Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015317.1 Kokia drynarioides strain JFW-HI SEQ_130362, 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: 666550
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 474 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:303 original size:60 final size:57
Alignment explanation
Indices: 209--370 Score: 170
Period size: 55 Copynumber: 2.8 Consensus size: 57
199 GGTGTGTTTG
* * * *
209 AAATTTTTTTTCTCAAAAAAGG-GGTGTCGACCATTGCATGGTCAACATAAAAAAAAATTT
1 AAATTTTTTTTCTC-AAAAAGGAGGTGTCGGCCATTCCATGGCCAAC---AAAAAAAATGT
* ***
269 AAATTTTTTTTCTCAAAAAGGAGGTGTCGGCCATTTCATGGCCAACACCCAAAATGT
1 AAATTTTTTTTCTCAAAAAGGAGGTGTCGGCCATTCCATGGCCAACAAAAAAAATGT
*
326 -AA-TTTTTTTCTCAAAAA-GAGGGTGTCGGCCATTCCATGACCAACA
1 AAATTTTTTTTCTCAAAAAGGA-GGTGTCGGCCATTCCATGGCCAACA
371 CAAATATTTT
Statistics
Matches: 91, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
54 2 0.02
55 38 0.42
56 2 0.02
57 7 0.08
59 7 0.08
60 35 0.38
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.30
Consensus pattern (57 bp):
AAATTTTTTTTCTCAAAAAGGAGGTGTCGGCCATTCCATGGCCAACAAAAAAAATGT
Found at i:3533 original size:6 final size:6
Alignment explanation
Indices: 3522--3552 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
3512 AATCGAAAGC
3522 TCTCTT TCTCTT TCTCTT TCTCTT TCTCTT T
1 TCTCTT TCTCTT TCTCTT TCTCTT TCTCTT T
3553 TACCGTTCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (6 bp):
TCTCTT
Found at i:10020 original size:176 final size:176
Alignment explanation
Indices: 9726--10079 Score: 629
Period size: 176 Copynumber: 2.0 Consensus size: 176
9716 AATATATATG
9726 TATATATAACTTTCCTGATTACAATATCCCTAGCTCTGAGTTGCCTCATTGGGAAGCATTTTAAG
1 TATATATAACTTTCCTGATTACAATATCCCTAGCTCTGAGTTGCCTCATTGGGAAGCATTTTAAG
9791 TCAAATATATGCATCAGTTTCCTTATCTGTTTCCTAGTGGCTTTTGGTTCTTTTCTTCAATGGTC
66 TCAAATATATGCATCAGTTTCCTTATCTGTTTCCTAGTGGCTTTTGGTTCTTTTCTTCAATGGTC
* *
9856 GGGTTTAAAGGCACTTTAGTGCATGTTACTGCACAATATCAGTTTA
131 GGGTCTAAAGGCACTTTAGTGCATGCTACTGCACAATATCAGTTTA
* **
9902 TATATATAACTTTCCTGGTTACAATATCCCTAGCTCTGAGTTGCCTCATTGGGAAGCATTTTCTG
1 TATATATAACTTTCCTGATTACAATATCCCTAGCTCTGAGTTGCCTCATTGGGAAGCATTTTAAG
* *
9967 TCAAGTATATGCATCAGTTTTC-TATTCTGTTTCCTAGTGGCTTTTGGTTCTTTTCTTCAATGGT
66 TCAAATATATGCATCAGTTTCCTTA-TCTGTTTCCTAGTGGCTTTTGGTTCTTTTCTTCAATGGT
10031 CGGGTCTAAAGGCACTTTAGTGCATGCTACTGCACAATATCAGTTTA
130 CGGGTCTAAAGGCACTTTAGTGCATGCTACTGCACAATATCAGTTTA
10078 TA
1 TA
10080 CATGTATATA
Statistics
Matches: 170, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
175 2 0.01
176 168 0.99
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.40
Consensus pattern (176 bp):
TATATATAACTTTCCTGATTACAATATCCCTAGCTCTGAGTTGCCTCATTGGGAAGCATTTTAAG
TCAAATATATGCATCAGTTTCCTTATCTGTTTCCTAGTGGCTTTTGGTTCTTTTCTTCAATGGTC
GGGTCTAAAGGCACTTTAGTGCATGCTACTGCACAATATCAGTTTA
Found at i:12623 original size:23 final size:24
Alignment explanation
Indices: 12594--12639 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
12584 GATGGGTTGA
*
12594 GAAGGGGAGGAAGGGAGA-GAAGG
1 GAAGGGGAGGAAAGGAGATGAAGG
12617 GAAGGGGAGGAAAGGAGATGAAG
1 GAAGGGGAGGAAAGGAGATGAAG
12640 AGATGGAAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.41, C:0.00, G:0.57, T:0.02
Consensus pattern (24 bp):
GAAGGGGAGGAAAGGAGATGAAGG
Found at i:19814 original size:69 final size:69
Alignment explanation
Indices: 19732--19869 Score: 276
Period size: 69 Copynumber: 2.0 Consensus size: 69
19722 TCTAATCACA
19732 CCAATATATTAAAAAAATCGAAAATCCTTGATACAAGGAATATGGGGATGTATAGAGTATGGATT
1 CCAATATATTAAAAAAATCGAAAATCCTTGATACAAGGAATATGGGGATGTATAGAGTATGGATT
19797 TGCT
66 TGCT
19801 CCAATATATTAAAAAAATCGAAAATCCTTGATACAAGGAATATGGGGATGTATAGAGTATGGATT
1 CCAATATATTAAAAAAATCGAAAATCCTTGATACAAGGAATATGGGGATGTATAGAGTATGGATT
19866 TGCT
66 TGCT
19870 GTCAAAGACA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.29
Consensus pattern (69 bp):
CCAATATATTAAAAAAATCGAAAATCCTTGATACAAGGAATATGGGGATGTATAGAGTATGGATT
TGCT
Found at i:23801 original size:30 final size:29
Alignment explanation
Indices: 23765--23831 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 29
23755 ACAACTAAAC
* *
23765 TTAAATTTTTTAAATTCAAAAA-ATAAAGAA
1 TTAAATTTTTGAAA-ACAAAAATATAAA-AA
*
