Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168087.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_334, 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: 34073
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.36
Found at i:2807 original size:14 final size:14
Alignment explanation
Indices: 2788--2901 Score: 68
Period size: 14 Copynumber: 7.9 Consensus size: 14
2778 AAGTTTGGAG
2788 ATTTTAGGGTTTTA
1 ATTTTAGGGTTTTA
* *
2802 ATTTTAAGGTTTGA
1 ATTTTAGGGTTTTA
* ** *
2816 AATTTAAAGTTTTG
1 ATTTTAGGGTTTTA
*
2830 GTTTTAGGG-TTTA
1 ATTTTAGGGTTTTA
*
2843 GAGGATTTAGGGTTTTA
1 -A--TTTTAGGGTTTTA
*
2860 ATTTTAGGATTTTA
1 ATTTTAGGGTTTTA
* *
2874 ATGTTTTAGGGATTTG
1 A--TTTTAGGGTTTTA
*
2890 ATTTTAAGGTTT
1 ATTTTAGGGTTT
2902 GATGTTTGAA
Statistics
Matches: 74, Mismatches: 20, Indels: 12
0.70 0.19 0.11
Matches are distributed among these distances:
13 3 0.04
14 48 0.65
16 19 0.26
17 4 0.05
ACGTcount: A:0.25, C:0.00, G:0.24, T:0.52
Consensus pattern (14 bp):
ATTTTAGGGTTTTA
Found at i:2864 original size:88 final size:87
Alignment explanation
Indices: 2760--2986 Score: 246
Period size: 88 Copynumber: 2.6 Consensus size: 87
2750 GCATGGAAGG
* * * * *
2760 TTTAGGATTTTGATTTTAAAGTTTGGAGATTTTAGGGTTTTAATTTTAAGGTTTGAAATTTAAAG
1 TTTAGGGTTTTAATTTTAAGGTTTAGAG-TTTTAGGGATTTAATTTTAAGGTTTGAAATTTAAAG
* *
2825 TTTTGGTTTTAGGGTTTAGAGGA
65 TTTTAGTTTTAGGATTTAGAGGA
* ** *
2848 TTTAGGGTTTTAATTTT-AGGATTTTA-ATGTTTTAGGGATTTGATTTTAAGGTTTGATGTTTGA
1 TTTAGGGTTTTAATTTTAAGG--TTTAGA-GTTTTAGGGATTTAATTTTAAGGTTTGAAATTTAA
*
2911 AGTTTTAGTTTTAGGATTTAGAGTA
63 AGTTTTAGTTTTAGGATTTAGAGGA
* * * *
2936 TTTAAGG-TTTAATTTTAGGGTTTAGAGGTTT-GAGATTTAATTTTAAGGTTT
1 TTTAGGGTTTTAATTTTAAGGTTTAGAGTTTTAGGGATTTAATTTTAAGGTTT
2987 AGATTTTTTA
Statistics
Matches: 117, Mismatches: 17, Indels: 13
0.80 0.12 0.09
Matches are distributed among these distances:
85 18 0.15
86 8 0.07
87 12 0.10
88 75 0.64
89 4 0.03
ACGTcount: A:0.25, C:0.00, G:0.24, T:0.51
Consensus pattern (87 bp):
TTTAGGGTTTTAATTTTAAGGTTTAGAGTTTTAGGGATTTAATTTTAAGGTTTGAAATTTAAAGT
TTTAGTTTTAGGATTTAGAGGA
Found at i:2916 original size:58 final size:57
Alignment explanation
Indices: 2831--2989 Score: 155
Period size: 57 Copynumber: 2.7 Consensus size: 57
2821 AAAGTTTTGG
* * * *
2831 TTTTAGGGTTTAGAGGATTTAGGGTTTTAATTTTAGGATTTTA-ATGT-TTTAGGGATTTGA
1 TTTTAAGGTTTAGAGG-TTT-GAGTTTTAATTTTAGGA-TTTAGA-GTATTTAAGG-TTTAA
* *
2891 TTTTAAGGTTT-GATGTTTGAAGTTTTAGTTTTAGGATTTAGAGTATTTAAGGTTTAA
1 TTTTAAGGTTTAGAGGTTTG-AGTTTTAATTTTAGGATTTAGAGTATTTAAGGTTTAA
* *
2948 TTTTAGGGTTTAGAGGTTTGAGATTTAATTTTAAGG-TTTAGA
1 TTTTAAGGTTTAGAGGTTTGAGTTTTAATTTT-AGGATTTAGA
2990 TTTTTTATTT
Statistics
Matches: 84, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
57 37 0.44
58 34 0.40
59 3 0.04
60 10 0.12
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (57 bp):
TTTTAAGGTTTAGAGGTTTGAGTTTTAATTTTAGGATTTAGAGTATTTAAGGTTTAA
Found at i:2959 original size:29 final size:28
Alignment explanation
Indices: 2831--2994 Score: 116
Period size: 28 Copynumber: 5.7 Consensus size: 28
2821 AAAGTTTTGG
* *
2831 TTTTAGGGTTTAGAGGATTTAGGGTTTTAA
1 TTTTAGGGTTTAGA-GTTTTAAGG-TTTAA
* * *
2861 TTTTAGGATTTTA-ATGTTTTAGGGATTTGA
1 TTTTAGG-GTTTAGA-GTTTTAAGG-TTTAA
* * * *
2891 TTTTAAGGTTT-GATGTTTGAAGTTTTAG
1 TTTTAGGGTTTAGA-GTTTTAAGGTTTAA
*
2919 TTTTAGGATTTAGAGTATTTAAGGTTTAA
1 TTTTAGGGTTTAGAGT-TTTAAGGTTTAA
* * *
2948 TTTTAGGGTTTAGAGGTTTGAGATTTAA
1 TTTTAGGGTTTAGAGTTTTAAGGTTTAA
* *
2976 TTTTAAGGTTTAGATTTTT
1 TTTTAGGGTTTAGAGTTTT
2995 TATTTTTATT
Statistics
Matches: 106, Mismatches: 24, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
28 40 0.38
29 36 0.34
30 26 0.25
31 4 0.04
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (28 bp):
TTTTAGGGTTTAGAGTTTTAAGGTTTAA
Found at i:3407 original size:17 final size:19
Alignment explanation
Indices: 3360--3409 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 19
3350 ATCATGCATA
3360 AATATATAAAAAAAAACTC
1 AATATATAAAAAAAAACTC
3379 AA-A-ATAACAAAAATAA-T-
1 AATATATAA-AAAAA-AACTC
3396 AATATATAAAAAAA
1 AATATATAAAAAAA
3410 TTCAAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
17 6 0.22
18 13 0.48
19 8 0.30
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.20
Consensus pattern (19 bp):
AATATATAAAAAAAAACTC
Found at i:4073 original size:13 final size:14
Alignment explanation
Indices: 4044--4079 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
4034 GGGAAGACTG
