels: 20
0.80 0.02 0.19
Matches are distributed among these distances:
37 37 0.43
38 5 0.06
39 3 0.03
40 5 0.06
41 1 0.01
42 1 0.01
43 5 0.06
44 6 0.07
45 5 0.06
46 18 0.21
ACGTcount: A:0.52, C:0.00, G:0.20, T:0.28
Consensus pattern (37 bp):
AAAAAGAATTTGGTAAAGTAAAAAGAATTTGGTAATT
Found at i:40014 original size:64 final size:66
Alignment explanation
Indices: 39916--40082 Score: 223
Period size: 64 Copynumber: 2.5 Consensus size: 66
39906 AAAGAATTTG
* *
39916 GTAATTAAAAAGAATTTGGTAAAGTAAAAAGAATTTGGTAATTAAAGAGTAAAAGTAAGATTGG-
1 GTAA-TAAAAAGAATTTGGT-AATTAAAAAGAATTTGGTAATTAAAGAGAAAAAGTAA-ATTGGT
39980 TAA-
63 TAAT
39983 GTAA-AAAAAGAATTTGGTAATTAAAAAGAATTTGGTAATTAAAGAGAAAAAGTAAATTGGTTAA
1 GTAATAAAAAGAATTTGGTAATTAAAAAGAATTTGGTAATTAAAGAGAAAAAGTAAATTGGTTAA
40047 TTT
66 --T
*
40050 GGTAATTAAAAAGAATTTGGTAATTAAAGAGAA
1 -GTAA-TAAAAAGAATTTGGTAATTAAAAAGAA
40083 AAAGTAAATT
Statistics
Matches: 90, Mismatches: 3, Indels: 11
0.87 0.03 0.11
Matches are distributed among these distances:
63 5 0.06
64 38 0.42
65 14 0.16
67 4 0.04
68 4 0.04
70 25 0.28
ACGTcount: A:0.51, C:0.00, G:0.20, T:0.29
Consensus pattern (66 bp):
GTAATAAAAAGAATTTGGTAATTAAAAAGAATTTGGTAATTAAAGAGAAAAAGTAAATTGGTTAA
T
Found at i:40051 original size:52 final size:52
Alignment explanation
Indices: 39993--40116 Score: 239
Period size: 52 Copynumber: 2.4 Consensus size: 52
39983 GTAAAAAAAG
39993 AATTTGGTAATTAAAAAGAATTTGGTAATTAAAGAGAAAAAGTAAATTGGTT
1 AATTTGGTAATTAAAAAGAATTTGGTAATTAAAGAGAAAAAGTAAATTGGTT
40045 AATTTGGTAATTAAAAAGAATTTGGTAATTAAAGAGAAAAAGTAAATTGGTT
1 AATTTGGTAATTAAAAAGAATTTGGTAATTAAAGAGAAAAAGTAAATTGGTT
*
40097 AATTTGGTAATTAAAGAGAA
1 AATTTGGTAATTAAAAAGAA
40117 AAAGTAAATT
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.48, C:0.00, G:0.19, T:0.32
Consensus pattern (52 bp):
AATTTGGTAATTAAAAAGAATTTGGTAATTAAAGAGAAAAAGTAAATTGGTT
Found at i:40103 original size:86 final size:86
Alignment explanation
Indices: 40011--40358 Score: 342
Period size: 86 Copynumber: 4.2 Consensus size: 86
40001 AATTAAAAAG
*
40011 AATTTGGTAATTAAAGAGAAAAAGTAAATTGGTTAATTTGGTAATTAAAAAGAATTTGGTAATTA
1 AATTTGGTAATTAAAGAGAAAAAGTAAATTGGTTAATTTGGTAATTAAAAAGAATTTGGTAAATA
*
40076 AAGAGAAAAAGTAAATTGGTT
66 AAGAGAAAAAGGAAATTGGTT
40097 AATTTGGTAATTAAAGAGAAAAAGTAAATTGGTTAATTTGGTAATTAAAAAGAATTTGGTAAATA
1 AATTTGGTAATTAAAGAGAAAAAGTAAATTGGTTAATTTGGTAATTAAAAAGAATTTGGTAAATA
*
40162 AAGAGTAAAAGGAAATTGGTT
66 AAGAGAAAAAGGAAATTGGTT
* * * ** * *
40183 AATTTGG----T-AAG-TAAAAAG-AATTTGG-TAA-TT--AAAGAGAAAAAGTAAATTGGTTAA
1 AATTTGGTAATTAAAGAGAAAAAGTAAATTGGTTAATTTGGTAA-TTAAAAAG-AATTTGGTAAA
*** * *
40237 TTTGGTA-ATTAAAAAGAATTTGG-T
64 TAAAG-AGA--AAAAGGAAATTGGTT