23795 TTAAATTCTTGAAAACAAAAATATAAAAA
1 TTAAATTTTTGAAAACAAAAATATAAAAA
23824 TTAAATTT
1 TTAAATTT
23832 CGAATATAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 15 0.47
30 17 0.53
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.36
Consensus pattern (29 bp):
TTAAATTTTTGAAAACAAAAATATAAAAA
Found at i:23843 original size:28 final size:29
Alignment explanation
Indices: 23781--23835 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
23771 TTTTTAAATT
*
23781 CAAAAAATAAAGAATTAAATTCTTGAAAA
1 CAAAAAATAAAGAATTAAATTCTCGAAAA
23810 CAAAAATATAAA-AATTAAATT-TCGAA
1 CAAAAA-ATAAAGAATTAAATTCTCGAA
23836 TATAAAAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 4 0.17
29 15 0.62
30 5 0.21
ACGTcount: A:0.62, C:0.07, G:0.05, T:0.25
Consensus pattern (29 bp):
CAAAAAATAAAGAATTAAATTCTCGAAAA
Found at i:23843 original size:29 final size:27
Alignment explanation
Indices: 23782--23835 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
23772 TTTTAAATTC
* *
23782 AAAAAATAAAGAATTAAATTCTTGAAA
1 AAAAAATAAAAAATTAAATTCTCGAAA
23809 ACAAAAATATAAAAATTAAATT-TCGAA
1 A-AAAAATA-AAAAATTAAATTCTCGAA
23836 TATAAAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 1 0.04
28 11 0.48
29 11 0.48
ACGTcount: A:0.63, C:0.06, G:0.06, T:0.26
Consensus pattern (27 bp):
AAAAAATAAAAAATTAAATTCTCGAAA
Found at i:25655 original size:21 final size:21
Alignment explanation
Indices: 25631--25677 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
25621 TCTAGGGTTT
25631 AAGGTTAAATGTCT-ATGATCC
1 AAGGTT-AATGTCTCATGATCC
* *
25652 AAGGTTCATGTTTCATGATCC
1 AAGGTTAATGTCTCATGATCC
25673 AAGGT
1 AAGGT
25678 CCAAGGTCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (21 bp):
AAGGTTAATGTCTCATGATCC
Found at i:25718 original size:21 final size:21
Alignment explanation
Indices: 25683--25737 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
25673 AAGGTCCAAG
* *
25683 GTCTAAGATTCAAAATCT-AA
1 GTCTAAAATTTAAAATCTAAA
*
25703 GATCTAAAATTTAAAATTTAAA
1 G-TCTAAAATTTAAAATCTAAA
*
25725 GTCCAAAATTTAA
1 GTCTAAAATTTAA
25738 GATTCAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 1 0.03
21 25 0.86
22 3 0.10
ACGTcount: A:0.49, C:0.11, G:0.07, T:0.33
Consensus pattern (21 bp):
GTCTAAAATTTAAAATCTAAA
Found at i:25724 original size:14 final size:14
Alignment explanation
Indices: 25707--25755 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
25697 ATCTAAGATC
*
25707 TAAAATTTAAAATT
1 TAAAATTCAAAATT
* *
25721 TAAAGTCCAAAATT
1 TAAAATTCAAAATT
*
25735 TAAGATTCAAAATT
1 TAAAATTCAAAATT
*
25749 CAAAATT
1 TAAAATT
25756 TAGAGTTTAG
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.35
Consensus pattern (14 bp):
TAAAATTCAAAATT
Found at i:25752 original size:21 final size:21
Alignment explanation
Indices: 25708--25757 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
25698 TCTAAGATCT
* *
25708 AAAATTTAAAATTTAAAGTCC
1 AAAATTTAAAATTCAAAATCC
* *
25729 AAAATTTAAGATTCAAAATTC
1 AAAATTTAAAATTCAAAATCC
25750 AAAATTTA
1 AAAATTTA
25758 GAGTTTAGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.54, C:0.08, G:0.04, T:0.34
Consensus pattern (21 bp):
AAAATTTAAAATTCAAAATCC
Found at i:26686 original size:21 final size:20
Alignment explanation
Indices: 26662--26726 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 20
26652 GTTCATGATA
26662 TAAGGTTTAAAGTTTAGAGTT
1 TAAGGTTTAAAGTTTAGA-TT
* **
26683 TAAGATTTAAAGTCGAGATT
1 TAAGGTTTAAAGTTTAGATT
* *
26703 TAAGGTCTAAAATTTAGAATT
1 TAAGGTTTAAAGTTTAG-ATT
26724 TAA
1 TAA
26727 AATTTAAGAT
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 14 0.40
21 21 0.60
ACGTcount: A:0.40, C:0.03, G:0.18, T:0.38
Consensus pattern (20 bp):
TAAGGTTTAAAGTTTAGATT
Found at i:26758 original size:14 final size:14
Alignment explanation
Indices: 26741--26775 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
26731 TAAGATTTAA
*
26741 GATTGAAGGTCGAG
1 GATTCAAGGTCGAG
*
26755 GATTCAAGGTCTAG
1 GATTCAAGGTCGAG
26769 GATTCAA
1 GATTCAA
26776 AGTTTGGGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.31, C:0.11, G:0.31, T:0.26
Consensus pattern (14 bp):
GATTCAAGGTCGAG
Found at i:45902 original size:3 final size:3
Alignment explanation
Indices: 45894--45925 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
45884 TATATCTATA
