Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012276.1 Kokia drynarioides strain JFW-HI SEQ_127277, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 679560
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Warning! 53 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:25358 original size:5 final size:5
Alignment explanation
Indices: 25348--25380 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
25338 AAAAAGATAA
25348 AAGAG AAGAG AA-AGG AAGAG AAGAG AAGAG AAG
1 AAGAG AAGAG AAGA-G AAGAG AAGAG AAGAG AAG
25381 GAAATAGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 1 0.04
5 24 0.92
6 1 0.04
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (5 bp):
AAGAG
Found at i:38610 original size:24 final size:24
Alignment explanation
Indices: 38578--38630 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
38568 TAATGCATGC
*
38578 TAAATAAGATACAAAAGAGACAAT
1 TAAAAAAGATACAAAAGAGACAAT
38602 TAAAAAAGATACAAAAGAGACAAT
1 TAAAAAAGATACAAAAGAGACAAT
38626 TAAAA
1 TAAAA
38631 CATCAATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.66, C:0.08, G:0.11, T:0.15
Consensus pattern (24 bp):
TAAAAAAGATACAAAAGAGACAAT
Found at i:39757 original size:15 final size:16
Alignment explanation
Indices: 39724--39773 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
39714 GTGCAGGTTC
39724 CTTCATTTCATTC-TCTT
1 CTTCA-TTC-TTCTTCTT
*
39741 CTTCCTTC-TCTTCTT
1 CTTCATTCTTCTTCTT
39756 CTTCATTCTTCTTCTT
1 CTTCATTCTTCTTCTT
39772 CT
1 CT
39774 GGCCATCTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
14 2 0.07
15 11 0.38
16 12 0.41
17 4 0.14
ACGTcount: A:0.06, C:0.34, G:0.00, T:0.60
Consensus pattern (16 bp):
CTTCATTCTTCTTCTT
Found at i:53961 original size:21 final size:22
Alignment explanation
Indices: 53918--53968 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
53908 AGTCTTCACT
*
53918 AACT-AAAATAAAAATAATTTC
1 AACTAAAAATAAAAATAATATC
*
53939 AACTAAAAATAAGAA-AATATC
1 AACTAAAAATAAAAATAATATC
*
53960 AATTAAAAA
1 AACTAAAAA
53969 GATCAGATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 17 0.65
22 9 0.35
ACGTcount: A:0.67, C:0.08, G:0.02, T:0.24
Consensus pattern (22 bp):
AACTAAAAATAAAAATAATATC
Found at i:61435 original size:29 final size:29
Alignment explanation
Indices: 61395--61457 Score: 119
Period size: 29 Copynumber: 2.2 Consensus size: 29
61385 TATTAAGGAG
61395 GAAAA-GGCAAGAACAAAGGAAAATGGTC
1 GAAAATGGCAAGAACAAAGGAAAATGGTC
61423 GAAAATGGCAAGAACAAAGGAAAATGGTC
1 GAAAATGGCAAGAACAAAGGAAAATGGTC
61452 GAAAAT
1 GAAAAT
61458 AATAATGATT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 5 0.15
29 29 0.85
ACGTcount: A:0.54, C:0.10, G:0.27, T:0.10
Consensus pattern (29 bp):
GAAAATGGCAAGAACAAAGGAAAATGGTC
Found at i:62679 original size:15 final size:12
Alignment explanation
Indices: 62647--62676 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
62637 ATATGCAAGG
62647 ATAGCATCAATA
1 ATAGCATCAATA
62659 ATAGCATCAATA
1 ATAGCATCAATA
62671 ATAGCA
1 ATAGCA
62677 GCAGTTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.50, C:0.17, G:0.10, T:0.23
Consensus pattern (12 bp):
ATAGCATCAATA
Found at i:69267 original size:17 final size:19
Alignment explanation
Indices: 69241--69286 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
69231 ATAGTTTGCA
69241 TGCA-TTTTTA-TTGTCAT
1 TGCATTTTTTATTTGTCAT
69258 TGC-TTTTTTATTTTGTCAT
1 TGCATTTTTTA-TTTGTCAT
69277 TGCATTTTTT
1 TGCATTTTTT
69287 GTTAATTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 9 0.36
19 10 0.40
20 6 0.24
ACGTcount: A:0.13, C:0.11, G:0.11, T:0.65
Consensus pattern (19 bp):
TGCATTTTTTATTTGTCAT
Found at i:77466 original size:14 final size:14
Alignment explanation
Indices: 77429--77466 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
77419 ATTTTTACAT
*
77429 TTTC-TTTTATTTG
1 TTTCGTTTTACTTG
77442 TTTCAGTTTTACTTG
1 TTTC-GTTTTACTTG
77457 TTTCGTTTTA
1 TTTCGTTTTA
77467 AATTTCTATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 4 0.18
14 6 0.27
15 12 0.55
ACGTcount: A:0.11, C:0.11, G:0.11, T:0.68
Consensus pattern (14 bp):
TTTCGTTTTACTTG
Found at i:80382 original size:12 final size:13
Alignment explanation
Indices: 80365--80393 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
80355 CAAAGAAATA
80365 AAAAGAAAAG-AG
1 AAAAGAAAAGAAG
80377 AAAAGAAAAGAAG
1 AAAAGAAAAGAAG
80390 AAAA
1 AAAA
80394 AATGTTTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAGAAG
Found at i:84868 original size:17 final size:17
Alignment explanation
Indices: 84835--84881 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
84825 TATTTTCGAG
* *
84835 ATATAAATATTAAAATTA
1 ATATAAAT-TTTAATTTA
84853 TATATAAATTTTAATTTA
1 -ATATAAATTTTAATTTA
84871 ATATAAATTTT
1 ATATAAATTTT
84882 GATATATGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 11 0.42
18 7 0.27
19 8 0.31
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATATAAATTTTAATTTA
Found at i:90222 original size:13 final size:13
Alignment explanation
Indices: 90201--90238 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
90191 AAATATAGTT
*
90201 TTTTTTCTTTTTC
1 TTTTCTCTTTTTC
*
90214 TTTTCTCTTTTTT
1 TTTTCTCTTTTTC
90227 TTTTCT-TTTTTC
1 TTTTCTCTTTTTC
90239 AAGTGACTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 5 0.23
13 17 0.77
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTCTCTTTTTC
Found at i:91321 original size:12 final size:12
Alignment explanation
Indices: 91306--91341 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
91296 CTTCTCTTTA
91306 TTCTCTTCTTCC
1 TTCTCTTCTTCC
91318 TTCTCTTCTT-C
1 TTCTCTTCTTCC
91329 TTC-CTT-TTCC
1 TTCTCTTCTTCC
91339 TTC
1 TTC
91342 AACTTGTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 2 0.09
10 7 0.30
11 4 0.17
12 10 0.43
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (12 bp):
TTCTCTTCTTCC
Found at i:106967 original size:13 final size:14
Alignment explanation
Indices: 106949--106978 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
106939 GTTAACGCAA
106949 TCAGAG-TTAAATG
1 TCAGAGATTAAATG
106962 TCAGAGATTAAATG
1 TCAGAGATTAAATG
106976 TCA
1 TCA
106979 TTGTACTGAA
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:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (14 bp):
TCAGAGATTAAATG
Found at i:115700 original size:24 final size:24
Alignment explanation
Indices: 115673--115723 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
115663 TTATATAAAT
115673 TTACAAGCATGAATGGTTATTTAA
1 TTACAAGCATGAATGGTTATTTAA
*
115697 TTACAAGCATGAATTGTTATTTAA
1 TTACAAGCATGAATGGTTATTTAA
115721 TTA
1 TTA
115724 TGGAGATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.41
Consensus pattern (24 bp):
TTACAAGCATGAATGGTTATTTAA
Found at i:118386 original size:23 final size:23
Alignment explanation
Indices: 118359--118409 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
118349 TGATACATAT
118359 ATGATGATGTTACAAGGTTTGAA
1 ATGATGATGTTACAAGGTTTGAA
118382 ATGATGATGTTACAAGGTTTGAA
1 ATGATGATGTTACAAGGTTTGAA
118405 ATGAT
1 ATGAT
118410 AATAAAATAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.35
Consensus pattern (23 bp):
ATGATGATGTTACAAGGTTTGAA
Found at i:119349 original size:22 final size:20
Alignment explanation
Indices: 119308--119349 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
119298 GGTCTGAAAC
*
119308 AGTTAAGTGTATGGTTGAAT
1 AGTTAAGTGTATAGTTGAAT
119328 AGTTAAGTTGTATAAGTTGAAT
1 AGTTAAG-TGTAT-AGTTGAAT
119350 TGAAATGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 5 0.26
22 7 0.37
ACGTcount: A:0.33, C:0.00, G:0.26, T:0.40
Consensus pattern (20 bp):
AGTTAAGTGTATAGTTGAAT
Found at i:123175 original size:14 final size:15
Alignment explanation
Indices: 123134--123180 Score: 78
Period size: 16 Copynumber: 3.1 Consensus size: 15
123124 TATTGTTTTT
123134 TATAGTTTTCACAGTC
1 TATAGTTTTCACA-TC
123150 TATAGTTTTCACATC
1 TATAGTTTTCACATC
123165 TATAG-TTTCACATC
1 TATAGTTTTCACATC
123179 TA
1 TA
123181 AAGAACACTC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.35
15 7 0.23
16 13 0.42
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.45
Consensus pattern (15 bp):
TATAGTTTTCACATC
Found at i:130704 original size:48 final size:48
Alignment explanation
Indices: 130633--130729 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
130623 ATAAGTGCAT
130633 ATTCTCAACAACTCATGTGAGCAGCATCGTTAGGGGACTGTTATATAG
1 ATTCTCAACAACTCATGTGAGCAGCATCGTTAGGGGACTGTTATATAG
130681 ATTCTCAACAACTCATGTGAGCAGCATCGTTAGGGGACTGTTATATAG
1 ATTCTCAACAACTCATGTGAGCAGCATCGTTAGGGGACTGTTATATAG
130729 A
1 A
130730 CAGACACCGT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.29
Consensus pattern (48 bp):
ATTCTCAACAACTCATGTGAGCAGCATCGTTAGGGGACTGTTATATAG
Found at i:136757 original size:12 final size:12
Alignment explanation
Indices: 136740--136764 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
136730 CTTCAAAGAT
136740 ATCATCATCATA
1 ATCATCATCATA
136752 ATCATCATCATA
1 ATCATCATCATA
136764 A
1 A
136765 ATGTCATATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (12 bp):
ATCATCATCATA
Found at i:140008 original size:4 final size:5
Alignment explanation
Indices: 139986--140018 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
139976 GTTGATGCAC
139986 TTTCT TTTCT TTTCT TTTC- TTTCTT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTC-T TTTCT TTT
140019 TTAATTTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.15
5 18 0.69
6 4 0.15
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTCT
Found at i:141627 original size:16 final size:18
Alignment explanation
Indices: 141606--141643 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
141596 AAGTTATCGA
141606 TTATTTACTT-GAAA-AT
1 TTATTTACTTAGAAATAT
*
141622 TTATTTTCTTAGAAATAT
1 TTATTTACTTAGAAATAT
141640 TTAT
1 TTAT
141644 GAAAAGATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 9 0.47
17 4 0.21
18 6 0.32
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.55
Consensus pattern (18 bp):