40261 AA--T--TA----AAGAGAAAAAGTAAATTGGTTAATTTGGTAATTAAAAAGAATTTGGTAAATA
1 AATTTGGTAATTAAAGAGAAAAAGTAAATTGGTTAATTTGGTAATTAAAAAGAATTTGGTAAATA
*
40318 AAGAGTAAAAGGAAATTGGTT
66 AAGAGAAAAAGGAAATTGGTT
* *
40339 AATTTGGTAAGTAAAAAGAA
1 AATTTGGTAATTAAAGAGAA
40359 TTTGGTAATT
Statistics
Matches: 209, Mismatches: 30, Indels: 46
0.73 0.11 0.16
Matches are distributed among these distances:
75 5 0.02
76 13 0.06
77 30 0.14
78 14 0.07
79 30 0.14
80 13 0.06
81 5 0.02
82 3 0.01
86 96 0.46
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.31
Consensus pattern (86 bp):
AATTTGGTAATTAAAGAGAAAAAGTAAATTGGTTAATTTGGTAATTAAAAAGAATTTGGTAAATA
AAGAGAAAAAGGAAATTGGTT
Found at i:40106 original size:34 final size:34
Alignment explanation
Indices: 40063--40150 Score: 167
Period size: 34 Copynumber: 2.6 Consensus size: 34
40053 AATTAAAAAG
40063 AATTTGGTAATTAAAGAGAAAAAGTAAATTGGTT
1 AATTTGGTAATTAAAGAGAAAAAGTAAATTGGTT
40097 AATTTGGTAATTAAAGAGAAAAAGTAAATTGGTT
1 AATTTGGTAATTAAAGAGAAAAAGTAAATTGGTT
*
40131 AATTTGGTAATTAAAAAGAA
1 AATTTGGTAATTAAAGAGAA
40151 TTTGGTAAAT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.19, T:0.32
Consensus pattern (34 bp):
AATTTGGTAATTAAAGAGAAAAAGTAAATTGGTT
Found at i:40153 original size:52 final size:52
Alignment explanation
Indices: 40097--40514 Score: 701
Period size: 52 Copynumber: 8.0 Consensus size: 52
40087 TAAATTGGTT
*
40097 AATTTGGTAATTAAAGAGAAAAAGTAAATTGGTTAATTTGGTAATTAAAAAG
1 AATTTGGTAATTAAAGAGTAAAAGTAAATTGGTTAATTTGGTAATTAAAAAG
* * *
40149 AATTTGGTAAATAAAGAGTAAAAGGAAATTGGTTAATTTGGTAAGTAAAAAG
1 AATTTGGTAATTAAAGAGTAAAAGTAAATTGGTTAATTTGGTAATTAAAAAG
*
40201 AATTTGGTAATTAAAGAGAAAAAGTAAATTGGTTAATTTGGTAATTAAAAAG
1 AATTTGGTAATTAAAGAGTAAAAGTAAATTGGTTAATTTGGTAATTAAAAAG
*
40253 AATTTGGTAATTAAAGAGAAAAAGTAAATTGGTTAATTTGGTAATTAAAAAG
1 AATTTGGTAATTAAAGAGTAAAAGTAAATTGGTTAATTTGGTAATTAAAAAG
* * *
40305 AATTTGGTAAATAAAGAGTAAAAGGAAATTGGTTAATTTGGTAAGTAAAAAG
1 AATTTGGTAATTAAAGAGTAAAAGTAAATTGGTTAATTTGGTAATTAAAAAG
*
40357 AATTTGGTAATTAAAGAGTTAAAAGTAAATTGGTTAATTTGGTAAGTAAAAAG
1 AATTTGGTAATTAAAGAG-TAAAAGTAAATTGGTTAATTTGGTAATTAAAAAG
40410 AATTTGGTAATTAAAGAGTAAAAGTAAATTGGTTAATTTGGTAATTAAAAAG
1 AATTTGGTAATTAAAGAGTAAAAGTAAATTGGTTAATTTGGTAATTAAAAAG
* * *
40462 AATTTGGTAATTAAAGAGTAAAAGGAAATCGATTAATTTGGTAATTAAGAAAG
1 AATTTGGTAATTAAAGAGTAAAAGTAAATTGGTTAATTTGGTAATTAA-AAAG
40515 TAAAATGAAA
Statistics
Matches: 346, Mismatches: 18, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
52 291 0.84
53 55 0.16
ACGTcount: A:0.47, C:0.00, G:0.21, T:0.32
Consensus pattern (52 bp):
AATTTGGTAATTAAAGAGTAAAAGTAAATTGGTTAATTTGGTAATTAAAAAG
Found at i:40206 original size:18 final size:18
Alignment explanation
Indices: 40183--40220 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