45894 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
45926 TAGGGCTATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:52963 original size:28 final size:29
Alignment explanation
Indices: 52922--52990 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
52912 GTCCCTGTAC
* *
52922 TTTTGTATATTTA-GAATTTACTCTCTTTA
1 TTTT-TATATTTAGGAATTTAATCTCCTTA
* *
52951 TTTTTATTTTTAGGAATTTAATCTCCTTC
1 TTTTTATATTTAGGAATTTAATCTCCTTA
*
52980 TTTTTAAATTT
1 TTTTTATATTT
52991 CAAAATTTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
28 7 0.21
29 26 0.79
ACGTcount: A:0.23, C:0.10, G:0.06, T:0.61
Consensus pattern (29 bp):
TTTTTATATTTAGGAATTTAATCTCCTTA
Found at i:52967 original size:29 final size:28
Alignment explanation
Indices: 52922--52999 Score: 75
Period size: 29 Copynumber: 2.7 Consensus size: 28
52912 GTCCCTGTAC
* *
52922 TTTTGTATATTTAGAATTTACTCTCTTTA
1 TTTT-TATATTTAGAATTTAATCTCCTTA
* *
52951 TTTTTATTTTTAGGAATTTAATCTCCTTC
1 TTTTTATATTTA-GAATTTAATCTCCTTA
* *
52980 TTTTTAAATTTCAAAATTTA
1 TTTTTATATTT-AGAATTTA
53000 TGTTCAATTG
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
28 7 0.17
29 32 0.80
30 1 0.03
ACGTcount: A:0.27, C:0.10, G:0.05, T:0.58
Consensus pattern (28 bp):
TTTTTATATTTAGAATTTAATCTCCTTA
Found at i:56800 original size:2 final size:2
Alignment explanation
Indices: 56793--56818 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
56783 TTGAATGATA
56793 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
56819 TCCTTCTAAC
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:60177 original size:21 final size:21
Alignment explanation
Indices: 60151--60190 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
60141 ATTAAGCGAC
60151 ACATTTTATTAATAATAAACT
1 ACATTTTATTAATAATAAACT
* *
60172 ACATTTTGTTAATAGTAAA
1 ACATTTTATTAATAATAAA
60191 AGTTATTGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
ACATTTTATTAATAATAAACT
Found at i:66186 original size:19 final size:20
Alignment explanation
Indices: 66148--66187 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
66138 ATTACACGTC
*
66148 TATTTACAATTTGATCCATA
1 TATTTACAATATGATCCATA
*
66168 TATTTA-AATATGCTCCATA
1 TATTTACAATATGATCCATA
66187 T
1 T
66188 CAAATTTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.35, C:0.15, G:0.05, T:0.45
Consensus pattern (20 bp):
TATTTACAATATGATCCATA
Found at i:66273 original size:22 final size:22
Alignment explanation
Indices: 66248--66292 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
66238 AACTTGATTT
66248 ATTTGATATT-AAATACTTTAAA
1 ATTTGA-ATTAAAATACTTTAAA
* *
66270 ATTTTAATTAAAATATTTTAAA
1 ATTTGAATTAAAATACTTTAAA
66292 A
1 A
66293 CTAAAAACAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (22 bp):
ATTTGAATTAAAATACTTTAAA
Found at i:68049 original size:30 final size:30
Alignment explanation
Indices: 68015--68077 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 30
68005 TTGACACACT
* *
68015 AATTTAATTATT-TTTAAAATTTTAAATTGA
1 AATTT-ATTATTATTGAAAATTTAAAATTGA
68045 AATTTATTATTAATTGAAAATTTAAAATTGA
1 AATTTATTATT-ATTGAAAATTTAAAATTGA
68076 AA
1 AA
68078 GATTCAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 6 0.21
30 5 0.17
31 18 0.62
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (30 bp):
AATTTATTATTATTGAAAATTTAAAATTGA
Found at i:73026 original size:18 final size:18
Alignment explanation
Indices: 73005--73039 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
72995 GGAACTTGTT
*
73005 TAGCATTAACAACTAGCC
1 TAGCACTAACAACTAGCC
*
73023 TAGCACTAGCAACTAGC
1 TAGCACTAACAACTAGC
73040 TCTGCCTGTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.29, G:0.14, T:0.20
Consensus pattern (18 bp):
TAGCACTAACAACTAGCC
Found at i:77520 original size:21 final size:23
Alignment explanation
Indices: 77496--77538 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
77486 AGAATTTTCA
*
77496 AAAAGAA-AAAGGAA-GAAAAAC
1 AAAAGAATAAAGAAAGGAAAAAC
77517 AAAAGAATAAAGAAAGGAAAAA
1 AAAAGAATAAAGAAAGGAAAAA
77539 TTAATTGGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 6 0.32
23 6 0.32
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02
Consensus pattern (23 bp):
AAAAGAATAAAGAAAGGAAAAAC
Found at i:80228 original size:16 final size:16
Alignment explanation