TTATTTACTTAGAAATAT
Found at i:145681 original size:31 final size:30
Alignment explanation
Indices: 145609--145710 Score: 104
Period size: 31 Copynumber: 3.4 Consensus size: 30
145599 ATAAAAAATA
* *
145609 AAAAAAAT-AGAATAAAACGG--TAATTTT
1 AAAAAAATAAAAATAAAAGGGTTTAATTTT
145636 AAAAAGGAATAAAAATAAAAGGGTTTAATTTT
1 AAAAA--AATAAAAATAAAAGGGTTTAATTTT
* *
145668 AACAAAAATAAAAATAGAAGGATTTAA-TTT
1 AA-AAAAATAAAAATAAAAGGGTTTAATTTT
*
145698 AAAAAAAAAAAAA
1 AAAAAAATAAAAA
145711 GAATAAATGG
Statistics
Matches: 64, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
27 5 0.08
29 13 0.20
30 15 0.23
31 19 0.30
32 9 0.14
33 3 0.05
ACGTcount: A:0.64, C:0.02, G:0.11, T:0.24
Consensus pattern (30 bp):
AAAAAAATAAAAATAAAAGGGTTTAATTTT
Found at i:148826 original size:32 final size:35
Alignment explanation
Indices: 148789--148920 Score: 180
Period size: 38 Copynumber: 3.7 Consensus size: 35
148779 AAAAGTCAGA
*
148789 ATGTTACC-TC-AATTTGTTAAA-AATGATGAACT
1 ATGTTACCTTCTAATTAGTTAAATAATGATGAACT
148821 ATGTTACCTTCTAATTAGTTAAATGTCAATGATGAACT
1 ATGTTACCTTCTAATTAGTTAAA--T-AATGATGAACT
148859 ATGTTACCTTCTAATTAGTTAAATGTCAATGATGAACT
1 ATGTTACCTTCTAATTAGTTAAA--T-AATGATGAACT
148897 ATGTTACCTTCTAATTAGTTAAAT
1 ATGTTACCTTCTAATTAGTTAAAT
148921 GTTAATGATA
Statistics
Matches: 93, Mismatches: 1, Indels: 8
0.91 0.01 0.08
Matches are distributed among these distances:
32 8 0.09
33 2 0.02
34 10 0.11
36 1 0.01
38 72 0.77
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (35 bp):
ATGTTACCTTCTAATTAGTTAAATAATGATGAACT
Found at i:148853 original size:38 final size:38
Alignment explanation
Indices: 148810--148929 Score: 231
Period size: 38 Copynumber: 3.2 Consensus size: 38
148800 ATTTGTTAAA
148810 AATGATGAACTATGTTACCTTCTAATTAGTTAAATGTC
1 AATGATGAACTATGTTACCTTCTAATTAGTTAAATGTC
148848 AATGATGAACTATGTTACCTTCTAATTAGTTAAATGTC
1 AATGATGAACTATGTTACCTTCTAATTAGTTAAATGTC
*
148886 AATGATGAACTATGTTACCTTCTAATTAGTTAAATGTT
1 AATGATGAACTATGTTACCTTCTAATTAGTTAAATGTC
148924 AATGAT
1 AATGAT
148930 AAACATGAGA
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
38 81 1.00
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (38 bp):
AATGATGAACTATGTTACCTTCTAATTAGTTAAATGTC
Found at i:151667 original size:54 final size:53
Alignment explanation
Indices: 151540--151812 Score: 242
Period size: 54 Copynumber: 5.1 Consensus size: 53
151530 GACCATGGTC
* * *
151540 ATGGCAAGTGAAGACCATATCGTGTAAGACCTAGTTTGGGACTATGGCATCAT
1 ATGGAAAGTGAAGACCATATAGTGTAAGACCTAGTTTAGGACTATGGCATCAT
** * ** *
151593 ATGGGGAAAG-GAAGTTCATATAGTGTAAGACCTAGTCATATTATTATGGCATCAT
1 AT--GGAAAGTGAAGACCATATAGTGTAAGACCTAGT-TTAGGACTATGGCATCAT
* * * *
151648 ATGGAAAGTGAAGACCATATAGTGTAAGACCTAGTTTGGGATTATGACATAAT
1 ATGGAAAGTGAAGACCATATAGTGTAAGACCTAGTTTAGGACTATGGCATCAT
*** *** * * **
151701 ATGGAGAAAAAAAGTTTATATAGTGTAAGGCCTAGTCGTATTACTATGGCATCAT
1 ATGGA-AAGTGAAGACCATATAGTGTAAGACCTAGT-TTAGGACTATGGCATCAT
* * * * *
151756 ATGGCAAGTGAATACCATATCGTGTAAGACCTAGTTTGGGACTATGGCATCAC
1 ATGGAAAGTGAAGACCATATAGTGTAAGACCTAGTTTAGGACTATGGCATCAT
151809 ATGG
1 ATGG
151813 GGAAATGAAG
Statistics
Matches: 168, Mismatches: 46, Indels: 12
0.74 0.20 0.05
Matches are distributed among these distances:
53 42 0.25
54 91 0.54
55 35 0.21
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.29
Consensus pattern (53 bp):
ATGGAAAGTGAAGACCATATAGTGTAAGACCTAGTTTAGGACTATGGCATCAT
Found at i:151735 original size:108 final size:108
Alignment explanation
Indices: 151540--151801 Score: 407
Period size: 108 Copynumber: 2.4 Consensus size: 108
151530 GACCATGGTC
* * * **
151540 ATGGCAAGTGAAGACCATATCGTGTAAGACCTAGTTTGGGACTATGGCATCATATGGGGAAAGGA
1 ATGGCAAGTGAAGACCATATCGTGTAAGACCTAGTTTGGGACTATGACATAATATGGAGAAAAAA
*
151605 AGTTCATATAGTGTAAGACCTAGTCATATTATTATGGCATCAT
66 AGTTCATATAGTGTAAGACCTAGTCATATTACTATGGCATCAT
* * *
151648 ATGGAAAGTGAAGACCATATAGTGTAAGACCTAGTTTGGGATTATGACATAATATGGAGAAAAAA
1 ATGGCAAGTGAAGACCATATCGTGTAAGACCTAGTTTGGGACTATGACATAATATGGAGAAAAAA
* * *
151713 AGTTTATATAGTGTAAGGCCTAGTCGTATTACTATGGCATCAT
66 AGTTCATATAGTGTAAGACCTAGTCATATTACTATGGCATCAT
*
151756 ATGGCAAGTGAATACCATATCGTGTAAGACCTAGTTTGGGACTATG
1 ATGGCAAGTGAAGACCATATCGTGTAAGACCTAGTTTGGGACTATG
151802 GCATCACATG
Statistics
Matches: 138, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
108 138 1.00
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (108 bp):
ATGGCAAGTGAAGACCATATCGTGTAAGACCTAGTTTGGGACTATGACATAATATGGAGAAAAAA
AGTTCATATAGTGTAAGACCTAGTCATATTACTATGGCATCAT
Found at i:152042 original size:58 final size:58
Alignment explanation
Indices: 151979--152091 Score: 154
Period size: 58 Copynumber: 1.9 Consensus size: 58
151969 TGTTTTGTTC
* * * * * *
151979 TGTGGAAGTCTTTGTGGTTGTTCTATTACGTGTGGGAGCTTTTGTGGTCGATCTGATA
1 TGTGGAAGCCTTTATGGATGTCCTATTACGTGTGGGAGCTCTTGTAGTCGATCTGATA
* *
152037 TGTGGAAGCCTTTATGGATGTCCTATTACGTGTGTGAGCTCTTGTAGTCGTTCTG
1 TGTGGAAGCCTTTATGGATGTCCTATTACGTGTGGGAGCTCTTGTAGTCGATCTG
152092 TTAAATGTGC
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
58 47 1.00
ACGTcount: A:0.14, C:0.13, G:0.31, T:0.42
Consensus pattern (58 bp):
TGTGGAAGCCTTTATGGATGTCCTATTACGTGTGGGAGCTCTTGTAGTCGATCTGATA
Found at i:153051 original size:23 final size:23
Alignment explanation
Indices: 153023--153074 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
153013 AAATTTTAAA
153023 ATTTATACTTAATACAATAAAAT
1 ATTTATACTTAATACAATAAAAT
** *
153046 ATTTATTTTTAATATAATAAAAT
1 ATTTATACTTAATACAATAAAAT
153069 ATTTAT
1 ATTTAT
153075 TATATTTATG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (23 bp):
ATTTATACTTAATACAATAAAAT
Found at i:153075 original size:23 final size:23
Alignment explanation
Indices: 153031--153075 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
153021 AAATTTATAC
153031 TTAATACAATAAAATATTTATTT
1 TTAATACAATAAAATATTTATTT
*
153054 TTAATATAATAAAATATTTATT
1 TTAATACAATAAAATATTTATT
153076 ATATTTATGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
TTAATACAATAAAATATTTATTT
Found at i:165531 original size:515 final size:514
Alignment explanation
Indices: 164086--165616 Score: 2258
Period size: 515 Copynumber: 3.0 Consensus size: 514
164076 CTACTCATTT
* * * *
164086 AGTGGTAAGGCTTCAACTTACCCTTTAGTTTTTAGTTCAAATTATCCCTACAGTTGCAAAATGGA
1 AGTGGTAAGGCTTCAGCTTACCCTTTGGTTTTTAGTTCGAATCATCCCTACAGTTGCAAAATGGA
* * * *
164151 AAATATTG-TTTTGTTCCGACGCTTGTGCCATCCATGTGTTGAAAATTGAGTTTAATTCAAATTC
66 AAATATTGTTTTTGTTCCCACTCTTGTGCCATCCATGTGTTGGAAATTGAGTCTAATTCAAATTC
* * * * *
164215 TGGATAAGTTACTGGGAGTGGATTTATTTGGTTTTCGGTTTGTAAATATCCTTTAAAAATCTCCT
131 TGGATAAGTTACTGAGAGTGGATTTATTTGGGTTTCGATTTGTAAATATCCCTTAAAAATCTCTT
* * *
164280 ATGTTTCCTTCTTTCTCTCTCTCTATTTCCTATCAATTATTTTTACTTTT-TTT-TCTTTTCCTT
196 ATGTTTCCTTCTTTCTCTCTC-CT-TTTCCTATCAGTCATTTTTACTTTTCTTTCTTTTTTCCTT
* * *
164343 TCTGCCATTTTTTCTTCTCTTCTTTTCCTTCTCCAAAAATTTTCCTTAGTTTCACGAAAGTTTTC
259 TCTGCCATTTTTTCTTCTCTTCTTTTCCTTCTCCAAAAATTTCCCTTGGTTACACGAAAG-TTTC
* * * * *
164408 TTTTTCCCATAGTGACTTTATCGTTTCATCTATTTTTGTCCTTTCCT-AGTTGTGGCTTTGTGAC
323 TTTTTCCCATAGTGACTCTGTCGTTTCATCTATTTTCGTTCTTTCCTCA-TTGTGGCTTTGTGAA
* * * ** *
164472 GAGTTCGGTAAGTTGTTTTGAAGGTTGTTTTTTCTGCAATATGGAAATTTTGTTAAGATAAGCAA
387 GAGTTCGATAAGTTGTTGTGAAGGTTGTTTTTTCTGTAATGGGGAAATTTTGTTAAGATAAGCGA
* * * *
164537 AGGTTCTTGTTAAATTATTTTGCGATTAGA-ATCGAAATTGTTTGTTCTTATTAAATTCTTGTTT
452 AGGTTCTTGTTAAATT-TTTTGTGATTA-ACATCGAAATTGTTCGTTCTTGTTAAATTCTTGTTC
* *
164601 AGTGGTAAGGCTTTAGTTTACCCTTTGGTTTTTAGTTCGAATCATCCCTACAGTTGCAAAATGGA
1 AGTGGTAAGGCTTCAGCTTACCCTTTGGTTTTTAGTTCGAATCATCCCTACAGTTGCAAAATGGA
*
164666 AAATATTGTTTTTGTT-CCA-TGCTTGTGCCATCCATGTGTTGGAAATTAAGTCTAATTCAAATT
66 AAATATTGTTTTTGTTCCCACT-CTTGTGCCATCCATGTGTTGGAAATTGAGTCTAATTCAAATT
*
164729 CTAGATAAGTTACT-AGGAGTGGATTTATTTGGGTTTCGATTTGTAAATAT-CCTTAAAAATCTC
130 CTGGATAAGTTACTGA-GAGTGGATTTATTTGGGTTTCGATTTGTAAATATCCCTTAAAAATCTC
*
164792 TTATGTTTCCTTCTTTCTCTCTCTTTTTCCTATCAGTCATTTTTACTTTTCTTTC-TTTTTCCTT
194 TTATGTTTCCTTCTTTCTCTCTCCTTTTCCTATCAGTCATTTTTACTTTTCTTTCTTTTTTCCTT
* * * *
164856 TCTACCATTTTGTCTTCTCTTCTTTTCCTTCTCCAAAAATTTCCCTTGGTTACACGAAATTTTTT
259 TCTGCCATTTTTTCTTCTCTTCTTTTCCTTCTCCAAAAATTTCCCTTGGTTACACGAAAGTTTCT
* *
164921 TTTTCCCATAGTGACTCTGTCGTTTCATCTATTTTCGTTCTTTCCTCATTGTGGCTTCGTGATGA
324 TTTTCCCATAGTGACTCTGTCGTTTCATCTATTTTCGTTCTTTCCTCATTGTGGCTTTGTGAAGA
*
164986 GTTCGATAAGTTGTTGTGAAGGTTGTTTTTTCTGTAATGGGGAAAATTTGTTAAGATAAGCGAAG
389 GTTCGATAAGTTGTTGTGAAGGTTGTTTTTTCTGTAATGGGGAAATTTTGTTAAGATAAGCGAAG
* * * *
165051 GTTCGTGTTAAATTTTGTTGTGATTAACATTGGAATTGTTCGTTCTTGTTAAGTTCTTGTTC
454 GTTCTTGTTAAATTTT-TTGTGATTAACATCGAAATTGTTCGTTCTTGTTAAATTCTTGTTC
* * * *
165113 AGTGGTAAGACTTCAGCTTACCCTTTGGTTTTTAGTTCGAATCATTCCTACAATTACAAAATGGA
1 AGTGGTAAGGCTTCAGCTTACCCTTTGGTTTTTAGTTCGAATCATCCCTACAGTTGCAAAATGGA
165178 AAATATTGTTTTTGTTCCCACTCTTGTGCCATCCATGTGTTGGAAATTGAGTCTAATT-AAAGTT
66 AAATATTGTTTTTGTTCCCACTCTTGTGCCATCCATGTGTTGGAAATTGAGTCTAATTCAAA-TT
* *
165242 CTGGATAAGTTACTGAGAGTGGATTTATTTGGGTTTCAATTTGTAAATATCCCTAAAAAATCTCT
130 CTGGATAAGTTACTGAGAGTGGATTTATTTGGGTTTCGATTTGTAAATATCCCTTAAAAATCTCT
* * * *
165307 TATGTTTCCTTCTTTCTCTCTCCTTTTCCTATTAGCCGTTTTTACTTTTCTTTCTTTTTTTCTTT
195 TATGTTTCCTTCTTTCTCTCTCCTTTTCCTATCAGTCATTTTTACTTTTCTTTCTTTTTTCCTTT
*
165372 CTGCCGTTTTTTCTTCTCTTCTTTTCCTTCTCCAAAAATTTCCCTTGGTTACGA-GAAAGTTTCT
260 CTGCCATTTTTTCTTCTCTTCTTTTCCTTCTCCAAAAATTTCCCTTGGTTAC-ACGAAAGTTTCT
*
165436 TTTTCCCATAGTGACTCTGTCGTTTCATCTATTTTCGTTCTTTCCTCATTGTGGCTTTGCGAAGA
324 TTTTCCCATAGTGACTCTGTCGTTTCATCTATTTTCGTTCTTTCCTCATTGTGGCTTTGTGAAGA
*
165501 GTTCGATAAGTTGTTGTGAAGGTTGTTTTTTCTGTAATGGGGAAATTTTTTTTAAGATAAGCGAA
389 GTTCGATAAGTTGTTGTGAAGGTTGTTTTTTCTGTAATGGGGAAA-TTTTGTTAAGATAAGCGAA
** * *
165566 TATTCTTGTTAAATTCTATTGTGATTAACATCAAAATTGTTCGTTCTTGTT
453 GGTTCTTGTTAAATT-TTTTGTGATTAACATCGAAATTGTTCGTTCTTGTT
165617 CTATTAGGAC
Statistics
Matches: 918, Mismatches: 81, Indels: 33
0.89 0.08 0.03
Matches are distributed among these distances:
511 3 0.00