*
4044 TTTGTCTTTATTTT
1 TTTGTTTTTATTTT
4058 TTTGTTTTTA-TTT
1 TTTGTTTTTATTTT
4071 TTTGTTTTT
1 TTTGTTTTT
4080 GTTTGGTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.06, C:0.03, G:0.08, T:0.83
Consensus pattern (14 bp):
TTTGTTTTTATTTT
Found at i:5072 original size:22 final size:23
Alignment explanation
Indices: 5047--5095 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
5037 AGGTCTTAGA
5047 AATCATGTTC-AGAGATCTTA-AG
1 AATCATGTTCGA-AGATCTTACAG
*
5069 AATCATGTTCGAAGGTCTTACAG
1 AATCATGTTCGAAGATCTTACAG
5092 AATC
1 AATC
5096 GATGGGATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 17 0.71
23 7 0.29
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (23 bp):
AATCATGTTCGAAGATCTTACAG
Found at i:5161 original size:218 final size:222
Alignment explanation
Indices: 4732--5294 Score: 570
Period size: 218 Copynumber: 2.6 Consensus size: 222
4722 ATGCCCAAAC
* * * ** * *
4732 GTCTTACAAAATCGACT-AGGACAACACTACAAGTCAAAAAATAAAAAAAAT--ATCAGGACAAC
1 GTCTTACAGAATCGACTGA-AACAACACCACAAGTCAAAAAATAAAACGAATCGATCGGGATAAC
* * * ** * ** * * *
4794 ACCGTAAATCAAAATTT-TGCCCTAAGGTTTTA-AGAATCATACTCTGAGGTCTTAGGAATCATG
65 ACTGCAAATC-GAATTTATGCCCGGAGGTCTTAGA-AATCATGTTCAGAGATCTTAAGAATCATG
* * *
4857 TCCGGAGGTCTTACAAAATCGACTGGGACAACACCGTAAGTCAAAAAATAAAGAATCGATCGTGA
128 TCCGAAGGTCTTACAAAATCGACTGGGACAACACCGCAAGTCAAAAAATAAAGAATCGATCGGGA
** ***
4922 CAACATTACAAATCAAATTTATGTTTGGAG
193 CAACACCACAAATCAAATTTATGCCGGGAG
* ** * * *
4952 GTCTTACAGAATCGATTGGGACAGCACCACAAGTC-AAAAA-ACAA-GAATCGATCGGGATAATA
1 GTCTTACAGAATCGACTGAAACAACACCACAAGTCAAAAAATAAAACGAATCGATCGGGATAACA
* *
5014 -TCGCGAATCGAATTTATGCCCGGAGGTCTTAGAAATCATGTTCAGAGATCTTAAGAATCATGTT
66 CT-GCAAATCGAATTTATGCCCGGAGGTCTTAGAAATCATGTTCAGAGATCTTAAGAATCATGTC
* * * * * *
5078 CGAAGGTCTTACAGAATCGA-TGGGATAACACCGCAAGTCGAAAAATAATGAATCGATTGGGATA
130 CGAAGGTCTTACAAAATCGACTGGGACAACACCGCAAGTCAAAAAATAAAGAATCGATCGGGACA
* **
5142 ACACCACGAATTGAATTTATGCCGGGAG
195 ACACCACAAATCAAATTTATGCCGGGAG
* *
5170 GTCTTACAGAATCGACTGAAACAACATCATAAGTCAAAAAATAAAACGAATCGATCGGGATAACA
1 GTCTTACAGAATCGACTGAAACAACACCACAAGTCAAAAAATAAAACGAATCGATCGGGATAACA
* ** *
5235 CTGTAAATCGAATTTATGCCCGGAGGTCTTAGAAATCATGTTTGGAGGTCTTACAGAATC
66 CTGCAAATCGAATTTATGCCCGGAGGTCTTAGAAATCATGTTCAGAGATCTTA-AGAATC
5295 GACTGGGATA
Statistics
Matches: 279, Mismatches: 53, Indels: 20
0.79 0.15 0.06
Matches are distributed among these distances:
217 3 0.01
218 94 0.34
219 79 0.28
220 33 0.12
221 63 0.23
222 7 0.03
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.24
Consensus pattern (222 bp):
GTCTTACAGAATCGACTGAAACAACACCACAAGTCAAAAAATAAAACGAATCGATCGGGATAACA
CTGCAAATCGAATTTATGCCCGGAGGTCTTAGAAATCATGTTCAGAGATCTTAAGAATCATGTCC
GAAGGTCTTACAAAATCGACTGGGACAACACCGCAAGTCAAAAAATAAAGAATCGATCGGGACAA
CACCACAAATCAAATTTATGCCGGGAG
Found at i:5361 original size:111 final size:111
Alignment explanation
Indices: 5160--5629 Score: 446
Period size: 111 Copynumber: 4.2 Consensus size: 111
5150 AATTGAATTT
* * * * * *
5160 ATGCCGGGAGGTCTTACAGAATCGACTGAAACAACA-TCATAAGTCAAAAAATAA-AACGAATCG
1 ATGCCCGGAGGTCTTACAAAATCGACTGAGATAACACT-ACAAGT-AAAAAA-AATAACAAATCG
*
5223 ATCGGGATAACA-CTGTAAATCGAATTTATGCCCGGAGGTCTTAGAAATC
63 ATCGGGATAACATC-GTAAATCGAATTTATGCCCAGAGGTCTTAGAAATC
*** * * * *
5272 ATGTTTGGAGGTCTTACAGAATCGACTGGGATAACACTACAAGTAAAAAAAATAACGAATCAATC
1 ATGCCCGGAGGTCTTACAAAATCGACTGAGATAACACTACAAGTAAAAAAAATAACAAATCGATC
* * *
5337 GAGATAACATCGTAAATCGAATTTATGCTC-GAAAGTCTTAGAAATC
66 GGGATAACATCGTAAATCGAATTTATGCCCAG-AGGTCTTAGAAATC
* * * * * * ** * *
5383 ATACTCGGAGGTCTTACAAAATCAACTCAGACAACACTATAAGTTGAAAAATTAAAAAATCGATC
1 ATGCCCGGAGGTCTTACAAAATCGACTGAGATAACACTACAAGTAAAAAAAATAACAAATCGATC
**
5448 GGGATAACATCGCGAATCGAATTTATGCCTCAGAGGTCTTAGAAATC
66 GGGATAACATCGTAAATCGAATTTATGCC-CAGAGGTCTTAGAAATC
* * * * * * * * *
5495 ATGCCCGAAGGTCTTACAAAATTGACCGAAATAATATTGCAAGTCAAAAAATTAA-AAATCGATC
1 ATGCCCGGAGGTCTTACAAAATCGACTGAGATAACACTACAAGTAAAAAAAATAACAAATCGATC
* * * * *
5559 GTGATAACATCATGAATCGAATTTATACCTAGAGGTCTTAGAAATC
66 GGGATAACATCGTAAATCGAATTTATGCCCAGAGGTCTTAGAAATC
* *
5605 ATGTCCGAAGGTCTTACAAAATCGA
1 ATGCCCGGAGGTCTTACAAAATCGA
5630 TCGGGATAAC
Statistics
Matches: 299, Mismatches: 53, Indels: 14
0.82 0.14 0.04
Matches are distributed among these distances:
110 42 0.14
111 165 0.55
112 90 0.30
113 2 0.01
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.24
Consensus pattern (111 bp):