40173 GAAATTGGTT
40183 AATTTGGTAAGTAAAAAG
1 AATTTGGTAAGTAAAAAG
* *
40201 AATTTGGTAATTAAAGAG
1 AATTTGGTAAGTAAAAAG
40219 AA
1 AA
40221 AAAGTAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (18 bp):
AATTTGGTAAGTAAAAAG
Found at i:40258 original size:18 final size:18
Alignment explanation
Indices: 40235--40272 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
40225 TAAATTGGTT
40235 AATTTGGTAATTAAAAAG
1 AATTTGGTAATTAAAAAG
*
40253 AATTTGGTAATTAAAGAG
1 AATTTGGTAATTAAAAAG
40271 AA
1 AA
40273 AAAGTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.18, T:0.32
Consensus pattern (18 bp):
AATTTGGTAATTAAAAAG
Found at i:40544 original size:87 final size:84
Alignment explanation
Indices: 40410--40684 Score: 214
Period size: 86 Copynumber: 3.3 Consensus size: 84
40400 AAGTAAAAAG
* **
40410 AATTTGGTAATTAA-AGAGTAAAA-GTAAATTGGTTAATT-TGGTAATTAAAAAGAATTTGGTAA
1 AATTTGGTAATTAAGAAAGTAAAATG-AAATTGG-TAATTAAAG--ATTAAAAAGAATTTGGTAA
*
40472 TTAAAGAGTAAAAGGAAATCGATT
62 TTAAAGAGTAAAAGGAAAT-GATA
*
40496 AATTTGGTAATTAAGAAAGTAAAATGAAATTGGGGTAATTAAAGATTAAAATGAA-TTGGATAAT
1 AATTTGGTAATTAAGAAAGTAAAATGAAATT--GGTAATTAAAGATTAAAAAGAATTTGG-TAAT
* **
40560 TAAAGGGTAATTGG---T-A-A
63 TAAAGAGTAAAAGGAAATGATA
* * * *
40577 AATTTGGTAATTAAG-AAGTAAAATGAACTTGGTAATTAAAGAGTAAAGTAA-AATTTGGCAATC
1 AATTTGGTAATTAAGAAAGTAAAATGAAATTGGTAATTAAAGATTAAA--AAGAATTTGGTAATT
* * *
40640 AAATAGTAAAAAGGAAATTGGTC
64 AAAGAGT-AAAAGGAAA-TGATA
*
40663 AACTTGGTAATTAA-AAAGTAAA
1 AATTTGGTAATTAAGAAAGTAAA
40685 TTGGGTAATT
Statistics
Matches: 152, Mismatches: 20, Indels: 34
0.74 0.10 0.17
Matches are distributed among these distances:
78 16 0.11
79 10 0.07
80 23 0.15
81 15 0.10
82 1 0.01
84 2 0.01
86 38 0.25
87 38 0.25
88 6 0.04
89 3 0.02
ACGTcount: A:0.48, C:0.02, G:0.20, T:0.30
Consensus pattern (84 bp):
AATTTGGTAATTAAGAAAGTAAAATGAAATTGGTAATTAAAGATTAAAAAGAATTTGGTAATTAA
AGAGTAAAAGGAAATGATA
Found at i:40576 original size:157 final size:156
Alignment explanation
Indices: 40097--40514 Score: 682
Period size: 157 Copynumber: 2.7 Consensus size: 156
40087 TAAATTGGTT
40097 AATTTGGTAATTAAAGAGAAAAAGTAAATTGGTTAATTTGGTAATTAAAAAGAATTTGGTAAATA
1 AATTTGGTAATTAAAGAGAAAAAGTAAATTGGTTAATTTGGTAATTAAAAAGAATTTGGTAAATA
40162 AAGAGTAAAAGGAAATTGGTTAATTTGGTAAGTAAAAAGAATTTGGTAATTAAAGAGAA--AAAG
66 AAGAGTAAAAGGAAATTGGTTAATTTGGTAAGTAAAAAGAATTTGGTAATT--AGAGAATTAAAG
40225 -TAAATTGGTTAATTTGGTAATTAAAAAG
129 ATAAATTGG-TAATTTGGTAATTAAAAAG
40253 AATTTGGTAATTAAAGAGAAAAAGTAAATTGGTTAATTTGGTAATTAAAAAGAATTTGGTAAATA
1 AATTTGGTAATTAAAGAGAAAAAGTAAATTGGTTAATTTGGTAATTAAAAAGAATTTGGTAAATA
* *
40318 AAGAGTAAAAGGAAATTGGTTAATTTGGTAAGTAAAAAGAATTTGGTAATTAAAGAGTTAAA-AG