512 269 0.29
513 153 0.17
514 99 0.11
515 326 0.36
516 67 0.07
517 1 0.00
ACGTcount: A:0.21, C:0.17, G:0.16, T:0.46
Consensus pattern (514 bp):
AGTGGTAAGGCTTCAGCTTACCCTTTGGTTTTTAGTTCGAATCATCCCTACAGTTGCAAAATGGA
AAATATTGTTTTTGTTCCCACTCTTGTGCCATCCATGTGTTGGAAATTGAGTCTAATTCAAATTC
TGGATAAGTTACTGAGAGTGGATTTATTTGGGTTTCGATTTGTAAATATCCCTTAAAAATCTCTT
ATGTTTCCTTCTTTCTCTCTCCTTTTCCTATCAGTCATTTTTACTTTTCTTTCTTTTTTCCTTTC
TGCCATTTTTTCTTCTCTTCTTTTCCTTCTCCAAAAATTTCCCTTGGTTACACGAAAGTTTCTTT
TTCCCATAGTGACTCTGTCGTTTCATCTATTTTCGTTCTTTCCTCATTGTGGCTTTGTGAAGAGT
TCGATAAGTTGTTGTGAAGGTTGTTTTTTCTGTAATGGGGAAATTTTGTTAAGATAAGCGAAGGT
TCTTGTTAAATTTTTTGTGATTAACATCGAAATTGTTCGTTCTTGTTAAATTCTTGTTC
Found at i:166180 original size:5 final size:5
Alignment explanation
Indices: 166170--166196 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
166160 ATAAGTTATG
166170 TGATA TGATA TGATA TGATA TGATA TG
1 TGATA TGATA TGATA TGATA TGATA TG
166197 TAAAAGTACG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.22, T:0.41
Consensus pattern (5 bp):
TGATA
Found at i:168683 original size:16 final size:16
Alignment explanation
Indices: 168662--168692 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
168652 GCTATCTAAT
168662 TATTAATCTGGTTAAA
1 TATTAATCTGGTTAAA
*
168678 TATTAATTTGGTTAA
1 TATTAATCTGGTTAA
168693 GAAATAAATT
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:0.35, C:0.03, G:0.13, T:0.48
Consensus pattern (16 bp):
TATTAATCTGGTTAAA
Found at i:171546 original size:73 final size:71
Alignment explanation
Indices: 171342--171582 Score: 236
Period size: 73 Copynumber: 3.3 Consensus size: 71
171332 AGTTACGCCT
*
171342 ACGGGCGTGTGTCAGACCGTGTGCCCATACTGTTT-TGAAAGTACAGAAACAGTGAGTTACATGG
1 ACGGGTGTGTGTCAGACCGTGTGCCCATACTGTTTGTGAAA--ACAGAAACAGTGAGTTACA-GG
*
171406 CCTAGACAC
63 GCTAGACAC
* * * *** * * * *
171415 ACGAGCGTGTGTCAGACCATGTGGATATGCTGTTTGTGGAATCAGAAACAGAGAGTTACACGGGC
1 ACGGGTGTGTGTCAGACCGTGTGCCCATACTGTTTGTGAAAACAGAAACAGTGAGTTACA-GGGC
171480 TAGACAC
65 TAGACAC
* *
171487 ACGGGTGTGTG-CTAGACCGTGTGCCCATACCAT-TTTGTGCAAACAGAAACAGTGAGTTACATG
1 ACGGGTGTGTGTC-AGACCGTGTGCCCATA-C-TGTTTGTGAAAACAGAAACAGTGAGTTACAGG
*
171550 GCTTGTACAC
63 GCTAG-ACAC
**
171560 ATTGGTGTGTGTCAGACCGTGTG
1 ACGGGTGTGTGTCAGACCGTGTG
171583 ACACACACGA
Statistics
Matches: 137, Mismatches: 25, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
71 1 0.01
72 52 0.38
73 78 0.57
74 6 0.04
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (71 bp):
ACGGGTGTGTGTCAGACCGTGTGCCCATACTGTTTGTGAAAACAGAAACAGTGAGTTACAGGGCT
AGACAC
Found at i:171726 original size:39 final size:39
Alignment explanation
Indices: 171683--171815 Score: 153
Period size: 39 Copynumber: 3.4 Consensus size: 39
171673 TAAACTGGCA
* *
171683 GTGACATTGTAAACACTACAATACAACACTAAACTGATG
1 GTGACACTGTAAACACTACAATACAATACTAAACTGATG
* ** *
171722 GTGACACTGTAAACAAC-ATAATACCGTACTAAACT-AGTA
1 GTGACACTGTAAAC-ACTACAATACAATACTAAACTGA-TG
* *
171761 GTGACACTGTAAACACTACAATACAATACTGAACTGACG
1 GTGACACTGTAAACACTACAATACAATACTAAACTGATG
*
171800 GTGACACTATAAACAC
1 GTGACACTGTAAACAC
171816 AATAGTACTG
Statistics
Matches: 77, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
38 3 0.04
39 71 0.92
40 3 0.04
ACGTcount: A:0.43, C:0.22, G:0.14, T:0.22
Consensus pattern (39 bp):
GTGACACTGTAAACACTACAATACAATACTAAACTGATG
Found at i:171838 original size:39 final size:39
Alignment explanation
Indices: 171790--171893 Score: 109
Period size: 39 Copynumber: 2.7 Consensus size: 39
171780 AATACAATAC
*
171790 TGAACTGACGGTGACACTATAAACACAATAGTACTGCAT
1 TGAACTGACGGTGACACTATAAACACAATAATACTGCAT
* ** * * *
171829 TGAATTGACGGTGACGTTATAAACACCATAATACTGTAC
1 TGAACTGACGGTGACACTATAAACACAATAATACTGCAT
* * * *
171868 TAAACTGGCAGTGACACTACAAACAC
1 TGAACTGACGGTGACACTATAAACAC
171894 TGCAATGCTA
Statistics
Matches: 51, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
39 51 1.00
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.23
Consensus pattern (39 bp):
TGAACTGACGGTGACACTATAAACACAATAATACTGCAT
Found at i:171843 original size:78 final size:78
Alignment explanation
Indices: 171672--171816 Score: 202
Period size: 78 Copynumber: 1.8 Consensus size: 78
171662 TATCAAATTG
* * * *
171672 CTAAACTGGCAGTGACATTGTAAACACTACAATACAACACTAAACTGATGGTGACACTGTAAACA
1 CTAAACTAG-AGTGACATTGTAAACACTACAATACAATACTAAACTGACGGTGACACTATAAACA
*
171737 -ACATAATACCGTA
65 CACATAATACCGCA
* *
171750 CTAAACTAGTAGTGACACTGTAAACACTACAATACAATACTGAACTGACGGTGACACTATAAACA
1 CTAAACTAG-AGTGACATTGTAAACACTACAATACAATACTAAACTGACGGTGACACTATAAACA
171815 CA
65 CA
171817 ATAGTACTGC
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
78 58 0.98
79 1 0.02
ACGTcount: A:0.43, C:0.22, G:0.14, T:0.21
Consensus pattern (78 bp):
CTAAACTAGAGTGACATTGTAAACACTACAATACAATACTAAACTGACGGTGACACTATAAACAC
ACATAATACCGCA
Found at i:174532 original size:51 final size:51
Alignment explanation
Indices: 174407--174695 Score: 339
Period size: 51 Copynumber: 5.6 Consensus size: 51
174397 TTTCATTTCA
** * *
174407 TACTCACGATGACA-TATAGTCATCGGACCTCTTGTTCCATATAGGAATTCATA
1 TACTCACGATGACACT-TAGTCATCGGACCT-TTAATCCATAAAGG-ATTCATT
** * * * *
174460 TACTCACGATGACACAAAGTCATCGGACCCTCAATCCATCATGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
* **
174511 TACTCACGATGACACTTAGTCATCAGACCTTTAATCTGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
* * * **
174562 TACTCACGATGACACTTAATCATCAGACATTTAATCTGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
* *
174613 TACTCACGATGACACTTAGTCATTGGACCTTTAATCCTTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
*
174664 T-CATCACGATGAGACTTAGTCATCGGACCTTT
1 TAC-TCACGATGACACTTAGTCATCGGACCTTT
174696 TCGTTTATAT
Statistics
Matches: 205, Mismatches: 29, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
50 1 0.00
51 170 0.83
52 8 0.04
53 26 0.13
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.32
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
Found at i:175512 original size:2 final size:2
Alignment explanation
Indices: 175505--175537 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
175495 TTCTTTTAAT
175505 TA TA TA 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 T
175538 TAATGGCAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:198293 original size:17 final size:18
Alignment explanation
Indices: 198273--198312 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
198263 TTAGTTTTAA
198273 TGCATTTT-TATTATCAT
1 TGCATTTTATATTATCAT
*
198290 TGCATTTTATTTTATCAT
1 TGCATTTTATATTATCAT
*
198308 CGCAT
1 TGCAT
198313 CATTTTGTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.23, C:0.15, G:0.07, T:0.55
Consensus pattern (18 bp):
TGCATTTTATATTATCAT
Found at i:202704 original size:422 final size:422
Alignment explanation
Indices: 201916--202750 Score: 1580
Period size: 422 Copynumber: 2.0 Consensus size: 422
201906 AGACTGATGA
*
201916 AAAGCATATTTTTACCGTTTCTCGGAAAGATTGTTACGGAGTTGTTTTTATATCGCTGTTAATTT
1 AAAGCATATTTTTACCGTTGCTCGGAAAGATTGTTACGGAGTTGTTTTTATATCGCTGTTAATTT
*
201981 TGATTAATTTTGTAAGTAATTGGAATTTCCTAAGCATTTAATATTCGGTGATATATTTGAAGGGT
66 TGATTAATTTTGTAAGTAATTAGAATTTCCTAAGCATTTAATATTCGGTGATATATTTGAAGGGT
* *
202046 TGGAATTGTTATTAATTAATTGCAACGGTTTTCTTTAGGCGAAGATCGTATCGTTAATGATATAT
131 TGGAATTGTTATTAATGAATTGCAACGGTTTTCTTTAGGCGAAGATCATATCGTTAATGATATAT
*
202111 CGTCAAGATAGTTCAGTAAATTCAACGTTAAGCGAGGTAAGTGTATTCTTGAGTTAGTAGTGAGA
196 CGTCAAGATAGTTCAGCAAATTCAACGTTAAGCGAGGTAAGTGTATTCTTGAGTTAGTAGTGAGA
*
202176 TTGTTACTAAGCTTTACGAATTGGTTTGGTTTAAGAATCGTTACGATTGGGGAATACGATGAGGA
261 TTGTTACTAAGCTTTACGAATTGGTTTGGTTTAAGAATCGTTACGATTGGGGAATACGATGAGAA
*
202241 ATTAATCTTATGACTTTAATTTAGGCTTCTGTTCGTGAGAGGAAGTTCACTTTTACTTCGGGATA
326 ATTAATCTTATGACTTTAATTTAGGCTTCTGTTCATGAGAGGAAGTTCACTTTTACTTCGGGATA
202306 GGTAGGGTACCCAAACCTTACTCAACTGACAG
391 GGTAGGGTACCCAAACCTTACTCAACTGACAG
202338 AAAGCATATTTTTACCGTTGCTCGGAAAGATTGTTACGGAGTTGTTTTTATATCGCTGTTAATTT
1 AAAGCATATTTTTACCGTTGCTCGGAAAGATTGTTACGGAGTTGTTTTTATATCGCTGTTAATTT
202403 TGATTAATTTTGTAAGTAATTAGAATTTCCTAAGCATTTAATATTCGGTGATATATTTGAAGGGT
66 TGATTAATTTTGTAAGTAATTAGAATTTCCTAAGCATTTAATATTCGGTGATATATTTGAAGGGT
* *
202468 TGGAATTGTTATTGATGAATTGCAATGGTTTTCTTTAGGCGAAGATCATATCGTTAATGATATAT
131 TGGAATTGTTATTAATGAATTGCAACGGTTTTCTTTAGGCGAAGATCATATCGTTAATGATATAT
202533 CGTCAAGATAGTTCAGCAAATTCAACGTTAAGCGAGGTAAGTGTATTCTTGAGTTAGTAGTGAGA
196 CGTCAAGATAGTTCAGCAAATTCAACGTTAAGCGAGGTAAGTGTATTCTTGAGTTAGTAGTGAGA
202598 TTGTTACTAAGCTTTACGAATTGGTTTGGTTTAAGAATCGTTACGATTGGGGAATACGATGAGAA
261 TTGTTACTAAGCTTTACGAATTGGTTTGGTTTAAGAATCGTTACGATTGGGGAATACGATGAGAA
202663 ATTAATCTTATGACTTTAATTTAGGCTTCTGTTCATGAGAGGAAGTTCACTTTTACTTCGGGATA
326 ATTAATCTTATGACTTTAATTTAGGCTTCTGTTCATGAGAGGAAGTTCACTTTTACTTCGGGATA
*
202728 GGTAGGGTACCGAAACCTTACTC
391 GGTAGGGTACCCAAACCTTACTC
202751 GTTTTCTGCA
Statistics
Matches: 403, Mismatches: 10, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
422 403 1.00
ACGTcount: A:0.29, C:0.11, G:0.22, T:0.38
Consensus pattern (422 bp):
AAAGCATATTTTTACCGTTGCTCGGAAAGATTGTTACGGAGTTGTTTTTATATCGCTGTTAATTT
TGATTAATTTTGTAAGTAATTAGAATTTCCTAAGCATTTAATATTCGGTGATATATTTGAAGGGT
TGGAATTGTTATTAATGAATTGCAACGGTTTTCTTTAGGCGAAGATCATATCGTTAATGATATAT
CGTCAAGATAGTTCAGCAAATTCAACGTTAAGCGAGGTAAGTGTATTCTTGAGTTAGTAGTGAGA
TTGTTACTAAGCTTTACGAATTGGTTTGGTTTAAGAATCGTTACGATTGGGGAATACGATGAGAA
ATTAATCTTATGACTTTAATTTAGGCTTCTGTTCATGAGAGGAAGTTCACTTTTACTTCGGGATA
GGTAGGGTACCCAAACCTTACTCAACTGACAG
Found at i:204862 original size:39 final size:38
Alignment explanation
Indices: 204813--205026 Score: 151
Period size: 39 Copynumber: 5.5 Consensus size: 38
204803 ACTGGCAGTA
* *
204813 ACACTGTAAACATTGCAATACAATACTAAACTGATGGTG
1 ACACTATAAACACTGCAATAC-ATACTAAACTGATGGTG
* * * * * *
204852 ACATTATAAACACCGTAATATCGTACTAAACTGGTAGTG
1 ACACTATAAACACTGCAATA-CATACTAAACTGATGGTG
* * * *
204891 ACACTGTAAACACTACAATACGACACTGAACTGATGGTG
1 ACACTATAAACACTGCAATAC-ATACTAAACTGATGGTG
* * * * *