Indices: 80207--80244 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
80197 TTTTGTTCAC
80207 TGTAATGGAATAAAAT
1 TGTAATGGAATAAAAT
*
80223 TGTAATGGAATATAAT
1 TGTAATGGAATAAAAT
80239 TGTAAT
1 TGTAAT
80245 TAGTAATTCA
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:0.45, C:0.00, G:0.18, T:0.37
Consensus pattern (16 bp):
TGTAATGGAATAAAAT
Found at i:80503 original size:26 final size:27
Alignment explanation
Indices: 80474--80551 Score: 77
Period size: 26 Copynumber: 2.8 Consensus size: 27
80464 TTAATCATGT
*
80474 TTTAACAAAATTATTATTAAAT-ACAA
1 TTTAATAAAATTATTATTAAATAACAA
* *
80500 TTTAATAAAATAATATATATTTAATAACAT
1 TTTAATAAAAT--TAT-TATTAAATAACAA
*
80530 TCTTAATATAATTATTATTAAA
1 T-TTAATAAAATTATTATTAAA
80552 ATATGAATTA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
26 10 0.24
28 9 0.21
29 10 0.24
30 4 0.10
31 9 0.21
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (27 bp):
TTTAATAAAATTATTATTAAATAACAA
Found at i:80547 original size:60 final size:59
Alignment explanation
Indices: 80423--80551 Score: 158
Period size: 60 Copynumber: 2.2 Consensus size: 59
80413 TTTTAATAAG
* * *
80423 ATTATTATTAAATATATTTTAATAAAATAATAATAAATAATTTAATCATGTTTTAACAAA
1 ATTATTATTAAATACAATTTAATAAAATAATAAT-AATAATTTAATCATGTCTTAACAAA
* *
80483 ATTATTATTAAATACAATTTAATAAAATAAT-AT-AT-ATTTAATAACAT-TCTTAATATA
1 ATTATTATTAAATACAATTTAATAAAATAATAATAATAATTTAAT--CATGTCTTAACAAA
80540 ATTATTATTAAA
1 ATTATTATTAAA
80552 ATATGAATTA
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
56 7 0.11
57 21 0.34
58 3 0.05
59 2 0.03
60 29 0.47
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (59 bp):
ATTATTATTAAATACAATTTAATAAAATAATAATAATAATTTAATCATGTCTTAACAAA
Found at i:83042 original size:60 final size:60
Alignment explanation
Indices: 82974--83093 Score: 231
Period size: 60 Copynumber: 2.0 Consensus size: 60
82964 CATAACATGA
*
82974 ATAAAATCTCGGGTTAGGATACTATATTTAAACCCTAAATCAATTAAATTATGTAAAAGG
1 ATAAAATCTCGAGTTAGGATACTATATTTAAACCCTAAATCAATTAAATTATGTAAAAGG
83034 ATAAAATCTCGAGTTAGGATACTATATTTAAACCCTAAATCAATTAAATTATGTAAAAGG
1 ATAAAATCTCGAGTTAGGATACTATATTTAAACCCTAAATCAATTAAATTATGTAAAAGG
83094 TATATATGGA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (60 bp):
ATAAAATCTCGAGTTAGGATACTATATTTAAACCCTAAATCAATTAAATTATGTAAAAGG
Found at i:89743 original size:35 final size:35
Alignment explanation
Indices: 89697--89767 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
89687 CAAAACGATC
89697 AAAACAGTCTACTGGCTTTGTCCATGGAACTAGAT
1 AAAACAGTCTACTGGCTTTGTCCATGGAACTAGAT
*
89732 AAAACAGTCTACTGGCTTTGTCCATGGGACTAGAT
1 AAAACAGTCTACTGGCTTTGTCCATGGAACTAGAT
89767 A
1 A
89768 TTGGTACCTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (35 bp):
AAAACAGTCTACTGGCTTTGTCCATGGAACTAGAT
Found at i:92184 original size:20 final size:21
Alignment explanation
Indices: 92147--92185 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
92137 TTTGACTTGA
* *
92147 TATATTTTTTTTCTTATGTAT
1 TATATTGTTTTTCATATGTAT
92168 TATATTGTTTTT-ATATGT
1 TATATTGTTTTTCATATGT
92186 TATATAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.21, C:0.03, G:0.08, T:0.69
Consensus pattern (21 bp):
TATATTGTTTTTCATATGTAT
Found at i:93352 original size:19 final size:19
Alignment explanation
Indices: 93330--93369 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
93320 TAATGTATAA
93330 TTTATACATAAATTTTGAT
1 TTTATACATAAATTTTGAT
*
93349 TTTATACATAAATTTTTAT
1 TTTATACATAAATTTTGAT
93368 TT
1 TT
93370 GATTCAATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (19 bp):
TTTATACATAAATTTTGAT
Found at i:99452 original size:29 final size:29
Alignment explanation
Indices: 99393--99452 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
99383 TATGATTTAA
* *
99393 TGTGTAATTGTGTACATGAAATTTGTTTT
1 TGTGTAATTGTATACATGAAATTTGTATT
* *
99422 TGTGTAATTTTATATATGAAAATTTG-ATT
1 TGTGTAATTGTATACATG-AAATTTGTATT
99451 TG
1 TG
99453 ATCTAATTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
29 19 0.73
30 7 0.27
ACGTcount: A:0.28, C:0.02, G:0.18, T:0.52
Consensus pattern (29 bp):
TGTGTAATTGTATACATGAAATTTGTATT
Found at i:99645 original size:29 final size:31
Alignment explanation
Indices: 99597--99658 Score: 101
Period size: 29 Copynumber: 2.1 Consensus size: 31
99587 GCACATTTAA
*
