Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2423
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: 25229
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.28
Found at i:5299 original size:29 final size:27
Alignment explanation
Indices: 5246--5299 Score: 65
Period size: 29 Copynumber: 1.9 Consensus size: 27
5236 TTTTGTTGGA
*
5246 AACAAACCAACATCTTTCTTGTCAAAT
1 AACAAACCAACATCTTTCTTATCAAAT
5273 AACAAACCATATCATCTTTAC-TATCAA
1 AACAAACCA-A-CATCTTT-CTTATCAA
5300 GCAAACCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 9 0.39
28 1 0.04
29 12 0.52
30 1 0.04
ACGTcount: A:0.43, C:0.26, G:0.02, T:0.30
Consensus pattern (27 bp):
AACAAACCAACATCTTTCTTATCAAAT
Found at i:6089 original size:61 final size:61
Alignment explanation
Indices: 6013--6319 Score: 243
Period size: 61 Copynumber: 4.9 Consensus size: 61
6003 TCTTTAAAGC
6013 AGCCCACTAACTCCGTGGCACCTTGTTTCCTTTTAAGTCCACAACTCCGTGGCAC-CCTTTCA
1 AGCCCAC-AACTCCGTGGCACCTT-TTTCCTTTTAAGTCCACAACTCCGTGGCACTCCTTTCA
* * * * * **
6075 AGCCCACGACTCCGTGGCA-C-TCTT--TTTAAAGCCCATAACTCCGT-GCACTTTTTTCCTCCT
1 AGCCCACAACTCCGTGGCACCTTTTTCCTTTTAAGTCCACAACTCCGTGGCAC-TCCTT--T-C-
6135 A
61 A
* * * *
6136 AGCCCACAACTCTGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGGCAC-CCTTTTTA
1 AGCCCACAACTCCGTGGCAC-CTTTTTCCTTTTAAGTCCACAACTCCGTGGCACTCC-TTTCA
* * * *
6198 AGCCCATAACTCCGTGGCA-CTTTTTCATCTTTAAGTCCACAACTCTGTGGCACATTTTTTTCTT
1 AGCCCACAACTCCGTGGCACCTTTTTCCT-TTTAAGTCCACAACTCCGTGGCAC-------TCCT
*
6262 TTAA
58 TTCA
6266 AGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAGTCCACAACTCCGTGGCA
1 AGCCCACAACTCCGTGGCAC-CTTTTT-CCTTTTAAGTCCACAACTCCGTGGCA
6320 TCTTTCTCCC
Statistics
Matches: 193, Mismatches: 27, Indels: 42
0.74 0.10 0.16
Matches are distributed among these distances:
55 4 0.02
56 17 0.09
57 2 0.01
58 2 0.01
59 2 0.01
60 10 0.05
61 50 0.26
62 25 0.13
63 1 0.01
64 4 0.02
66 19 0.10
67 4 0.02
68 22 0.11
69 1 0.01
70 28 0.15
71 2 0.01
ACGTcount: A:0.20, C:0.35, G:0.13, T:0.32
Consensus pattern (61 bp):
AGCCCACAACTCCGTGGCACCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACTCCTTTCA
Found at i:6175 original size:95 final size:96
Alignment explanation
Indices: 6074--6292 Score: 320
Period size: 95 Copynumber: 2.3 Consensus size: 96
6064 GCACCCTTTC
* *
6074 AAGCCCACGACTCCGTGGCACTCTTTTTAAAGCCCATAACTCCGT-GCACTTTTTTCCTC-CTAA
1 AAGCCCACAACTCCGTGGCACTCTTTTT-AAGCCCATAACTCCGTGGCAC-TTTTTCATCTCTAA
6137 GCCCACAACTCTGTGGCAC-TCTTTTTCCTTCT-
64 GCCCACAACTCTGTGGCACAT-TTTTTCCTTCTA
* * *
6169 AAGCCCACAACTCCGTGGCACCCTTTTTAAGCCCATAACTCCGTGGCACTTTTTCATCTTTAAGT
1 AAGCCCACAACTCCGTGGCACTCTTTTTAAGCCCATAACTCCGTGGCACTTTTTCATCTCTAAGC
* *
6234 CCACAACTCTGTGGCACATTTTTTTCTTTTA
66 CCACAACTCTGTGGCACATTTTTTCCTTCTA
6265 AAGCCCACAACTCCGTGGCACTCTTTTT
1 AAGCCCACAACTCCGTGGCACTCTTTTT
6293 CCCTTTTAAG
Statistics
Matches: 112, Mismatches: 8, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
94 24 0.21
95 60 0.54
96 28 0.25
ACGTcount: A:0.21, C:0.33, G:0.13, T:0.33
Consensus pattern (96 bp):
AAGCCCACAACTCCGTGGCACTCTTTTTAAGCCCATAACTCCGTGGCACTTTTTCATCTCTAAGC
CCACAACTCTGTGGCACATTTTTTCCTTCTA
Found at i:6273 original size:35 final size:33
Alignment explanation
Indices: 6013--6324 Score: 255
Period size: 35 Copynumber: 9.7 Consensus size: 33
6003 TCTTTAAAGC
*