204930 ACACTATAAACACTGTAATACTGTAATGAACTGACGGTG
1 ACACTATAAACACTGCAATAC-ATACTAAACTGATGGTG
* * * * *
204969 ACACTGTAAACAGC-GTAATACTATACTGAACTGGTAGTG
1 ACACTATAAACA-CTGCAATAC-ATACTAAACTGATGGTG
**
205008 ACACTGCAAACACTGCAAT
1 ACACTATAAACACTGCAAT
205027 GCTATCTTGA
Statistics
Matches: 137, Mismatches: 34, Indels: 8
0.77 0.19 0.04
Matches are distributed among these distances:
38 2 0.01
39 133 0.97
40 2 0.01
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (38 bp):
ACACTATAAACACTGCAATACATACTAAACTGATGGTG
Found at i:204931 original size:78 final size:78
Alignment explanation
Indices: 204797--204980 Score: 235
Period size: 78 Copynumber: 2.4 Consensus size: 78
204787 GTTATCAAAT
* * * * *
204797 TACTGAACTGGCAGTAACACTGTAAACATTGCAATACAATACTAAACTGATGGTGACATTATAAA
1 TACTGAACTGGCAGTGACACTGTAAACACTACAATACAACACTAAACTGATGGTGACACTATAAA
204862 CACCGTAATA-TCG
66 CACCGTAATACT-G
* * * *
204875 TACTAAACTGGTAGTGACACTGTAAACACTACAATACGACACTGAACTGATGGTGACACTATAAA
1 TACTGAACTGGCAGTGACACTGTAAACACTACAATACAACACTAAACTGATGGTGACACTATAAA
*
204940 CACTGTAATACTG
66 CACCGTAATACTG
* * *
204953 TAATGAACTGACGGTGACACTGTAAACA
1 TACTGAACTGGCAGTGACACTGTAAACA
204981 GCGTAATACT
Statistics
Matches: 90, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
78 89 0.99
79 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (78 bp):
TACTGAACTGGCAGTGACACTGTAAACACTACAATACAACACTAAACTGATGGTGACACTATAAA
CACCGTAATACTG
Found at i:204989 original size:78 final size:77
Alignment explanation
Indices: 204813--205058 Score: 208
Period size: 78 Copynumber: 3.2 Consensus size: 77
204803 ACTGGCAGTA
* * * * *
204813 ACACTGTAAACATTGCAATACAATACTAAACTGATGGTGACATTATAAACACCGTAATA-TCGTA
1 ACACTGTAAACA-CGTAATACAATACTGAACTGATGGTGACACTATAAACACTGTAATACT-GTA
* * ***
204877 CTAAACTGGTAGTG
64 ATGAACTGACGGTG
* *
204891 ACACTGTAAACAC-TACAATACGACACTGAACTGATGGTGACACTATAAACACTGTAATACTGTA
1 ACACTGTAAACACGT--AATACAATACTGAACTGATGGTGACACTATAAACACTGTAATACTGTA
204955 ATGAACTGACGGTG
64 ATGAACTGACGGTG
* * * ** * * * **
204969 ACACTGTAAACAGCGTAATACTATACTGAACTGGTAGTGACACTGCAAACACTGCAATGCTATCT
1 ACACTGTAAACA-CGTAATACAATACTGAACTGATGGTGACACTATAAACACTGTAATACTGTAA
* * *
205034 TGATCCGACGATG
65 TGAACTGACGGTG
205047 ACACTGTAAACA
1 ACACTGTAAACA
205059 TAACACGGTT
Statistics
Matches: 137, Mismatches: 26, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
78 134 0.98
79 2 0.01
80 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.24
Consensus pattern (77 bp):
ACACTGTAAACACGTAATACAATACTGAACTGATGGTGACACTATAAACACTGTAATACTGTAAT
GAACTGACGGTG
Found at i:205049 original size:117 final size:117
Alignment explanation
Indices: 204841--205058 Score: 260
Period size: 117 Copynumber: 1.9 Consensus size: 117
204831 TACAATACTA
* * * *
204841 AACTGATGGTGACATTATAAACACCGTAATATCGTACTAAACTGGTAGTGACACTGTAAACACTA
1 AACTGACGGTGACACTATAAACACCGTAATATCATACTAAACTGGTAGTGACACTGCAAACACTA
* * *
204906 CAATACGACACTGAACTGATGGTGACACTATAAACACTGTAATACTGTAATG
66 CAATACGACACTGAACCGACGATGACACTATAAACACTGTAATACTGTAATG
* * *
204958 AACTGACGGTGACACTGTAAACAGCGTAATA-CTATACTGAACTGGTAGTGACACTGCAAACACT
1 AACTGACGGTGACACTATAAACACCGTAATATC-ATACTAAACTGGTAGTGACACTGCAAACACT
* * * * * *
205022 GCAATGCTATC-TTGATCCGACGATGACACTGTAAACA
65 ACAATACGA-CACTGAACCGACGATGACACTATAAACA
205059 TAACACGGTT
Statistics
Matches: 83, Mismatches: 16, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
116 1 0.01
117 81 0.98
118 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.24
Consensus pattern (117 bp):
AACTGACGGTGACACTATAAACACCGTAATATCATACTAAACTGGTAGTGACACTGCAAACACTA
CAATACGACACTGAACCGACGATGACACTATAAACACTGTAATACTGTAATG
Found at i:207194 original size:18 final size:18
Alignment explanation
Indices: 207138--207194 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 18
207128 TTAAACATAC
207138 AAACAATCGATTCAAAAG
1 AAACAATCGATTCAAAAG
* * * *
207156 AAA-TAT-TATTCCAACG
1 AAACAATCGATTCAAAAG
*
207172 TAACAATCGATTCAAAAG
1 AAACAATCGATTCAAAAG
207190 AAACA
1 AAACA
207195 GTATTTCAAC
Statistics
Matches: 27, Mismatches: 10, Indels: 4
0.66 0.24 0.10
Matches are distributed among these distances:
16 9 0.33
17 4 0.15
18 14 0.52
ACGTcount: A:0.53, C:0.18, G:0.09, T:0.21
Consensus pattern (18 bp):
AAACAATCGATTCAAAAG
Found at i:209292 original size:23 final size:23
Alignment explanation
Indices: 209266--209312 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
209256 TTTATTTAAC
*
209266 TTAACCAAACATATTTACGAACA
1 TTAAACAAACATATTTACGAACA
* * *
209289 TTAAACGAACATGTTTATGAACA
1 TTAAACAAACATATTTACGAACA
209312 T
1 T
209313 ATAATTGAAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.45, C:0.17, G:0.09, T:0.30
Consensus pattern (23 bp):
TTAAACAAACATATTTACGAACA
Found at i:209334 original size:24 final size:23
Alignment explanation
Indices: 209273--209335 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 23
209263 AACTTAACCA
*
209273 AACATATTTACGAACATTAAACG
1 AACATGTTTACGAACATTAAACG
* **
209296 AACATGTTTATGAACATATAATTG
1 AACATGTTTACGAACAT-TAAACG
*
209320 AACATGTTCACGAACA
1 AACATGTTTACGAACA
209336 ATGTTAATGA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 15 0.45
24 18 0.55
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.29
Consensus pattern (23 bp):
AACATGTTTACGAACATTAAACG
Found at i:212943 original size:32 final size:31
Alignment explanation
Indices: 212875--212945 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
212865 AATAACTAAT
* **
212875 TAAATTTTTTTAAATAATCTAGTGACTTAAA
1 TAAATTTTTTTAAATAATCTAATGACAAAAA
* *
212906 TAAATTTTTTTGAATAATTTAATGACAAAAA
1 TAAATTTTTTTAAATAATCTAATGACAAAAA
*
212937 TAAAATTTT
1 TAAATTTTT
212946 AATCATAATA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (31 bp):
TAAATTTTTTTAAATAATCTAATGACAAAAA
Found at i:215543 original size:2 final size:2
Alignment explanation
Indices: 215536--215570 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
215526 CTCTTGCCCT
215536 TA TA TA TA 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 T
215571 GTAAGCTCTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:221951 original size:23 final size:23
Alignment explanation
Indices: 221591--221950 Score: 463
Period size: 23 Copynumber: 15.7 Consensus size: 23
221581 TCTAATTGCA
*
221591 CATAAATCGCATTAATATTTAAG
1 CATAAATCACATTAATATTTAAG
*
221614 CAAAAATCACATTAATATTTAAG
1 CATAAATCACATTAATATTTAAG
* * *
221637 CATAAATCATATTTACATTTAAG
1 CATAAATCACATTAATATTTAAG
* * *
221660 CATAAATCATATTTACATTTAAG
1 CATAAATCACATTAATATTTAAG
221683 CATAAATCACATTAATATTTAAG
1 CATAAATCACATTAATATTTAAG
*
221706 CACAAATCACATTAATATTTAAG
1 CATAAATCACATTAATATTTAAG
* *
221729 CACAAATCACGTTAACT-TTTAAG
1 CATAAATCACATTAA-TATTTAAG
* *
221752 CATAAATCATATTAACATTTAAG
1 CATAAATCACATTAATATTTAAG
221775 CATAAATCACATTAATATTTAAG
1 CATAAATCACATTAATATTTAAG
*
221798 TATAAATCACATTAATATTTAAG
1 CATAAATCACATTAATATTTAAG
*
221821 CAGAAATCACATTAATATTTAAG
1 CATAAATCACATTAATATTTAAG
*
221844 CAGAAATCACATTAATATTTAAG
1 CATAAATCACATTAATATTTAAG
* * *
221867 TAGAAAGCACATTAATATTTAAG
1 CATAAATCACATTAATATTTAAG
* * *
221890 TAGAAATCACATTAATATTTATG
1 CATAAATCACATTAATATTTAAG
* * *
221913 CACAAATTACATTAACT-TTTATG
1 CATAAATCACATTAA-TATTTAAG
221936 CATAAATCACATTAA
1 CATAAATCACATTAA
221951 CATCTAACAT
Statistics
Matches: 305, Mismatches: 29, Indels: 6
0.90 0.09 0.02
Matches are distributed among these distances:
23 303 0.99
24 2 0.01
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.34
Consensus pattern (23 bp):
CATAAATCACATTAATATTTAAG
Found at i:222466 original size:36 final size:35
Alignment explanation
Indices: 222386--222485 Score: 139
Period size: 36 Copynumber: 2.8 Consensus size: 35
222376 CTATCACATT
**
222386 GCATGAATAACATACACCACATATTTAC-TCTTTTG
1 GCATGAATAACATAC-CCACATATTTACTTCTCATG
*
222421 GCATGAATAACGTACCCACATATTTACTGTCTCATG
1 GCATGAATAACATACCCACATATTTACT-TCTCATG
*
222457 GCATGAATAACATACCCATATATTTACTT
1 GCATGAATAACATACCCACATATTTACTT
222486 TCACAACAGT
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
34 12 0.21
35 15 0.26
36 31 0.53
ACGTcount: A:0.34, C:0.23, G:0.10, T:0.33
Consensus pattern (35 bp):
GCATGAATAACATACCCACATATTTACTTCTCATG
Found at i:224342 original size:20 final size:20
Alignment explanation
Indices: 224300--224352 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
224290 AACGGATGAG
** *
224300 GATATGATATGATTCGTTAT
1 GATATGATATGACACATTAT
*
224320 GATATGATATGACACATTTT
1 GATATGATATGACACATTAT
224340 GATTTATGATATG
1 GA--TATGATATG
224353 CTCTGATATG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 18 0.67
22 9 0.33
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.43
Consensus pattern (20 bp):
GATATGATATGACACATTAT
Found at i:226894 original size:21 final size:22
Alignment explanation
Indices: 226870--226910 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
226860 CTAACCTCTT
226870 TGTCACAACA-CGACTCCTGTG
1 TGTCACAACATCGACTCCTGTG
* *
226891 TGTCACCACATTGACTCCTG
1 TGTCACAACATCGACTCCTG
226911 GACGCAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.22, C:0.34, G:0.17, T:0.27
Consensus pattern (22 bp):
TGTCACAACATCGACTCCTGTG
Found at i:229287 original size:15 final size:15
Alignment explanation
Indices: 229267--229299 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
229257 TATGGTTTTC
229267 TTTATTTTT-TATTAT
1 TTTATTTTTAT-TTAT
229282 TTTATTTTTATTTAT
1 TTTATTTTTATTTAT
229297 TTT
1 TTT
229300 TCAACTTTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 16 0.94
16 1 0.06
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTATTTTTATTTAT
Found at i:235593 original size:5 final size:5
Alignment explanation
Indices: 235577--235620 Score: 54
Period size: 5 Copynumber: 8.8 Consensus size: 5
235567 TGGAAAAAGA
* *
235577 TTTAT TTCAT TTTA- TTTAT TTTAT TTTCAT TTTAT TTTAG TTTA
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT-AT TTTAT TTTAT TTTA
235621 ACATTTATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
4 4 0.12
5 25 0.74
