Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1265
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: 436287
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
File 3 of 3
Found at i:345660 original size:14 final size:14
Alignment explanation
Indices: 345642--345723 Score: 103
Period size: 14 Copynumber: 5.6 Consensus size: 14
345632 TGATGAAAAA
345642 AAAAAACAAACAAAC
1 AAAAAA-AAACAAAC
*
345657 AAAAAAAAACACAC
1 AAAAAAAAACAAAC
345671 AAAAAAAAAC-AAC
1 AAAAAAAAACAAAC
*
345684 AAAAAACACAAAAAAC
1 AAAAAA-A-AACAAAC
345700 AAAAAAAAACAAAC
1 AAAAAAAAACAAAC
345714 ACAAAAAAAA
1 A-AAAAAAAA
345724 GTGCAAAGGT
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
13 8 0.14
14 25 0.42
15 17 0.29
16 9 0.15
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAAAAACAAAC
Found at i:345680 original size:24 final size:24
Alignment explanation
Indices: 345653--345723 Score: 94
Period size: 24 Copynumber: 3.1 Consensus size: 24
345643 AAAAACAAAC
345653 AAACAAAAAAAAACACACAAAAAA
1 AAACAAAAAAAAACACACAAAAAA
* *
345677 AAACAACAAAAAACACA-AAAAAC
1 AAACAAAAAAAAACACACAAAAAA
*
345700 AAA-AAAAAACAA-ACACAAAAAA
1 AAACAAAAAAAAACACACAAAAAA
345722 AA
1 AA
345724 GTGCAAAGGT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
21 3 0.07
22 14 0.34
23 8 0.20
24 16 0.39
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (24 bp):
AAACAAAAAAAAACACACAAAAAA
Found at i:345702 original size:43 final size:45
Alignment explanation
Indices: 345640--345723 Score: 136
Period size: 44 Copynumber: 1.9 Consensus size: 45
345630 AGTGATGAAA
*
345640 AAAAAAAACAAACAAACAAAAAAAAACACACA-AAAAAAAACAAC
1 AAAAAAAACAAACAAACAAAAAAAAACAAACACAAAAAAAACAAC
*
345684 AAAAAACACAAA-AAACAAAAAAAAACAAACACAAAAAAAA
1 AAAAAAAACAAACAAACAAAAAAAAACAAACACAAAAAAAA
345724 GTGCAAAGGT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
43 18 0.49
44 19 0.51
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (45 bp):
AAAAAAAACAAACAAACAAAAAAAAACAAACACAAAAAAAACAAC
Found at i:345706 original size:10 final size:10
Alignment explanation
Indices: 345639--345712 Score: 80
Period size: 10 Copynumber: 7.3 Consensus size: 10
345629 AAGTGATGAA
345639 AAAAAAAAAC
1 AAAAAAAAAC
345649 AAACAAACAAA-
1 AAA-AAA-AAAC
*
345660 AAAAAACACAC
1 AAAAAA-AAAC
345671 AAAAAAAAAC
1 AAAAAAAAAC
*
345681 AACAAAAAAC
1 AAAAAAAAAC
*
345691 -ACAAAAAAC
1 AAAAAAAAAC
345700 AAAAAAAAAC
1 AAAAAAAAAC
345710 AAA
1 AAA
345713 CACAAAAAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
9 9 0.16
10 32 0.57
11 12 0.21
12 3 0.05
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:345717 original size:6 final size:6
Alignment explanation
Indices: 345637--345720 Score: 52
Period size: 6 Copynumber: 13.8 Consensus size: 6
345627 AGAAGTGATG
*
345637 AAAAAA AAAAAC AAACAAAC AAAAA- AAAACAC ACAAAA- AAAAAC AACAAA-
1 AAAAAC AAAAAC -AA-AAAC AAAAAC AAAA-AC A-AAAAC AAAAAC AA-AAAC
* *
345687 AAACAC AAAAA- ACAAAA- AAAAAC AAACAC AAAAA
1 AAAAAC AAAAAC A-AAAAC AAAAAC AAAAAC AAAAA
345721 AAAGTGCAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
5 15 0.24
6 32 0.51
7 9 0.14
8 7 0.11
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:345745 original size:47 final size:42
Alignment explanation
Indices: 345641--345723 Score: 130
Period size: 43 Copynumber: 1.9 Consensus size: 42
345631 GTGATGAAAA
*
345641 AAAAAAACAAACAAACAAAAAAAAACACACAAAAAAAAACAAC
1 AAAAAAACAAA-AAACAAAAAAAAACAAACAAAAAAAAACAAC
345684 AAAAAACACAAAAAACAAAAAAAAACAAACACAAAAAAAA
1 AAAAAA-ACAAAAAACAAAAAAAAACAAACA-AAAAAAAA
345724 GTGCAAAGGT
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
43 24 0.65
44 13 0.35
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (42 bp):
AAAAAAACAAAAAACAAAAAAAAACAAACAAAAAAAAACAAC
Found at i:346998 original size:31 final size:30
Alignment explanation
Indices: 346960--347137 Score: 218
Period size: 32 Copynumber: 5.7 Consensus size: 30
346950 AAAAAAAAAG
346960 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
1 AAAGTCCACGACTCAGTGGC-ATCTCTTCTC
*
346991 AAAGTCCACGACTCAGTGGCAATCTCTACTC
1 AAAGTCCACGACTCAGTGGC-ATCTCTTCTC
*
347022 AAAGTCCACGACGCAGTGGCATC-CTTCTC
1 AAAGTCCACGACTCAGTGGCATCTCTTCTC
*
347051 TTTAAAGTCCACGACGCAGTGGCATC-CTTCTC
1 ---AAAGTCCACGACTCAGTGGCATCTCTTCTC
*
347083 TTTAAAGTCCACGACTCAGTGGCAT-TTTGTCTC
1 ---AAAGTCCACGACTCAGTGGCATCTCT-TCTC
347116 AAAGTCCACGACTCAGTGGCAT
1 AAAGTCCACGACTCAGTGGCAT
347138 TTTCTTTTTA
Statistics
Matches: 137, Mismatches: 5, Indels: 11
0.90 0.03 0.07
Matches are distributed among these distances:
29 5 0.04
30 25 0.18
31 49 0.36
32 54 0.39
33 4 0.03
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (30 bp):
AAAGTCCACGACTCAGTGGCATCTCTTCTC
Found at i:347074 original size:94 final size:91
Alignment explanation
Indices: 346960--347155 Score: 259
Period size: 94 Copynumber: 2.1 Consensus size: 91
346950 AAAAAAAAAG
*
346960 AAAGTCCACGACTCAGTGGCAATCTCTTCTC-AAAGTCCACGACTCAGTGGCAATCTCTACTCAA
1 AAAGTCCACGACGCAGTGGC-ATC-CTTCTCTAAAGTCCACGACTCAGTGGCAATCTCT-CTCAA
347024 AGTCCACGACGCAGTGGCATCCTTCTCTTT
63 AGTCCACGACGCAGTGGCAT-CTTCTCTTT
* * *
347054 AAAGTCCACGACGCAGTGGCATCCTTCTCTTTAAAGTCCACGACTCAGTGGCATTTTGTCTCAAA
1 AAAGTCCACGACGCAGTGGCATCCTTCTC--TAAAGTCCACGACTCAGTGGCAATCTCTCTCAAA
* * *
347119 GTCCACGACTCAGTGGCATTTTCTTTTT
64 GTCCACGACGCAGTGGCATCTTCTCTTT
*
347147 AAAGCCCAC
1 AAAGTCCAC
347156 AACTTTGTGG
Statistics
Matches: 91, Mismatches: 8, Indels: 7
0.86 0.08 0.07
Matches are distributed among these distances:
92 6 0.07
93 18 0.20
94 43 0.47
95 24 0.26
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.28
Consensus pattern (91 bp):
AAAGTCCACGACGCAGTGGCATCCTTCTCTAAAGTCCACGACTCAGTGGCAATCTCTCTCAAAGT
CCACGACGCAGTGGCATCTTCTCTTT
Found at i:347223 original size:27 final size:27
Alignment explanation
Indices: 347190--347359 Score: 160
Period size: 27 Copynumber: 5.9 Consensus size: 27
347180 TTTTCAAAGC
*
347190 CCACAACTCCGTGGCACCCTTTTAAGT
1 CCACAACTACGTGGCACCCTTTTAAGT
* *
347217 CCACAACTACGTGGCACTCTTTTCCTTCTAAGC
1 CCACAACTACGTGGCA--C----CCTTTTAAGT
*
347250 CCACAACTCCGTGGCACCCTTTTAAGT
1 CCACAACTACGTGGCACCCTTTTAAGT
* *
347277 CCACAACTACGTGGCACTCTTTTCCTTCTAAGC
1 CCACAACTACGTGGCA--C----CCTTTTAAGT
*
347310 CCACAACTCCGTGGCACCCTTTTAAGT
1 CCACAACTACGTGGCACCCTTTTAAGT
*
347337 CCACAACTACGTGGCACTCTTTT
1 CCACAACTACGTGGCACCCTTTT
347360 CCTTCTAAGC
Statistics
Matches: 117, Mismatches: 14, Indels: 24
0.75 0.09 0.15