6013 AGCCCACTAACTCCGTGGCACCTTGTTTCCTTTTA
1 AGCCCAC-AACTCCGTGGCA-CTTTTTTCCTTTTA
* *
6048 AGTCCACAACTCCGTGGCAC------CCTTTCA
1 AGCCCACAACTCCGTGGCACTTTTTTCCTTTTA
* * *
6075 AGCCCACGACTCCGTGGCAC--TCTT--TTTAA
1 AGCCCACAACTCCGTGGCACTTTTTTCCTTTTA
* **
6104 AGCCCATAACTCCGT-GCACTTTTTTCCTCCTA
1 AGCCCACAACTCCGTGGCACTTTTTTCCTTTTA
* *
6136 AGCCCACAACTCTGTGGCACTCTTTTTCCTTCTA
1 AGCCCACAACTCCGTGGCACT-TTTTTCCTTTTA
6170 AGCCCACAACTCCGTGGCAC------CCTTTTTA
1 AGCCCACAACTCCGTGGCACTTTTTTCC-TTTTA
* *
6198 AGCCCATAACTCCGTGGCAC-TTTTTCATCTTTA
1 AGCCCACAACTCCGTGGCACTTTTTTCCT-TTTA
* * *
6231 AGTCCACAACTCTGTGGCACATTTTTTTCTTTTAA
1 AGCCCACAACTCCGTGGCAC-TTTTTTCCTTTT-A
6266 AGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTA
1 AGCCCACAACTCCGTGGCACT-TTTTT-CCTTTTA
*
6301 AGTCCACAACTCCGTGGCATCTTT
1 AGCCCACAACTCCGTGGCA-CTTT
6325 CTCCCTTCCT
Statistics
Matches: 227, Mismatches: 27, Indels: 46
0.76 0.09 0.15
Matches are distributed among these distances:
27 26 0.11
28 27 0.12
29 17 0.07
30 3 0.01
32 16 0.07
33 28 0.12
34 46 0.20
35 57 0.25
36 7 0.03
ACGTcount: A:0.20, C:0.34, G:0.13, T:0.33
Consensus pattern (33 bp):
AGCCCACAACTCCGTGGCACTTTTTTCCTTTTA
Found at i:6420 original size:33 final size:33
Alignment explanation
Indices: 6327--6429 Score: 158
Period size: 32 Copynumber: 3.2 Consensus size: 33
6317 GCATCTTTCT
*
6327 CCCTTC-CTAAAGCCCACACAAGTTGGTGGCAA
1 CCCTTCTCTAAAGCCCACACAAGTCGGTGGCAA
*
6359 CCCTTCTC-GAAGCCCACAC-AGTCGGTGGCAA
1 CCCTTCTCTAAAGCCCACACAAGTCGGTGGCAA
*
6390 CCATTCTCTAAAGCCCACACAAGTCGGTGGCAA
1 CCCTTCTCTAAAGCCCACACAAGTCGGTGGCAA
6423 CCCTTCT
1 CCCTTCT
6430 AACCCCAATA
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
31 18 0.29
32 26 0.41
33 19 0.30
ACGTcount: A:0.25, C:0.37, G:0.18, T:0.19
Consensus pattern (33 bp):
CCCTTCTCTAAAGCCCACACAAGTCGGTGGCAA
Found at i:6493 original size:49 final size:49
Alignment explanation
Indices: 6442--6898 Score: 575
Period size: 49 Copynumber: 9.5 Consensus size: 49
6432 CCCCAATATC
* * *
6442 GCTGGCCTTGAATCAGCATATTGGTACCTTCATCTTTAAGTCCAATGTC
1 GCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTA
* *
6491 GCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATC
1 GCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTA
* * *
6534 GCTGGCCTTGAATCAGCATATTGGCATCATCATCTTTAAGTCCAATGTA
1 GCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTA
*
6583 GCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCCCAATGTA
1 GCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT--CCAATGTA
*
6634 GCTGGCCTTGACTCAG-ACATATGGCGACCTTCATCTTTAAGTCCAATGTA
1 GCTGGCCTTGAATCAGCACAT-TGGC-ACCTTCATCTTTAAGTCCAATGTA
6684 GCTGGCCTTGAATCAGCACATTGGCACC-TCATCTTTAAGTCCAATGTA
1 GCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTA
* *
6732 GCTGGCCTTGACTCAGCACATTGGCATCTTCATCTTTAAGTCCAATGTA
1 GCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTA
* *
6781 GCTGTCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATA
1 GCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTA
* * * *
6824 GCTGG-CTTGAATCAGCATATTGGCACATTTTCCATCTTTACGTTCAATGTA
1 GCTGGCCTTGAATCAGCACATTGGCAC--CTT-CATCTTTAAGTCCAATGTA
6875 CGCTGGCCTTGAATCAGCACATTG
1 -GCTGGCCTTGAATCAGCACATTG
6899 ACATCCTTTT
Statistics
Matches: 363, Mismatches: 22, Indels: 42
0.85 0.05 0.10
Matches are distributed among these distances:
42 19 0.05