ATGCCCGGAGGTCTTACAAAATCGACTGAGATAACACTACAAGTAAAAAAAATAACAAATCGATC
GGGATAACATCGTAAATCGAATTTATGCCCAGAGGTCTTAGAAATC
Found at i:5567 original size:222 final size:222
Alignment explanation
Indices: 5166--5627 Score: 522
Period size: 222 Copynumber: 2.1 Consensus size: 222
5156 ATTTATGCCG
* * *
5166 GGAGGTCTTACAGAATCGACTGAAACAACATCATAAGTCAAAAAATAAAACGAATCGATCGGGAT
1 GGAGGTCTTACAAAATCAACTCAAACAACATCATAAGTCAAAAAATAAAAC-AATCGATCGGGAT
* * *** * *
5231 AACACTGTAAATCGAATTTATGCCCGGAGGTCTTAGAAATCATGTTTGGAGGTCTTACAGAATCG
65 AACACTGCAAATCGAATTTATGCCCAGAGGTCTTAGAAATCATGCCCGAAGGTCTTACAAAATCG
* ** * *
5296 ACTGGGATAACACTACAAGTAAAAAAAATAACGAATCAATCGAGATAACATCGTAAATCGAATTT
130 ACCGAAATAACACTACAAGTAAAAAAAATAACAAATCAATCGAGATAACATCATAAATCGAATTT
*
5361 ATGCTCGA-AAGTCTTAGAAATCATACT-C
195 ATAC-CGAGAAGTCTTAGAAATCAT-CTCC
* * *
5389 GGAGGTCTTACAAAATCAACTCAGACAACA-CTATAAGTTGAAAAATTAAAA-AATCGATCGGGA
1 GGAGGTCTTACAAAATCAACTCAAACAACATC-ATAAG-TCAAAAAATAAAACAATCGATCGGGA
*
5452 TAACA-TCGCGAATCGAATTTATGCCTCAGAGGTCTTAGAAATCATGCCCGAAGGTCTTACAAAA
64 TAACACT-GCAAATCGAATTTATGCC-CAGAGGTCTTAGAAATCATGCCCGAAGGTCTTACAAAA
* * * * * * * * *
5516 TTGACCGAAATAATATTGCAAGTCAAAAAATTAA-AAATCGATCGTGATAACATCATGAATCGAA
127 TCGACCGAAATAACACTACAAGTAAAAAAAATAACAAATCAATCGAGATAACATCATAAATCGAA
* * *
5580 TTTATACCTAGAGGTCTTAGAAATCATGTCC
192 TTTATACCGAGAAGTCTTAGAAATCATCTCC
*
5611 GAAGGTCTTACAAAATC
1 GGAGGTCTTACAAAATC
5628 GATCGGGATA
Statistics
Matches: 200, Mismatches: 33, Indels: 13
0.81 0.13 0.05
Matches are distributed among these distances:
221 4 0.02
222 97 0.49
223 88 0.44
224 11 0.05
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.24
Consensus pattern (222 bp):
GGAGGTCTTACAAAATCAACTCAAACAACATCATAAGTCAAAAAATAAAACAATCGATCGGGATA
ACACTGCAAATCGAATTTATGCCCAGAGGTCTTAGAAATCATGCCCGAAGGTCTTACAAAATCGA
CCGAAATAACACTACAAGTAAAAAAAATAACAAATCAATCGAGATAACATCATAAATCGAATTTA
TACCGAGAAGTCTTAGAAATCATCTCC
Found at i:6179 original size:137 final size:135
Alignment explanation
Indices: 5947--6230 Score: 367
Period size: 137 Copynumber: 2.1 Consensus size: 135
5937 AAGATCTGTG
* * *
5947 AATTTTGAAAATTTAAAAATCTTTTGCTCGAAAATCTTGAAAGTTGTGCCTGAAAGTTTTAGAGA
1 AATTTT-AAAATTTAAAAATCTTTTGCCCGAAAATCTTGAAAGTTGTGCCTAAAAGTATTAGAGA
* *
6012 TTACGCTCAGAGGTCTTATAAATCTCAAAATCTTTGAATGCCTC-TCATAATTAGAGGCAATAAA
65 TTACGCTCAGAGGTCTTACAAATCTCAAAATCTTTGAATG-CTCATCATAATCAGAGGCAATAAA
6076 ACTTTTAAA
129 AC-TTT-AA
* * **
6085 AATTTTAAAATTTTAAAATCTTTTGCCCGGAGGTCTTGAAAGTTGTG-CTCAAAAGTATTAGAGA
1 AATTTTAAAATTTAAAAATCTTTTGCCCGAAAATCTTGAAAGTTGTGCCT-AAAAGTATTAGAGA
* * * *
6149 TTATGC-CCGTATGTCTTACAAATCTCAAAATCTTTGAATGCTCATCATAATCAGAGGCAATGAA
65 TTACGCTCAG-AGGTCTTACAAATCTCAAAATCTTTGAATGCTCATCATAATCAGAGGCAATAAA
6213 ACTTTAA
129 ACTTTAA
*
6220 AATTTAAAAAT
1 AATTTTAAAAT
6231 CTTTTTAAAT
Statistics
Matches: 129, Mismatches: 14, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
135 12 0.09
136 10 0.08
137 101 0.78
138 6 0.05
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (135 bp):
AATTTTAAAATTTAAAAATCTTTTGCCCGAAAATCTTGAAAGTTGTGCCTAAAAGTATTAGAGAT
TACGCTCAGAGGTCTTACAAATCTCAAAATCTTTGAATGCTCATCATAATCAGAGGCAATAAAAC
TTTAA
Found at i:9129 original size:9 final size:9
Alignment explanation
Indices: 9115--9149 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
9105 GTAGAAAACT
*
9115 TTTTTTTGA
1 TTTTTTTAA
9124 TTTTTTTAA
1 TTTTTTTAA
9133 TTTTTTTTAA
1 -TTTTTTTAA
9143 TTTTTTT
1 TTTTTTT
9150 TTGAAATCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 15 0.62
10 9 0.38
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.83
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:9129 original size:10 final size:10
Alignment explanation
Indices: 9114--9150 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
9104 AGTAGAAAAC
*
9114 TTTTTTTTGA
1 TTTTTTTTAA
9124 -TTTTTTTAA
1 TTTTTTTTAA
9133 TTTTTTTTAA
1 TTTTTTTTAA
9143 TTTTTTTT
1 TTTTTTTT
9151 TGAAATCTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 8 0.32
10 17 0.68
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.84
Consensus pattern (10 bp):
TTTTTTTTAA
Found at i:10143 original size:38 final size:38
Alignment explanation
Indices: 10092--10165 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
10082 AAATATGGGA
*
10092 TAATATTTAGGCCAATCTTGTGCTATAGTAATTATTTT
1 TAATAATTAGGCCAATCTTGTGCTATAGTAATTATTTT
10130 TAATAATTAGGCCAATCTTGTGCTATAGTAATTATT
1 TAATAATTAGGCCAATCTTGTGCTATAGTAATTATT