Matches are distributed among these distances:
27 67 0.57
29 2 0.02
31 2 0.02
33 46 0.39
ACGTcount: A:0.22, C:0.36, G:0.14, T:0.28
Consensus pattern (27 bp):
CCACAACTACGTGGCACCCTTTTAAGT
Found at i:347263 original size:33 final size:33
Alignment explanation
Indices: 347148--347562 Score: 411
Period size: 34 Copynumber: 12.8 Consensus size: 33
347138 TTTCTTTTTA
** *
347148 AAGCCCACAACTTTGTGGCACTCTTTTTTCCCTTTTCA
1 AAGCCCACAACTCCGTGGCACTC--TTTT-CC--TTCT
*
347186 AAGCCCACAACTCCGTGGCA--C----CCTTTT
1 AAGCCCACAACTCCGTGGCACTCTTTTCCTTCT
* *
347213 AAGTCCACAACTACGTGGCACTCTTTTCCTTCT
1 AAGCCCACAACTCCGTGGCACTCTTTTCCTTCT
*
347246 AAGCCCACAACTCCGTGGCA--C----CCTTTT
1 AAGCCCACAACTCCGTGGCACTCTTTTCCTTCT
* *
347273 AAGTCCACAACTACGTGGCACTCTTTTCCTTCT
1 AAGCCCACAACTCCGTGGCACTCTTTTCCTTCT
*
347306 AAGCCCACAACTCCGTGGCA--C----CCTTTT
1 AAGCCCACAACTCCGTGGCACTCTTTTCCTTCT
* *
347333 AAGTCCACAACTACGTGGCACTCTTTTCCTTCT
1 AAGCCCACAACTCCGTGGCACTCTTTTCCTTCT
347366 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT
1 AAGCCCACAACTCCGTGGCACTC-TTTTCCTTCT
347400 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT
1 AAGCCCACAACTCCGTGGCACTC-TTTTCCTTCT
*
347434 AAGCCCACAACTCCGTGGCATTCTTTTTCCTTCT
1 AAGCCCACAACTCCGTGGCACTC-TTTTCCTTCT
*
347468 AAGCCCACAACTCCGTGGCACTCTTTTTTCCCTTTT
1 AAGCCCACAACTCCGTGGCACTC--TTTT-CCTTCT
* *
347504 AAAGCCCACAACTCCGTGGCAC-CTTGTTCTTTTT
1 -AAGCCCACAACTCCGTGGCACTCTT-TTCCTTCT
* *
347538 AAGTCCACAACTTCGTGGCA-TCTTT
1 AAGCCCACAACTCCGTGGCACTCTTT
347563 CACCCTTTCT
Statistics
Matches: 326, Mismatches: 27, Indels: 54
0.80 0.07 0.13
Matches are distributed among these distances:
27 66 0.20
29 5 0.02
31 2 0.01
32 1 0.00
33 93 0.29
34 106 0.33
35 7 0.02
36 7 0.02
37 21 0.06
38 18 0.06
ACGTcount: A:0.20, C:0.35, G:0.13, T:0.32
Consensus pattern (33 bp):
AAGCCCACAACTCCGTGGCACTCTTTTCCTTCT
Found at i:347266 original size:60 final size:60
Alignment explanation
Indices: 347186--347562 Score: 450
Period size: 60 Copynumber: 5.9 Consensus size: 60
347176 TCCCTTTTCA
347186 AAGCCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTACGTGGCACTCTTTTCCTTCT
1 AAGCCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTACGTGGCACTCTTTTCCTTCT
347246 AAGCCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTACGTGGCACTCTTTTCCTTCT
1 AAGCCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTACGTGGCACTCTTTTCCTTCT
347306 AAGCCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTACGTGGCACTCTTTTCCTTCT
1 AAGCCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTACGTGGCACTCTTTTCCTTCT
* * *
347366 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGGCACTCTTTTTCCT
1 AAGCCCACAACTCCGTGGCA--C-----CCTTTTAAGTCCACAACTACGTGGCACTC-TTTTCCT
347431 TCT
58 TCT
* * *
347434 AAGCCCACAACTCCGTGGCATTCTTTTTCCTTCTAAGCCCACAACTCCGTGGCACTCTTTTTTCC
1 AAGCCCACAACTCCGTGGCA--C-----CCTTTTAAGTCCACAACTACGTGGCACTC--TTTT-C
*
347499 CTTTT
56 CTTCT
*
347504 AAAGCCCACAACTCCGTGGCACCTTGTTCTTTTTAAGTCCACAACTTCGTGGCA-TCTTT
1 -AAGCCCACAACTCCGTGGCACC-----C-TTTTAAGTCCACAACTACGTGGCACTCTTT
347563 CACCCTTTCT
Statistics
Matches: 292, Mismatches: 8, Indels: 27
0.89 0.02 0.08
Matches are distributed among these distances:
60 140 0.48
62 1 0.00
64 1 0.00
67 29 0.10
68 66 0.23
69 9 0.03
70 26 0.09
71 20 0.07
ACGTcount: A:0.20, C:0.36, G:0.13, T:0.31
Consensus pattern (60 bp):
AAGCCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTACGTGGCACTCTTTTCCTTCT
Found at i:347710 original size:32 final size:33
Alignment explanation
Indices: 347564--347733 Score: 249
Period size: 32 Copynumber: 5.2 Consensus size: 33
347554 GGCATCTTTC
*
347564 ACCCTT-TCTAAAGCCCACACAAGTCGATGGCA
1 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCA
*
347596 AACCTTCTCTAAAGCCCACACAAGTCGGTGGCAA
1 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGC-A
*
347630 ACCCTTCTCTAAAGCCCACACAAGTTGGTGGCA
1 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCA
* *
347663 ACCC-CCTC-AAAGCCCACACAAGTCGATGGCA
1 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCA
*
347694 ACCCTTGTC-AAAGCCCACACAAGTCGGTGGCA
1 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCA
347726 ACCCTTCT
1 ACCCTTCT
347734 AAGCCCAATA
Statistics
Matches: 124, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
31 25 0.20
32 39 0.31
33 29 0.23
34 31 0.25
ACGTcount: A:0.29, C:0.36, G:0.17, T:0.18
Consensus pattern (33 bp):
ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCA
Found at i:347797 original size:49 final size:49
Alignment explanation
Indices: 347733--348621 Score: 1124
Period size: 49 Copynumber: 18.7 Consensus size: 49
347723 GCAACCCTTC
* * * *
347733 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
347782 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
347830 TAAGTCTAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
347873 TAAGACCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
347922 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
347965 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCATCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
348014 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * *
348057 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
348106 TAAGTCCAACGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * *
348149 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
348198 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * * *
348241 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
348290 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCAT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * * *
348339 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
348388 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA-CTTGCACCAT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTT-CATCTT
* * *
348437 TAAGTCC-ATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
348485 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * *
348534 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CATCTT
*
348586 TAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTG
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTG
348622 ACATCCTTTT
Statistics
Matches: 731, Mismatches: 73, Indels: 69
0.84 0.08 0.08
Matches are distributed among these distances:
43 196 0.27
45 5 0.01
47 5 0.01
48 84 0.11
49 402 0.55
51 2 0.00
52 37 0.05
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.30