43 59 0.16
45 2 0.01
47 1 0.00
48 46 0.13
49 123 0.34
50 31 0.09
51 45 0.12
52 21 0.06
53 16 0.04
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (49 bp):
GCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTA
Found at i:6591 original size:92 final size:93
Alignment explanation
Indices: 6434--6907 Score: 596
Period size: 92 Copynumber: 5.0 Consensus size: 93
6424 CCTTCTAACC
* * *
6434 CCAATATCGCTGGCCTTGAATCAGCATATTGGTACCTTCATCTTTAAGTCCAATGTCGCTGGCCT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCT
6499 TGAATCAGCACATTGGCA-CCTTTAAGT
66 TGAATCAGCACATTGGCACCCTTTAAGT
* * *
6526 CCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTTTAAGTCCAATGTAGCTGGCCT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCT
*
6591 TGACTCAGCACATTGGCACCTTCATCTTTAAGT
66 TGAATCAGCACATTGGCA-C--C--CTTTAAGT
* *
6624 CCCCAATGTAGCTGGCCTTGACTCAGACATA-TGGCGACCTTCATCTTTAAGTCCAATGTAGCTG
1 --CCAATATAGCTGGCCTTGAATCAG-CATATTGGC-ACCTTCATCTTTAAGTCCAATGTAGCTG
6688 GCCTTGAATCAGCACATTGGCACCTCATCTTTAAGT
62 GCCTTGAATCAGCACATTGGCA-C-C--CTTTAAGT
* * * * *
6724 CCAATGTAGCTGGCCTTGACTCAGCACATTGGCATCTTCATCTTTAAGTCCAATGTAGCTGTCCT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCT
6789 TGAATCAGCACATTGGCA-CCTTTAAGT
66 TGAATCAGCACATTGGCACCCTTTAAGT
* * *
6816 CCAATATAGCTGG-CTTGAATCAGCATATTGGCACATTTTCCATCTTTACGTTCAATGTACGCTG
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCAC--CTT-CATCTTTAAGTCCAATGTA-GCTG
* *
6880 GCCTTGAATCAGCACATTGACATCCTTT
62 GCCTTGAATCAGCACATTGGCACCCTTT
6908 TTCTCATCAT
Statistics
Matches: 343, Mismatches: 23, Indels: 28
0.87 0.06 0.07
Matches are distributed among these distances:
91 18 0.05
92 98 0.29
93 2 0.01
94 18 0.05
95 24 0.07
96 6 0.02
97 51 0.15
98 36 0.10
100 37 0.11
101 53 0.15
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.31
Consensus pattern (93 bp):
CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCT
TGAATCAGCACATTGGCACCCTTTAAGT
Found at i:6955 original size:198 final size:193
Alignment explanation
Indices: 6433--6959 Score: 596
Period size: 198 Copynumber: 2.7 Consensus size: 193
6423 CCCTTCTAAC
* * *
6433 CCCAATATCGCTGGCCTTGAATCAG-CATATTGG-TACCTTCATCTTTAAGTCCAATGTCGCTGG
1 CCCAATATAGCTGGCCTTGAATCAGACATA-TGGCGACCTTCATCTTTAAGTCCAATGTAGCTGG
*
6496 CCTTGAATCAGCACATTGGCA-C-C-T--TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATT
65 CCTTGAATCAGCACATTGACACCTCATCATTAAGTCCAATATCGCTGGCCTTGAATCAGCATATT
* *
6556 GGCATCATCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTA
130 GGCATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C--CA-CTTTA
6621 AGT
191 AGT
* *
6624 CCCCAATGTAGCTGGCCTTGACTCAGACATATGGCGACCTTCATCTTTAAGTCCAATGTAGCTGG
1 -CCCAATATAGCTGGCCTTGAATCAGACATATGGCGACCTTCATCTTTAAGTCCAATGTAGCTGG
* * * * * *
6689 CCTTGAATCAGCACATTGGCACCTCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATT
65 CCTTGAATCAGCACATTGACACCTCATCATTAAGTCCAATATCGCTGGCCTTGAATCAGCATATT
*
6754 GGCATCTTCATCTTTAAGTCCAATGTAGCTGTCCTTGAATCAGCACATTGGCA-C-CTTTAAGT
130 GGCATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCACTTTAAGT
* * *
6816 -CCAATATAGCTGG-CTTGAATCAG-CATATTGGC-ACATTTTCCATCTTTACGTTCAATGTACG
1 CCCAATATAGCTGGCCTTGAATCAGACATA-TGGCGAC--CTT-CATCTTTAAGTCCAATGTA-G
* * * *
6877 CTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCATCATTAAGCCCCATATCGTTGGCCGTGA