99597 ACCACAATTAGAGTTTCATGTATATAATTGC
1 ACCACAATTAAAGTTTCATGTATATAATTGC
99628 ACCA-AATTAAAG-TTCATGTATATAATTGC
1 ACCACAATTAAAGTTTCATGTATATAATTGC
99657 AC
1 AC
99659 ATTAAATCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 19 0.63
30 7 0.23
31 4 0.13
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (31 bp):
ACCACAATTAAAGTTTCATGTATATAATTGC
Found at i:106928 original size:41 final size:41
Alignment explanation
Indices: 106869--106946 Score: 95
Period size: 41 Copynumber: 1.9 Consensus size: 41
106859 ATACCTTTGG
*
106869 CATTATCCACAAGACTCTCAGTCGGGGTCCCATTTTCATGA
1 CATTATCCACAAGACTCTCAGTCCGGGTCCCATTTTCATGA
* * * *
106910 CATTAT-CATCAAGGCTCTCGGTCCGTGTCTCATTTTC
1 CATTATCCA-CAAGACTCTCAGTCCGGGTCCCATTTTC
106947 TCAACATTGT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
40 2 0.06
41 29 0.94
ACGTcount: A:0.21, C:0.29, G:0.17, T:0.33
Consensus pattern (41 bp):
CATTATCCACAAGACTCTCAGTCCGGGTCCCATTTTCATGA
Found at i:114554 original size:36 final size:35
Alignment explanation
Indices: 114506--114612 Score: 126
Period size: 36 Copynumber: 3.0 Consensus size: 35
114496 CCATGTGAAG
* * *
114506 CACACAGCTGTGTAGAAACATGCAGGTCGTGTGGGG
1 CACACAACTGTGT-GAAACATGCAGGCCGTGTGGGA
* *
114542 CACACGAA-TGTGTGAAAACATGTAGGCCATGTGGGA
1 CACAC-AACTGTGTG-AAACATGCAGGCCGTGTGGGA
114578 CACACAACTGTGTGGAAACATGCAGGCCGTGTGGG
1 CACACAACTGTGT-GAAACATGCAGGCCGTGTGGG
114613 TCAAACATGT
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
35 3 0.05
36 55 0.92
37 2 0.03
ACGTcount: A:0.28, C:0.20, G:0.34, T:0.19
Consensus pattern (35 bp):
CACACAACTGTGTGAAACATGCAGGCCGTGTGGGA
Found at i:115339 original size:20 final size:20
Alignment explanation
Indices: 115314--115396 Score: 67
Period size: 20 Copynumber: 3.9 Consensus size: 20
115304 ATGATACAAA
115314 TCGTTATGATATTATATGAT
1 TCGTTATGATATTATATGAT
* * *
115334 TTGTTATGTTATGATATGGCAAGGT
1 TCGTTATGATATTATAT-G--A--T
* *
115359 TCATTATGATATGATATGAT
1 TCGTTATGATATTATATGAT
*
115379 TCGTTATGATATGATATG
1 TCGTTATGATATTATATG
115397 GTATGATTTG
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
20 32 0.63
21 1 0.02
22 1 0.02
23 1 0.02
24 1 0.02
25 15 0.29
ACGTcount: A:0.29, C:0.05, G:0.20, T:0.46
Consensus pattern (20 bp):
TCGTTATGATATTATATGAT
Found at i:115373 original size:5 final size:5
Alignment explanation
Indices: 115363--115415 Score: 54
Period size: 5 Copynumber: 10.6 Consensus size: 5
115353 CAAGGTTCAT
* * * *
115363 TATGA TATGA TATGA T-TCGT TATGA TATGA TATGG TATGA TTTGT TATGA
1 TATGA TATGA TATGA TAT-GA TATGA TATGA TATGA TATGA TATGA TATGA
115413 TAT
1 TAT
115416 TAACATGTTC
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
4 1 0.03
5 36 0.95
6 1 0.03
ACGTcount: A:0.30, C:0.02, G:0.21, T:0.47
Consensus pattern (5 bp):
TATGA
Found at i:115391 original size:25 final size:25
Alignment explanation
Indices: 115363--115415 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
115353 CAAGGTTCAT
115363 TATGATATGATATGATTCGTTATGA
1 TATGATATGATATGATTCGTTATGA
* *
115388 TATGATATGGTATGATTTGTTATGA
1 TATGATATGATATGATTCGTTATGA
115413 TAT
1 TAT
115416 TAACATGTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.30, C:0.02, G:0.21, T:0.47
Consensus pattern (25 bp):
TATGATATGATATGATTCGTTATGA
Found at i:115411 original size:45 final size:45
Alignment explanation
Indices: 115314--115415 Score: 132
Period size: 45 Copynumber: 2.3 Consensus size: 45
115304 ATGATACAAA
* * * *
115314 TCGTTATGATATTATATGATTTGTTATGTTATGATATGGCAAGGT
1 TCGTTATGATATGATATGATTCGTTATGATATGATATGGCAAGAT
* * *
115359 TCATTATGATATGATATGATTCGTTATGATATGATATGGTATGAT
1 TCGTTATGATATGATATGATTCGTTATGATATGATATGGCAAGAT
*
115404 TTGTTATGATAT
1 TCGTTATGATAT
115416 TAACATGTTC
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.28, C:0.04, G:0.21, T:0.47
Consensus pattern (45 bp):
TCGTTATGATATGATATGATTCGTTATGATATGATATGGCAAGAT
Found at i:121777 original size:12 final size:12
Alignment explanation
Indices: 121756--121789 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
121746 GCTCTATTCT
*
121756 TTTTCTTTTTTG
1 TTTTCATTTTTG
121768 TTTTCA-TTTTG
1 TTTTCATTTTTG
121779 TTTTCATTTTT
1 TTTTCATTTTT
121790 TCTTTTTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.06, C:0.09, G:0.06, T:0.79