Consensus pattern (49 bp):
TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
Found at i:347958 original size:92 final size:92
Alignment explanation
Indices: 347779--348630 Score: 1213
Period size: 92 Copynumber: 9.0 Consensus size: 92
347769 GCACCTTTAT
* * *
347779 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCATCTTTAAGTCTAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
347843 GCTGGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* * * *
347870 CTTTAAGACCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
347935 GCTGGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* * * *
347962 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCATCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
348027 GCTGGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* * *
348054 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAACGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
348119 GCTGGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* *
348146 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
348211 GCTGGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* * *
348238 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
*
348303 GCTGGCCTTGACTCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* * *
348330 CTTCACCATTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTTTATCTTTAAGTCC
1 C-T-----TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCC
*
348395 AATGTAGCTGGCCTTGACTCAGCACATTGGCACTTGCAC
60 AATGTAGCTGGCCTTGAATCAGCACATT-G-----GCAC
* *
348434 CATTAAGTCC-ATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
*
348498 GCTGGCCTTGACTCAGCACATTGGCACCTTC
66 GCTGGCCTTGAATCAGCACATTGGCA----C
* * *
348529 ATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTTTAAGTTCA
1 --CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--TT-CATCTTTAAGTCCA
*
348594 ATGTAGCTGGCCTTGAATCAGCACATTGACATC
61 ATGTAGCTGGCCTTGAATCAGCACATTGGCA-C
348627 CTTT
1 CTTT
348631 TTCTCATCTT
Statistics
Matches: 707, Mismatches: 31, Indels: 41
0.91 0.04 0.05
Matches are distributed among these distances:
91 45 0.06
92 403 0.57
93 1 0.00
95 1 0.00
96 5 0.01
97 84 0.12
98 119 0.17
99 1 0.00
100 2 0.00
101 41 0.06
104 5 0.01
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (92 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
GCTGGCCTTGAATCAGCACATTGGCAC
Found at i:347986 original size:22 final size:22
Alignment explanation
Indices: 347919--347986 Score: 54
Period size: 22 Copynumber: 3.1 Consensus size: 22
347909 GCACCTTCAT
347919 CTTTAAGTCCAATGTAGCTGGC
1 CTTTAAGTCCAATGTAGCTGGC
* * *
347941 CTTGAA-TCAGCACAT-TGGC--AC
1 CTTTAAGTC--CA-ATGTAGCTGGC
347962 CTTTAAGTCCAATGTAGCTGGC
1 CTTTAAGTCCAATGTAGCTGGC
347984 CTT
1 CTT
347987 GACTCAGCAC
Statistics
Matches: 33, Mismatches: 6, Indels: 14
0.62 0.11 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 8 0.24
22 11 0.33
23 5 0.15
24 2 0.06
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.31
Consensus pattern (22 bp):
CTTTAAGTCCAATGTAGCTGGC
Found at i:348666 original size:55 final size:53
Alignment explanation
Indices: 348238--348668 Score: 174
Period size: 49 Copynumber: 8.6 Consensus size: 53
348228 ACATTGGCAC
* * *
348238 CTTTAAGTCC-AATATCGCTGGCCTTGAATCAGCATATTGGCA-----TCATCAT
1 CTTTAAG-CCTAATATCGCTGGCCTTGAATCAGCACATCGACACCTTTTC-TCAT
* * * * * *
348287 CTTTAAGTCC-AATGTAGCTGGCCTTGACTCAGCACATTGGCACC---T-TCAC
1 CTTTAAG-CCTAATATCGCTGGCCTTGAATCAGCACATCGACACCTTTTCTCAT
* * * * * *
348336 CATTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-C-TTT-T-AT
1 CTTTAAGCCTAATATCGCTGGCCTTGAATCAGCACATCGACACCTTTTCTCAT
* * * * * * *
348385 CTTTAAGTCC-AATGTAGCTGGCCTTGACTCAGCACATTGGCA-C--TT-GCAC
1 CTTTAAG-CCTAATATCGCTGGCCTTGAATCAGCACATCGACACCTTTTCTCAT
* * * * *
348434 CATTAAGTCC--ATATAGCTGGCCTTGAATCAGCATATTGGCACC--TT-T-AT
1 CTTTAAG-CCTAATATCGCTGGCCTTGAATCAGCACATCGACACCTTTTCTCAT
* * * * *
348482 CTTTAAGTCC-AATGTAGCTGGCCTTGACTCAGCACATTGGCACC---T-TCAT
1 CTTTAAG-CCTAATATCGCTGGCCTTGAATCAGCACATCGACACCTTTTCTCAT
* *
348531 CTTTAAGTCC-AATATCGCTGGCCTTGAATCAGCATATCGGCACCTTTTC-CAT
1 CTTTAAG-CCTAATATCGCTGGCCTTGAATCAGCACATCGACACCTTTTCTCAT
* * * *
348583 CTTTAAG-TTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGCCT-AATATCGCTGGCCTTGAATCAGCACATCGACA-CC-TTTTCTCAT
* *
348638 CTTTAAGCCTAATATCGTTGGCCGTGAATCA
1 CTTTAAGCCTAATATCGCTGGCCTTGAATCA
348669 ACATATTGGC
Statistics
Matches: 320, Mismatches: 42, Indels: 34
0.81 0.11 0.09
Matches are distributed among these distances:
48 45 0.14
49 197 0.62
50 4 0.01
51 1 0.00
52 38 0.12
53 2 0.01
54 5 0.02
55 27 0.08
56 1 0.00
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (53 bp):
CTTTAAGCCTAATATCGCTGGCCTTGAATCAGCACATCGACACCTTTTCTCAT
Found at i:349579 original size:13 final size:13
Alignment explanation
Indices: 349561--349585 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
349551 CATAAAATGT
349561 TGTATCGATACAA
1 TGTATCGATACAA
349574 TGTATCGATACA
1 TGTATCGATACA
349586 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:349583 original size:33 final size:33
Alignment explanation
Indices: 349541--349610 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
349531 TTCAACGATT
349541 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
349574 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
349607 TGTA
1 TGTA
349611 AGCTACTGCC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:349669 original size:13 final size:13
Alignment explanation
Indices: 349651--349675 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
349641 ATTACTCACA
349651 TGTATCGATACAT
1 TGTATCGATACAT
349664 TGTATCGATACA
1 TGTATCGATACA
349676 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:349740 original size:52 final size:52
Alignment explanation
Indices: 349684--349804 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
349674 CACTGATCTT
*
349684 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
349736 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
349788 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
349805 TAACTTTTCA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:352932 original size:28 final size:28
Alignment explanation
Indices: 352892--353140 Score: 269
Period size: 28 Copynumber: 8.9 Consensus size: 28
352882 CGTTACGACA
*
352892 CCACGGAA-TTGTGGACTTTAAAAGGGTG
1 CCAC-GAAGTTGTGGACTTTAAAAGGATG