66 AAGAGTAAAAGGAAATTGGTTAATTTGGTAAGTAAAAAGAATTTGGTAATTAGAGAATTAAAGA-
*
40382 TAAATTGGTTAATTTGGTAAGTAAAAAG
130 TAAATTGG-TAATTTGGTAATTAAAAAG
* *
40410 AATTTGGTAATTAAAGAGTAAAAGTAAATTGGTTAATTTGGTAATTAAAAAGAATTTGGTAATTA
1 AATTTGGTAATTAAAGAGAAAAAGTAAATTGGTTAATTTGGTAATTAAAAAGAATTTGGTAAATA
* * *
40475 AAGAGTAAAAGGAAATCGATTAATTTGGTAATTAAGAAAG
66 AAGAGTAAAAGGAAATTGGTTAATTTGGTAAGTAA-AAAG
40515 TAAAATGAAA
Statistics
Matches: 249, Mismatches: 8, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
154 4 0.02
156 119 0.48
157 122 0.49
158 4 0.02
ACGTcount: A:0.47, C:0.00, G:0.21, T:0.32
Consensus pattern (156 bp):
AATTTGGTAATTAAAGAGAAAAAGTAAATTGGTTAATTTGGTAATTAAAAAGAATTTGGTAAATA
AAGAGTAAAAGGAAATTGGTTAATTTGGTAAGTAAAAAGAATTTGGTAATTAGAGAATTAAAGAT
AAATTGGTAATTTGGTAATTAAAAAG
Found at i:40586 original size:53 final size:51
Alignment explanation
Indices: 40499--40634 Score: 141
Period size: 53 Copynumber: 2.6 Consensus size: 51
40489 ATCGATTAAT
* * * * *
40499 TTGGTAATTAAGAAAGTAAAATGAAATTGGGGTAATTAA-AGATTAAAATGAA-
1 TTGGTAATTAA-AGAGTAAAGTAAAATT-TGGTAATTAAGA-AGTAAAATGAAC
* *
40551 TTGGATAATTAAAGGGTAATTGGTAAAATTTGGTAATTAAGAAGTAAAATGAAC
1 TTGG-TAATTAAAGAGTAA--AGTAAAATTTGGTAATTAAGAAGTAAAATGAAC
40605 TTGGTAATTAAAGAGTAAAGTAAAATTTGG
1 TTGGTAATTAAAGAGTAAAGTAAAATTTGG
40635 CAATCAAATA
Statistics
Matches: 70, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
51 11 0.16
52 9 0.13
53 39 0.56
54 11 0.16
ACGTcount: A:0.46, C:0.01, G:0.22, T:0.31
Consensus pattern (51 bp):
TTGGTAATTAAAGAGTAAAGTAAAATTTGGTAATTAAGAAGTAAAATGAAC
Found at i:40634 original size:26 final size:25
Alignment explanation
Indices: 40496--40650 Score: 98
Period size: 25 Copynumber: 5.9 Consensus size: 25
40486 GAAATCGATT
*
40496 AATTTGGTAATTAAGAAAGTAAAATGA
1 AATTTGGTAATTAA-AGAGTAAAAT-A
* * *
40523 AATTGGGGTAATTAAAGATTAAAATG
1 AATT-TGGTAATTAAAGAGTAAAATA
* **
40549 AA-TTGGATAATTAAAGGGTAATTGGTAA
1 AATTTGG-TAATTAAAGAGTAA--AAT-A
*
40577 AATTTGGTAATT-AAGAAGTAAAATG
1 AATTTGGTAATTAAAG-AGTAAAATA
* *
40602 AACTTGGTAATTAAAGAGTAAAGTAA
1 AATTTGGTAATTAAAGAGTAAAAT-A
* * *
40628 AATTTGGCAATCAAATAGTAAAA
1 AATTTGGTAATTAAAGAGTAAAA
40651 AGGAAATTGG
Statistics
Matches: 97, Mismatches: 22, Indels: 19
0.70 0.16 0.14
Matches are distributed among these distances:
24 2 0.02
25 31 0.32
26 24 0.25
27 16 0.16
28 20 0.21
29 4 0.04
ACGTcount: A:0.48, C:0.02, G:0.20, T:0.30
Consensus pattern (25 bp):
AATTTGGTAATTAAAGAGTAAAATA
Found at i:40649 original size:51 final size:52
Alignment explanation
Indices: 40542--40650 Score: 134
Period size: 51 Copynumber: 2.1 Consensus size: 52
40532 AATTAAAGAT
* * * *
40542 TAAAATGAATTGGATAATTAAAGGGTAATTGGTAAAATTTGGTAATTAAGAAG