61 CTGGCCTTGAATCAGCACATTGACA--C-----CTCATCATTAAGTCCAATATCGCTGGCCTTGA
6942 ATCA-CATATTGGCATCTT
119 ATCAGCATATTGGCATCTT
6960 TATCACTTTT
Statistics
Matches: 289, Mismatches: 27, Indels: 32
0.83 0.08 0.09
Matches are distributed among these distances:
188 6 0.02
189 13 0.04
190 14 0.05
191 17 0.06
192 58 0.20
193 53 0.18
194 3 0.01
195 1 0.00
196 1 0.00
198 95 0.33
199 28 0.10
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.32
Consensus pattern (193 bp):
CCCAATATAGCTGGCCTTGAATCAGACATATGGCGACCTTCATCTTTAAGTCCAATGTAGCTGGC
CTTGAATCAGCACATTGACACCTCATCATTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTG
GCATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCACTTTAAGT
Found at i:6960 original size:241 final size:233
Alignment explanation
Indices: 6433--6961 Score: 500
Period size: 241 Copynumber: 2.2 Consensus size: 233
6423 CCCTTCTAAC
* * * *
6433 CCCAATATCGCTGGCCTTGAATCAGCATATTGGTACCTTCATCTTTAAGTCCAATGTCGCTGGCC
1 CCCAATATAGCTGGCCGTGAATCAGCACATTGG---C--CATCTTTAAGTCCAATGTAGCTGGCC
* *
6498 TTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCA
61 TTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGG-A-CA
* *
6563 TCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCCC
124 TCA-CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT-CCC
* * *
6628 AATGTAGCTGGCCTTGACTCAGACATATGGCGACCTTCATCTTTAAG
187 AATGTAGCTGGCCTTGAATCAGACATATGACGACCTTCATCATTAAG
* * *
6675 TCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCATCTTTAAGTCCAATGTAGCTGGCCT
1 CCCAATATAGCTGGCCGTGAATCAGCACATTGG---C-CATCTTTAAGTCCAATGTAGCTGGCCT
* * *
6740 TGACTCAGCACATTGGCATCTTCATCTTTAAGTCCAATGTAGCTGTCCTTGAATCAGCACATTGG
62 TGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGG
* * *
6805 -CA-C-CTTTAAGTCCAATATAGCTGG-CTTGAATCAGCATATTGGCACATTTTCCATCTTTACG
121 ACATCACTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC--CTT-CATCTTTAAG
*
6866 T-TCAATGTACGCTGGCCTTGAATCAGCACAT-TGAC-ATCCTTTTTCTCATCATTAAG
183 TCCCAATGTA-GCTGGCCTTGAATCAG-ACATATGACGA-CC----T-TCATCATTAAG
* * * *
6922 CCCCATATCGTTGGCCGTGAATCA-CATATTGG-CATCTTTA
1 CCCAATATAGCTGGCCGTGAATCAGCACATTGGCCATCTTTA
6962 TCACTTTTCT
Statistics
Matches: 243, Mismatches: 27, Indels: 35
0.80 0.09 0.11
Matches are distributed among these distances:
240 19 0.08
241 80 0.33
242 54 0.22
243 15 0.06
244 2 0.01
245 1 0.00
246 8 0.03
247 64 0.26
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (233 bp):
CCCAATATAGCTGGCCGTGAATCAGCACATTGGCCATCTTTAAGTCCAATGTAGCTGGCCTTGAA
TCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGACATCACTTT
AAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCCAATGTAGCT
GGCCTTGAATCAGACATATGACGACCTTCATCATTAAG
Found at i:7860 original size:33 final size:33
Alignment explanation
Indices: 7823--7889 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
7813 CACAACGATT
7823 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
7856 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
7889 T
1 T
7890 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:7861 original size:13 final size:13
Alignment explanation
Indices: 7843--7867 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7833 CATAAAATGT
7843 TGTATCGATACAA
1 TGTATCGATACAA
7856 TGTATCGATACA
1 TGTATCGATACA
7868 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:7950 original size:13 final size:13
