Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1748
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: 63510
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:3261 original size:1 final size:1
Alignment explanation
Indices: 3255--3348 Score: 89
Period size: 1 Copynumber: 94.0 Consensus size: 1
3245 CGTCCTCCAC
* * * * * * *
3255 AAAAAAAAAACAAAAAAAAAACAAAACAAAAAAAAACAAAAACAAAAAAAAAACAAAACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * *
3320 ACAAAACAAAACAAAAAAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3349 GGGGTCCGGA
Statistics
Matches: 71, Mismatches: 22, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 71 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3274 original size:16 final size:16
Alignment explanation
Indices: 3255--3347 Score: 132
Period size: 16 Copynumber: 5.6 Consensus size: 16
3245 CGTCCTCCAC
3255 AAAAAAAAAACAAAAA
1 AAAAAAAAAACAAAAA
*
3271 AAAAACAAAACAAAAA
1 AAAAAAAAAACAAAAA
*
3287 AAAACAAAAACAAAAA
1 AAAAAAAAAACAAAAA
*
3303 AAAAACAAAACAAAAA
1 AAAAAAAAAACAAAAA
3319 AACAAAACAAAACAAAAA
1 AA-AAAA-AAAACAAAAA
3337 AAACAAAAAAA
1 AAA-AAAAAAA
3348 AGGGGTCCGG
Statistics
Matches: 68, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
16 45 0.66
17 8 0.12
18 15 0.22
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAACAAAAA
Found at i:3302 original size:40 final size:38
Alignment explanation
Indices: 3253--3348 Score: 131
Period size: 40 Copynumber: 2.5 Consensus size: 38
3243 GGCGTCCTCC
* *
3253 ACAAAAAAAAAACAAAAAAAA-AACAAAACAAAAAAAA
1 ACAAAAAAAAAAAAAAAAAAACAAAAAAACAAAAAAAA
*
3290 ACAAAAACAAAAAAAAAACAAAACAAAAAAACAAAACAAA
1 ACAAAAA-AAAAAAAAAA-AAAACAAAAAAACAAAAAAAA
*
3330 ACAAAAAAAACAAAAAAAA
1 ACAAAAAAAAAAAAAAAAA
3349 GGGGTCCGGA
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
37 7 0.13
38 11 0.21
39 13 0.25
40 21 0.40
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (38 bp):
ACAAAAAAAAAAAAAAAAAAACAAAAAAACAAAAAAAA
Found at i:3310 original size:43 final size:43
Alignment explanation
Indices: 3255--3348 Score: 120
Period size: 45 Copynumber: 2.1 Consensus size: 43
3245 CGTCCTCCAC
3255 AAAAAAAAAACAAAAAAAAAACAAAACAAAAAAA-AACAA-AAA
1 AAAAAAAAAACAAAAAAAAAACAAAACAAAAAAACAA-AACAAA
*
3297 CAAAAAAAAAACAAAACAAAAAAACAAAACAAAACAAAAAAAACAAA
1 -AAAAAAAAAAC-AAA-AAAAAAACAAAACAAAA-AAACAAAACAAA
3344 AAAAA
1 AAAAA
3349 GGGGTCCGGA
Statistics
Matches: 46, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
43 11 0.24
44 3 0.07
45 17 0.37
46 10 0.22
47 5 0.11
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (43 bp):
AAAAAAAAAACAAAAAAAAAACAAAACAAAAAAACAAAACAAA
Found at i:4770 original size:29 final size:29
Alignment explanation
Indices: 4731--4963 Score: 247
Period size: 29 Copynumber: 8.0 Consensus size: 29
4721 TCACCCTTCA
* *
4731 AAAGTCCACAAGTCAGTGGCATATTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
4760 AAAGCCCACAAGTCAGTGGCAAC-CTTTA
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* *
4788 AAAGCCTACAAGTTAGTGGCATCTTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
*
4817 AAAGCCCACAAGTCAGTGGCATTTTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
* *
4847 AAAAGCCCACAAGTCAGTGGCAAC--CTTC
1 -AAAGCCCACAAGTCAGTGGCATCTTTTTC
* *
4875 AAAGCCCACAAATCAGTGGCACCTTTTTCC
1 AAAGCCCACAAGTCAGTGGCATCTTTTT-C
* * *
4905 GAAGCCCACAAGTCGGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
4934 AAAGTCCACAACTCTGTGGCACTCTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
4964 TTTTGTAAAC
Statistics
Matches: 168, Mismatches: 29, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
27 21 0.12
28 26 0.15
29 62 0.37
30 38 0.23
31 21 0.12
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (29 bp):
AAAGCCCACAAGTCAGTGGCATCTTTTTC
Found at i:4818 original size:57 final size:58
Alignment explanation
Indices: 4727--4954 Score: 239
Period size: 57 Copynumber: 3.9 Consensus size: 58
4717 TTCCTCACCC
* *
4727 TTCAAAAGTCCACAAGTCAGTGGCATATTTTTCAAAGCCCACAAGTCAGTGGCAACCT
1 TTCAAAAGCCCACAAGTCAGTGGCATCTTTTTCAAAGCCCACAAGTCAGTGGCAACCT
* * ***
4785 TT-AAAAGCCTACAAGTTAGTGGCATCTTTTTCAAAGCCCACAAGTCAGTGGCATTTTTT
1 TTCAAAAGCCCACAAGTCAGTGGCATCTTTTTCAAAGCCCACAAGTCAGTGGCA--ACCT
* * *
4844 TTCAAAAGCCCACAAGTCAGTGGCAAC--CTTCAAAGCCCACAAATCAGTGGC-ACCTTT
1 TTCAAAAGCCCACAAGTCAGTGGCATCTTTTTCAAAGCCCACAAGTCAGTGGCAACC--T
** * * * * *
4901 TTCCGAAGCCCACAAGTCGGTGGCATCTTTTCCAAAGTCCACAACTCTGTGGCA
1 TTCAAAAGCCCACAAGTCAGTGGCATCTTTTTCAAAGCCCACAAGTCAGTGGCA
4955 CTCTTTTTCT
Statistics
Matches: 138, Mismatches: 24, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