10166 AAATACGGGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.45
Consensus pattern (38 bp):
TAATAATTAGGCCAATCTTGTGCTATAGTAATTATTTT
Found at i:13605 original size:29 final size:28
Alignment explanation
Indices: 13558--13666 Score: 85
Period size: 30 Copynumber: 3.7 Consensus size: 28
13548 AAGATTCGGA
* *
13558 TTTTAAGGGTTTAGATTTAAGTTTTGATGG
1 TTTT-AGGGTTTAGTTTTAAG-TTTGAAGG
* *
13588 TTTTAGGGTTTGGTTTTAAGGTATGAAAGG
1 TTTTAGGGTTTAGTTTTAA-GTTTG-AAGG
* *
13618 -TTTAGGGTTTTAATTTTAGAGTTTGAAGA
1 TTTTAGGG-TTTAGTTTTA-AGTTTGAAGG
*
13647 TTTTAGGGTTTCGGTTTTAA
1 TTTTAGGGTTT-AGTTTTAA
13667 AATTTGAGGT
Statistics
Matches: 63, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
29 30 0.48
30 32 0.51
31 1 0.02
ACGTcount: A:0.23, C:0.01, G:0.28, T:0.49
Consensus pattern (28 bp):
TTTTAGGGTTTAGTTTTAAGTTTGAAGG
Found at i:13763 original size:17 final size:17
Alignment explanation
Indices: 13729--13764 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
13719 AGGTTTGAGA
**
13729 TTTTGGATTTTAGGGGT
1 TTTTGGATTTTAAAGGT
13746 TTTTGGATTTTAAAGGT
1 TTTTGGATTTTAAAGGT
13763 TT
1 TT
13765 CGAATTTTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.28, T:0.56
Consensus pattern (17 bp):
TTTTGGATTTTAAAGGT
Found at i:15241 original size:3 final size:3
Alignment explanation
Indices: 15221--15259 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
15211 TAAACCAATT
* *
15221 TTA TTT TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
15260 AAATCATTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (3 bp):
TTA
Found at i:15285 original size:24 final size:24
Alignment explanation
Indices: 15241--15286 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
15231 TTTTATTATT
*
15241 ATTATTATTATTATTATTAAAATC
1 ATTATTATTATTATTAATAAAATC
*
15265 ATTATTGTTA-TATATAATAAAA
1 ATTATTATTATTAT-TAATAAAA
15287 CAAATATCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 3 0.16
24 16 0.84
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (24 bp):
ATTATTATTATTATTAATAAAATC
Found at i:15765 original size:67 final size:67
Alignment explanation
Indices: 15687--15915 Score: 239
Period size: 67 Copynumber: 3.4 Consensus size: 67
15677 GATTAAAGCA
* * * *
15687 ATCGAGATTAAATCACGAGTCAGAATAACATCAACTTGGATTGAATCACAAGTCAGAAAACAAAG
1 ATCGGGATTAAACCACGAGTCAGAATAACATCAACTTGGATTAAATCACAAGTCAGAAAATAAAG
15752 AG
66 AG
* * * * ** ** **
15754 A-CTGGGATTAAACCACGAGTCAGAAAATAACAACAA-TCGAGATTAAATTATGATTTTTGAATT
1 ATC-GGGATTAAACCACGAGTCAG--AATAACATCAACTTG-GATTAAATCA-CAAGTCAGAAAA
15817 TAAAGAG
61 TAAAGAG
* *
15824 ATCGGGA-TAGAACCGCGAGTCAGAATAACATCAACTTGGATTAAATCACAAGTCATAAAATAAA
1 ATCGGGATTA-AACCACGAGTCAGAATAACATCAACTTGGATTAAATCACAAGTCAGAAAATAAA
15888 GAG
65 GAG
15891 ATCGGGATTAAACCACGAGTCAGAA
1 ATCGGGATTAAACCACGAGTCAGAA
15916 AATAACAATA
Statistics
Matches: 126, Mismatches: 27, Indels: 18
0.74 0.16 0.11
Matches are distributed among these distances:
66 1 0.01
67 51 0.40
68 23 0.18
69 22 0.17
70 28 0.22
71 1 0.01
ACGTcount: A:0.45, C:0.15, G:0.19, T:0.21
Consensus pattern (67 bp):
ATCGGGATTAAACCACGAGTCAGAATAACATCAACTTGGATTAAATCACAAGTCAGAAAATAAAG
AG
Found at i:15775 original size:34 final size:32
Alignment explanation
Indices: 15692--15787 Score: 102
Period size: 33 Copynumber: 2.9 Consensus size: 32
15682 AAGCAATCGA
* *
15692 GATTAAATCACGAGTCAGAATAACATCAACTTG
1 GATTAAATCACGAGTCAGAA-AACAACAACTGG
* * *
15725 GATTGAATCACAAGTCAGAAAACAAAGAGACTGG
1 GATTAAATCACGAGTCAGAAAAC-AACA-ACTGG
* *
15759 GATTAAACCACGAGTCAGAAAATAACAAC
1 GATTAAATCACGAGTCAGAAAACAACAAC
15788 AATCGAGATT
Statistics
Matches: 51, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
32 5 0.10
33 23 0.45
34 23 0.45
ACGTcount: A:0.47, C:0.18, G:0.18, T:0.18
Consensus pattern (32 bp):
GATTAAATCACGAGTCAGAAAACAACAACTGG
Found at i:15863 original size:137 final size:134
Alignment explanation
Indices: 15586--15936 Score: 451
Period size: 137 Copynumber: 2.6 Consensus size: 134
15576 ATCAGGATTG
* * * * * *
15586 AACTTAGATTGAGTCATAAGTCAAAATATAAAGAGACCGAGATTAAACCACGAGT-A-AAAAAAA
1 AACTTGGATTGAATCACAAGTCAAAA-ATAAAGAGACTGGGATTAAACCACGAGTCAGAAAATAA
* * * *
15649 TAACAATCAAGATTAAATTACGATTTTGGATTAAAGCAATCGAGATTAAATCACGAGTCAGAATA
65 CAACAATCGAGATTAAATTACGATTTTGAATTAAAGCAATCGAGATTAAACCACGAGTCAGAATA
15714 ACATC
130 ACATC
*
15719 AACTTGGATTGAATCACAAGTCAGAAAACAAAGAGACTGGGATTAAACCACGAGTCAGAAAATAA
1 AACTTGGATTGAATCACAAGTCA-AAAATAAAGAGACTGGGATTAAACCACGAGTCAGAAAATAA
* * *