6 5 0.15
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (5 bp):
TTTAT
Found at i:235595 original size:14 final size:15
Alignment explanation
Indices: 235576--235613 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
235566 TTGGAAAAAG
235576 ATTTATTTCATTTT-
1 ATTTATTTCATTTTC
*
235590 ATTTATTTTATTTTC
1 ATTTATTTCATTTTC
235605 ATTTTATTT
1 A-TTTATTT
235614 TAGTTTAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.62
15 1 0.05
16 7 0.33
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (15 bp):
ATTTATTTCATTTTC
Found at i:236636 original size:32 final size:32
Alignment explanation
Indices: 236600--236662 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
236590 ACTCAAGCTC
236600 ATTTTCTT-TTTCTTTCTT-TGTTTGTTTGCTTT
1 ATTTTCTTGTTT-TTTCTTGT-TTTGTTTGCTTT
*
236632 ATTTTGTTGTTTTTTCTTGTTTTGTTTGCTT
1 ATTTTCTTGTTTTTTCTTGTTTTGTTTGCTT
236663 GAGGCAAGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 24 0.86
33 4 0.14
ACGTcount: A:0.03, C:0.10, G:0.13, T:0.75
Consensus pattern (32 bp):
ATTTTCTTGTTTTTTCTTGTTTTGTTTGCTTT
Found at i:241971 original size:16 final size:16
Alignment explanation
Indices: 241952--241999 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 16
241942 CTCTTTGTGC
*
241952 TTCTTTTTCTTGTCCT
1 TTCTTTTTCTTTTCCT
* *
241968 TTCTCTTTCTTTTCTT
1 TTCTTTTTCTTTTCCT
241984 TTC-TTTTCTTTTCCT
1 TTCTTTTTCTTTTCCT
241999 T
1 T
242000 GGAGTCAACC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
15 11 0.41
16 16 0.59
ACGTcount: A:0.00, C:0.25, G:0.02, T:0.73
Consensus pattern (16 bp):
TTCTTTTTCTTTTCCT
Found at i:241982 original size:21 final size:20
Alignment explanation
Indices: 241956--241996 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
241946 TTGTGCTTCT
241956 TTTTCTTGTCCTTTCTCTTTC
1 TTTTCTTGTCCTTTCT-TTTC
* *
241977 TTTTCTTTTCTTTTCTTTTC
1 TTTTCTTGTCCTTTCTTTTC
241997 CTTGGAGTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.73
Consensus pattern (20 bp):
TTTTCTTGTCCTTTCTTTTC
Found at i:241983 original size:5 final size:5
Alignment explanation
Indices: 241956--241996 Score: 55
Period size: 5 Copynumber: 8.0 Consensus size: 5
241946 TTGTGCTTCT
* *
241956 TTTTC TTGTC CTTTC TCTTTC TTTTC TTTTC TTTTC TTTTC
1 TTTTC TTTTC TTTTC T-TTTC TTTTC TTTTC TTTTC TTTTC
241997 CTTGGAGTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
5 26 0.84
6 5 0.16
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.73
Consensus pattern (5 bp):
TTTTC
Found at i:244176 original size:7 final size:7
Alignment explanation
Indices: 244160--244202 Score: 65
Period size: 7 Copynumber: 6.6 Consensus size: 7
244150 GAAATGAATG
244160 AAAA-TA
1 AAAAGTA
244166 AAAAGTA
1 AAAAGTA
244173 AAAAGT-
1 AAAAGTA
244179 AAAAGTA
1 AAAAGTA
244186 AAAAGT-
1 AAAAGTA
244192 AAAAGTA
1 AAAAGTA
244199 AAAA
1 AAAA
244203 TTACAATGAC
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
6 16 0.47
7 18 0.53
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.14
Consensus pattern (7 bp):
AAAAGTA
Found at i:244182 original size:13 final size:13
Alignment explanation
Indices: 244166--244202 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
244156 AATGAAAATA
244166 AAAAGTAAAAAGT
1 AAAAGTAAAAAGT
244179 AAAAGTAAAAAGT
1 AAAAGTAAAAAGT
244192 AAAAGTAAAAA
1 AAAAGTAAAAA
244203 TTACAATGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.14
Consensus pattern (13 bp):
AAAAGTAAAAAGT
Found at i:248571 original size:18 final size:18
Alignment explanation
Indices: 248550--248589 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
248540 TTATATGACT
*
248550 GCATCTGATTTTGTGATC
1 GCATCTGATCTTGTGATC
* *
248568 GCATCTGGTCTTGTGGTC
1 GCATCTGATCTTGTGATC
248586 GCAT
1 GCAT
248590 ATTATCTGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.12, C:0.20, G:0.28, T:0.40
Consensus pattern (18 bp):
GCATCTGATCTTGTGATC
Found at i:258657 original size:25 final size:24
Alignment explanation
Indices: 258629--258690 Score: 56
Period size: 25 Copynumber: 2.5 Consensus size: 24
258619 AGACTTGAAC
258629 AATAACAAAAATAAAATAAAATAAA
1 AATAACAAAAAT-AAATAAAATAAA
**
258654 AAT-ACATAATAATAAATTCAATAAA
1 AATAACA-AA-AATAAATAAAATAAA
258679 AATTAA-AAAAAT
1 AA-TAACAAAAAT
258691 TTGACCAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
24 6 0.19
25 19 0.61
26 5 0.16
27 1 0.03
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.23
Consensus pattern (24 bp):
AATAACAAAAATAAATAAAATAAA
Found at i:258667 original size:16 final size:17
Alignment explanation
Indices: 258629--258669 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
258619 AGACTTGAAC
*
258629 AATAACAAAAATAAAAT
1 AATAATAAAAATAAAAT
*
258646 AA-AATAAAAAT-ACAT
1 AATAATAAAAATAAAAT
258661 AATAATAAA
1 AATAATAAA
258670 TTCAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 5 0.24
16 14 0.67
17 2 0.10
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.20
Consensus pattern (17 bp):
AATAATAAAAATAAAAT
Found at i:259396 original size:37 final size:37
Alignment explanation
Indices: 259346--259419 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
259336 TTACTACTAA
* * *
259346 TGTCACTGCATGAGCACTTTTAGATTGCACCCAAAAC
1 TGTCACCGCATGAGCACTTCTAGACTGCACCCAAAAC
259383 TGTCACCGCATGAGCACTTCTAGACTGCACCCAAAAC
1 TGTCACCGCATGAGCACTTCTAGACTGCACCCAAAAC
259420 AGTCGTCATA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.30, C:0.31, G:0.16, T:0.23
Consensus pattern (37 bp):
TGTCACCGCATGAGCACTTCTAGACTGCACCCAAAAC
Found at i:259472 original size:37 final size:38
Alignment explanation
Indices: 259431--259549 Score: 102
Period size: 38 Copynumber: 3.2 Consensus size: 38
259421 GTCGTCATAG
259431 AAATATT-TTCAGATTGCACCTAAGACTATCACTGGAT
1 AAATATTCTTCAGATTGCACCTAAGACTATCACTGGAT
* * **
259468 AAATATTCTTCAAATTGCATCT-AGAACTATTGC-GGCAT
1 AAATATTCTTCAGATTGCACCTAAG-ACTATCACTGG-AT
* * * * *
259506 AAGTATTCTTCA-ATTGCACCCAAGAATGTCACTGCAT
1 AAATATTCTTCAGATTGCACCTAAGACTATCACTGGAT
*
259543 GAATATT
1 AAATATT
259550 TCCAGAATTG
Statistics
Matches: 63, Mismatches: 14, Indels: 10
0.72 0.16 0.11
Matches are distributed among these distances:
37 29 0.46
38 34 0.54
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.33
Consensus pattern (38 bp):
AAATATTCTTCAGATTGCACCTAAGACTATCACTGGAT
Found at i:259497 original size:38 final size:38
Alignment explanation
Indices: 259431--259549 Score: 102
Period size: 37 Copynumber: 3.2 Consensus size: 38
259421 GTCGTCATAG
*
259431 AAATATT-TTCAGATTGCACCTAAGACTATCACTGG-AT
1 AAATATTCTTCAAATTGCACCTAAGACTATCAC-GGCAT
* **
259468 AAATATTCTTCAAATTGCATCT-AGAACTATTGCGGCAT
1 AAATATTCTTCAAATTGCACCTAAG-ACTATCACGGCAT
* * * * *
259506 AAGTATTCTTC-AATTGCACCCAAGAATGTCACTGCAT
1 AAATATTCTTCAAATTGCACCTAAGACTATCACGGCAT
*
259543 GAATATT
1 AAATATT
259550 TCCAGAATTG
Statistics
Matches: 64, Mismatches: 14, Indels: 8
0.74 0.16 0.09
Matches are distributed among these distances:
37 32 0.50
38 32 0.50
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.33
Consensus pattern (38 bp):
AAATATTCTTCAAATTGCACCTAAGACTATCACGGCAT
Found at i:259566 original size:26 final size:26
Alignment explanation
Indices: 259528--259585 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
259518 ATTGCACCCA
* * *
259528 AGAA-TGTCACTGCATGAATATTTCC
1 AGAATTGTAACTGCATGAACATGTCC
*
259553 AGAATTGTAACTGCATGAACGTGTCC
1 AGAATTGTAACTGCATGAACATGTCC
259579 AGAATTG
1 AGAATTG
259586 CGCCCAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 4 0.14
26 24 0.86
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (26 bp):
AGAATTGTAACTGCATGAACATGTCC
Found at i:262261 original size:48 final size:48
Alignment explanation
Indices: 262190--262289 Score: 191
Period size: 48 Copynumber: 2.1 Consensus size: 48
262180 GCGTAAAAAA
262190 ATCTAGGTAGGCTAGCAAGTGGAGGTAAACGTATCCTACAGTGTTATT
1 ATCTAGGTAGGCTAGCAAGTGGAGGTAAACGTATCCTACAGTGTTATT
*
262238 ATCTAGGTAGGCTAGCAAGTGGAGGTAAAGGTATCCTACAGTGTTATT
1 ATCTAGGTAGGCTAGCAAGTGGAGGTAAACGTATCCTACAGTGTTATT
262286 ATCT
1 ATCT
262290 CTAAGATAGA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (48 bp):
ATCTAGGTAGGCTAGCAAGTGGAGGTAAACGTATCCTACAGTGTTATT
Found at i:289366 original size:43 final size:43
Alignment explanation
Indices: 289279--289457 Score: 184
Period size: 43 Copynumber: 4.1 Consensus size: 43
289269 TTAATGACAT
* * * * *
289279 TGAGAGGAACAGTGTTTCCTAAATATTGAATGTATGTGACTGAA
1 TGAGAGGAAAACTATTTCCT-AATATTGAAAGTATGTGATTGAA
*
289323 TGAGAGGAAAACTATTTCCTAATATTAAAAGTATGTGATTGAA
1 TGAGAGGAAAACTATTTCCTAATATTGAAAGTATGTGATTGAA
* * * * *
289366 TGA-ATGAAACATTGTTTCCTAATACTGAAAGTATGTGATCGAA
1 TGAGAGGAAA-ACTATTTCCTAATATTGAAAGTATGTGATTGAA
* *
289409 TGA-ATGGAACACTATTTCCTAATATTGATAGTATGTGATT-AA
1 TGAGA-GGAAAACTATTTCCTAATATTGAAAGTATGTGATTGAA
289451 TTGAGAG
1 -TGAGAG
289458 CATGATAAAT
Statistics
Matches: 112, Mismatches: 19, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
42 7 0.06
43 84 0.75
44 21 0.19
ACGTcount: A:0.37, C:0.09, G:0.21, T:0.34
Consensus pattern (43 bp):
TGAGAGGAAAACTATTTCCTAATATTGAAAGTATGTGATTGAA
Found at i:289925 original size:21 final size:21
Alignment explanation
Indices: 289899--289969 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
289889 TAGGTATGAG
289899 ATTGTTTATGTTTGATGCTTT
1 ATTGTTTATGTTTGATGCTTT
** **
289920 ATTGTTTA-GTCTCAAT-CTGAG
1 ATTGTTTATGT-TTGATGCT-TT
289941 ATTGTTTATGTTTGATGCTTT
1 ATTGTTTATGTTTGATGCTTT
289962 ATTGTTTA
1 ATTGTTTA
289970 GTCTCAATTT
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
20 4 0.11
21 30 0.79
22 4 0.11
ACGTcount: A:0.18, C:0.07, G:0.18, T:0.56
Consensus pattern (21 bp):
ATTGTTTATGTTTGATGCTTT
Found at i:289954 original size:42 final size:42
Alignment explanation
Indices: 289895--289988 Score: 170
Period size: 42 Copynumber: 2.2 Consensus size: 42
289885 TTGCTAGGTA
289895 TGAGATTGTTTATGTTTGATGCTTTATTGTTTAGTCTCAATC
1 TGAGATTGTTTATGTTTGATGCTTTATTGTTTAGTCTCAATC
*
289937 TGAGATTGTTTATGTTTGATGCTTTATTGTTTAGTCTCAATT
1 TGAGATTGTTTATGTTTGATGCTTTATTGTTTAGTCTCAATC