57 71 0.51
58 24 0.17
59 22 0.16
60 21 0.15
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (58 bp):
TTCAAAAGCCCACAAGTCAGTGGCATCTTTTTCAAAGCCCACAAGTCAGTGGCAACCT
Found at i:4910 original size:88 final size:87
Alignment explanation
Indices: 4731--4954 Score: 283
Period size: 88 Copynumber: 2.6 Consensus size: 87
4721 TCACCCTTCA
* * *
4731 AAAGTCCACAAGTCAGTGGCA-TATTTTTCAAAGCCCACAAGTCAGTGGCAACCTTTAAAAGCCT
1 AAAGCCCACAAGTCAGTGGCATTTTTTTTCAAAGCCCACAAGTCAGTGGCAACCTTTAAAAGCCC
* * *
4795 ACAAGTTAGTGGCATCTTTTTC
66 ACAAATCAGTGGCACCTTTTTC
*
4817 AAAGCCCACAAGTCAGTGGCATTTTTTTTCAAAAGCCCACAAGTCAGTGGCAACC-TTCAAAGCC
1 AAAGCCCACAAGTCAGTGGCATTTTTTTTC-AAAGCCCACAAGTCAGTGGCAACCTTTAAAAGCC
4881 CACAAATCAGTGGCACCTTTTTCC
65 CACAAATCAGTGGCACCTTTTT-C
* * * * * * *
4905 GAAGCCCACAAGTCGGTGGCA-TCTTTTCCAAAGTCCACAACTCTGTGGCA
1 AAAGCCCACAAGTCAGTGGCATTTTTTTTCAAAGCCCACAAGTCAGTGGCA
4955 CTCTTTTTCT
Statistics
Matches: 121, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
86 38 0.31
87 39 0.32
88 44 0.36
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (87 bp):
AAAGCCCACAAGTCAGTGGCATTTTTTTTCAAAGCCCACAAGTCAGTGGCAACCTTTAAAAGCCC
ACAAATCAGTGGCACCTTTTTC
Found at i:4910 original size:117 final size:117
Alignment explanation
Indices: 4727--4963 Score: 291
Period size: 117 Copynumber: 2.0 Consensus size: 117
4717 TTCCTCACCC
* ** *
4727 TTCAAAAGTCCACAAGTCAGTGGCATATTTTTCAAAGCCCACAAGTCAGTGGCAACCTTTAAAAG
1 TTCAAAAGCCCACAAGTCAGTGGCATATCCTTCAAAGCCCACAAATCAGTGGCAACCTTTAAAAG
* * * * * *
4792 CCTACAAGTTAGTGGCATCTTTTTCAAAGCCCACAAGTCAGTGGCATTTTTT
66 CCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAACTCAGTGGCACTCTTT
**
4844 TTCAAAAGCCCACAAGTCAGTGGCA-A-CCTTCAAAGCCCACAAATCAGTGGC-ACCTTTTTCCG
1 TTCAAAAGCCCACAAGTCAGTGGCATATCCTTCAAAGCCCACAAATCAGTGGCAACC--TTT-AA
* * *
4906 AAGCCCACAAGTCGGTGGCATCTTTTCCAAAGTCCACAACTCTGTGGCACTCTTT
63 AAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAACTCAGTGGCACTCTTT
4961 TTC
1 TTC
4964 TTTTGTAAAC
Statistics
Matches: 102, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
114 3 0.03
115 22 0.22
116 4 0.04
117 73 0.72
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (117 bp):
TTCAAAAGCCCACAAGTCAGTGGCATATCCTTCAAAGCCCACAAATCAGTGGCAACCTTTAAAAG
CCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAACTCAGTGGCACTCTTT
Found at i:5030 original size:34 final size:36
Alignment explanation
Indices: 4939--5030 Score: 111
Period size: 35 Copynumber: 2.7 Consensus size: 36
4929 TTTCCAAAGT
4939 CCACAACTCT-GTGGCACTCTTTTTCTTTTGTAAAC
1 CCACAACTCTAGTGGCACTCTTTTTCTTTTGTAAAC
* * *
4974 TCACAACTCTA-TAGCACTCTTTTTCTTTT-TAAGC
1 CCACAACTCTAGTGGCACTCTTTTTCTTTTGTAAAC
* *
5008 CCACAAGT-TAGTGGCACCCTTTT
1 CCACAACTCTAGTGGCACTCTTTT
5031 CAAAAGCCCA
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
33 2 0.04
34 20 0.42
35 26 0.54
ACGTcount: A:0.22, C:0.28, G:0.11, T:0.39
Consensus pattern (36 bp):
CCACAACTCTAGTGGCACTCTTTTTCTTTTGTAAAC
Found at i:5220 original size:43 final size:43
Alignment explanation
Indices: 5159--5243 Score: 143
Period size: 43 Copynumber: 2.0 Consensus size: 43
5149 CACTTTCATA
*
5159 TTTAAGTCCAATGTAGCTGACCTTGAATCAGCACATTGGCACC
1 TTTAAGTCCAATATAGCTGACCTTGAATCAGCACATTGGCACC
* *
5202 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 TTTAAGTCCAATATAGCTGACCTTGAATCAGCACATTGGCAC
5244 ATTTTCCATC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (43 bp):
TTTAAGTCCAATATAGCTGACCTTGAATCAGCACATTGGCACC
Found at i:5242 original size:92 final size:94
Alignment explanation
Indices: 5108--5290 Score: 298
Period size: 92 Copynumber: 2.0 Consensus size: 94
5098 TGGCACCTTG
*
5108 CCTTTAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGGCAC-TTT-CATATTTAAGTCCAAT
1 CCTTTAAGTCCAATATAGCTGGCCTTAAATCAGCATATTGGCACATTTCCATATTTAAGTCCAAT
5171 GTAGCTGACCTTGAATCAGCACATTGGCA
66 GTAGCTGACCTTGAATCAGCACATTGGCA
* * *
5200 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAGTTCAA
1 CCTTTAAGTCCAATATAGCTGGCCTTAAATCAGCATATTGGCACA-TTTCCATATTTAAGTCCAA
*
5265 TGTAGCTGGCCTTGAATCAGCACATT
65 TGTAGCTGACCTTGAATCAGCACATT
5291 TACATCCTTT
Statistics
Matches: 83, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
92 42 0.51
94 3 0.04
95 38 0.46
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.33
Consensus pattern (94 bp):
CCTTTAAGTCCAATATAGCTGGCCTTAAATCAGCATATTGGCACATTTCCATATTTAAGTCCAAT
GTAGCTGACCTTGAATCAGCACATTGGCA
Found at i:5271 original size:52 final size:54
Alignment explanation
Indices: 5201--5349 Score: 176
Period size: 52 Copynumber: 2.8 Consensus size: 54