Consensus pattern (12 bp):
TTTTCATTTTTG
Found at i:131813 original size:80 final size:80
Alignment explanation
Indices: 131728--131939 Score: 298
Period size: 80 Copynumber: 2.6 Consensus size: 80
131718 CTTTTGTGGC
*
131728 TTATCCGCTAGGCACTGGGTGCCAAGATTTGACGGATATTTGTTGGTTAATCCAACTAGAGCTGA
1 TTATCCACTAGGCACTGGGTGCCAAGATTTGACGGATATTTGTTGGTTAATCCAACTAGAGCTGA
*
131793 GATCACTTTTACAGT
66 GATCACATTTACAGT
* * * * *
131808 TTATCCACTAAGCACTGGGTGCCAGGATTTGACGGATATTTGTTAGTTAATCCAACTAGAGTTGG
1 TTATCCACTAGGCACTGGGTGCCAAGATTTGACGGATATTTGTTGGTTAATCCAACTAGAGCTGA
* * *
131873 GCTCACATTTGCGGT
66 GATCACATTTACAGT
* * *
131888 TTATCCTCTAGGCACTAGGTGCCAAGATTTGACGGATTAGTTGTTGGTTAAT
1 TTATCCACTAGGCACTGGGTGCCAAGATTTGACGGA-TATTTGTTGGTTAAT
131940 GTGCCAGGAT
Statistics
Matches: 115, Mismatches: 16, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
80 102 0.89
81 13 0.11
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (80 bp):
TTATCCACTAGGCACTGGGTGCCAAGATTTGACGGATATTTGTTGGTTAATCCAACTAGAGCTGA
GATCACATTTACAGT
Found at i:132136 original size:82 final size:82
Alignment explanation
Indices: 131984--132147 Score: 231
Period size: 82 Copynumber: 2.0 Consensus size: 82
131974 AGCGCAAAAC
* ** *
131984 CGTTCGTTAATCCAACTAGAGTTGGGCTCACTTATTGCGGTTTATCCGCTAGGTACTAGGTACCA
1 CGTTCGTTAATCCAACTAGAGCTACGCTCACTTATTGCGGTTTATCCGCTAGGCACTAGGTACCA
132049 AGAATTGACAGAATTAT
66 AGAATTGACAGAATTAT
* * * *
132066 CGTTGGTTAATCCAACTAGAGCTACGCTCACTTATTGCGGTTTATCTGCTAGGCACTGGGT-GCA
1 CGTTCGTTAATCCAACTAGAGCTACGCTCACTTATTGCGGTTTATCCGCTAGGCACTAGGTACCA
*
132130 ATGAATTGACAGATTTAT
66 A-GAATTGACAGAATTAT
132148 ACGGTGATAA
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
81 3 0.04
82 69 0.96
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.32
Consensus pattern (82 bp):
CGTTCGTTAATCCAACTAGAGCTACGCTCACTTATTGCGGTTTATCCGCTAGGCACTAGGTACCA
AGAATTGACAGAATTAT
Found at i:139894 original size:78 final size:78
Alignment explanation
Indices: 139749--139894 Score: 177
Period size: 78 Copynumber: 1.9 Consensus size: 78
139739 GAAACTTGAT
* * * * **
139749 TAAATTCTATTGAATGATAAGAATAAATCCTAAAACAGAATTGTTTAATTAAATTCTGCTTGGAA
1 TAAATTCTATTGAATGACAAGAATAAATCCTAAAACAGAATTATTCAATTAAATTCTACTTACAA
139814 ACAAAAAATTAAA
66 ACAAAAAATTAAA
* ** * *
139827 TAAATTCTATTGAATGACGAGAATAAAT-CTCGGAACAGAATTATTCAATTAATTTCTATTTACA
1 TAAATTCTATTGAATGACAAGAATAAATCCT-AAAACAGAATTATTCAATTAAATTCTACTTACA
139891 AACA
65 AACA
139895 GAATACAATT
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
77 2 0.04
78 54 0.96
ACGTcount: A:0.46, C:0.11, G:0.10, T:0.33
Consensus pattern (78 bp):
TAAATTCTATTGAATGACAAGAATAAATCCTAAAACAGAATTATTCAATTAAATTCTACTTACAA
ACAAAAAATTAAA
Found at i:143476 original size:24 final size:24
Alignment explanation
Indices: 143448--143504 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
143438 TAGACTAATA
143448 AGAGTTTAACCAAAACAAATAAAC
1 AGAGTTTAACCAAAACAAATAAAC
*** *
143472 AGAGTTTAATTGAAACAAATAAGC
1 AGAGTTTAACCAAAACAAATAAAC
143496 AGAGTTTAA
1 AGAGTTTAA
143505 TTGGAAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.53, C:0.11, G:0.14, T:0.23
Consensus pattern (24 bp):
AGAGTTTAACCAAAACAAATAAAC
Found at i:143505 original size:24 final size:24
Alignment explanation
Indices: 143460--143507 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
143450 AGTTTAACCA
143460 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
*
143484 AAACAAATAAGCAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
143508 GAAAATTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.52, C:0.08, G:0.15, T:0.25
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:145806 original size:21 final size:21
Alignment explanation
Indices: 145780--145822 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
145770 GGATTTCTAC
145780 AACTCAAATTTACTTTATTTT
1 AACTCAAATTTACTTTATTTT
145801 AACTCAAATTTACTTTATTTT
1 AACTCAAATTTACTTTATTTT
145822 A
1 A
145823 TTTCTATCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.14, G:0.00, T:0.51
Consensus pattern (21 bp):
AACTCAAATTTACTTTATTTT
Found at i:150245 original size:2 final size:2
Alignment explanation
Indices: 150233--150262 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
150223 ACCCAAATTA