15784 CAACAATCGAGATTAAATTATGATTTTTGAATTTAAAG-AGATCGGGA-TAGAACCGCGAGTCAG
65 CAACAATCGAGATTAAATTACGA-TTTTGAA-TTAAAGCA-ATCGAGATTA-AACCACGAGTCAG
15847 AATAACATC
126 AATAACATC
*
15856 AACTTGGATTAAATCACAAGTCATAAAATAAAGAGA-TCGGGATTAAACCACGAGTCAGAAAATA
1 AACTTGGATTGAATCACAAGTCA-AAAATAAAGAGACT-GGGATTAAACCACGAGTCAGAAAATA
*
15920 ACAATAATCGAGATTAA
64 ACAACAATCGAGATTAA
15937 CCGGGATTAA
Statistics
Matches: 192, Mismatches: 18, Indels: 12
0.86 0.08 0.05
Matches are distributed among these distances:
133 45 0.23
134 4 0.02
135 26 0.14
136 10 0.05
137 107 0.56
ACGTcount: A:0.47, C:0.14, G:0.17, T:0.22
Consensus pattern (134 bp):
AACTTGGATTGAATCACAAGTCAAAAATAAAGAGACTGGGATTAAACCACGAGTCAGAAAATAAC
AACAATCGAGATTAAATTACGATTTTGAATTAAAGCAATCGAGATTAAACCACGAGTCAGAATAA
CATC
Found at i:15955 original size:45 final size:45
Alignment explanation
Indices: 15893--15981 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
15883 ATAAAGAGAT
*
15893 CGGGATTAAACCACGAGTCAGAAAATAACAATAATCGAGATTAAC
1 CGGGATTAAACCACGAGTCAAAAAATAACAATAATCGAGATTAAC
* *
15938 CGGGATTAAATCGCGAGTCAAAAAATAACAATAATCGAGATTAA
1 CGGGATTAAACCACGAGTCAAAAAATAACAATAATCGAGATTAA
15982 ACTACGATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.47, C:0.16, G:0.18, T:0.19
Consensus pattern (45 bp):
CGGGATTAAACCACGAGTCAAAAAATAACAATAATCGAGATTAAC
Found at i:16057 original size:66 final size:68
Alignment explanation
Indices: 15970--16098 Score: 165
Period size: 68 Copynumber: 1.9 Consensus size: 68
15960 AAATAACAAT
*
15970 AATCGAGATTAAACTACGA-TTTTGGA-TTAAAAAAATCAGGATTAAATCGTGAA-TCAAAATAA
1 AATCAAGATTAAACTACGATTTTTGGATTTAAAAAAATCAGGATTAAATCGT-AAGTCAAAATAA
16032 CGTC
65 CGTC
* * * * * *
16036 AATCAAGATTAAATTATGATTTTTGGATTTAAAGAGATCGGGATTTAATCGTAAGTCAAAATA
1 AATCAAGATTAAACTACGATTTTTGGATTTAAAAAAATCAGGATTAAATCGTAAGTCAAAATA
16099 TAAAGAGATT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
66 16 0.30
67 9 0.17
68 28 0.53
ACGTcount: A:0.43, C:0.09, G:0.16, T:0.31
Consensus pattern (68 bp):
AATCAAGATTAAACTACGATTTTTGGATTTAAAAAAATCAGGATTAAATCGTAAGTCAAAATAAC
GTC
Found at i:16113 original size:34 final size:35
Alignment explanation
Indices: 16065--16147 Score: 100
Period size: 34 Copynumber: 2.4 Consensus size: 35
16055 TTTTTGGATT
* *
16065 TAAAGAGATCGGGATTTA-ATCGTAAGTCA-AAATA
1 TAAAGAGATTGGGATTTAGATCGTAAATCATAAA-A
*
16099 TAAAGAGATTGGGA-TTAGATCGTAAATTATAAAA
1 TAAAGAGATTGGGATTTAGATCGTAAATCATAAAA
*
16133 TAAAGAGACTGGGAT
1 TAAAGAGATTGGGAT
16148 CAAACTATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
33 3 0.07
34 36 0.86
35 3 0.07
ACGTcount: A:0.45, C:0.06, G:0.23, T:0.27
Consensus pattern (35 bp):
TAAAGAGATTGGGATTTAGATCGTAAATCATAAAA
Found at i:16295 original size:109 final size:109
Alignment explanation
Indices: 16166--16845 Score: 817
Period size: 109 Copynumber: 6.2 Consensus size: 109
16156 AATTTGAAAA
* * * * * * *
16166 CTATAAAAATGATCAGGATTAAAACAGGAGTCAAAGATTAAAGATAATTGGGACTGAATC-TCAA
1 CTATAAGAATGATCGGGATTAAACCACGAGTCAAAGATTAAAGATAACTGAGACTGAACCGT-AA
* *
16230 CTCAAA-AATATAAAAGCGACTAGGATTAAACTGTAAGTCGAGAAG
65 GTCAAAGAA-ATAAAAGCGACTAGGATTAAACCGTAAGTCGAGAAG
* * * * * * *
16275 CTATAAGAATGATCGGGATTAAATCACAAGTTAAAGATTAAAAATAACTGAAACTGAATCGCAAG
1 CTATAAGAATGATCGGGATTAAACCACGAGTCAAAGATTAAAGATAACTGAGACTGAACCGTAAG
*
16340 TCAAAGAAATAAAAACGACTAGGATTAAACCGTAAGTCGAGAAG
66 TCAAAGAAATAAAAGCGACTAGGATTAAACCGTAAGTCGAGAAG
* * * *
16384 CTATAAGAATGATCGAGATTAAACCACGAGTCAAAGATTAACGATGATCCG-GACTGAACCGTAA
1 CTATAAGAATGATCGGGATTAAACCACGAGTCAAAGATTAAAGAT-AACTGAGACTGAACCGTAA
* * **
16448 GTCAAAGAAATAAAAGTGACTAGGATTAAACCGTAAATTAAGAAG
65 GTCAAAGAAATAAAAGCGACTAGGATTAAACCGTAAGTCGAGAAG
* * * * *
16493 CTATAAGAATGATCGGGATTAAACCACGAGTCAAAGATTAAAAATAATTGAAACTGAACTGCAAG
1 CTATAAGAATGATCGGGATTAAACCACGAGTCAAAGATTAAAGATAACTGAGACTGAACCGTAAG
*
16558 TCAAAGAAATAAAAGCGACTAGGATTAAACCATAAGTCGAGAAG
66 TCAAAGAAATAAAAGCGACTAGGATTAAACCGTAAGTCGAGAAG
* * * * * * ** * *
16602 CTATAAAAATGATCGAGATTAAACCATGAATCAAATATTAACGACGACCGGGACTGAACCGTAAG
1 CTATAAGAATGATCGGGATTAAACCACGAGTCAAAGATTAAAGATAACTGAGACTGAACCGTAAG
* * *
16667 TCAAAGAAATAAAAGCGACTAGGATTAAATCGAAAGTCGAAAAG
66 TCAAAGAAATAAAAGCGACTAGGATTAAACCGTAAGTCGAGAAG
* * * * *
16711 CTATAAAAATGAACGCGATTATACCATGAGTCAAAGATTAAAGATAACTGAGACTGAACCGTAAG
1 CTATAAGAATGATCGGGATTAAACCACGAGTCAAAGATTAAAGATAACTGAGACTGAACCGTAAG
* *
16776 TCAAAGAAATAAAAGTGACTAGGTTTAAACCGTAAGTCGAGAAG
66 TCAAAGAAATAAAAGCGACTAGGATTAAACCGTAAGTCGAGAAG