5191 ACATTGGCAC
5201 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CATTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCATTTTCTCAT
* * * ** *
5253 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTTACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CCATTTTCTCAT
* * * * *
5308 CTTTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA
5350 TCTTTATCAC
Statistics
Matches: 78, Mismatches: 16, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
52 37 0.47
54 6 0.08
55 35 0.45
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.35
Consensus pattern (54 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCATTTTCTCAT
Found at i:6174 original size:13 final size:13
Alignment explanation
Indices: 6156--6180 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6146 CATAAAGTGT
6156 TGTATCGATACAA
1 TGTATCGATACAA
6169 TGTATCGATACA
1 TGTATCGATACA
6181 TGTTTTTTTG
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:6240 original size:13 final size:13
Alignment explanation
Indices: 6222--6246 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6212 TGCCAAAAAA
6222 TGTATCGATACAT
1 TGTATCGATACAT
6235 TGTATCGATACA
1 TGTATCGATACA
6247 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:6313 original size:52 final size:52
Alignment explanation
Indices: 6235--6429 Score: 251
Period size: 52 Copynumber: 3.9 Consensus size: 52
6225 ATCGATACAT
**
6235 TGTATCGATACACTGA-TCTTTGTATCGATACATGCAGGCAAATTTGCCTAGA
1 TGTATCGATACACT-ATTCAATGTATCGATACATGCAGGCAAATTTGCCTAGA
* *
6287 TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTT-TC-ATA
1 TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTTGCCTAGA
** * * *
6337 T-T-TCG--GGACTTTTTAGTGTATCGATACATGCAGGCAAATTTGCCTAGA
1 TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTTGCCTAGA
6385 TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTT
6430 TCATATTTCG
Statistics
Matches: 120, Mismatches: 16, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
46 31 0.26
47 1 0.01
48 6 0.05
49 2 0.02
50 6 0.05
51 2 0.02
52 72 0.60
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (52 bp):
TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTTGCCTAGA
Found at i:6359 original size:98 final size:98
Alignment explanation
Indices: 6255--6448 Score: 388
Period size: 98 Copynumber: 2.0 Consensus size: 98
6245 CACTGATCTT
6255 TGTATCGATACATGCAGGCAAATTTGCCTAGATGTATCGATACACTATTCAATGTATCGATACAT
1 TGTATCGATACATGCAGGCAAATTTGCCTAGATGTATCGATACACTATTCAATGTATCGATACAT
6320 GCAGGCAAATTTTCATATTTCGGGACTTTTTAG
66 GCAGGCAAATTTTCATATTTCGGGACTTTTTAG
6353 TGTATCGATACATGCAGGCAAATTTGCCTAGATGTATCGATACACTATTCAATGTATCGATACAT
1 TGTATCGATACATGCAGGCAAATTTGCCTAGATGTATCGATACACTATTCAATGTATCGATACAT
6418 GCAGGCAAATTTTCATATTTCGGGACTTTTT
66 GCAGGCAAATTTTCATATTTCGGGACTTTTT
6449 CTTCCTTTTC
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 96 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (98 bp):
TGTATCGATACATGCAGGCAAATTTGCCTAGATGTATCGATACACTATTCAATGTATCGATACAT
GCAGGCAAATTTTCATATTTCGGGACTTTTTAG
Found at i:6374 original size:46 final size:46
Alignment explanation
Indices: 6305--6448 Score: 171
Period size: 46 Copynumber: 3.0 Consensus size: 46
6295 TACACTATTC
6305 AATGTATCGATACATGCAGGCAAATTTTCATATTTCGGGACTTTTT
1 AATGTATCGATACATGCAGGCAAATTTTCATATTTCGGGACTTTTT
* * * ** * *
6351 AGTGTATCGATACATGCAGGCAAATTTGCCTAGATGTATCGATACACTATTC
1 AATGTATCGATACATGCAGGCAAATTT-TC-ATAT-T-TCG--GGACTTTTT
6403 AATGTATCGATACATGCAGGCAAATTTTCATATTTCGGGACTTTTT
1 AATGTATCGATACATGCAGGCAAATTTTCATATTTCGGGACTTTTT
6449 CTTCCTTTTC
Statistics
Matches: 78, Mismatches: 14, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
46 31 0.40
47 1 0.01
48 6 0.08
49 2 0.03
50 6 0.08
51 1 0.01
52 31 0.40
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (46 bp):
AATGTATCGATACATGCAGGCAAATTTTCATATTTCGGGACTTTTT
Found at i:13683 original size:24 final size:25
Alignment explanation
Indices: 13656--13710 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
13646 TACCATAACG
*
13656 TTAAATAAATTTAAAATTTT-AATT
1 TTAAATAAATATAAAATTTTCAATT
* * *
13680 TTAAATATATATAATATTTTCATTT
1 TTAAATAAATATAAAATTTTCAATT
13705 TTAAAT
1 TTAAAT
13711 TATAATTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 17 0.65
25 9 0.35
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (25 bp):
TTAAATAAATATAAAATTTTCAATT
Found at i:14281 original size:16 final size:17
Alignment explanation
Indices: 14260--14291 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
14250 TATTATAATA