1 TAAAATGAATTGGATAATTAAAGAGTAA-TAGTAAAATTTGGCAATCAAGAAG
40595 TAAAATGAACTTGG-TAATTAAAGAGTAA-AGTAAAATTTGGCAATCAA-ATAG
1 TAAAATGAA-TTGGATAATTAAAGAGTAATAGTAAAATTTGGCAATCAAGA-AG
40646 TAAAA
1 TAAAA
40651 AGGAAATTGG
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
50 1 0.02
51 23 0.46
53 22 0.44
54 4 0.08
ACGTcount: A:0.49, C:0.03, G:0.19, T:0.29
Consensus pattern (52 bp):
TAAAATGAATTGGATAATTAAAGAGTAATAGTAAAATTTGGCAATCAAGAAG
Found at i:40705 original size:19 final size:20
Alignment explanation
Indices: 40668--40707 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
40658 TGGTCAACTT
40668 GGTAATTAAAAAGTAAATTG
1 GGTAATTAAAAAGTAAATTG
*
40688 GGTAATTAAAGAGT-AATTG
1 GGTAATTAAAAAGTAAATTG
40707 G
1 G
40708 TAAAATGAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.45, C:0.00, G:0.25, T:0.30
Consensus pattern (20 bp):
GGTAATTAAAAAGTAAATTG
Found at i:42916 original size:22 final size:23
Alignment explanation
Indices: 42891--42943 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
42881 GTTTGGCATC
42891 GTTTTTGTTTTC-TTGTTT-TTTT
1 GTTTTTGTTTTCGTT-TTTATTTT
42913 GTTTTTG-TTTCGTTTTTATTTT
1 GTTTTTGTTTTCGTTTTTATTTT
42935 GTTTTTGTT
1 GTTTTTGTT
42944 GTGTTGTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
21 7 0.25
22 20 0.71
23 1 0.04
ACGTcount: A:0.02, C:0.04, G:0.15, T:0.79
Consensus pattern (23 bp):
GTTTTTGTTTTCGTTTTTATTTT
Found at i:42927 original size:11 final size:11
Alignment explanation
Indices: 42889--42943 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
42879 TCGTTTGGCA
42889 TCGTTTTTGTTT
1 TCGTTTTTG-TT
42901 TC-TTGTTT-TT
1 TCGTT-TTTGTT
*
42911 TTGTTTTTGTT
1 TCGTTTTTGTT
*
42922 TCGTTTTTATT
1 TCGTTTTTGTT
*
42933 TTGTTTTTGTT
1 TCGTTTTTGTT
42944 GTGTTGTCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
10 6 0.17
11 24 0.69
12 5 0.14
ACGTcount: A:0.02, C:0.05, G:0.15, T:0.78
Consensus pattern (11 bp):
TCGTTTTTGTT
Found at i:43190 original size:25 final size:25
Alignment explanation
Indices: 43155--43206 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
43145 AGAAATATTT
43155 TTTATTATTTTCT-T-AAATTCTTATC
1 TTTATTATTTT-TATCAAATTCTT-TC
*
43180 TTTATTTTTTTTATCAAATTCTTTC
1 TTTATTATTTTTATCAAATTCTTTC
43205 TT
1 TT
43207 CCCTATATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 1 0.04
25 15 0.62
26 8 0.33
ACGTcount: A:0.21, C:0.12, G:0.00, T:0.67
Consensus pattern (25 bp):
TTTATTATTTTTATCAAATTCTTTC
Found at i:43217 original size:2 final size:2
Alignment explanation
Indices: 43210--43239 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
43200 CTTTCTTCCC
*
43210 TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
43240 AAAGGCGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:44109 original size:20 final size:21