* * **
16820 TTATAAGAATAATCATGATTAAACCA
1 CTATAAGAATGATCGGGATTAAACCA
16846 TAAGTTAAAA
Statistics
Matches: 482, Mismatches: 85, Indels: 8
0.84 0.15 0.01
Matches are distributed among these distances:
108 2 0.00
109 475 0.99
110 5 0.01
ACGTcount: A:0.47, C:0.14, G:0.19, T:0.21
Consensus pattern (109 bp):
CTATAAGAATGATCGGGATTAAACCACGAGTCAAAGATTAAAGATAACTGAGACTGAACCGTAAG
TCAAAGAAATAAAAGCGACTAGGATTAAACCGTAAGTCGAGAAG
Found at i:16377 original size:36 final size:35
Alignment explanation
Indices: 16337--16813 Score: 115
Period size: 36 Copynumber: 13.1 Consensus size: 35
16327 ACTGAATCGC
*
16337 AAGTCAAAGAAATAAAAACGACTAGGATTAAACCGT
1 AAGTCAAAGAAATAAAAATGA-TAGGATTAAACCGT
** * * **
16373 AAGTCGAGAAGCTATAAGAATGATCGAGATTAAACCAC
1 AAGTC-A-AAGAAATAAAAATGATAG-GATTAAACCGT
* * ** * * *
16411 GAGTCAAAG-ATTAACGATGATCCGGACTGAACCGT
1 AAGTCAAAGAAATAAAAATGAT-AGGATTAAACCGT
*
16446 AAGTCAAAGAAATAAAAGTGACTAGGATTAAACCGT
1 AAGTCAAAGAAATAAAAATGA-TAGGATTAAACCGT
* * * * **
16482 AAAT-TAAGAAGCTATAAGAATGATCGGGATTAAACCAC
1 AAGTCAAAGAA---ATAAAAATGAT-AGGATTAAACCGT
* * * * * * * * *
16520 GAGTCAAAG-ATTAAAAATAATTGAAACTGAACTGC
1 AAGTCAAAGAAATAAAAATGATAG-GATTAAACCGT
** *
16555 AAGTCAAAGAAATAAAAGCGACTAGGATTAAACCAT
1 AAGTCAAAGAAATAAAAATGA-TAGGATTAAACCGT
** * *
16591 AAGTCGAGAAGCTATAAAAATGATCGAGATTAAACCAT
1 AAGTC-A-AAGAAATAAAAATGATAG-GATTAAACCGT
* * ** * ** * *
16629 GAA-TCAAA-TATTAACGACGACCGGGACTGAACCGT
1 -AAGTCAAAGAAATAAAAATGA-TAGGATTAAACCGT
** * *
16664 AAGTCAAAGAAATAAAAGCGACTAGGATTAAATCGA
1 AAGTCAAAGAAATAAAAATGA-TAGGATTAAACCGT
** * *
16700 AAGTCGAAAAGCTATAAAAATGA-ACGCGATTATACCAT
1 AAGTC--AAAGAAATAAAAATGATA-G-GATTAAACCGT
* * * * * *
16738 GAGTCAAAG-ATTAAAGATAACT-GAGACTGAACCGT
1 AAGTCAAAGAAATAAAAATGA-TAG-GATTAAACCGT
* *
16773 AAGTCAAAGAAATAAAAGTGACTAGGTTTAAACCGT
1 AAGTCAAAGAAATAAAAATGA-TAGGATTAAACCGT
16809 AAGTC
1 AAGTC
16814 GAGAAGTTAT
Statistics
Matches: 304, Mismatches: 108, Indels: 58
0.65 0.23 0.12
Matches are distributed among these distances:
34 3 0.01
35 92 0.30
36 98 0.32
37 14 0.05
38 92 0.30
39 5 0.02
ACGTcount: A:0.47, C:0.14, G:0.19, T:0.19
Consensus pattern (35 bp):
AAGTCAAAGAAATAAAAATGATAGGATTAAACCGT
Found at i:16404 original size:38 final size:36
Alignment explanation
Indices: 16362--16850 Score: 107
Period size: 35 Copynumber: 13.4 Consensus size: 36
16352 AAACGACTAG
*
16362 GATTAAACCGTAAGTCGAGAAGCTATAAGAATGATCGA
1 GATTAAACCGTAAGTC-A-AAGATATAAGAATGATCGA
***
16400 GATTAAACCACGAGTCAAAGAT-TAACG-ATGATCCG-
1 GATTAAACCGTAAGTCAAAGATATAA-GAATGAT-CGA
* * * *
16435 GACTGAACCGTAAGTCAAAGAAATAA-AAGTGA-CTA
1 GATTAAACCGTAAGTCAAAGATATAAGAA-TGATCGA
* * * *
16470 GGATTAAACCGTAAATTAAGAAGCTATAAGAATGATCGG
1 -GATTAAACCGT-AAGTCA-AAGATATAAGAATGATCGA
*** * * *
16509 GATTAAACCACGAGTCAAAGAT-TAAAAATAATTGA
1 GATTAAACCGTAAGTCAAAGATATAAGAATGATCGA
* * * * * * * *
16544 AACTGAACTGCAAGTCAAAGAAATAA-AAGCGA-CTA
1 GATTAAACCGTAAGTCAAAGATATAAGAA-TGATCGA
* * *
16579 GGATTAAACCATAAGTCGAGAAGCTATAAAAATGATCGA
1 -GATTAAACCGTAAGTC-A-AAGATATAAGAATGATCGA
* * * * *
16618 GATTAAACCATGAA-TCAAATAT-TAACG-ACGACCGG
1 GATTAAACCGT-AAGTCAAAGATATAA-GAATGATCGA
* * * * *
16653 GACTGAACCGTAAGTCAAAGAAATAA-AAGCGA-CTA
1 GATTAAACCGTAAGTCAAAGATATAAGAA-TGATCGA
* * * * * *
16688 GGATTAAATCGAAAGTCGAAAAGCTATAAAAATGAACGC
1 -GATTAAACCGTAAGTC--AAAGATATAAGAATGATCGA
* * * *
16727 GATTATACCATGAGTCAAAGAT-TAA-AGAT-AACTGA
1 GATTAAACCGTAAGTCAAAGATATAAGA-ATGATC-GA
* * * *
16762 GACTGAACCGTAAGTCAAAGAAATAA-AAGTGA-CTA
1 GATTAAACCGTAAGTCAAAGATATAAGAA-TGATCGA
* * *
16797 GGTTTAAACCGTAAGTCGAGAAGTTATAAGAATAATC-A
1 -GATTAAACCGTAAGTC-A-AAGATATAAGAATGATCGA
*
16835 TGATTAAACCATAAGT
1 -GATTAAACCGTAAGT
16851 TAAAAATTAA
Statistics
Matches: 317, Mismatches: 95, Indels: 78
0.65 0.19 0.16
Matches are distributed among these distances:
34 7 0.02
35 100 0.32
36 85 0.27
37 12 0.04
38 98 0.31
39 15 0.05
ACGTcount: A:0.46, C:0.14, G:0.19, T:0.20
Consensus pattern (36 bp):
GATTAAACCGTAAGTCAAAGATATAAGAATGATCGA
Found at i:16768 original size:327 final size:327
Alignment explanation
Indices: 16166--16845 Score: 900
Period size: 327 Copynumber: 2.1 Consensus size: 327
16156 AATTTGAAAA
* * * * **
16166 CTATAAAAATGATCAGGATTAAAACAGGAGTCAAAGATTAAAGATAATTGGGACTGAATCTCAAC
1 CTATAAGAATGATCAGGATTAAACCACGAGTCAAAGATTAAAAATAATTGAAACTGAATCTCAAC
** * *
16231 TCAAAAATATAAAAGCGACTAGGATTAAACTGTAAGTCGAGAAGCTATAAGAATGATCGGGATTA
66 TCAAAAATATAAAAGCGACTAGGATTAAACCATAAGTCGAGAAGCTATAAAAATGATCGAGATTA