14260 TTATAT-ATATAAATTT
1 TTATATAATATAAATTT
14276 TTATATAATATAAATT
1 TTATATAATATAAATT
14292 ATATAATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTATATAATATAAATTT
Found at i:14293 original size:14 final size:14
Alignment explanation
Indices: 14253--14301 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 14
14243 TTATTCATAT
14253 TATAATATTATAT-A
1 TATAA-ATTATATAA
14267 TATAAATTTTTATATAA
1 TATAAA---TTATATAA
14284 TATAAATTATATAA
1 TATAAATTATATAA
14298 TATA
1 TATA
14302 TGTAAATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
13 1 0.03
14 17 0.55
16 6 0.19
17 7 0.23
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TATAAATTATATAA
Found at i:17376 original size:13 final size:13
Alignment explanation
Indices: 17358--17390 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
17348 TCTTTAACAT
17358 ATATATAATGTTA
1 ATATATAATGTTA
*
17371 ATATATAATTTTA
1 ATATATAATGTTA
17384 ATATATA
1 ATATATA
17391 TCTAATATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (13 bp):
ATATATAATGTTA
Found at i:18198 original size:18 final size:19
Alignment explanation
Indices: 18177--18219 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
18167 TTAAAATGTT
*
18177 ATTTTTTAATTTTTATT-A
1 ATTTTGTAATTTTTATTAA
*
18195 ATTTTGTATTTTTTATTAA
1 ATTTTGTAATTTTTATTAA
18214 ATTTTG
1 ATTTTG
18220 ACTTATCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.70
Consensus pattern (19 bp):
ATTTTGTAATTTTTATTAA
Found at i:18302 original size:5 final size:5
Alignment explanation
Indices: 18292--18316 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
18282 ACATAAATAA
18292 TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT
18317 AATTAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:18511 original size:18 final size:17
Alignment explanation
Indices: 18482--18552 Score: 63
Period size: 18 Copynumber: 4.1 Consensus size: 17
18472 GATCTAAAAT
18482 TAAATTTA-TTTTTAAA
1 TAAATTTATTTTTTAAA
**
18498 TAAATTTTATTTTTTATT
1 TAAA-TTTATTTTTTAAA
*
18516 TAAATTTATTTTTATAAT
1 TAAATTTATTTTT-TAAA
* *
18534 TTAATATTATTATTTAAA
1 TAAAT-TTATTTTTTAAA
18552 T
1 T
18553 TATATAAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
16 4 0.09
17 13 0.29
18 21 0.47
19 7 0.16
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TAAATTTATTTTTTAAA
Found at i:18543 original size:19 final size:18
Alignment explanation
Indices: 18478--18553 Score: 61
Period size: 17 Copynumber: 4.3 Consensus size: 18
18468 GTTAGATCTA
*
18478 AAATTAAAT-TTATTTTT
1 AAATTTAATATTATTTTT
* *
18495 AAA-TAAATTTTATTTTT
1 AAATTTAATATTATTTTT
*
18512 -TATTTAA-ATTTATTTTT
1 AAATTTAATA-TTATTTTT
18529 ATAATTTAATATTATTATTT
1 A-AATTTAATATTATT-TTT
18549 AAATT
1 AAATT
18554 ATATAAAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
16 6 0.12
17 22 0.46
19 15 0.31
20 5 0.10
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
AAATTTAATATTATTTTT
Found at i:19724 original size:23 final size:24
Alignment explanation
Indices: 19683--19729 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
19673 AAAATAAAAT
*
19683 TATAACTATTCTTATAAAAATATA
1 TATAACTATTATTATAAAAATATA
19707 TATAACTA-TATTATAAAAATATA
1 TATAACTATTATTATAAAAATATA
19730 AATTTTATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.40
Consensus pattern (24 bp):
TATAACTATTATTATAAAAATATA
Found at i:24680 original size:19 final size:18
Alignment explanation
Indices: 24651--24711 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 18
24641 ATAATAATTT
*
24651 ATTTTATAAATTA-AAATA
1 ATTTT-TAAAATATAAATA
*
24669 ATTTTTACAAATATAATTA
1 ATTTTTA-AAATATAAATA
*
24688 ATTTATAAAAATATAAATA
1 ATTT-TTAAAATATAAATA
24707 ATTTT
1 ATTTT
24712 GTTTACTTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
17 2 0.06
18 10 0.28
19 22 0.61
20 2 0.06
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTTTTAAAATATAAATA
Found at i:31559 original size:2 final size:2
Alignment explanation
Indices: 31543--31578 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
31533 AACAATTATG
*
31543 TA TA CA TA T- TA 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 TA TA TA T
31579 TCACATATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:33159 original size:16 final size:16
Alignment explanation
Indices: 33138--33168 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
33128 TATATCTTTA
*
33138 TTATATGTAAATATAT
1 TTATATATAAATATAT
33154 TTATATATAAATATA
1 TTATATATAAATATA
33169 AGTTCTAAAA
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:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (16 bp):