**
352920 CCACGAAGTTGTGGAC-TTAAAACAATG
1 CCACGAAGTTGTGGACTTTAAAAGGATG
*
352947 CCACGGAA-TTGTGGACTTTAAAAGGGTG
1 CCAC-GAAGTTGTGGACTTTAAAAGGATG
* *
352975 CCACGGAGTTGTGGAC-TTAAAACGATG
1 CCACGAAGTTGTGGACTTTAAAAGGATG
*
353002 CCACAGAA-TTGTGGACTTTAAAAGGGTG
1 CCAC-GAAGTTGTGGACTTTAAAAGGATG
*
353030 CCACGGAGTTGTGGACTTTAAAAGGATG
1 CCACGAAGTTGTGGACTTTAAAAGGATG
* *
353058 CCACGGAGTTATGGACTTTAAAAGGATG
1 CCACGAAGTTGTGGACTTTAAAAGGATG
* *
353086 CCACGGAGTTGTGGAC-TTAAAAGAAAATG
1 CCACGAAGTTGTGGACTTTAAAAG--GATG
*
353115 CCACTG-AGTCGTGGACTTTGAAAAGG
1 CCAC-GAAGTTGTGGACTTT-AAAAGG
353141 TCACAGTACT
Statistics
Matches: 190, Mismatches: 19, Indels: 23
0.82 0.08 0.10
Matches are distributed among these distances:
27 55 0.29
28 111 0.58
29 16 0.08
30 3 0.02
31 5 0.03
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (28 bp):
CCACGAAGTTGTGGACTTTAAAAGGATG
Found at i:352976 original size:55 final size:55
Alignment explanation
Indices: 352892--353140 Score: 354
Period size: 55 Copynumber: 4.5 Consensus size: 55
352882 CGTTACGACA
*
352892 CCACGGAATTGTGGACTTTAAAAGGGTGCCACGAAGTTGTGGACTTAAAACAATG
1 CCACGGAATTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAACAATG
*
352947 CCACGGAATTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAACGATG
1 CCACGGAATTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAACAATG
* **
353002 CCACAGAATTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGATG
1 CCACGGAATTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAACAATG
* * * *
353058 CCACGGAGTTATGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGAAAATG
1 CCACGGAATTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTT-AAA-ACAATG
* * *
353115 CCACTGAGTCGTGGACTTTGAAAAGG
1 CCACGGAATTGTGGACTTT-AAAAGG
353141 TCACAGTACT
Statistics
Matches: 177, Mismatches: 13, Indels: 5
0.91 0.07 0.03
Matches are distributed among these distances:
55 98 0.55
56 53 0.30
57 20 0.11
58 6 0.03
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (55 bp):
CCACGGAATTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAACAATG
Found at i:353032 original size:83 final size:82
Alignment explanation
Indices: 352892--353140 Score: 311
Period size: 83 Copynumber: 3.0 Consensus size: 82
352882 CGTTACGACA
* * *
352892 CCACGGAATTGTGGACTTTAAAAGGGTGCCACGAAGTTGTGGACTTAAAACAATGCCACGGAATT
1 CCACGGAGTTGTGGACTTTAAAAGGATGCCACGAA-TTGTGGACTTAAAAGAATGCCACGGAATT
*
352957 GTGGACTTTAAAAGGGTG
65 GTGGACTTTAAAAGGATG
* ** *
352975 CCACGGAGTTGTGGAC-TTAAAACGATGCCACAGAATTGTGGACTTTAAAAGGGTGCCACGGAGT
1 CCACGGAGTTGTGGACTTTAAAAGGATGCCAC-GAATTGTGGAC-TTAAAAGAATGCCACGGAAT
353039 TGTGGACTTTAAAAGGATG
64 TGTGGACTTTAAAAGGATG
* * * *
353058 CCACGGAGTTATGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGAAAATGCCACTGAG
1 CCACGGAGTTGTGGACTTTAAAAGGATGCCAC-GAATTGTGGACTTAAAAG--AATGCCACGGAA
*
353123 TCGTGGACTTTGAAAAGG
63 TTGTGGACTTT-AAAAGG
353141 TCACAGTACT
Statistics
Matches: 144, Mismatches: 16, Indels: 9
0.85 0.09 0.05
Matches are distributed among these distances:
82 21 0.15
83 74 0.51
84 24 0.17
85 19 0.13
86 6 0.04
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (82 bp):
CCACGGAGTTGTGGACTTTAAAAGGATGCCACGAATTGTGGACTTAAAAGAATGCCACGGAATTG
TGGACTTTAAAAGGATG
Found at i:354176 original size:11 final size:11
Alignment explanation
Indices: 354160--354192 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
354150 GGGTGAAAAG
354160 GTTTTTTTTTT
1 GTTTTTTTTTT
354171 GTTTTTTTTTCT
1 GTTTTTTTTT-T
354183 -TTTTTTTTTT
1 GTTTTTTTTTT
354193 TAGGATTAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.05
11 19 0.90
12 1 0.05
ACGTcount: A:0.00, C:0.03, G:0.06, T:0.91
Consensus pattern (11 bp):
GTTTTTTTTTT
Found at i:354516 original size:14 final size:13
Alignment explanation
Indices: 354462--354515 Score: 53
Period size: 14 Copynumber: 4.3 Consensus size: 13
354452 TCCTTTTTTA
354462 TTTTGCTTTTGCAC
1 TTTTGCTTTTG-AC
*
354476 TTTTGCTTTTCA-
1 TTTTGCTTTTGAC
354488 TTTT--TTTGTG-C
1 TTTTGCTTT-TGAC
354499 TTTTGCTTTTGAC
1 TTTTGCTTTTGAC
354512 TTTT
1 TTTT
354516 TTTTGTCATT
Statistics
Matches: 33, Mismatches: 2, Indels: 11
0.72 0.04 0.24
Matches are distributed among these distances:
10 3 0.09
11 5 0.15
12 6 0.18
13 9 0.27
14 10 0.30
ACGTcount: A:0.06, C:0.15, G:0.13, T:0.67
Consensus pattern (13 bp):
TTTTGCTTTTGAC
Found at i:361470 original size:20 final size:20
Alignment explanation
Indices: 361445--361494 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
361435 TTTTAACTAG
361445 ATGTATCGATACATTATTCA
1 ATGTATCGATACATTATTCA
361465 ATGTATCGATACATTATTCA
1 ATGTATCGATACATTATTCA
361485 ATGTATCGAT
1 ATGTATCGAT
361495 GCATCCAGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTATTCA
Found at i:365476 original size:18 final size:18
Alignment explanation
Indices: 365436--365477 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
365426 GATGGTTTAG
*
365436 AAAAAAAAATGTTAAATTC
1 AAAAAAAAATCTTAAA-TC
365455 AAAAAAAAATCTTAAA-C
1 AAAAAAAAATCTTAAATC
365472 AAAAAA
1 AAAAAA
365478 TTAGGCTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.32
19 15 0.68
ACGTcount: A:0.71, C:0.07, G:0.02, T:0.19
Consensus pattern (18 bp):
AAAAAAAAATCTTAAATC
Found at i:369334 original size:15 final size:15
Alignment explanation
Indices: 369297--369330 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
369287 TTTAATAATA
369297 TTAAATTATTTAAAT
1 TTAAATTATTTAAAT
*
369312 TTAAATTA-TTAACT
1 TTAAATTATTTAAAT
369326 TTAAA
1 TTAAA
369331 ATTAAATCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
TTAAATTATTTAAAT
Found at i:369451 original size:67 final size:67
Alignment explanation
Indices: 369309--369453 Score: 150
Period size: 67 Copynumber: 2.2 Consensus size: 67
369299 AAATTATTTA
* * * * * ***
369309 AATTTAAATTATTAACTTTAAAATTAAATCATTTTTAATTATATTAAATTTAGTGTTAAATTGTT
1 AATTCAAATCATTAACTTTAAAATTAAATAATTTTTAATTATATTAAAATTAGTGTCAAATTAAA
*
369374 TG
66 TC
* * *
369376 AGTCCAAATCATTAACTTTGAAATTAAATAATTTTTAATTATA-TAAAATTAGAT-TCAAATTAA
1 AATTCAAATCATTAACTTTAAAATTAAATAATTTTTAATTATATTAAAATTAG-TGTCAAATT-A
369439 AATC
64 AATC
369443 AATTCAAATCA
1 AATTCAAATCA
369454 AACATAAACA
Statistics
Matches: 62, Mismatches: 14, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
66 14 0.23
67 48 0.77
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (67 bp):
AATTCAAATCATTAACTTTAAAATTAAATAATTTTTAATTATATTAAAATTAGTGTCAAATTAAA
TC