Alignment explanation
Indices: 44078--44118 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
44068 GTTTGTTTTC
44078 AAAACATGAAAATGGCAACAA
1 AAAACATGAAAATGGCAACAA
44099 AAAACAT-AAAATGGCAACAA
1 AAAACATGAAAATGGCAACAA
44119 TGCCAAACGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.63, C:0.15, G:0.12, T:0.10
Consensus pattern (21 bp):
AAAACATGAAAATGGCAACAA
Found at i:46325 original size:2 final size:2
Alignment explanation
Indices: 46318--46347 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
46308 GACCCTTTTA
46318 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
46348 ATTATTATTA
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):
AT
Found at i:51943 original size:32 final size:32
Alignment explanation
Indices: 51907--51972 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
51897 AGATCTTGCC
* *
51907 ATATGAGAGAAGATCTGAACAAAATATGGATG
1 ATATGAGAAAAGATCTGAACAAAATATGAATG
51939 ATATGAGAAAAGATCTGAACAAAATATGAATG
1 ATATGAGAAAAGATCTGAACAAAATATGAATG
51971 AT
1 AT
51973 TAATGACTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.50, C:0.06, G:0.21, T:0.23
Consensus pattern (32 bp):
ATATGAGAAAAGATCTGAACAAAATATGAATG
Found at i:52699 original size:20 final size:20
Alignment explanation
Indices: 52676--52713 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
52666 ATTCAAAATA
*
52676 AAATAAAAACTACTCATTTT
1 AAATAAAAACTACCCATTTT
*
52696 AAATTAAAACTACCCATT
1 AAATAAAAACTACCCATT
52714 AGAGAATGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (20 bp):
AAATAAAAACTACCCATTTT
Found at i:61832 original size:24 final size:21
Alignment explanation
Indices: 61785--61828 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
61775 CGTAGGCTCT
61785 CGCCGTGGCGGCGGTCCTAAA
1 CGCCGTGGCGGCGGTCCTAAA
61806 CGCCGTGGCGGCGGTCCTAAA
1 CGCCGTGGCGGCGGTCCTAAA
61827 CG
1 CG
61829 ACGCGCTCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.14, C:0.34, G:0.39, T:0.14
Consensus pattern (21 bp):
CGCCGTGGCGGCGGTCCTAAA
Found at i:73582 original size:2 final size:2
Alignment explanation
Indices: 73571--73599 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
73561 TTAGTAACTT
73571 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
73600 AAAGGTTATG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:74676 original size:50 final size:50
Alignment explanation
Indices: 74616--74715 Score: 191
Period size: 50 Copynumber: 2.0 Consensus size: 50
74606 AATTTTTTTC
*
74616 ACCTCAAATTAAATCTTTCGAAATTTTTTAACATCAATTAAGGCAAAGTT
1 ACCTCAAATTAAATCTTTCGAAATTTTTTAACATCAATTAAGACAAAGTT
74666 ACCTCAAATTAAATCTTTCGAAATTTTTTAACATCAATTAAGACAAAGTT