TTATATATAAATATAT
Found at i:33797 original size:29 final size:30
Alignment explanation
Indices: 33747--33804 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
33737 AAGTATTATT
*
33747 TAATTAAAAATATTTTTATTT-ATATTTAA
1 TAATTAAAAATATATTTATTTAATATTTAA
*
33776 TAATATAAAAATA-ATTTCTTTAATATTTA
1 TAAT-TAAAAATATATTTATTTAATATTTA
33805 TGAATAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (30 bp):
TAATTAAAAATATATTTATTTAATATTTAA
Found at i:34025 original size:15 final size:15
Alignment explanation
Indices: 33979--34027 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 15
33969 GAATAAAGCG
33979 TTTTAATTTTT-TAT
1 TTTTAATTTTTATAT
* *
33993 TATTAGA-TTTAATA-
1 TTTTA-ATTTTTATAT
34007 TTTTAATTTTTATAT
1 TTTTAATTTTTATAT
34022 TTTTAA
1 TTTTAA
34028 AATTATAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 7
0.71 0.11 0.18
Matches are distributed among these distances:
13 1 0.04
14 17 0.63
15 9 0.33
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (15 bp):
TTTTAATTTTTATAT
Found at i:34046 original size:17 final size:19
Alignment explanation
Indices: 34026--34071 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 19
34016 TTATATTTTT
34026 AAAATTATAATAA-A-TAA
1 AAAATTATAATAATATTAA
*
34043 AAAATAATTAATAATATTAA
1 AAAATTA-TAATAATATTAA
34063 ATAAATTAT
1 A-AAATTAT
34072 TTAAATATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
17 6 0.26
18 6 0.26
19 1 0.04
20 5 0.22
21 5 0.22
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAATTATAATAATATTAA
Found at i:34063 original size:20 final size:19
Alignment explanation
Indices: 34040--34095 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 19
34030 TTATAATAAA
34040 TAAAAAATAATTAATAATAT
1 TAAAAAAT-ATTAATAATAT
*
34060 TAAATAAATTATTTA-AATAT
1 TAAA-AAA-TATTAATAATAT
34080 TAATAAAATATTAATA
1 TAA-AAAATATTAATA
34096 TTTTTTATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
19 5 0.17
20 16 0.53
21 8 0.27
22 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TAAAAAATATTAATAATAT
Found at i:34242 original size:22 final size:21
Alignment explanation
Indices: 34192--34270 Score: 71
Period size: 19 Copynumber: 4.0 Consensus size: 21
34182 TTATATTACG
*
34192 TAATATATT-AAT-ATTTTAT
1 TAATATATTAAATAATTTTTT
34211 TAATAT-TTAAATAATTTTTT
1 TAATATATTAAATAATTTTTT
*
34231 TAATATAATTAATTAATTATTTT
1 TAATAT-ATTAAATAATT-TTTT
*
34254 T-ATTTATT--ATAATTTTT
1 TAATATATTAAATAATTTTT
34271 AAAATATAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
18 5 0.10
19 14 0.27
20 12 0.24
21 3 0.06
22 12 0.24
23 5 0.10
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TAATATATTAAATAATTTTTT
Found at i:34301 original size:41 final size:41
Alignment explanation
Indices: 34221--34303 Score: 98
Period size: 41 Copynumber: 2.0 Consensus size: 41
34211 TAATATTTAA
** * *
34221 ATAATTTTTTTAATATAATTAATTAATTATTTTTATTTATT
1 ATAATTTTTAAAATATAATAAATTAAATATTTTTATTTATT
34262 ATAATTTTTAAAATATAA-AAATTAAAATATATTTT-TTTATT
1 ATAATTTTTAAAATATAATAAATT-AAATAT-TTTTATTTATT
34303 A
1 A
34304 CAACATAAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
40 4 0.11
41 28 0.78
42 4 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (41 bp):
ATAATTTTTAAAATATAATAAATTAAATATTTTTATTTATT
Found at i:34794 original size:20 final size:20
Alignment explanation
Indices: 34769--34811 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
34759 TTGAAAAAAA
*
34769 AATTATAATTT-ATATATTAT
1 AATTAT-ATTTAAAATATTAT
34789 AATTATATTTAAAATATTAT
1 AATTATATTTAAAATATTAT
34809 AAT
1 AAT
34812 ATTTATATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AATTATATTTAAAATATTAT
Found at i:35115 original size:30 final size:31
Alignment explanation
Indices: 35045--35115 Score: 76
Period size: 30 Copynumber: 2.3 Consensus size: 31
35035 TAAAAAATTA
* * *
35045 ATAATATATTTTTTAGTTTTTTAAATTTATTT
1 ATAATA-ATTTTTTAATTTATTAAATTTATCT
35077 ATAA-AATTTTTTAATTTATT-AATTT-TCT
1 ATAATAATTTTTTAATTTATTAAATTTATCT
35105 ATTAATAATTT
1 A-TAATAATTT
35116 ATATCATTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
28 3 0.09
29 8 0.24
30 18 0.53
31 1 0.03
32 4 0.12
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (31 bp):
ATAATAATTTTTTAATTTATTAAATTTATCT
Found at i:37907 original size:2 final size:2
Alignment explanation
Indices: 37889--37927 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
37879 TATACAAGTC
* *
37889 TA TA TA CA TA TA CA 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 TA TA TA TA T
37928 TTCTATTAGC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:39429 original size:2 final size:2