Found at i:370750 original size:22 final size:25
Alignment explanation
Indices: 370707--370752 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
370697 ATATGTATTT
370707 AAAAATCAGAATTTAACTAACTTAA
1 AAAAATCAGAATTTAACTAACTTAA
370732 AAAAAT-A-AATTTAAC-AACTTA
1 AAAAATCAGAATTTAACTAACTTA
370753 CAACTTTTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 6 0.29
23 8 0.38
24 1 0.05
25 6 0.29
ACGTcount: A:0.59, C:0.11, G:0.02, T:0.28
Consensus pattern (25 bp):
AAAAATCAGAATTTAACTAACTTAA
Found at i:372173 original size:19 final size:20
Alignment explanation
Indices: 372129--372174 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
372119 TTTAAATTAA
372129 ATTATA-TTAAATAATTATT
1 ATTATATTTAAATAATTATT
372148 ATT-TATTTAAATAATT-TT
1 ATTATATTTAAATAATTATT
*
372166 TTTATATTT
1 ATTATATTT
372175 TTTATTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 6 0.25
19 18 0.75
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
ATTATATTTAAATAATTATT
Found at i:372222 original size:18 final size:17
Alignment explanation
Indices: 372187--372226 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
372177 TATTTTAAAT
*
372187 AAATAAATTTTAAGATA
1 AAATAAATTATAAGATA
*
372204 AAATCAAATTATAATATA
1 AAAT-AAATTATAAGATA
372222 AAATA
1 AAATA
372227 TCAGATGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (17 bp):
AAATAAATTATAAGATA
Found at i:372622 original size:20 final size:20
Alignment explanation
Indices: 372594--372639 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 20
372584 CGAATATAAT
372594 ATAAAAAA-ATAATTAAATATA
1 ATAAAAAATATAA-TAAA-ATA
372615 ATAAAAAATATAATAAAATA
1 ATAAAAAATATAATAAAATA
372635 ATAAA
1 ATAAA
372640 TATATTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 8 0.33
21 12 0.50
22 4 0.17
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (20 bp):
ATAAAAAATATAATAAAATA
Found at i:372634 original size:17 final size:17
Alignment explanation
Indices: 372586--372651 Score: 64
Period size: 17 Copynumber: 3.8 Consensus size: 17
372576 ACTCGACTCG
372586 AATATAATATAAA-AAAA
1 AATATAATA-AAATAAAA
*
372603 TAAT-TAAATATAATAAAA
1 -AATAT-AATAAAATAAAA
*
372621 AATATAATAAAATAATA
1 AATATAATAAAATAAAA
*
372638 AATATATTAAAATA
1 AATATAATAAAATA
372652 TATATATAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
17 29 0.71
18 12 0.29
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AATATAATAAAATAAAA
Found at i:372649 original size:29 final size:30
Alignment explanation
Indices: 372591--372660 Score: 97
Period size: 29 Copynumber: 2.3 Consensus size: 30
372581 ACTCGAATAT
*
372591 AATATAAAAAAATAATTAAATATAATAAAA
1 AATATAATAAAATAATTAAATATAATAAAA
*
372621 AATATAATAAAATAA-TAAATATATTAAAA
1 AATATAATAAAATAATTAAATATAATAAAA
*
372650 TATATATATAA
1 AATATA-ATAA
372661 TATTTTATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 18 0.50
30 18 0.50
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (30 bp):
AATATAATAAAATAATTAAATATAATAAAA
Found at i:372659 original size:33 final size:32
Alignment explanation
Indices: 372586--372662 Score: 97
Period size: 30 Copynumber: 2.4 Consensus size: 32
372576 ACTCGACTCG
*
372586 AATATAATATAAAAAAATAATTAAATATAATA
1 AATATAATATAATAAAATAATTAAATATAATA
*
372618 AA-A-AATATAATAAAATAA-TAAATATATTAA
1 AATATAATATAATAAAATAATTAAATATAAT-A
372648 AATATATATATAATA
1 AATATA-ATATAATA
372663 TTTTATATGA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
29 9 0.23
30 17 0.44
31 2 0.05
32 3 0.08
33 8 0.21
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (32 bp):
AATATAATATAATAAAATAATTAAATATAATA
Found at i:372729 original size:30 final size:29
Alignment explanation
Indices: 372689--372751 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 29
372679 AATTCTTATC
372689 ATAATAAAAAATAATATA-A-ATATTAATAT
1 ATAATAAAAAA-AATA-ACATATATTAATAT
*
372718 ATAATTAAAAAAATTAACATATATTAATAT
1 ATAA-TAAAAAAAATAACATATATTAATAT
372748 ATAA
1 ATAA
372752 CTACATAAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 1 0.03
29 8 0.27
30 21 0.70
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (29 bp):
ATAATAAAAAAAATAACATATATTAATAT
Found at i:372899 original size:2 final size:2
Alignment explanation
Indices: 372887--372930 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
372877 TTAGAGTCTG
372887 AT AT A- 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
372928 AT A
1 AT A
372931 CGCCATACAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:373685 original size:2 final size:2
Alignment explanation
Indices: 373678--373705 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
373668 TTAACTAATG
373678 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
373706 GGAGAAAGGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:374102 original size:15 final size:16
Alignment explanation
Indices: 374075--374104 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
374065 TTAATATTTT
374075 TAATTTGTTAAACTTG
1 TAATTTGTTAAACTTG
374091 TAATTT-TTAAACTT
1 TAATTTGTTAAACTT
374105 TATCATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (16 bp):
TAATTTGTTAAACTTG
Found at i:377852 original size:2 final size:2
Alignment explanation
Indices: 377845--377883 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
377835 AATGGAGGGG
377845 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
377884 TTAAGGTGTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:379562 original size:3 final size:3
Alignment explanation
Indices: 379554--379600 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
379544 AGGTATCTAT
* *
379554 ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA ATC ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
379601 GCTTCTAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:379742 original size:2 final size:2
Alignment explanation
Indices: 379735--379770 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
379725 TCACTTTGAA
379735 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
379771 TATTCGTTCG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:380238 original size:23 final size:23
Alignment explanation
Indices: 380195--380239 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
380185 AGATGCAAAG
*
380195 TTTCTTTTTCTTTTTCCTTTTTC
1 TTTCTTTTTCTTTTTCATTTTTC
* *
380218 TTTCTTTTTTTTTTTTATTTTT
1 TTTCTTTTTCTTTTTCATTTTT
380240 TAATTTTTGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.02, C:0.13, G:0.00, T:0.84