*
289979 TGAGTTTGTT
1 TGAGATTGTT
289989 AAGCTTACCC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.18, C:0.07, G:0.20, T:0.54
Consensus pattern (42 bp):
TGAGATTGTTTATGTTTGATGCTTTATTGTTTAGTCTCAATC
Found at i:300888 original size:20 final size:20
Alignment explanation
Indices: 300848--300917 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
300838 AGTTTGAAAC
*
300848 AATTTTAAAATCAAGTTAAAAT
1 AATTTT-AAA-CAAGTCAAAAT
*
300870 TATTTTAAACAAGTCAAAAT
1 AATTTTAAACAAGTCAAAAT
** *
300890 AATTGGAACCAAGTCAAAAT
1 AATTTTAAACAAGTCAAAAT
*
300910 CATTTTAA
1 AATTTTAA
300918 CACTTCAAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 31 0.79
21 3 0.08
22 5 0.13
ACGTcount: A:0.50, C:0.10, G:0.07, T:0.33
Consensus pattern (20 bp):
AATTTTAAACAAGTCAAAAT
Found at i:303778 original size:16 final size:16
Alignment explanation
Indices: 303745--303787 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
303735 CCAAAGTATT
*
303745 CTAAATTAAACT-AAA
1 CTAAATTAAATTAAAA
*
303760 CTAAGTTAAATTAAAA
1 CTAAATTAAATTAAAA
303776 CTAAATTAAATT
1 CTAAATTAAATT
303788 TCTATGCACG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.56, C:0.09, G:0.02, T:0.33
Consensus pattern (16 bp):
CTAAATTAAATTAAAA
Found at i:323930 original size:3 final size:3
Alignment explanation
Indices: 323922--323947 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
323912 TCAAAACCCA
323922 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
323948 GTAAAACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:324378 original size:28 final size:29
Alignment explanation
Indices: 324329--324388 Score: 95
Period size: 28 Copynumber: 2.1 Consensus size: 29
324319 AAATCTACAG
* *
324329 AATAACGAATAAATGCGATAAAGATTGCC
1 AATAACAAATAAATGCGATAAAGATCGCC
324358 AATAACAAAT-AATGCGATAAAGATCGCC
1 AATAACAAATAAATGCGATAAAGATCGCC
324386 AAT
1 AAT
324389 CCACTCAGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 20 0.69
29 9 0.31
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.20
Consensus pattern (29 bp):
AATAACAAATAAATGCGATAAAGATCGCC
Found at i:324663 original size:43 final size:42
Alignment explanation
Indices: 324597--324745 Score: 178
Period size: 43 Copynumber: 3.5 Consensus size: 42
324587 ACAAACTATC
* * *
324597 AATAATAGGAAATAGTGTTCCATTCATTCGACCACATACTTTT
1 AATATTAGGAAACAGTGTTCCATTCATTC-ATCACATACTTTT
*
324640 AGTATTAGGAAACAGTGTTCCATTCATTCAATCACATACTTTT
1 AATATTAGGAAACAGTGTTCCATTCATTC-ATCACATACTTTT
* *
324683 AATATTAGGAAACA--GTTCC-TCTCATTCAGTCACATACATTC
1 AATATTAGGAAACAGTGTTCCAT-TCATTCA-TCACATACTTTT
324724 AATATTTAGGAAACAGTGTTCC
1 AATA-TTAGGAAACAGTGTTCC
324746 TCTCAATGTC
Statistics
Matches: 93, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
40 2 0.02
41 25 0.27
42 10 0.11
43 51 0.55
44 5 0.05
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.34
Consensus pattern (42 bp):
AATATTAGGAAACAGTGTTCCATTCATTCATCACATACTTTT
Found at i:324692 original size:86 final size:85
Alignment explanation
Indices: 324583--324745 Score: 188
Period size: 84 Copynumber: 1.9 Consensus size: 85
324573 GCTCTCAATT
* * * *
324583 AATCACAAACTATCAATAATAGGAAATAGTGTTCCAT-TCATTC-GACCACATACTTTTAGTA-T
1 AATCACAAACTATCAATAATAGGAAACA--GTTCC-TCTCATTCAG-CCACATACATTCAATATT
324645 TAGGAAACAGTGTTCCATTCATTC
62 TAGGAAACAGTGTTCCATTCATTC
* * * * *
324669 AATCACATACTTTTAATATTAGGAAACAGTTCCTCTCATTCAGTCACATACATTCAATATTTAGG
1 AATCACAAACTATCAATAATAGGAAACAGTTCCTCTCATTCAGCCACATACATTCAATATTTAGG
324734 AAACAGTGTTCC
66 AAACAGTGTTCC
324746 TCTCAATGTC
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
83 1 0.02
84 23 0.35
85 18 0.28
86 23 0.35
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.33
Consensus pattern (85 bp):
AATCACAAACTATCAATAATAGGAAACAGTTCCTCTCATTCAGCCACATACATTCAATATTTAGG
AAACAGTGTTCCATTCATTC
Found at i:324716 original size:41 final size:42
Alignment explanation
Indices: 324574--324750 Score: 164
Period size: 43 Copynumber: 4.1 Consensus size: 42
324564 ATTTATCATG
* * * * *
324574 CTCTCAATT-AATCACAAACTATCAATAATAGGAAATAGTGTTC
1 CTCTC-ATTCAATCACATACTTTTAATATTAGGAAACAG-GTTC
* * *
324617 CAT-TCATTCGACCACATACTTTTAGTATTAGGAAACAGTGTTC
1 C-TCTCATTCAATCACATACTTTTAATATTAGGAAACAG-GTTC
324660 CAT-TCATTCAATCACATACTTTTAATATTAGGAAACA-GTTC
1 C-TCTCATTCAATCACATACTTTTAATATTAGGAAACAGGTTC
* * *
324701 CTCTCATTCAGTCACATACATTCAATATTTAGGAAACAGTGTTC
1 CTCTCATTCAATCACATACTTTTAATA-TTAGGAAACAG-GTTC
324745 CTCTCA
1 CTCTCA
324751 ATGTCATTAA
Statistics
Matches: 114, Mismatches: 14, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
40 1 0.01
41 26 0.23
42 13 0.11
43 63 0.55
44 11 0.10
ACGTcount: A:0.34, C:0.21, G:0.10, T:0.34
Consensus pattern (42 bp):
CTCTCATTCAATCACATACTTTTAATATTAGGAAACAGGTTC
Found at i:331135 original size:26 final size:25
Alignment explanation
Indices: 331060--331135 Score: 59
Period size: 25 Copynumber: 3.1 Consensus size: 25
331050 TGTAATAGGG
* * *
331060 GAATTTTTTGGA-ATAAGATTCAAA
1 GAATTTTTTTGAGACAACATTCAAA
* * * *
331084 G--TTTTTTTTATACAACATTTAGA
1 GAATTTTTTTGAGACAACATTCAAA
331107 GAATTTTTTTGAGACATACATTCAAA
1 GAATTTTTTTGAGACA-ACATTCAAA
331133 GAA
1 GAA
331136 AATTCAAAAC
Statistics
Matches: 38, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
22 7 0.18
23 9 0.24
24 1 0.03
25 11 0.29
26 10 0.26
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.41
Consensus pattern (25 bp):
GAATTTTTTTGAGACAACATTCAAA
Found at i:331485 original size:13 final size:13
Alignment explanation
Indices: 331459--331508 Score: 55
Period size: 13 Copynumber: 3.6 Consensus size: 13
331449 ACATTTAATT
*
331459 TTTATTTTTATTTA
1 TTTA-TTTTGTTTA
331473 TTTATTTTGTTTA
1 TTTATTTTGTTTA
*
331486 TTTATCTTGTTGTTA
1 TTTATTTTG-T-TTA
331501 TTTATTTT
1 TTTATTTT
331509 CATGTCATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
13 16 0.52
14 5 0.16
15 10 0.32
ACGTcount: A:0.16, C:0.02, G:0.06, T:0.76
Consensus pattern (13 bp):
TTTATTTTGTTTA
Found at i:343326 original size:24 final size:24
Alignment explanation
Indices: 343294--343345 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
343284 AAAGAAGAAG
343294 GATAAGCATCCTCATGCGCCCATA
1 GATAAGCATCCTCATGCGCCCATA
343318 GATAAGCATCCTCATGCGCCCATA
1 GATAAGCATCCTCATGCGCCCATA
343342 GATA
1 GATA
343346 CTCAACTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.21
Consensus pattern (24 bp):
GATAAGCATCCTCATGCGCCCATA
Found at i:349518 original size:13 final size:12
Alignment explanation
Indices: 349496--349525 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
349486 GTTGAATGAG
349496 AAAAAGAAAAGA
1 AAAAAGAAAAGA
349508 AAAAGAGAAAAGA
1 AAAA-AGAAAAGA
349521 AAAAA
1 AAAAA
349526 ATAAATATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAGA
Found at i:354743 original size:20 final size:20
Alignment explanation
Indices: 354718--354758 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
354708 CATTGCTACT
354718 TAGTGAAGTCAGTGATACAC
1 TAGTGAAGTCAGTGATACAC
354738 TAGTGAAGTCAGTGATACAC
1 TAGTGAAGTCAGTGATACAC
354758 T
1 T
354759 CCATTCTTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (20 bp):
TAGTGAAGTCAGTGATACAC
Found at i:357179 original size:17 final size:17
Alignment explanation
Indices: 357159--357212 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
357149 TGTCCCTACC
357159 TTTTTATTGTCATTGCA
1 TTTTTATTGTCATTGCA
* *
357176 TTTTTATTGTCACTACA
1 TTTTTATTGTCATTGCA
* **
357193 TCTACATTGTCATTGCA
1 TTTTTATTGTCATTGCA
357210 TTT
1 TTT
357213 CCATATATAT
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.20, C:0.17, G:0.09, T:0.54
Consensus pattern (17 bp):
TTTTTATTGTCATTGCA
Found at i:369514 original size:26 final size:26
Alignment explanation
Indices: 369478--369531 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
369468 ATTTTAGGTG
*
369478 CAATTCTTGACACGTTCATGCAGCGA
1 CAATTCTTGACACGTTCATGCAACGA
*
369504 CAATTCTTGACATGTTCATGCAACGA
1 CAATTCTTGACACGTTCATGCAACGA
369530 CA
1 CA
369532 TTCCTAGGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.28
Consensus pattern (26 bp):
CAATTCTTGACACGTTCATGCAACGA
Found at i:369562 original size:37 final size:38
Alignment explanation
Indices: 369521--369592 Score: 96
Period size: 37 Copynumber: 1.9 Consensus size: 38
369511 TGACATGTTC
369521 ATGCAACGACA-TTCCTAGG-TGCAA-TTGAAGAATACAT
1 ATGCAACGACAGTT-C-AGGATGCAATTTGAAGAATACAT
*
369558 ATGCAACGATAGTTCAGGATGCAATTTGAAGAATA
1 ATGCAACGACAGTTCAGGATGCAATTTGAAGAATA
369593 TTTATGCTGC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
36 3 0.10
37 16 0.52
38 12 0.39
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (38 bp):
ATGCAACGACAGTTCAGGATGCAATTTGAAGAATACAT
Found at i:369675 original size:37 final size:37
Alignment explanation
Indices: 369634--369709 Score: 89
Period size: 37 Copynumber: 2.1 Consensus size: 37
369624 AAAATATTCC
* * * *
369634 TGCGATGACAATTTTGGGTGCAATCTGGAAGTACTCA
1 TGCGACGACAATTTTGAGTGAAATCTAGAAGTACTCA
* * *
369671 TGCGACGATAGTTTTGAGTGAAATCTAGAAGTGCTCA
1 TGCGACGACAATTTTGAGTGAAATCTAGAAGTACTCA
369708 TG
1 TG
369710 TAGCGACATT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (37 bp):
TGCGACGACAATTTTGAGTGAAATCTAGAAGTACTCA
Found at i:373068 original size:16 final size:16
Alignment explanation
Indices: 373047--373077 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
373037 ATAATGTGAA
373047 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
373063 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
373078 GGATTCACAA
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:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:373911 original size:26 final size:25
Alignment explanation
Indices: 373871--373925 Score: 83
Period size: 26 Copynumber: 2.2 Consensus size: 25
373861 TTTAGGTCCA
373871 ATTCTAGACACGTTCATGCAGCGAC
1 ATTCTAGACACGTTCATGCAGCGAC
* *
373896 TATTCTGGACATGTTCATGCAGCGAC
1 -ATTCTAGACACGTTCATGCAGCGAC
373922 ATTC
1 ATTC
373926 GAAGGTGCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 4 0.15