* * * * *
16296 AATCACAAGTTAAAGATTAAAAATAACTGAAACTGAATCGCAAGTCAAAGAAATAAAAACGACTA
131 AACCACAAGTCAAAGATTAAAAACAACCGAAACTGAACCGCAAGTCAAAGAAATAAAAACGACTA
* * * * *
16361 GGATTAAACCGTAAGTCGAGAAGCTATAAGAATGATCGAGATTAAACCACGAGTCAAAGATTAAC
196 GGATTAAACCGAAAGTCGAAAAGCTATAAAAATGAACGAGATTAAACCACGAGTCAAAGATTAAA
* *
16426 GATGATCCGGACTGAACCGTAAGTCAAAGAAATAAAAGTGACTAGGATTAAACCGTAAATTAAGA
261 GATGAACCGGACTGAACCGTAAGTCAAAGAAATAAAAGTGACTAGGATTAAACCGTAAATCAAGA
16491 AG
326 AG
*
16493 CTATAAGAATGATCGGGATTAAACCACGAGTCAAAGATTAAAAATAATTGAAACTGAA-CTGCAA
1 CTATAAGAATGATCAGGATTAAACCACGAGTCAAAGATTAAAAATAATTGAAACTGAATCT-CAA
*
16557 GTCAAAGAA-ATAAAAGCGACTAGGATTAAACCATAAGTCGAGAAGCTATAAAAATGATCGAGAT
65 CTCAAA-AATATAAAAGCGACTAGGATTAAACCATAAGTCGAGAAGCTATAAAAATGATCGAGAT
* * ** * ** * *
16621 TAAACCATGAA-TCAAATATTAACGACGACCGGGACTGAACCGTAAGTCAAAGAAATAAAAGCGA
129 TAAACCA-CAAGTCAAAGATTAAAAACAACCGAAACTGAACCGCAAGTCAAAGAAATAAAAACGA
* * * *
16685 CTAGGATTAAATCGAAAGTCGAAAAGCTATAAAAATGAACGCGATTATACCATGAGTCAAAGATT
193 CTAGGATTAAACCGAAAGTCGAAAAGCTATAAAAATGAACGAGATTAAACCACGAGTCAAAGATT
* * *
16750 AAAGAT-AACTGAGACTGAACCGTAAGTCAAAGAAATAAAAGTGACTAGGTTTAAACCGTAAGTC
258 AAAGATGAACCG-GACTGAACCGTAAGTCAAAGAAATAAAAGTGACTAGGATTAAACCGTAAATC
*
16814 GAGAAG
322 AAGAAG
* * *
16820 TTATAAGAATAATCATGATTAAACCA
1 CTATAAGAATGATCAGGATTAAACCA
16846 TAAGTTAAAA
Statistics
Matches: 304, Mismatches: 45, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
326 5 0.02
327 295 0.97
328 4 0.01
ACGTcount: A:0.47, C:0.14, G:0.19, T:0.21
Consensus pattern (327 bp):
CTATAAGAATGATCAGGATTAAACCACGAGTCAAAGATTAAAAATAATTGAAACTGAATCTCAAC
TCAAAAATATAAAAGCGACTAGGATTAAACCATAAGTCGAGAAGCTATAAAAATGATCGAGATTA
AACCACAAGTCAAAGATTAAAAACAACCGAAACTGAACCGCAAGTCAAAGAAATAAAAACGACTA
GGATTAAACCGAAAGTCGAAAAGCTATAAAAATGAACGAGATTAAACCACGAGTCAAAGATTAAA
GATGAACCGGACTGAACCGTAAGTCAAAGAAATAAAAGTGACTAGGATTAAACCGTAAATCAAGA
AG
Found at i:17940 original size:10 final size:10
Alignment explanation
Indices: 17925--17976 Score: 67
Period size: 10 Copynumber: 5.6 Consensus size: 10
17915 TTACTTCTTT
*
17925 TTTTTTTCTC
1 TTTTTTTCTA
17935 TTTTTTTCTA
1 TTTTTTTCTA
17945 TTTTTTTCTA
1 TTTTTTTCTA
17955 -TTTTTT-TA
1 TTTTTTTCTA
17963 -TTTTTTCT-
1 TTTTTTTCTA
17971 TTTTTT
1 TTTTTT
17977 AAGCAAAATA
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
8 8 0.21
9 12 0.31
10 19 0.49
ACGTcount: A:0.06, C:0.10, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTTCTA
Found at i:17958 original size:18 final size:19
Alignment explanation
Indices: 17926--17970 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
17916 TACTTCTTTT
*
17926 TTTTTTCTCTTTTTTTCTA
1 TTTTTTCTCTATTTTTCTA
*
17945 TTTTTT-TCTATTTTTTTA
1 TTTTTTCTCTATTTTTCTA
17963 TTTTTTCT
1 TTTTTTCT
17971 TTTTTTAAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.07, C:0.11, G:0.00, T:0.82
Consensus pattern (19 bp):
TTTTTTCTCTATTTTTCTA
Found at i:29279 original size:140 final size:139
Alignment explanation
Indices: 29006--29279 Score: 446
Period size: 140 Copynumber: 2.0 Consensus size: 139
28996 ATGTAAAATG
29006 AAATGCAATTTAAGAGTTGGATTCTTAAATATAATGAGACCACCCCAACTTCCAACATCTAGGCA
1 AAATGCAATTTAAGAGTTGGATTCTTAAATATAATGAGACCACCCCAACTTCCAACATCTAGGCA
* *
29071 AAGCTTAGGTGCGACTGTTTATATTTAAGATCCCAATTTTATTATACTTTTTATTATTAATCTTA
66 AAGCTTAGGTGCGACTGTTTATATTTAAAATCCCAATTTTATTATACTTTTTATTATTAATCTAA
29136 TTTTTAATA
131 TTTTTAATA
*
29145 AAATGCAATTTAAAGAGTTGGATTCTTAAATATAATGAGACCA-CCCGACTCTCCAACATCTAGG
1 AAATGCAATTT-AAGAGTTGGATTCTTAAATATAATGAGACCACCCCAACT-TCCAACATCTAGG
* *
29209 CAGAGCTTAGGTGCGACTGTTTATATTTAAAATCCCAATTTTATTATAAC-TTTTATTTATTTAT
64 CAAAGCTTAGGTGCGACTGTTTATATTTAAAATCCCAATTTTATTAT-ACTTTTTA-TTATTAAT
29273 -TAATTTT
127 CTAATTTT
29280 ATTATTAATA
Statistics
Matches: 126, Mismatches: 5, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
139 17 0.13
140 100 0.79
141 9 0.07
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.39
Consensus pattern (139 bp):
AAATGCAATTTAAGAGTTGGATTCTTAAATATAATGAGACCACCCCAACTTCCAACATCTAGGCA
AAGCTTAGGTGCGACTGTTTATATTTAAAATCCCAATTTTATTATACTTTTTATTATTAATCTAA
TTTTTAATA
Found at i:29483 original size:16 final size:16
Alignment explanation
Indices: 29416--29483 Score: 66
Period size: 16 Copynumber: 4.2 Consensus size: 16
29406 TTTTTCGGAC
*
29416 TTTGGACTTCAAGGAT
1 TTTGGATTTCAAGGAT
* *
29432 TTTGGATTTCGAGCGGT
1 TTTGGATTTCAAG-GAT
29449 TTTGGATTT-AATGGAT