Consensus pattern (23 bp):
TTTCTTTTTCTTTTTCATTTTTC
Found at i:380730 original size:13 final size:13
Alignment explanation
Indices: 380712--380738 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
380702 ATAGAGAGAA
380712 AAAGAGATTAAAT
1 AAAGAGATTAAAT
380725 AAAGAGATTAAAT
1 AAAGAGATTAAAT
380738 A
1 A
380739 TTTAATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.15, T:0.22
Consensus pattern (13 bp):
AAAGAGATTAAAT
Found at i:382083 original size:2 final size:2
Alignment explanation
Indices: 382078--382106 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
382068 TATATTCTTT
382078 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
382107 TTTTTTCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:382764 original size:2 final size:2
Alignment explanation
Indices: 382757--382792 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
382747 CTCTTCAACC
382757 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
382793 GCTGAAGCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:383100 original size:2 final size:2
Alignment explanation
Indices: 383088--383116 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
383078 ATCATCATAG
383088 AT AT A- 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
383117 TTTCAATAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:383486 original size:15 final size:15
Alignment explanation
Indices: 383441--383497 Score: 52
Period size: 15 Copynumber: 4.1 Consensus size: 15
383431 TATGATTTAC
383441 ATAAA-TAAA-AAAT
1 ATAAATTAAATAAAT
*
383454 A-AAATACAAAT-AAT
1 ATAAAT-TAAATAAAT
383468 -TAAATTAAATAAAT
1 ATAAATTAAATAAAT
*
383482 ATAAATTATATAAAT
1 ATAAATTAAATAAAT
383497 A
1 A
383498 ATTATATAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
12 3 0.09
13 5 0.14
14 13 0.37
15 14 0.40
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (15 bp):
ATAAATTAAATAAAT
Found at i:383487 original size:23 final size:22
Alignment explanation
Indices: 383450--383522 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 22
383440 CATAAATAAA
*
383450 AAATAAAATACAAATAATTAAATT
1 AAAT-AAATAAAAAT-ATTAAATT
*
383474 AAATAAATATAAATTATATAAA-T
1 AAATAAATA-AAAATAT-TAAATT
* * *
383497 AATTATATAAAAATATAAAATT
1 AAATAAATAAAAATATTAAATT
383519 AAAT
1 AAAT
383523 TAATTATACA
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
21 3 0.08
22 10 0.26
23 15 0.38
24 11 0.28
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (22 bp):
AAATAAATAAAAATATTAAATT
Found at i:387289 original size:13 final size:14
Alignment explanation
Indices: 387260--387289 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
387250 ATTTTGTGTA
387260 TTAAAATTATGTTT
1 TTAAAATTATGTTT
387274 TTAAAATTAT-TTT
1 TTAAAATTATGTTT
387287 TTA
1 TTA
387290 TTATTTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (14 bp):
TTAAAATTATGTTT
Found at i:387704 original size:2 final size:2
Alignment explanation
Indices: 387691--387725 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
387681 AACAAGTACG
* *
387691 TA TA TG TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
387726 CACTTTTGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (2 bp):
TA
Found at i:388979 original size:19 final size:19
Alignment explanation
Indices: 388955--389006 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
388945 TAATAAAATC
388955 TTTTAAAATA-AAAGAATAA
1 TTTTAAAATATAAAGAA-AA
* *
388974 TTTTAAAATATTAAGAACA
1 TTTTAAAATATAAAGAAAA
*
388993 TTTTAAAATTTAAA
1 TTTTAAAATATAAA
389007 AATTAACTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 23 0.82
20 5 0.18
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (19 bp):
TTTTAAAATATAAAGAAAA
Found at i:390554 original size:15 final size:16
Alignment explanation
Indices: 390531--390563 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
390521 GCCAAAAATG
*
390531 AAAACACAATAAT-AA
1 AAAAAACAATAATGAA
390546 AAAAAACAATAATGAA
1 AAAAAACAATAATGAA
390562 AA
1 AA
390564 CTAGGGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.76, C:0.09, G:0.03, T:0.12
Consensus pattern (16 bp):
AAAAAACAATAATGAA
Found at i:395076 original size:2 final size:2
Alignment explanation
Indices: 395069--395100 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
395059 GGGAGGAAGG
395069 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
395101 CCCTTGATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:403745 original size:12 final size:14
Alignment explanation
Indices: 403719--403748 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
403709 ATAAAGTGAT
403719 ATATATTTAATAAA
1 ATATATTTAATAAA
403733 ATATATTTAA-AAA
1 ATATATTTAATAAA
403746 ATA
1 ATA
403749 AATAAATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
ATATATTTAATAAA
Found at i:404032 original size:34 final size:35
Alignment explanation
Indices: 403984--404056 Score: 121
Period size: 34 Copynumber: 2.1 Consensus size: 35
403974 AAGATTTAAC
*
403984 TATTCATCGAAAAAACTAACCGCCAAAGTCACTCA
1 TATTCATCGAAAAAACTAACCACCAAAGTCACTCA
*
404019 TATT-ATCGAAAAAACTAACCACCAAAGTTACTCA
1 TATTCATCGAAAAAACTAACCACCAAAGTCACTCA
404053 TATT
1 TATT
404057 TTTTAAAATC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
34 32 0.89
35 4 0.11
ACGTcount: A:0.44, C:0.25, G:0.07, T:0.25
Consensus pattern (35 bp):
TATTCATCGAAAAAACTAACCACCAAAGTCACTCA
Found at i:410131 original size:21 final size:23
Alignment explanation
Indices: 410093--410134 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
410083 TATGTTTGAA
*
410093 AAATAATACATTTTATTTTATTT
1 AAATAATACATTTCATTTTATTT
410116 AAATAA-A-ATTTCATTTTAT
1 AAATAATACATTTCATTTTAT
410135 GCAAAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
22 1 0.06
23 6 0.33
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (23 bp):
AAATAATACATTTCATTTTATTT
Found at i:410711 original size:29 final size:28
Alignment explanation
Indices: 410677--410736 Score: 84
Period size: 30 Copynumber: 2.1 Consensus size: 28
410667 AAATTTAGCT
*
410677 TAAAAACTTAAATTATTATTTATAAATTAA
1 TAAAAACTTAAA-AATTATTT-TAAATTAA
*
410707 TAAAAATTTAAAAATTATTTTAAATTAA
1 TAAAAACTTAAAAATTATTTTAAATTAA
410735 TA
1 TA
410737 TTTTTATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 10 0.36
29 7 0.25
30 11 0.39
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (28 bp):
TAAAAACTTAAAAATTATTTTAAATTAA
Found at i:420678 original size:18 final size:20
Alignment explanation