Alignment explanation
Indices: 39422--39486 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
39412 AAATTTCAAA
39422 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39464 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
39487 AGACTCAACC
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:40701 original size:22 final size:22
Alignment explanation
Indices: 40660--40701 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
40650 AATAATAATT
*
40660 TAATTTTAACACTAATTAAAAA
1 TAATTTTAACACTAACTAAAAA
* *
40682 TAATTTTAAGATTAACTAAA
1 TAATTTTAACACTAACTAAA
40702 TCTAATTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.38
Consensus pattern (22 bp):
TAATTTTAACACTAACTAAAAA
Found at i:41205 original size:12 final size:12
Alignment explanation
Indices: 41188--41219 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
41178 CATGGAGTGG
41188 AGAGCAATGTGT
1 AGAGCAATGTGT
41200 AGAGCAATGTGT
1 AGAGCAATGTGT
*
41212 GGAGCAAT
1 AGAGCAAT
41220 TTACCTCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.34, C:0.09, G:0.34, T:0.22
Consensus pattern (12 bp):
AGAGCAATGTGT
Found at i:42392 original size:3 final size:3
Alignment explanation
Indices: 42381--42428 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
42371 ATGATGATGC
*
42381 TAA TCA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
42429 AGCAATTTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:47826 original size:20 final size:20
Alignment explanation
Indices: 47801--47851 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
47791 CCACAAATAC
47801 AATATATTTAATATAAAAAT
1 AATATATTTAATATAAAAAT
* * * *
47821 AATATAATAAATATTAATAT
1 AATATATTTAATATAAAAAT
*
47841 AATGTATTTAA
1 AATATATTTAA
47852 ATACGATTAA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
AATATATTTAATATAAAAAT
Found at i:48033 original size:24 final size:25
Alignment explanation
Indices: 47990--48052 Score: 78
Period size: 24 Copynumber: 2.6 Consensus size: 25
47980 TTAAGCATAA
*
47990 ATATTATATGTATA-TTAAATATGTC
1 ATATTATAT-TATATTTAAATATATC
*
48015 ATATTA-ATTATATTTAAATATATT
1 ATATTATATTATATTTAAATATATC
48039 ATATTATATT-TATT
1 ATATTATATTATATT
48053 ATATTATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
23 4 0.12
24 21 0.62
25 9 0.26
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (25 bp):
ATATTATATTATATTTAAATATATC
Found at i:48054 original size:9 final size:9
Alignment explanation
Indices: 48015--48073 Score: 55
Period size: 9 Copynumber: 6.1 Consensus size: 9
48005 TAAATATGTC
*
48015 ATATTAATT
1 ATATTTATT
*
48024 ATATTTAAAT
1 ATATTT-ATT
48034 ATATTATATT
1 ATATT-TATT
48044 ATATTTATT
1 ATATTTATT
*
48053 ATATTATTTTT
1 ATA-T-TTATT
48064 ATATTTATT
1 ATATTTATT
48073 A
1 A
48074 AGTATCACAT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
9 17 0.41
10 16 0.39
11 8 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (9 bp):
ATATTTATT
Found at i:48054 original size:14 final size:14
Alignment explanation
Indices: 47991--48065 Score: 60
Period size: 14 Copynumber: 5.2 Consensus size: 14
47981 TAAGCATAAA
47991 TATTATATGTATATT
1 TATTATAT-TATATT
* * * *
48006 AAATATGTCATATT
1 TATTATATTATATT
* * *
48020 AATTATATTTAAATA
1 TATTATA-TTATATT
48035 TATTATATTATATT
1 TATTATATTATATT
*
48049 TATTATATTATTTT
1 TATTATATTATATT
48063 TAT
1 TAT
48066 ATTTATTAAG
Statistics
Matches: 46, Mismatches: 13, Indels: 3
0.74 0.21 0.05
Matches are distributed among these distances:
14 31 0.67
15 15 0.33
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (14 bp):
TATTATATTATATT
Found at i:48071 original size:20 final size:19
Alignment explanation
Indices: 47991--48073 Score: 78
Period size: 20 Copynumber: 4.3 Consensus size: 19
47981 TAAGCATAAA
* *
47991 TATTATATGTATATTAAATA
1 TATTATAT-TATATTATATT
* *
48011 TGTCATATTA-ATTATATT
1 TATTATATTATATTATATT
*
48029 TAAATATATTATATTATATT
1 T-ATTATATTATATTATATT
*
48049 TATTATATTATTTTTATATT
1 TATTATATTA-TATTATATT
48069 TATTA
1 TATTA
48074 AGTATCACAT
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
18 7 0.14
19 16 0.31
20 28 0.55
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.58
Consensus pattern (19 bp):
TATTATATTATATTATATT
Found at i:48449 original size:32 final size:31
Alignment explanation
Indices: 48413--48481 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 31
48403 AATAATAAGA
*
48413 ATATATATGAGAA-TATAAATATTTTAAAATTT
1 ATATATAT-A-AATTATAAATATATTAAAATTT
*
48445 ATATAATATAAATTATTAATATATTAAAATTT
1 ATAT-ATATAAATTATAAATATATTAAAATTT
48477 ATATA