Alignment explanation
Indices: 7932--7956 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7922 ATTACTCAAA
7932 TGTATCGATACAT
1 TGTATCGATACAT
7945 TGTATCGATACA
1 TGTATCGATACA
7957 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:8058 original size:52 final size:52
Alignment explanation
Indices: 7965--8088 Score: 207
Period size: 52 Copynumber: 2.4 Consensus size: 52
7955 CACTGATCTT
*
7965 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACA-TTTTAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATT-AAA
8016 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
*
8068 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
8089 CTTTTCATAT
Statistics
Matches: 69, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
51 19 0.28
52 47 0.68
53 3 0.04
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
Found at i:10912 original size:13 final size:13
Alignment explanation
Indices: 10894--10919 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10884 CATATTTTTG
10894 TGTATCGATACAT
1 TGTATCGATACAT
10907 TGTATCGATACAT
1 TGTATCGATACAT
10920 ACATTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:10932 original size:32 final size:33
Alignment explanation
Indices: 10874--10937 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
10864 TACAAGCCAA
**
10874 TGTATCGATACATATTTTTGTGTATCGATACAT
1 TGTATCGATACATATCATTGTGTATCGATACAT
10907 TGTATCGATACATA-CATTGTGTATCGATACA
1 TGTATCGATACATATCATTGTGTATCGATACA
10938 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.41
Consensus pattern (33 bp):
TGTATCGATACATATCATTGTGTATCGATACAT
Found at i:13793 original size:33 final size:33
Alignment explanation
Indices: 13756--13822 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
13746 TTCAACGATT
13756 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
13789 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
13822 T
1 T
13823 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:13794 original size:13 final size:13
Alignment explanation
Indices: 13776--13800 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13766 CATAAAATGT
13776 TGTATCGATACAA
1 TGTATCGATACAA
13789 TGTATCGATACA
1 TGTATCGATACA
13801 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:13881 original size:13 final size:13
Alignment explanation
Indices: 13863--13887 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13853 ATTACTCAAA
13863 TGTATCGATACAT
1 TGTATCGATACAT
13876 TGTATCGATACA
1 TGTATCGATACA
13888 CTAATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:13989 original size:52 final size:52
Alignment explanation
Indices: 13876--14019 Score: 211
Period size: 52 Copynumber: 2.8 Consensus size: 52
13866 ATCGATACAT
* ***
13876 TGTATCGATACACTAATCTTTGTATCGATACATGCAGGC-AATTTGCCCAGA
1 TGTATCGATACACTATTAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
*
13927 TGTATCGATACA-TTTTAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTATT-AAATGTATCGATACATGCAGGCAAATTTGCCCAGA
*
13979 TGTATCGATACACTATTAAATGTATCGATACATGCAAGCAA
1 TGTATCGATACACTATTAAATGTATCGATACATGCAGGCAA
14020 CTTTTCATAT
Statistics
Matches: 83, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
50 2 0.02
51 31 0.37
52 47 0.57
53 3 0.04
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.31