150233 CT CT GCT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT -CT CT CT CT CT CT CT CT CT CT CT CT C
150263 AAAGTAGAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.00, C:0.50, G:0.03, T:0.47
Consensus pattern (2 bp):
CT
Found at i:157271 original size:3 final size:3
Alignment explanation
Indices: 157263--157297 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
157253 ATAAGGACAA
157263 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
157298 CCTTACTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:177287 original size:24 final size:24
Alignment explanation
Indices: 177259--177321 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
177249 AGAAATAATC
177259 TTTCAGTTAAACTCTGTTTAATTG
1 TTTCAGTTAAACTCTGTTTAATTG
* *
177283 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTAATTG
* *
177307 TTTAAGTCAAACTCT
1 TTTCAGTTAAACTCT
177322 TATTAGTCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.27, C:0.14, G:0.10, T:0.49
Consensus pattern (24 bp):
TTTCAGTTAAACTCTGTTTAATTG
Found at i:177752 original size:24 final size:24
Alignment explanation
Indices: 177724--177798 Score: 114
Period size: 24 Copynumber: 3.1 Consensus size: 24
177714 AGAAATAATC
* * *
177724 TTTCAGTTAAACTCTGTTTAATTA
1 TTTCAATTAAACTCTGTTTATTTG
177748 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
*
177772 TTTCAATTAAACTTTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
177796 TTT
1 TTT
177799 AAGTCAAACT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.25, C:0.11, G:0.08, T:0.56
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:177807 original size:24 final size:24
Alignment explanation
Indices: 177732--177810 Score: 97
Period size: 24 Copynumber: 3.3 Consensus size: 24
177722 TCTTTCAGTT
* * *
177732 AAACTCTGTTTAATTATTTCAATT
1 AAACTCTGTTTATTTGTTTCAATC
*
177756 AAACTCTGTTTATTTGTTTCAATT
1 AAACTCTGTTTATTTGTTTCAATC
*
177780 AAACTTTGTTTATTTGTTT-AAGTC
1 AAACTCTGTTTATTTGTTTCAA-TC
177804 AAACTCT
1 AAACTCT
177811 TATTAGTCTA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
23 2 0.04
24 47 0.96
ACGTcount: A:0.29, C:0.13, G:0.08, T:0.51
Consensus pattern (24 bp):
AAACTCTGTTTATTTGTTTCAATC
Found at i:177991 original size:489 final size:489
Alignment explanation
Indices: 177259--178155 Score: 1512
Period size: 489 Copynumber: 1.8 Consensus size: 489
177249 AGAAATAATC
*
177259 TTTCAGTTAAACTCTGTTTAATTGTTTCAATTAAACTCTGTTTATTTGTTTAAGTCAAACTCTTA
1 TTTCAATTAAACTCTGTTTAATTGTTTCAATTAAACTCTGTTTATTTGTTTAAGTCAAACTCTTA
*
177324 TTAGTCTAGATTATTTTATTATTATTTGACCTAAAAATTTAGCCTATAAATAGACTCTTTTACAA
66 TTAGTCTAGATTATTTTATTATTATTTGACCTAAAAATTTAACCTATAAATAGACTCTTTTACAA
*
177389 CCTTAGAAAAAACACTCATTAGATACACCCATTAAAGTTTAGAACTCTTAACACTCTAGGAGAAT
131 CCTTAGAAAAAACACTCATTAGATACACCCATTAAAGTTTAGAACTCCTAACACTCTAGGAGAAT
* * * *
177454 TTAGTGTTTATGTTTTGAGGGTTATTAATTTTTCGGCTTTCGGGGTTTAGTTTTTATCTCCATCT
196 TTAGTGTTTACGTTTTGAAGGTTATTAATTTTTCGGCTTTCAGGGTTTAGTTTTTATCTCAATCT
* *
177519 TTTGTACTCTTCATTCTTTTGCCATTATAGTAAAATTATCTTTGCCCGTGGTTTTTTATCCTCTT
261 TTTATACTCTTCATTCTTTTGCCATTATAATAAAATTATCTTTGCCCGTGGTTTTTTATCCTCTT
* *
177584 CGGAGGCATTTTTCCACGTTAAATTTGTGTGTTCAATTTCTCAATTTATTCCG-CTATATTTCAC
326 CAGAGGCAGTTTTCCACGTTAAATTTGTGTGTTCAATTTCTCAATTTATT-CGACTATATTTCAC
177648 TTGTTCGTTGCTTAATAGGGTTGATCACCAACACTATCTTATGACTCCTATTTCAAGTCAAATTT
390 TTGTTCGTTGCTTAATAGGGTTGATCACCAACACTATCTTATGACTCCTATTTCAAGTCAAATTT
177713 GAGAAATAATCTTTCAGTTAAACTCTGTTTAATTA
455 GAGAAATAATCTTTCAGTTAAACTCTGTTTAATTA
* *
177748 TTTCAATTAAACTCTGTTTATTTGTTTCAATTAAACTTTGTTTATTTGTTTAAGTCAAACTCTTA
1 TTTCAATTAAACTCTGTTTAATTGTTTCAATTAAACTCTGTTTATTTGTTTAAGTCAAACTCTTA
*
177813 TTAGTCTAGATTATTTTATTATTATTTGACC-AAGAAATTTAACCTATAAATAGGCTCTTTTACA
66 TTAGTCTAGATTATTTTATTATTATTTGACCTAA-AAATTTAACCTATAAATAGACTCTTTTACA
* * * *
177877 ATCTTAGAAAAAACATTCATTAGATACACCCATTAAAGTTTAGAA-TCCTAACACTTTTGGAGAA
130 ACCTTAGAAAAAACACTCATTAGATACACCCATTAAAGTTTAGAACTCCTAACACTCTAGGAGAA
* ** *
177941 TTTAGTGTTTACGTTTTGAAGGTTTTTTGTTTTTCGAGTTTTCAGGGTTTAGTTTTTATCTCAAT
195 TTTAGTGTTTACGTTTTGAAGGTTATTAATTTTTCG-GCTTTCAGGGTTTAGTTTTTATCTCAAT
178006 CTTTTATACTCTTCATTCTTTTGCCATTATAATAAAATTATCTTTGCCCGTGGTTTTTTATCCTC
259 CTTTTATACTCTTCATTCTTTTGCCATTATAATAAAATTATCTTTGCCCGTGGTTTTTTATCCTC
* ** *