1 TTTGGATTTCAA-GGAT
* *
29465 TTTGGATTTTAAGGGT
1 TTTGGATTTCAAGGAT
29481 TTT
1 TTT
29484 AAAAACCTAG
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
16 29 0.67
17 14 0.33
ACGTcount: A:0.19, C:0.06, G:0.28, T:0.47
Consensus pattern (16 bp):
TTTGGATTTCAAGGAT
Found at i:29996 original size:38 final size:37
Alignment explanation
Indices: 29945--30021 Score: 100
Period size: 38 Copynumber: 2.1 Consensus size: 37
29935 AACGATGGTC
* * * *
29945 CGGGCGGTCTGACCAGTTCGGCGGTTGGATCGGCGGTT
1 CGGGCGATCTGACCAGTTCGACGG-TCGATAGGCGGTT
*
29983 CGGGCGATCTGACCGGTTCGACGGTCGATAGGCGGTT
1 CGGGCGATCTGACCAGTTCGACGGTCGATAGGCGGTT
30020 CG
1 CG
30022 TATAAACCGG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
37 13 0.38
38 21 0.62
ACGTcount: A:0.10, C:0.25, G:0.43, T:0.22
Consensus pattern (37 bp):
CGGGCGATCTGACCAGTTCGACGGTCGATAGGCGGTT
Found at i:30598 original size:10 final size:10
Alignment explanation
Indices: 30583--30607 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
30573 GTGGCGGTTC
30583 TGTTTATGGT
1 TGTTTATGGT
30593 TGTTTATGGT
1 TGTTTATGGT
30603 TGTTT
1 TGTTT
30608 TGGGTTGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.28, T:0.64
Consensus pattern (10 bp):
TGTTTATGGT
Found at i:30994 original size:17 final size:17
Alignment explanation
Indices: 30969--31015 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
30959 TGTTTACTTG
30969 TTTTG-TTTTTTTTCTA
1 TTTTGTTTTTTTTTCTA
*
30985 TTTTGTTTTTTTTTCTT
1 TTTTGTTTTTTTTTCTA
31002 TTTTGTTTTGTTTT
1 TTTTGTTTT-TTTT
31016 GTTAAATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
16 5 0.18
17 19 0.68
18 4 0.14
ACGTcount: A:0.02, C:0.04, G:0.09, T:0.85
Consensus pattern (17 bp):
TTTTGTTTTTTTTTCTA
Found at i:30994 original size:22 final size:22
Alignment explanation
Indices: 30966--31015 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
30956 GTTTGTTTAC
*
30966 TTGTTTTGTTTT-TTTTCTATT
1 TTGTTTTTTTTTCTTTTCTATT
* *
30987 TTGTTTTTTTTTCTTTTTTGTT
1 TTGTTTTTTTTTCTTTTCTATT
31009 TTGTTTT
1 TTGTTTT
31016 GTTAAATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.02, C:0.04, G:0.10, T:0.84
Consensus pattern (22 bp):
TTGTTTTTTTTTCTTTTCTATT
Found at i:31006 original size:33 final size:34
Alignment explanation
Indices: 30952--31015 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 34
30942 CTTTCTTTTT
30952 TTTTGTTTGTTTACTTGTTTTGTTTT-TTTTCTA
1 TTTTGTTTGTTTACTTGTTTTGTTTTGTTTTCTA
* *
30985 TTTTGTTTTTTTTTCTT-TTTTGTTTTGTTTT
1 TTTTG-TTTGTTTACTTGTTTTGTTTTGTTTT
31016 GTTAAATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
33 14 0.52
34 13 0.48
ACGTcount: A:0.03, C:0.05, G:0.11, T:0.81
Consensus pattern (34 bp):
TTTTGTTTGTTTACTTGTTTTGTTTTGTTTTCTA
Found at i:31249 original size:48 final size:48
Alignment explanation
Indices: 31177--31694 Score: 721
Period size: 48 Copynumber: 10.8 Consensus size: 48
31167 TGGTTTTACA
* * *
31177 GAAAAAGGCTCCTCTTAGCAGAGGCTCAACAACTTTAAAATTTCTTCTT
1 GAAAAA-GCTCCTCTCAACAGAGGCTCCACAACTTTAAAATTTCTTCTT
* *
31226 GAAAAAGCTCCTCTCAACAGAGGCTCCACAACTTTAAAAATCTCATC-T
1 GAAAAAGCTCCTCTCAACAGAGGCTCCACAACTTT-AAAATTTCTTCTT
* *
31274 GAAAAAGCTCCTCTCAACAGAGGCTTCATAACTTTAAAATTTCATT-TT
1 GAAAAAGCTCCTCTCAACAGAGGCTCCACAACTTTAAAATTTC-TTCTT
* * *
31322 GAAAAAGCTCCTCTCAACAGAGGCTCTACAACTTTAAAAATCTCATC-T
1 GAAAAAGCTCCTCTCAACAGAGGCTCCACAACTTT-AAAATTTCTTCTT
* *
31370 GAAAAAGCTCCTCTCAACAGAGGCTTCATAACTTTAAAATTTCATT-TT
1 GAAAAAGCTCCTCTCAACAGAGGCTCCACAACTTTAAAATTTC-TTCTT
31418 GAAAAAGCTCCTCTCAACAGAGGCTCCACAACTTTAAAATTTCTTC-T
1 GAAAAAGCTCCTCTCAACAGAGGCTCCACAACTTTAAAATTTCTTCTT
* *
31465 GAAAAAGCTCCTCTCAACAGAGGCTTCATAACTTTAAAATTTCATT-TT
1 GAAAAAGCTCCTCTCAACAGAGGCTCCACAACTTTAAAATTTC-TTCTT
* *
31513 GAAAAAGCTCCTCTCAACAGAGGCTCTACAACTTTAAAATTCTCATT-TC
1 GAAAAAGCTCCTCTCAACAGAGGCTCCACAACTTTAAAATT-TC-TTCTT
* *
31562 GGAAAAGCTCCTCTCAACAGAGGCTCCACAACTTTAAAA-TTCTTTTT
1 GAAAAAGCTCCTCTCAACAGAGGCTCCACAACTTTAAAATTTCTTCTT
*
31609 GAAAAAGCTCCTCTCAACAGAGGCTCAACAACTTTAAAATTT-TTCTT
1 GAAAAAGCTCCTCTCAACAGAGGCTCCACAACTTTAAAATTTCTTCTT
*
31656 GAAAAAGCTCATCTCAACAGAGGCTCCACAACTTTAAAA
1 GAAAAAGCTCCTCTCAACAGAGGCTCCACAACTTTAAAA
31695 AAATCTCATT
Statistics
Matches: 421, Mismatches: 35, Indels: 28
0.87 0.07 0.06
Matches are distributed among these distances:
46 2 0.00
47 139 0.33
48 215 0.51
49 65 0.15
ACGTcount: A:0.36, C:0.25, G:0.11, T:0.29
Consensus pattern (48 bp):
GAAAAAGCTCCTCTCAACAGAGGCTCCACAACTTTAAAATTTCTTCTT
Done.