1 ATATA
48482 AATATAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
31 3 0.09
32 26 0.79
33 4 0.12
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (31 bp):
ATATATATAAATTATAAATATATTAAAATTT
Found at i:48766 original size:16 final size:18
Alignment explanation
Indices: 48735--48768 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
48725 AAATTATATC
48735 AAATAATTATATTATTTA
1 AAATAATTATATTATTTA
48753 AAAT-ATTA-ATTATTTA
1 AAATAATTATATTATTTA
48769 TTATATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 4 0.25
18 4 0.25
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AAATAATTATATTATTTA
Found at i:48777 original size:23 final size:24
Alignment explanation
Indices: 48744--48799 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
48734 CAAATAATTA
*
48744 TATTATTTAAAAT-ATTAATTATT
1 TATTATATAAAATAATTAATTATT
*
48767 TATTATAT-AAATAATTAATTTTT
1 TATTATATAAAATAATTAATTATT
*
48790 TAATATATAA
1 TATTATATAA
48800 TTAAATAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.14
23 23 0.82
24 1 0.04
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TATTATATAAAATAATTAATTATT
Found at i:48781 original size:19 final size:19
Alignment explanation
Indices: 48727--48802 Score: 66
Period size: 19 Copynumber: 3.8 Consensus size: 19
48717 TATCGTTTAA
48727 ATTATATCAAATAATTATATT
1 ATTATAT-AAATAATTAT-TT
*
48748 ATT-TAAAATATTAATTATTT
1 ATTATATAA-A-TAATTATTT
48768 ATTATATAAATAATTAATTT
1 ATTATATAAATAATT-ATTT
* *
48788 TTTA-ATATATAATTA
1 ATTATATAAATAATTA
48803 AATAATATAG
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
18 1 0.02
19 16 0.34
20 16 0.34
21 14 0.30
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (19 bp):
ATTATATAAATAATTATTT
Found at i:48808 original size:23 final size:23
Alignment explanation
Indices: 48735--48817 Score: 64
Period size: 23 Copynumber: 3.6 Consensus size: 23
48725 AAATTATATC
*
48735 AAATAATTATATT-ATTTA-AAAT
1 AAATAATTAT-TTAATATATAAAT
* *
48757 -ATTAATTATTTATTATATAAAT
1 AAATAATTATTTAATATATAAAT
* * *
48779 AATTAATTTTTTAATATATAATT
1 AAATAATTATTTAATATATAAAT
48802 AAATAATATAGTTTAA
1 AAATAAT-TA-TTTAA
48818 ATAAAAAATT
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
20 2 0.04
21 11 0.23
22 4 0.08
23 25 0.52
24 1 0.02
25 5 0.10
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (23 bp):
AAATAATTATTTAATATATAAAT
Found at i:49279 original size:14 final size:13
Alignment explanation
Indices: 49235--49282 Score: 55
Period size: 14 Copynumber: 3.7 Consensus size: 13
49225 TTAGTTTAAA
49235 TTTAAATTTAA-T
1 TTTAAATTTAATT
*
49247 TTT-AATATAATAT
1 TTTAAATTTAAT-T
49260 TTTAAATTTAATT
1 TTTAAATTTAATT
49273 TTATAAATTT
1 TT-TAAATTT
49283 TTATTAACTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
11 6 0.20
12 3 0.10
13 7 0.23
14 14 0.47
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TTTAAATTTAATT
Found at i:49767 original size:20 final size:19
Alignment explanation
Indices: 49722--49766 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 19
49712 TGAGAATCAG
49722 AAAAAGAAAGAGAAAGGAA
1 AAAAAGAAAGAGAAAGGAA
*
49741 AGAAAAGAATGAGGAAAGAGAA
1 A-AAAAGAAAGA-GAAAG-GAA
49763 AAAA
1 AAAA
49767 GTAAAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 1 0.05
20 9 0.41
21 8 0.36
22 4 0.18
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (19 bp):
AAAAAGAAAGAGAAAGGAA
Found at i:50755 original size:20 final size:21
Alignment explanation
Indices: 50686--50756 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
50676 AAAATATGTA
* * *
50686 TTTGGATAAAATAATACAATG
1 TTTGAATAAAAAAATACAATT
* * *
50707 GTTGAATAAAAGAATACACTT
1 TTTGAATAAAAAAATACAATT
*
50728 TTTGAATAAAAAAATATAATT
1 TTTGAATAAAAAAATACAATT
50749 TTT-AATAA
1 TTTGAATAA
50757 TCAAAAGTTG
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
20 5 0.12
21 36 0.88
ACGTcount: A:0.51, C:0.04, G:0.10, T:0.35
Consensus pattern (21 bp):
TTTGAATAAAAAAATACAATT
Found at i:51727 original size:22 final size:22
Alignment explanation
Indices: 51702--51744 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
51692 TTTAAAAAAA
51702 ATATTTTTAT-ATTAATATTTAC
1 ATATTTTTATAATTAA-ATTTAC
51724 ATATTTTTATAATTAAATTTA
1 ATATTTTTATAATTAAATTTA
51745 AATAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
ATATTTTTATAATTAAATTTAC
Found at i:52548 original size:21 final size:21
Alignment explanation
Indices: 52520--52577 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
52510 AAAAAAATTC
*
52520 CAAATGTATCGATACATTTGTA
1 CAAATGTATCGATACA-TTCTA
*
52542 -GAATGTATCGATACATTCTA
1 CAAATGTATCGATACATTCTA