Indices: 420655--420694 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
420645 TATAAATTAA
420655 TTATTTT-AATTT-ATTTTT
1 TTATTTTGAATTTAATTTTT
*
420673 TTATTTTGATTTTAATTTTT
1 TTATTTTGAATTTAATTTTT
420693 TT
1 TT
420695 TTATTCACCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 4 0.21
20 8 0.42
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.78
Consensus pattern (20 bp):
TTATTTTGAATTTAATTTTT
Found at i:420801 original size:16 final size:16
Alignment explanation
Indices: 420765--420802 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
420755 AATTAAGATA
*
420765 AAATCAAATGATATTT
1 AAATTAAATGATATTT
420781 AAATTAAATGATATTT
1 AAATTAAATGATATTT
420797 AAATTA
1 AAATTA
420803 CTTAATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (16 bp):
AAATTAAATGATATTT
Found at i:424976 original size:22 final size:21
Alignment explanation
Indices: 424934--424984 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
424924 TCATAGTTTT
*
424934 ATAATTTTAAAAAATATAAAA
1 ATAATTTTAAAAAATAAAAAA
*
424955 ATAATTTTGAAAACATAAAAAA
1 ATAATTTT-AAAAAATAAAAAA
424977 AT-ATTTTA
1 ATAATTTTA
424985 TGACCATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 1 0.04
21 13 0.48
22 13 0.48
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (21 bp):
ATAATTTTAAAAAATAAAAAA
Found at i:425721 original size:19 final size:19
Alignment explanation
Indices: 425681--425722 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
425671 ATTGATAAAC
* *
425681 AAATTATTTTTAATTAATT
1 AAATTATTTTTAATGAAAT
*
425700 AAATTATTTTTCATGAAAT
1 AAATTATTTTTAATGAAAT
425719 AAAT
1 AAAT
425723 AATAAAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (19 bp):
AAATTATTTTTAATGAAAT
Found at i:426178 original size:26 final size:26
Alignment explanation
Indices: 426149--426232 Score: 68
Period size: 26 Copynumber: 3.2 Consensus size: 26
426139 GAACTAAGAT
426149 ATTAAATTATAATAAGATTGTGATTA
1 ATTAAATTATAATAAGATTGTGATTA
* * **
426175 ATTAAAGGTGT-TCAT-AGAACTAAGA-T-
1 ATTAAA--T-TATAATAAG-ATTGTGATTA
426201 ATTAAATTATAATAAGATTGTGATTA
1 ATTAAATTATAATAAGATTGTGATTA
426227 ATTAAA
1 ATTAAA
426233 GGTGTTCATG
Statistics
Matches: 42, Mismatches: 8, Indels: 16
0.64 0.12 0.24
Matches are distributed among these distances:
23 1 0.02
24 8 0.19
25 3 0.07
26 18 0.43
27 3 0.07
28 8 0.19
29 1 0.02
ACGTcount: A:0.46, C:0.02, G:0.13, T:0.38
Consensus pattern (26 bp):
ATTAAATTATAATAAGATTGTGATTA
Found at i:426197 original size:52 final size:52
Alignment explanation
Indices: 426135--426241 Score: 214
Period size: 52 Copynumber: 2.1 Consensus size: 52
426125 ATATAAAATA
426135 CATAGAACTAAGATATTAAATTATAATAAGATTGTGATTAATTAAAGGTGTT
1 CATAGAACTAAGATATTAAATTATAATAAGATTGTGATTAATTAAAGGTGTT
426187 CATAGAACTAAGATATTAAATTATAATAAGATTGTGATTAATTAAAGGTGTT
1 CATAGAACTAAGATATTAAATTATAATAAGATTGTGATTAATTAAAGGTGTT
426239 CAT
1 CAT
426242 GATTTGGGGA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 55 1.00
ACGTcount: A:0.44, C:0.05, G:0.15, T:0.36
Consensus pattern (52 bp):
CATAGAACTAAGATATTAAATTATAATAAGATTGTGATTAATTAAAGGTGTT
Found at i:427374 original size:23 final size:22
Alignment explanation
Indices: 427347--427406 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 22
427337 TTTGTATTTA
427347 AAAATATAATTATTTTAATATT
1 AAAATATAATTATTTTAATATT
*
427369 ACAAATAT-A-TA-TTAAATATT
1 A-AAATATAATTATTTTAATATT
427389 AAAATAAATAATTATTTT
1 AAAAT--ATAATTATTTT
427407 TTAATTCAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
19 4 0.13
20 9 0.30
21 4 0.13
22 3 0.10
23 8 0.27
24 2 0.07
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
AAAATATAATTATTTTAATATT
Found at i:428934 original size:3 final size:3
Alignment explanation
Indices: 428926--428961 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
428916 CACAAAAACA
428926 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
428962 TTTGGAGCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:430561 original size:2 final size:2
Alignment explanation
Indices: 430554--430581 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
430544 ATAGATATGT
430554 AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC
430582 CAAAATACTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:431174 original size:29 final size:29
Alignment explanation
Indices: 431120--431175 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
431110 AATAAAATTT
* *
431120 TAAATATTATAAAAATAATTTTAATAAAA
1 TAAATATTATAAAAATAATATAAATAAAA
*
431149 TAAATATTATATACAATAA-ATAAATAA
1 TAAATATTATA-AAAATAATATAAATAA
431176 TTAAAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 17 0.74
30 6 0.26
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (29 bp):
TAAATATTATAAAAATAATATAAATAAAA
Found at i:431217 original size:30 final size:31
Alignment explanation
Indices: 431175--431253 Score: 74
Period size: 30 Copynumber: 2.6 Consensus size: 31
431165 TAAATAAATA
431175 ATTAAA-AAAAAATTTTTTAA-AAAATACTC
1 ATTAAATAAAAAATTTTTTAATAAAATACTC
* * ** *
431204 ATTAAATATAAAA-TTATTAATTTAATTCTC
1 ATTAAATAAAAAATTTTTTAATAAAATACTC
*
431234 ATTAAATACAAAATTATTTT
1 ATTAAATAAAAAATT-TTTT
431254 TTTAAAAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
29 12 0.31
30 23 0.59
31 1 0.03
32 3 0.08
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (31 bp):
ATTAAATAAAAAATTTTTTAATAAAATACTC
Found at i:434116 original size:4 final size:4
Alignment explanation
Indices: 434107--434175 Score: 50
Period size: 4 Copynumber: 16.5 Consensus size: 4
434097 TTTAATGATA
* * * * *
434107 ATTT ATTT ATTT AATT ATTA ATTT ATTT ATGT AATT ATAT ATTTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT A-TTT ATTT
434156 -TTAT ATTTT CATTT ATTT AT
1 ATT-T A-TTT -ATTT ATTT AT
434176 AACTATTTTT
Statistics
Matches: 50, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
3 2 0.04
4 38 0.76
5 7 0.14
6 3 0.06
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (4 bp):
ATTT
Found at i:434392 original size:26 final size:23
Alignment explanation
Indices: 434331--434393 Score: 60
Period size: 24 Copynumber: 2.7 Consensus size: 23
434321 GAGATTAAAA
434331 ATAACAGTAACGATAAGATTATTT
1 ATAACAGTAA-GATAAGATTATTT
434355 ATTAA-AGT--GATAAGATTAGATATT
1 A-TAACAGTAAGATAAGATT--AT-TT
434379 ATAACAGTAAGATAA
1 ATAACAGTAAGATAA
434394 AAATTAGTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
21 9 0.28
23 5 0.16
24 10 0.31
25 3 0.09
26 5 0.16
ACGTcount: A:0.49, C:0.05, G:0.14, T:0.32