1 ACCTCAAATTAAATCTTTCGAAATTTTTTAACATCAATTAAGACAAAGTT
74716 GTAAAGAAAC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.36
Consensus pattern (50 bp):
ACCTCAAATTAAATCTTTCGAAATTTTTTAACATCAATTAAGACAAAGTT
Found at i:76508 original size:206 final size:199
Alignment explanation
Indices: 76145--76545 Score: 721
Period size: 206 Copynumber: 2.0 Consensus size: 199
76135 AACTTTGGGG
76145 AATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATACAAAACATT
1 AATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATACAAAACATT
*
76210 ATTATTATATATAAAACTATACAAAAAAAATAGTTGAACATTAGTGGTTGATTTATTAAATTAAA
66 ACTATTATATATAAAACTATACAAAAAAAATAGTTGAACATTAGTGGTTGATTTATTAAATTAAA
76275 TTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCCGATTTATTTATCAA
131 TTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATT-AAGATCCGATTTATTTATCAA
76340 TGGTA
195 TGGTA
*
76345 AATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATACAACACATT
1 AATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATACAAAACATT
76410 ACTATTATATATATAGAACTATACCAAAAAAAAAATTAGTTGAACATTAGTGGTTGATTTATTAA
66 ACTATTATATATA-A-AACTATA-C--AAAAAAAA-TAGTTGAACATTAGTGGTTGATTTATTAA
76475 ATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATCCGATTTATTT
125 ATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATCCGATTTATTT
76540 ATCAAT
190 ATCAAT
76546 AAGGAACAAT
Statistics
Matches: 193, Mismatches: 2, Indels: 7
0.96 0.01 0.03
Matches are distributed among these distances:
200 76 0.39
201 1 0.01
202 7 0.04
203 1 0.01
205 30 0.16
206 78 0.40
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.36
Consensus pattern (199 bp):
AATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATACAAAACATT
ACTATTATATATAAAACTATACAAAAAAAATAGTTGAACATTAGTGGTTGATTTATTAAATTAAA
TTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATCCGATTTATTTATCAAT
GGTA
Found at i:76654 original size:24 final size:25
Alignment explanation
Indices: 76610--76656 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
76600 ACGTTTGCAC
76610 AAATACCTAAAGATTTGAATTAAAA
1 AAATACCTAAAGATTTGAATTAAAA
76635 AAATACCT-AAGAATTT-AATTAA
1 AAATACCTAAAG-ATTTGAATTAA
76657 TGTAAGTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30
Consensus pattern (25 bp):
AAATACCTAAAGATTTGAATTAAAA
Found at i:76701 original size:39 final size:40
Alignment explanation
Indices: 76647--76727 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
76637 ATACCTAAGA
*
76647 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
*
76686 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
76726 AT
1 AT
76728 AGGAATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.51
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
Done.