26 23 0.85
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.29
Consensus pattern (25 bp):
ATTCTAGACACGTTCATGCAGCGAC
Found at i:374001 original size:38 final size:37
Alignment explanation
Indices: 373931--374002 Score: 90
Period size: 38 Copynumber: 1.9 Consensus size: 37
373921 CATTCGAAGG
* *
373931 TGCAATTGAAGAATACTTATGCAACGATAGTTTTGGA
1 TGCAATTGAAGAATACTTATGCAACAACAGTTTTGGA
* **
373968 TGCAATTTGAAGAATATTTATGCTGCAACAGTTTT
1 TGCAA-TTGAAGAATACTTATGCAACAACAGTTTT
374003 AGGTGTATTC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
37 5 0.17
38 24 0.83
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.36
Consensus pattern (37 bp):
TGCAATTGAAGAATACTTATGCAACAACAGTTTTGGA
Found at i:374525 original size:45 final size:45
Alignment explanation
Indices: 374457--374901 Score: 457
Period size: 45 Copynumber: 9.8 Consensus size: 45
374447 CCCCAAATCT
* * * * *
374457 AATCTTATACACCTAATCCAGAGGGGTATATTGAAGCCACCATCC
1 AATCTTTTACCCCTAATCTAGAGGGGAAGATTGAAGCCACCATCC
* * * *
374502 AATCTTTTACCTCTAATCTAGAGGAGAAGATTAAAGCCACCATATGC
1 AATCTTTTACCCCTAATCTAGAGGGGAAGATTGAAGCCACC--ATCC
* * *
374549 AATCATTTACCCCTATTCCAGAGGGGAAGATTGAAGCCACCATCC
1 AATCTTTTACCCCTAATCTAGAGGGGAAGATTGAAGCCACCATCC
** * * * *
374594 AATCTTTTACCCCTAATCTAGAGAAGCAGATTGAAACCATCATCA
1 AATCTTTTACCCCTAATCTAGAGGGGAAGATTGAAGCCACCATCC
* *
374639 AATCTTTTACCCCTAATCCAGATGGGTAA-ATTGAAGCCACCATCC
1 AATCTTTTACCCCTAATCTAGA-GGGGAAGATTGAAGCCACCATCC
* * *
374684 AATCTTATACCCCTAATCTAGAGGGGTAGATTGAAGCCACCATCA
1 AATCTTTTACCCCTAATCTAGAGGGGAAGATTGAAGCCACCATCC
* * * *
374729 AATCTTTTACCCCTAATCTAGAAGGGCAGATTTAAGCTACCATCC
1 AATCTTTTACCCCTAATCTAGAGGGGAAGATTGAAGCCACCATCC
* * * *
374774 AATCTTTTACCCTTAAATCTAAAAGGAAAGATTGAAGCCACCATCC
1 AATCTTTTACCCCT-AATCTAGAGGGGAAGATTGAAGCCACCATCC
* * * *
374820 AATTTTTTA-CCCTCAATCCAAAAGGGG-AGATTGAAGCCACTATCC
1 AATCTTTTACCCCT-AAT-CTAGAGGGGAAGATTGAAGCCACCATCC
* *
374865 ACTCTCTTACCCCTAAATCTAGAGGGGCAA-ATTGAAG
1 AATCTTTTACCCCT-AATCTAGAGGGG-AAGATTGAAG
374902 TTACAGAAAG
Statistics
Matches: 328, Mismatches: 63, Indels: 17
0.80 0.15 0.04
Matches are distributed among these distances:
44 4 0.01
45 229 0.70
46 56 0.17
47 39 0.12
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.26
Consensus pattern (45 bp):
AATCTTTTACCCCTAATCTAGAGGGGAAGATTGAAGCCACCATCC
Found at i:375739 original size:21 final size:21
Alignment explanation
Indices: 375690--375732 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
375680 GTTAGTCTTT
*
375690 TTTA-TTA-TTATTATTTATA
1 TTTAGTTATTTATTATTTACA
375709 TTTAGTTATTTATTA-TTACA
1 TTTAGTTATTTATTATTTACA
375729 TTTA
1 TTTA
375733 ATTTATTGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 4 0.19
20 11 0.52
21 6 0.29
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (21 bp):
TTTAGTTATTTATTATTTACA
Found at i:375912 original size:44 final size:47
Alignment explanation
Indices: 375828--375919 Score: 109
Period size: 48 Copynumber: 2.0 Consensus size: 47
375818 TCTTTTAGCA
* * * *
375828 TTTTATTTTTATTTTTATTTATTTTGTTTATTTATCTTGTTGTTATCTC
1 TTTTATTATTATTTTTATTTAATTTG-TCATTTA-CTTGTTATTATCTC
375877 TTTTATTATTA-TTTTATTTAATTTG-CATTTA-TTGTTATTATCT
1 TTTTATTATTATTTTTATTTAATTTGTCATTTACTTGTTATTATCT
375920 TGTTTGTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
44 11 0.28
46 5 0.13
48 13 0.33
49 10 0.26
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.71
Consensus pattern (47 bp):
TTTTATTATTATTTTTATTTAATTTGTCATTTACTTGTTATTATCTC
Found at i:376045 original size:16 final size:16
Alignment explanation
Indices: 376024--376054 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
376014 ATTTTGTATA
376024 TTTATTTATTGATATT
1 TTTATTTATTGATATT
*
376040 TTTATTTATTTATAT
1 TTTATTTATTGATAT
376055 CTCATATTTT
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:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (16 bp):
TTTATTTATTGATATT
Found at i:385245 original size:2 final size:2
Alignment explanation
Indices: 385238--385263 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
385228 TTATTGAATA
385238 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
385264 TCTTCTTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:390562 original size:62 final size:62
Alignment explanation
Indices: 390465--390588 Score: 203
Period size: 62 Copynumber: 2.0 Consensus size: 62
390455 TAATGGGCAC
* *
390465 CTCTTTATCAACTTCACAATCAATTATAATGAAATCTGCTGGGAACACAAACTTATCGACAT
1 CTCTTTATCAACTTCACAATCAAGTATAATGAAATCTACTGGGAACACAAACTTATCGACAT
* * *
390527 CTCTTTATCAGCTTCACAATCAAGTATGATGAAATCTACTGGGAACACAAACTTGTCGACAT
1 CTCTTTATCAACTTCACAATCAAGTATAATGAAATCTACTGGGAACACAAACTTATCGACAT
390589 GGACGAGAAC
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 57 1.00
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.30
Consensus pattern (62 bp):
CTCTTTATCAACTTCACAATCAAGTATAATGAAATCTACTGGGAACACAAACTTATCGACAT
Found at i:403535 original size:26 final size:26
Alignment explanation
Indices: 403506--403559 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
403496 CACCCAGGAA
*
403506 TGTCGCTGCATGAACATGTCCAGAAT
1 TGTCGCTGCAAGAACATGTCCAGAAT
* *
403532 TGTCGTTGCAAGAACGTGTCCAGAAT
1 TGTCGCTGCAAGAACATGTCCAGAAT
403558 TG
1 TG
403560 CACCCAGAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (26 bp):
TGTCGCTGCAAGAACATGTCCAGAAT
Found at i:411921 original size:18 final size:18
Alignment explanation
Indices: 411880--411922 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
411870 GTGCAACCTG
411880 ATCAGATGCAGTCACATA
1 ATCAGATGCAGTCACATA
** * *
411898 CCCAGATGTAGTCATATA
1 ATCAGATGCAGTCACATA
411916 ATCAGAT
1 ATCAGAT
411923 ACAACCACAT
Statistics
Matches: 19, Mismatches: 6, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (18 bp):
ATCAGATGCAGTCACATA
Found at i:413671 original size:27 final size:27
Alignment explanation
Indices: 413633--413686 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
413623 CACGATGGTA
413633 AGCAATGATAAAAATAAACTAATCCCT
1 AGCAATGATAAAAATAAACTAATCCCT
* *
413660 AGCAATGATAAAAATGAAGTAATCCCT
1 AGCAATGATAAAAATAAACTAATCCCT
413687 TCTCGTATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.50, C:0.17, G:0.11, T:0.22
Consensus pattern (27 bp):
AGCAATGATAAAAATAAACTAATCCCT
Found at i:421757 original size:23 final size:23
Alignment explanation
Indices: 421722--421793 Score: 99
Period size: 23 Copynumber: 3.1 Consensus size: 23
421712 ATCTTAATTC
* * *
421722 TTTAAGAAAAAATCACATTAATA
1 TTTAAGCACAAATCATATTAATA
* *
421745 TTTAATCATAAATCATATTAATA
1 TTTAAGCACAAATCATATTAATA
421768 TTTAAGCACAAATCATATTAATA
1 TTTAAGCACAAATCATATTAATA
421791 TTT
1 TTT
421794 GATCTACTAG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.39
Consensus pattern (23 bp):
TTTAAGCACAAATCATATTAATA
Found at i:424305 original size:22 final size:21
Alignment explanation
Indices: 424271--424312 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
424261 AACAAGAAAA
* *
424271 TAGAAGAGCTTGAGGTCATAT
1 TAGAAGAGATTGAGATCATAT
424292 TAGATAGAGATTGAGATCATA
1 TAGA-AGAGATTGAGATCATA
424313 GCATGTATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.38, C:0.07, G:0.26, T:0.29
Consensus pattern (21 bp):
TAGAAGAGATTGAGATCATAT
Found at i:427310 original size:17 final size:17
Alignment explanation
Indices: 427278--427357 Score: 79
Period size: 17 Copynumber: 4.6 Consensus size: 17
427268 GCACTAACAC
*
427278 AATGACCAATGGAAATGT
1 AATGA-CAATGCAAATGT
*
427296 AATGACAATGCAAATGC
1 AATGACAATGCAAATGT
**
427313 AATGACAATTAAAATGT
1 AATGACAATGCAAATGT
* **
427330 CATGACAATGGGAATGT
1 AATGACAATGCAAATGT
*
427347 GATGACAATGC
1 AATGACAATGC
427358 TTACTCACAA
Statistics
Matches: 51, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
17 46 0.90
18 5 0.10
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.23
Consensus pattern (17 bp):
AATGACAATGCAAATGT
Found at i:445007 original size:15 final size:15
Alignment explanation
Indices: 444987--445021 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
444977 CACCCACGAT
*
444987 GAATGCTCGATTGAG
1 GAATGCGCGATTGAG
445002 GAATGCGCGATTGAG
1 GAATGCGCGATTGAG
445017 GAATG
1 GAATG
445022 ATATTACGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.29, C:0.11, G:0.37, T:0.23
Consensus pattern (15 bp):
GAATGCGCGATTGAG
Found at i:464663 original size:16 final size:18
Alignment explanation
Indices: 464637--464669 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
464627 TAATTGTCAT
464637 TGCATTTTTA-TTGTTTC
1 TGCATTTTTATTTGTTTC
464654 TGCA-TTTTATTTGTTT
1 TGCATTTTTATTTGTTT
464670 TAGCATATGC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.12, C:0.09, G:0.12, T:0.67
Consensus pattern (18 bp):
TGCATTTTTATTTGTTTC
Found at i:465257 original size:13 final size:14
Alignment explanation
Indices: 465239--465273 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
465229 TCAGTCGCAT
465239 AAAGAAAAGAAAA-
1 AAAGAAAAGAAAAG
465252 AAAGAAAA-AAAAG
1 AAAGAAAAGAAAAG
465265 AAAGAAAAG
1 AAAGAAAAG
465274 TTGATGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 4 0.20
13 16 0.80
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (14 bp):
AAAGAAAAGAAAAG
Found at i:470261 original size:22 final size:22
Alignment explanation
Indices: 470236--470290 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 22
470226 TGTGATTAAA
470236 CTGTTTCAAACCTAGCACGTCT
1 CTGTTTCAAACCTAGCACGTCT
470258 CTG-TT---ACCATAGCACGTCT
1 CTGTTTCAAACC-TAGCACGTCT
470277 CTGTTTCAAACCTA
1 CTGTTTCAAACCTA
470291 ATGTGGTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
18 3 0.11
19 13 0.46
20 2 0.07
21 2 0.07
22 5 0.18
23 3 0.11
ACGTcount: A:0.24, C:0.31, G:0.13, T:0.33
Consensus pattern (22 bp):
CTGTTTCAAACCTAGCACGTCT
Found at i:470743 original size:13 final size:13
Alignment explanation
Indices: 470727--470761 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
470717 CCTCAGTCAC
470727 ATAAAGAAAAGAG
1 ATAAAGAAAAGAG
470740 ATAAAGAAAAGAG
1 ATAAAGAAAAGAG
470753 ATAAAGAAA