52562 CAAATGTATCGATACA
1 CAAATGTATCGATACA
52578 GGGTCCCAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.12
21 28 0.88
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.33
Consensus pattern (21 bp):
CAAATGTATCGATACATTCTA
Found at i:52637 original size:19 final size:19
Alignment explanation
Indices: 52613--52712 Score: 107
Period size: 19 Copynumber: 5.9 Consensus size: 19
52603 AATTCAACGA
52613 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
52632 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
52647 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
52664 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
52679 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
52696 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
52713 TTAGCTACTG
Statistics
Matches: 69, Mismatches: 0, Indels: 24
0.74 0.00 0.26
Matches are distributed among these distances:
13 22 0.32
15 4 0.06
17 4 0.06
19 39 0.57
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:52651 original size:32 final size:32
Alignment explanation
Indices: 52615--52709 Score: 181
Period size: 32 Copynumber: 3.0 Consensus size: 32
52605 TTCAACGATT
52615 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTTTTGTATCGATACAA
52647 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTTTTGTATCGATACAA
*
52679 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTTTTGTATCGATACA
52710 TAATTAGCTA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 62 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTTTTGTATCGATACAA
Found at i:52652 original size:13 final size:13
Alignment explanation
Indices: 52634--52690 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
52624 ACATAAGTTT
52634 TGTATCGATACAA
1 TGTATCGATACAA
52647 TGTATCGATACATAA
1 TGTATCGATAC--AA
52662 GTTTTGTATCGATACAA
1 ----TGTATCGATACAA
52679 TGTATCGATACA
1 TGTATCGATACA
52691 TAAGTATTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:52770 original size:13 final size:13
Alignment explanation
Indices: 52752--52777 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
52742 CATTTTTCTG
52752 TGTATCGATACAT
1 TGTATCGATACAT
52765 TGTATCGATACAT
1 TGTATCGATACAT
52778 GGATCTTTGT
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:52774 original size:33 final size:33
Alignment explanation
Indices: 52732--52798 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
52722 GCCAAGGAAA
***
52732 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
52765 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
52798 T
1 T
52799 TGGAAATTTT
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:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:55304 original size:27 final size:26
Alignment explanation
Indices: 55246--55315 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 26
55236 CTTCACAATT
*
55246 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCA-C
*
55273 GGGGATACTCCAACCCCGTTATTTC-C
1 GGGGATACTCCAACCCCGTTA-ATCAC
55299 GAGGGAATACTCCAACC
1 G-GGG-ATACTCCAACC
55316 TCGACTTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
26 2 0.05
27 23 0.61
28 13 0.34
ACGTcount: A:0.26, C:0.34, G:0.20, T:0.20
Consensus pattern (26 bp):
GGGGATACTCCAACCCCGTTAATCAC
Found at i:55364 original size:51 final size:51
Alignment explanation
Indices: 55305--55472 Score: 201
Period size: 51 Copynumber: 3.3 Consensus size: 51
55295 TTCCGAGGGA
* *
55305 ATACTCCAACCTCGACTTTATTTCCAAAATATTGATTTTTCATAATCGGGG
1 ATACTCCAACCCCGGCTTTATTTCCAAAATATTGATTTTTCATAATCGGGG
* * * *** * *
55356 ATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGG
1 ATACTCCAACCCCGGCTTTATTTCCAAAATATTGATTTTTC-ATAATCGGGG
* * * *
55408 ATACTCCAACCCCGGCTTTATTCCCAAAATATTGATTTCTCATTATTGGGG
1 ATACTCCAACCCCGGCTTTATTTCCAAAATATTGATTTTTCATAATCGGGG
55459 ATACTCCAACCCCG
1 ATACTCCAACCCCG
55473 TTATTTTCGA
Statistics
Matches: 94, Mismatches: 22, Indels: 2
0.80 0.19 0.02
Matches are distributed among these distances:
51 53 0.56
52 41 0.44
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.34
Consensus pattern (51 bp):
ATACTCCAACCCCGGCTTTATTTCCAAAATATTGATTTTTCATAATCGGGG
Found at i:62290 original size:17 final size:17
Alignment explanation
Indices: 62268--62301 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
62258 CAGAGGTAAG
*
62268 AAGGAAGGCAAAGTCAA
1 AAGGAAGCCAAAGTCAA
*
62285 AAGGAAGCCACAGTCAA
1 AAGGAAGCCAAAGTCAA
62302 GAATCGATGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.18, G:0.26, T:0.06
Consensus pattern (17 bp):
AAGGAAGCCAAAGTCAA
Done.