Consensus pattern (52 bp):
TGTATCGATACACTATTAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:23614 original size:1 final size:1
Alignment explanation
Indices: 23608--23661 Score: 63
Period size: 1 Copynumber: 54.0 Consensus size: 1
23598 CCTTCTCTTC
* ** * *
23608 AAAAAAAAAAAGAGCAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
23662 CAAAGGAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.91, C:0.06, G:0.04, T:0.00
Consensus pattern (1 bp):
A
Found at i:23629 original size:16 final size:14
Alignment explanation
Indices: 23607--23665 Score: 77
Period size: 13 Copynumber: 4.3 Consensus size: 14
23597 GCCTTCTCTT
*
23607 CAAAAAAAAAAAGAG
1 CAAAAAAAAAAA-AA
23622 CAAAAAAAAAAAAA
1 CAAAAAAAAAAAAA
23636 -AAAAAAAAAAAAA
1 CAAAAAAAAAAAAA
*
23649 C-AAAAAAACAAAA
1 CAAAAAAAAAAAAA
23662 CAAA
1 CAAA
23666 GGAAAAGAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
13 25 0.62
14 3 0.08
15 12 0.30
ACGTcount: A:0.88, C:0.08, G:0.03, T:0.00
Consensus pattern (14 bp):
CAAAAAAAAAAAAA
Found at i:24793 original size:55 final size:55
Alignment explanation
Indices: 24655--25229 Score: 944
Period size: 55 Copynumber: 10.6 Consensus size: 55
24645 TCCGCTTTTT
**
24655 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGC-CCTT-C
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTCC
24708 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTCC
24763 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
24818 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
24873 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGC--TTTCC
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTCC
24926 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
24981 AGTCC-CAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGC--TTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
25033 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTCC
* *
25088 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACCCAAGTTGGTGGCATTTTCT
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
*
25143 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
*
25198 AGTCCCCAAAGAGC-GGACACCTTTCAAAGCCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCC
Statistics
Matches: 499, Mismatches: 8, Indels: 29
0.93 0.01 0.05
Matches are distributed among these distances:
52 12 0.02
53 139 0.28
54 65 0.13
55 276 0.55
56 7 0.01
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
Found at i:24843 original size:27 final size:27
Alignment explanation
Indices: 24758--24895 Score: 68
Period size: 27 Copynumber: 5.0 Consensus size: 27
24748 TTGGTGGCAT
24758 TTTCCAGTCCTCAAAGAGCAGGACACC
1 TTTCCAGTCCTCAAAGAGCAGGACACC
* * * * ** *
24785 TTTCAAAGCCCACACAAGTTGGTGG-CA-T
1 TTTC-CAGTCCTCA-AAG-AGCAGGACACC
24813 TTTCCAGTCCTCAAAGAGCAGGACACC
1 TTTCCAGTCCTCAAAGAGCAGGACACC
* * * * ** *
24840 TTTCAAAGCCCACACAAGTTGGTGG-CA-T
1 TTTC-CAGTCCTCA-AAG-AGCAGGACACC
24868 TTTCCAGTCCTCAAAGAGCAGGACACC
1 TTTCCAGTCCTCAAAGAGCAGGACACC
24895 T
1 T
24896 CTTAAAGCCC
Statistics
Matches: 73, Mismatches: 28, Indels: 20
0.60 0.23 0.17
Matches are distributed among these distances:
25 6 0.08
26 10 0.14
27 21 0.29
28 20 0.27
29 10 0.14
30 6 0.08
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.22
Consensus pattern (27 bp):
TTTCCAGTCCTCAAAGAGCAGGACACC
Done.