1 ATAAAGAAA
470762 GAAAAGGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.71, C:0.00, G:0.20, T:0.09
Consensus pattern (13 bp):
ATAAAGAAAAGAG
Found at i:476801 original size:18 final size:18
Alignment explanation
Indices: 476756--476802 Score: 76
Period size: 19 Copynumber: 2.6 Consensus size: 18
476746 CACAAGTCAC
476756 TTGGTATTAGATATATAA
1 TTGGTATTAGATATATAA
*
476774 TTGTGTATTAGATATATGA
1 TTG-GTATTAGATATATAA
476793 TTGGTATTAG
1 TTGGTATTAG
476803 TGTTAGTGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 10 0.37
19 17 0.63
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (18 bp):
TTGGTATTAGATATATAA
Found at i:488931 original size:106 final size:107
Alignment explanation
Indices: 488790--488998 Score: 366
Period size: 106 Copynumber: 2.0 Consensus size: 107
488780 TTTACTGAAT
*
488790 ATAATTTAACGTAATTATAATTATTAATTATAATGATTTCGTTAAATATT-AAAACATGGAAGTT
1 ATAATTTAACGTAATTATAATTATTAATTATAATGATTTCGTTAAATATTAAAAACATGAAAGTT
*
488854 AATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCA
66 AATATACTTTTGGAAAGGATATAATGTTTTAATAAACCTTCA
*
488896 ATAATTTAACGTAATTATAATTATTAATTATAATGATTTCGTTCAATATTAAAAAACATGAAAGT
1 ATAATTTAACGTAATTATAATTATTAATTATAATGATTTCGTTAAATATT-AAAAACATGAAAGT
*
488961 TAATATACTTTTGGAAATGATATAATGTTTTAATAAAC
65 TAATATACTTTTGGAAAGGATATAATGTTTTAATAAAC
488999 TTTCCATATA
Statistics
Matches: 97, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
106 49 0.51
108 48 0.49
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.41
Consensus pattern (107 bp):
ATAATTTAACGTAATTATAATTATTAATTATAATGATTTCGTTAAATATTAAAAACATGAAAGTT
AATATACTTTTGGAAAGGATATAATGTTTTAATAAACCTTCA
Found at i:489072 original size:121 final size:126
Alignment explanation
Indices: 488940--489171 Score: 343
Period size: 121 Copynumber: 1.9 Consensus size: 126
488930 GATTTCGTTC
* *
488940 AATATTAAAAAACAT-GAAAGTTAATATACTTTTGGAAATGATATAATGTTTTAATAAA-CTTTC
1 AATATTAAAAAACATAG-AAGTTAATATACTTTTGAAAAGGATATAATGTTTTAATAAATCTTT-
*
489003 CATATATTT-TTTAAAG-GA-ATATTTCCA-TTTAATATGAGATATTATATAAAAAGAAATTG
64 CATATATTTCTCTAAAGAGATATATTTCCATTTTAATATGAGATATTATATAAAAAGAAATTG
*
489062 AATATT-AAAAACATAGAAGTTAATATCCTTTTGAAAAGGATATAATGTTTTAATAAATCTTTCA
1 AATATTAAAAAACATAGAAGTTAATATACTTTTGAAAAGGATATAATGTTTTAATAAATCTTTCA
* *
489126 TATATTTCTCTAAAGATATATATTTTCATTTTAATATGAGATATTA
66 TATATTTCTCTAAAGAGATATATTTCCATTTTAATATGAGATATTA
489172 AAATAAAAGG
Statistics
Matches: 98, Mismatches: 6, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
121 55 0.56
122 17 0.17
123 1 0.01
124 8 0.08
125 17 0.17
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (126 bp):
AATATTAAAAAACATAGAAGTTAATATACTTTTGAAAAGGATATAATGTTTTAATAAATCTTTCA
TATATTTCTCTAAAGAGATATATTTCCATTTTAATATGAGATATTATATAAAAAGAAATTG
Found at i:491772 original size:17 final size:17
Alignment explanation
Indices: 491731--491807 Score: 54
Period size: 17 Copynumber: 4.6 Consensus size: 17
491721 TCCACATGTA
* *
491731 ATGT-GAACCCTCATGT
1 ATGTGGAACCCCCATGC
491747 A-GTGCGAACCCCCATGC
1 ATGTG-GAACCCCCATGC
*
491764 ATGTGGAA-CCCC-TAC
1 ATGTGGAACCCCCATGC
* *
491779 ATGTGTAAACCCCCTTGC
1 ATGTG-GAACCCCCATGC
*
491797 ATGTGAAACCC
1 ATGTGGAACCC
491808 TATAGGTAAG
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
15 9 0.18
16 7 0.14
17 24 0.48
18 10 0.20
ACGTcount: A:0.26, C:0.32, G:0.19, T:0.22
Consensus pattern (17 bp):
ATGTGGAACCCCCATGC
Found at i:492366 original size:27 final size:27
Alignment explanation
Indices: 492296--492402 Score: 126
Period size: 27 Copynumber: 3.8 Consensus size: 27
492286 ACCATCTACA
* *
492296 AACCCCTAGGTGTGAACCATATAAGTGTG
1 AACCCCTAGGTGTGAACCCTAT--GTGCG
*
492325 AATCCCTAGGTGTGTGAACCCTATGTGCG
1 AACCCCTA-G-GTGTGAACCCTATGTGCG
*
492354 AGCCCCTAGGTGTGAACCC-ATTGTGCG
1 AACCCCTAGGTGTGAACCCTA-TGTGCG
492381 AACCCCTAGGTGTGAACCCTAT
1 AACCCCTAGGTGTGAACCCTAT
492403 ATGTGCTAAC
Statistics
Matches: 68, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
26 1 0.01
27 35 0.51
28 2 0.03
29 17 0.25
30 1 0.01
31 12 0.18
ACGTcount: A:0.24, C:0.26, G:0.25, T:0.24
Consensus pattern (27 bp):
AACCCCTAGGTGTGAACCCTATGTGCG
Found at i:492399 original size:14 final size:14
Alignment explanation
Indices: 492296--492399 Score: 77
Period size: 14 Copynumber: 7.4 Consensus size: 14
492286 ACCATCTACA
492296 AACCCCTAGGTGTG
1 AACCCCTAGGTGTG
** *
492310 AACCATATAAGTGTG
1 AACC-CCTAGGTGTG
*
492325 AATCCCTAGGTGTGTG
1 AACCCCTA-G-GTGTG
* *
492341 AA-CCCTATGTGCG
1 AACCCCTAGGTGTG
*
492354 AGCCCCTAGGTGTG
1 AACCCCTAGGTGTG
* * *
492368 AACCCAT-TGTGCG
1 AACCCCTAGGTGTG
492381 AACCCCTAGGTGTG
1 AACCCCTAGGTGTG
492395 AACCC
1 AACCC
492400 TATATGTGCT
Statistics
Matches: 66, Mismatches: 19, Indels: 10
0.69 0.20 0.11
Matches are distributed among these distances:
13 15 0.23
14 29 0.44
15 15 0.23
16 7 0.11
ACGTcount: A:0.24, C:0.27, G:0.26, T:0.23
Consensus pattern (14 bp):
AACCCCTAGGTGTG
Found at i:495619 original size:148 final size:146
Alignment explanation
Indices: 495137--495789 Score: 834
Period size: 147 Copynumber: 4.4 Consensus size: 146
495127 TTTTTAAAAC
* * * *
495137 AAAATCACTATTTTTCTTAAAAATCAAAACTTTTATTTCGAAATAGTTTAAAGGAAATC-AAATT
1 AAAATCACTATTTTTCTTAAAACTCCAAACTTTTATTTCGAAATAG-TTAAA-AAAATCAAAACT
* * *
495201 TTGTTTAAAAACTTAAACTTTTCTCTTTTAAAAT-ACCTAAAAAATATATTTTTATTTTTAAAAA
64 TTATTTAAAAATTTAAACTTTT-TC-TTTAAAATGA-CTAAAAAACATATTTTTATTTTTAAAAA
* *
495265 TCTAAACTTCCTTTTTTTTTT
126 TCTAAACTTTCTTTTTTTTAT
* * * **
495286 AAAAAACACTAATTTAT-TTAACAA-TCCAAATTTTTATTTCGAACA-AGTTAAAAATTTTCAAA
1 -AAAATCACT-ATTTTTCTTAA-AACTCCAAACTTTTATTTCGAA-ATAGTTAAAAA-AATCAAA
* * *
495348 ATTTTGTTTAAAAATTTAAACTTTTTCTTT-AAATGACTAAAAAACATATTTTTATTTTTGAAAA
61 ACTTTATTTAAAAATTTAAACTTTTTCTTTAAAATGACTAAAAAACATATTTTTATTTTTAAAAA
495412 TCTAAACTTTCTTTTTTTTAT
126 TCTAAACTTTCTTTTTTTTAT
*
495433 GAAATCACTATTTTTCTTAAAACTCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
1 AAAATCACTATTTTTCTTAAAACTCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
* *
495498 ACTTAAAAATTTAAACTTTTTCTTTAAAATGACTAAAAAAACATATTTTTATTTTTAAAAATCAA
66 ATTTAAAAATTTAAACTTTTTCTTTAAAATGACT-AAAAAACATATTTTTATTTTTAAAAATCTA
*
495563 AACTTTCTTTTCTTTTTT
130 AACTTTCTTTT-TTTTAT
* * *
495581 TAAATCACTATTTTTCTTAAAACTCCAAACTTTCATTTCGAAATAGTTAAAAAAATTAAAACTTT
1 AAAATCACTATTTTTCTTAAAACTCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
* ** *
495646 ATTTAAAAATTTAAATTTTTTCTTTAAAATGACTAAAAAACCGATTTGTATTTTTAAAAATCTAA
66 ATTTAAAAATTTAAACTTTTTCTTTAAAATGACTAAAAAACATATTTTTATTTTTAAAAATCTAA
* *
495711 ACTTTCTTTTTTTAAAG
131 ACTTTCTTTTTTT-TAT
* * *
495728 AAAATCATTATTTTTCTTAAAACTCAAAACTTTTATTTCGAAATTA-TTAAAAAAATGAAAAC
1 AAAATCACTATTTTTCTTAAAACTCCAAACTTTTATTTCGAAA-TAGTTAAAAAAATCAAAAC
495790 ATTTCTCAAG
Statistics
Matches: 448, Mismatches: 41, Indels: 31
0.86 0.08 0.06
Matches are distributed among these distances:
145 40 0.09
146 49 0.11
147 179 0.40
148 106 0.24
149 9 0.02
150 57 0.13
151 8 0.02
ACGTcount: A:0.42, C:0.11, G:0.03, T:0.44
Consensus pattern (146 bp):
AAAATCACTATTTTTCTTAAAACTCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
ATTTAAAAATTTAAACTTTTTCTTTAAAATGACTAAAAAACATATTTTTATTTTTAAAAATCTAA
ACTTTCTTTTTTTTAT
Found at i:496213 original size:3 final size:3
Alignment explanation
Indices: 496205--496232 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
496195 CACGAAATCC
496205 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
496233 GATGATGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:496769 original size:42 final size:42
Alignment explanation
Indices: 496711--497050 Score: 484
Period size: 42 Copynumber: 8.1 Consensus size: 42
496701 AAATAATAAT
* *
496711 TGGACCTCTACCCCTAGGCCTCTAAATGCAATGAAAAGTAAA
1 TGGACCTCCACACCTAGGCCTCTAAATGCAATGAAAAGTAAA
* * * *
496753 TGCACCTCCACACCTAGGTCTCTAAATGCGATTAAAAGTAAA
1 TGGACCTCCACACCTAGGCCTCTAAATGCAATGAAAAGTAAA
* *
496795 TGGACCTCCACACCTGGGCCTCTAAATGCGATGAAAAGTAAA
1 TGGACCTCCACACCTAGGCCTCTAAATGCAATGAAAAGTAAA
* * *
496837 TGGACTTTCACACCTAGGCCTCTAAATGTAATGAAAAGTAAA
1 TGGACCTCCACACCTAGGCCTCTAAATGCAATGAAAAGTAAA
* * * * * *
496879 TGGACCTCAACACCTGGGTCTTTAAATGTAATGAAGAGTAAA
1 TGGACCTCCACACCTAGGCCTCTAAATGCAATGAAAAGTAAA
**
496921 TGGACCTCCATGCCTAGGCCTCTAAATGCAATGAAAAGTAAA
1 TGGACCTCCACACCTAGGCCTCTAAATGCAATGAAAAGTAAA
496963 TGGACCTCCACACCT-GAGCCTCTAAATGCAATGAAAAGTAAA
1 TGGACCTCCACACCTAG-GCCTCTAAATGCAATGAAAAGTAAA
*
497005 TGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAGTAAA
1 TGGACCTCCACACCTAGGCCTCTAAATGCAATGAAAAGTAAA
497047 TGGA
1 TGGA
497051 AATGCGATGA
Statistics
Matches: 264, Mismatches: 32, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
41 1 0.00
42 262 0.99
43 1 0.00
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.22
Consensus pattern (42 bp):
TGGACCTCCACACCTAGGCCTCTAAATGCAATGAAAAGTAAA
Found at i:497060 original size:22 final size:22
Alignment explanation
Indices: 497028--497069 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
497018 CTGGGCCTCT
497028 AAATGCAATGAAAAGTAAATGG
1 AAATGCAATGAAAAGTAAATGG
*
497050 AAATGCGATGAAAAGTAAAT
1 AAATGCAATGAAAAGTAAAT
497070 AGACCTCCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.55, C:0.05, G:0.21, T:0.19
Consensus pattern (22 bp):
AAATGCAATGAAAAGTAAATGG
Found at i:497065 original size:64 final size:64
Alignment explanation
Indices: 496986--497113 Score: 202
Period size: 64 Copynumber: 2.0 Consensus size: 64
496976 CTGAGCCTCT
* *
496986 AAATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAGTAAATGG
1 AAATGCAATGAAAAGTAAATAGACCTCCACACCTGAGCCTCTAAATGCAATGAAAAGTAAATGG
* * **
497050 AAATGCGATGAAAAGTAAATAGACCTCCACATCTGAGCCTCTAAATGTGATGAAAAGTAAATGG
1 AAATGCAATGAAAAGTAAATAGACCTCCACACCTGAGCCTCTAAATGCAATGAAAAGTAAATGG
497114 GCCTCCACAC
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 58 1.00
ACGTcount: A:0.42, C:0.17, G:0.20, T:0.20
Consensus pattern (64 bp):
AAATGCAATGAAAAGTAAATAGACCTCCACACCTGAGCCTCTAAATGCAATGAAAAGTAAATGG
Done.