Consensus pattern (23 bp):
ATAACAGTAAGATAAGATTATTT
Found at i:434707 original size:8 final size:8
Alignment explanation
Indices: 434675--434737 Score: 55
Period size: 8 Copynumber: 8.2 Consensus size: 8
434665 ATTCAACATT
434675 TATTTATA
1 TATTTATA
*
434683 TAATTATA
1 TATTTATA
434691 TATTT-TA
1 TATTTATA
434698 T-TTT-TA
1 TATTTATA
434704 TATTTGCATA
1 TATTT--ATA
434714 TATTTATA
1 TATTTATA
434722 TA-TTAT-
1 TATTTATA
*
434728 TAATTATA
1 TATTTATA
434736 TA
1 TA
434738 AAAATTATTT
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
6 8 0.17
7 14 0.30
8 18 0.38
10 7 0.15
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (8 bp):
TATTTATA
Found at i:434744 original size:18 final size:18
Alignment explanation
Indices: 434723--434767 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
434713 ATATTTATAT
434723 ATTATTAATTATATAA-AA
1 ATTATT-ATTATATAATAA
*
434741 ATTATT-TTATATAATTA
1 ATTATTATTATATAATAA
434758 ATTATTATTA
1 ATTATTATTA
434768 AATTAAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 8 0.33
17 7 0.29
18 9 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTATTATTATATAATAA
Found at i:435146 original size:65 final size:64
Alignment explanation
Indices: 435032--435170 Score: 167
Period size: 65 Copynumber: 2.1 Consensus size: 64
435022 TTTTTATAAA
* *
435032 TTAATTAAATTTAAAAAATTTAATAAATAATAATATATTAATTATTATTTTTAATAAA-AAAATA
1 TTAATTAAATTTAAAAAATTTAATAAATAATAAAATATTAA-TATTATTTTTAA-AAATAAAAAA
435096 T
64 T
* *
435097 TTAATTAACTTTAAAAAATTTACATTAATAAATTAAAATATT-A-ATTATTTTTAAAAATAAAAA
1 TTAATTAAATTTAAAAAATTTA-ATAAAT-AA-TAAAATATTAATATTATTTTTAAAAATAAAAA
435160 AT
63 AT
*
435162 TAAATTAAA
1 TTAATTAAA
435171 AAGGGTTTAT
Statistics
Matches: 64, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
64 3 0.05
65 45 0.70
66 5 0.08
67 3 0.05
68 8 0.12
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (64 bp):
TTAATTAAATTTAAAAAATTTAATAAATAATAAAATATTAATATTATTTTTAAAAATAAAAAAT
Found at i:435237 original size:114 final size:111
Alignment explanation
Indices: 435086--435361 Score: 335
Period size: 110 Copynumber: 2.5 Consensus size: 111
435076 TTATTTTTAA
* *
435086 TAAAAA-AATATTTAATTAACTTTAAAAAATTTACATTAATAAATTAAAATATTAATTAT-T-TT
1 TAAAAATAATATTTAATTAAATTTAAAAAATTTACATTAACAAATTAAAATATTAATTATATATT
435148 TAAAAATAAAAAATTAAATTAAAAAGGGTTTATTATTATTTTTTAATAAAAT
66 T--AAAT-AAAAA-TAAA--AAAAAGGGTTTATTATTATTTTTTAATAAAAT
435200 TAAAAATAATATTTAATTAAATTTAAAAAA-TTACATTAACAAATTAAAATATTAATTATATATT
1 TAAAAATAATATTTAATTAAATTTAAAAAATTTACATTAACAAATTAAAATATTAATTATATATT
** ** *** *
435264 TTTATAAAAATAAAAAGTATTTTTTATTGTTATTTTTTAATAAAAT
66 TAAATAAAAATAAAAAAAAGGGTTTATTATTATTTTTTAATAAAAT
* * *
435310 AAAAAATGATATTTAATTAAGTTTAAAAAAATTTACATTAACAAATTTAAAA
1 TAAAAATAATATTTAATTAAATTT-AAAAAATTTACATTAACAAA-TTAAAA
435362 AATAACATTT
Statistics
Matches: 143, Mismatches: 13, Indels: 13
0.85 0.08 0.08
Matches are distributed among these distances:
110 47 0.33
111 6 0.04
112 17 0.12
113 11 0.08
114 36 0.25
115 23 0.16
116 3 0.02
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (111 bp):
TAAAAATAATATTTAATTAAATTTAAAAAATTTACATTAACAAATTAAAATATTAATTATATATT
TAAATAAAAATAAAAAAAAGGGTTTATTATTATTTTTTAATAAAAT
Found at i:435369 original size:22 final size:23
Alignment explanation
Indices: 435332--435387 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
435322 TTAATTAAGT
*
435332 TTAAAAAAATTTACA-TTAACA-AA
1 TTAAAAAAA-TAACATTTAA-AGAA
*
435355 TTTAAAAAATAACATTTAAAGAA
1 TTAAAAAAATAACATTTAAAGAA
435378 TTAAAAAAAT
1 TTAAAAAAAT
435388 TTATCATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 5 0.18
23 23 0.82
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.30
Consensus pattern (23 bp):
TTAAAAAAATAACATTTAAAGAA
Found at i:435893 original size:117 final size:117
Alignment explanation
Indices: 435680--436017 Score: 385
Period size: 117 Copynumber: 2.9 Consensus size: 117
435670 AAAAAATATT
* *
435680 ATTATAATAAAAAACTTTTTTTAATTTAAAATTTTTTATTTTTTAAAATATAATAATTAATATTT
1 ATTATAATAAAAAAC-TATTTT-ATTTTAAATTTTTTA-TTTTT-AAA-A-AATAATTAATATTT
* **
435745 TAATTTATTAATGTAAAATTTTAAACTTAATTAAATATTTATTTTT-ATTTTATTAAAA
60 TAATTTGTTAATGTAATTTTTTAAACTTAATTAAATA-TTATTTTTAATTTTATTAAAA
*
435803 ATTATAATAAAAAACCTATTTTATTTTAAATTTTTTTATTTTTATAAAAA-CA-T-ATATTTTAA
1 ATTATAATAAAAAA-CTATTTTATTTTAAA-TTTTTTATTTTTA-AAAAATAATTAATATTTTAA
435865 TTTGTTAATGTAATTTTTTAAACTTAATTAAATATTATTTTTAATTTTATTAAAA
63 TTTGTTAATGTAATTTTTTAAACTTAATTAAATATTATTTTTAATTTTATTAAAA
* * *
435920 A-AATAATAATAAA--A-TCT-TTTT--A-TTTTTATTTTTAAAAAATAATTAATATTTTAATTT
1 ATTATAATAAAAAACTATTTTATTTTAAATTTTTTATTTTTAAAAAATAATTAATATTTTAATTT
* *
435977 GTTAATATAAATTTCTTTAAAGTTAATTAAATATTATTTTT
66 GTTAATGT-AATTT-TTTAAACTTAATTAAATATTATTTTT
436018 TACTAAAAAT
Statistics
Matches: 194, Mismatches: 12, Indels: 30
0.82 0.05 0.13
Matches are distributed among these distances:
106 5 0.03
107 13 0.07
108 1 0.01
109 20 0.10
110 5 0.03
111 29 0.15
112 2 0.01
113 1 0.01
116 18 0.09
117 53 0.27
118 1 0.01
119 1 0.01
120 2 0.01
121 2 0.01
122 14 0.07
123 26 0.13
124 1 0.01
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (117 bp):
ATTATAATAAAAAACTATTTTATTTTAAATTTTTTATTTTTAAAAAATAATTAATATTTTAATTT
GTTAATGTAATTTTTTAAACTTAATTAAATATTATTTTTAATTTTATTAAAA
Found at i:436029 original size:101 final size:101
Alignment explanation
Indices: 435835--436052 Score: 235
Period size: 111 Copynumber: 2.1 Consensus size: 101
435825 ATTTTAAATT
* *
435835 TTTTTATTTTTATAAAAACATATATTTTAATTTGTTAATGTAATTTTTTAAACTTAATTAAATAT
1 TTTTTATTTTTATAAAAAAATATATTTTAATTTGTTAATATAATTTTTTAAACTTAATTAAATAT
*
435900 TATTTTTAATTTTATTAAAAAAATAATAATAAAATCTTTTTA
66 TA--TTT-ATTTTACT---AAAATAATAATAAAATCTTTTTA
*
435942 TTTTTATTTTTA-AAAAATAATTAATATTTTAATTTGTTAATATAAATTTCTTTAAAGTTAATTA
1 TTTTTATTTTTATAAAAA-AA-T-ATATTTTAATTTGTTAATAT-AATTT-TTTAAACTTAATTA
* * *
436006 AATATTA-TT-TTTTACTAAAAATAATAATTAATTCATTATTA
61 AATATTATTTATTTTACT-AAAATAATAATAAAATC-TTTTTA
436047 TTTTTA
1 TTTTTA
436053 AAATTTAATT
Statistics
Matches: 98, Mismatches: 7, Indels: 14
0.82 0.06 0.12
Matches are distributed among these distances:
104 16 0.16
105 11 0.11
106 11 0.11
107 13 0.13
108 3 0.03
109 19 0.19
110 5 0.05
111 20 0.20
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.54
Consensus pattern (101 bp):
TTTTTATTTTTATAAAAAAATATATTTTAATTTGTTAATATAATTTTTTAAACTTAATTAAATAT
TATTTATTTTACTAAAATAATAATAAAATCTTTTTA
Done.