178071 TTTAGAGGGGGTTTTCCACGTTAAATTTGTGTGTTCAATTTCTCAATTTATTCGACTATATTTTA
324 TTCAGAGGCAGTTTTCCACGTTAAATTTGTGTGTTCAATTTCTCAATTTATTCGACTATATTTCA
178136 CTTGTTCGTTGCTTAATAGG
389 CTTGTTCGTTGCTTAATAGG
178156 ATCGATCCTC
Statistics
Matches: 379, Mismatches: 26, Indels: 6
0.92 0.06 0.01
Matches are distributed among these distances:
488 51 0.13
489 328 0.87
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (489 bp):
TTTCAATTAAACTCTGTTTAATTGTTTCAATTAAACTCTGTTTATTTGTTTAAGTCAAACTCTTA
TTAGTCTAGATTATTTTATTATTATTTGACCTAAAAATTTAACCTATAAATAGACTCTTTTACAA
CCTTAGAAAAAACACTCATTAGATACACCCATTAAAGTTTAGAACTCCTAACACTCTAGGAGAAT
TTAGTGTTTACGTTTTGAAGGTTATTAATTTTTCGGCTTTCAGGGTTTAGTTTTTATCTCAATCT
TTTATACTCTTCATTCTTTTGCCATTATAATAAAATTATCTTTGCCCGTGGTTTTTTATCCTCTT
CAGAGGCAGTTTTCCACGTTAAATTTGTGTGTTCAATTTCTCAATTTATTCGACTATATTTCACT
TGTTCGTTGCTTAATAGGGTTGATCACCAACACTATCTTATGACTCCTATTTCAAGTCAAATTTG
AGAAATAATCTTTCAGTTAAACTCTGTTTAATTA
Found at i:181728 original size:24 final size:24
Alignment explanation
Indices: 181701--181763 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
181691 ATAAATAATC
*
181701 TTTTAGTTAAACTCTATTTAATTG
1 TTTTAATTAAACTCTATTTAATTG
*
181725 TTTTAATTAAACTCTATTTATTTG
1 TTTTAATTAAACTCTATTTAATTG
* *
181749 TTTCAATGAAACTCT
1 TTTTAATTAAACTCT
181764 TATTAGTCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.30, C:0.11, G:0.06, T:0.52
Consensus pattern (24 bp):
TTTTAATTAAACTCTATTTAATTG
Found at i:182232 original size:23 final size:23
Alignment explanation
Indices: 182206--182249 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
182196 TTGGATGTGG
182206 TAGTTGTGGATAGA-TAGGATTGT
1 TAGTTGTGGATA-ATTAGGATTGT
182229 TAGTTGTGGATAATTAGGATT
1 TAGTTGTGGATAATTAGGATT
182250 ATATGTGTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.27, C:0.00, G:0.32, T:0.41
Consensus pattern (23 bp):
TAGTTGTGGATAATTAGGATTGT
Found at i:184611 original size:56 final size:56
Alignment explanation
Indices: 184520--184630 Score: 213
Period size: 56 Copynumber: 2.0 Consensus size: 56
184510 GTATGTGTTC
*
184520 TTAGTGACCTAGAATTGAAGCGAGATACTTTGTTAGAGGCTCATAGTAACACTTAA
1 TTAGCGACCTAGAATTGAAGCGAGATACTTTGTTAGAGGCTCATAGTAACACTTAA
184576 TTAGCGACCTAGAATTGAAGCGAGATACTTTGTTAGAGGCTCATAGTAACACTTA
1 TTAGCGACCTAGAATTGAAGCGAGATACTTTGTTAGAGGCTCATAGTAACACTTA
184631 CATCATTCAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (56 bp):
TTAGCGACCTAGAATTGAAGCGAGATACTTTGTTAGAGGCTCATAGTAACACTTAA
Found at i:187058 original size:25 final size:25
Alignment explanation
Indices: 187011--187102 Score: 103
Period size: 25 Copynumber: 3.7 Consensus size: 25
187001 ATATTTTGAT
* ** *
187011 TCTGGCTCGTAAAAACGTAATTCTA
1 TCTGGCTCGTAAGAGTGTAATTCTG
* *
187036 TTTGGCTCGTAAGAGTGTGATTCTG
1 TCTGGCTCGTAAGAGTGTAATTCTG
** *
187061 TCTGGCTTATAAGAGCGTAATTCTG
1 TCTGGCTCGTAAGAGTGTAATTCTG
187086 TCTGGCTCGTAAGAGTG
1 TCTGGCTCGTAAGAGTG
187103 ATACTTTGTT
Statistics
Matches: 53, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 53 1.00
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.35
Consensus pattern (25 bp):
TCTGGCTCGTAAGAGTGTAATTCTG
Found at i:187855 original size:21 final size:21
Alignment explanation
Indices: 187831--187874 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
187821 TAGAAGCATG
* *
187831 ACTTGTTTCGGTAGAAGTTAC
1 ACTTGTATCGGTAGAAGTAAC
187852 ACTTGTATCGGTAGAAGTAAC
1 ACTTGTATCGGTAGAAGTAAC
187873 AC
1 AC
187875 AAGTTTTGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.32
Consensus pattern (21 bp):
ACTTGTATCGGTAGAAGTAAC
Found at i:192596 original size:59 final size:59
Alignment explanation
Indices: 192439--192597 Score: 300
Period size: 59 Copynumber: 2.7 Consensus size: 59
192429 CTTTAATAAG
* *
192439 TCTTGAACACTTGAATGGGCAGCTTGTTAATTGATGTGCATGTTCATATACAAAATTAC
1 TCTTGAACACTTGAATGGACAGCTTGTTAATTGATGTGCCTGTTCATATACAAAATTAC
192498 TCTTGAACACTTGAATGGACAGCTTGTTAATTGATGTGCCTGTTCATATACAAAATTAC
1 TCTTGAACACTTGAATGGACAGCTTGTTAATTGATGTGCCTGTTCATATACAAAATTAC
192557 TCTTGAACACTTGAATGGACAGCTTGTTAATTGATGTGCCT
1 TCTTGAACACTTGAATGGACAGCTTGTTAATTGATGTGCCT
192598 TAAGGAGATG
Statistics
Matches: 98, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 98 1.00
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (59 bp):
TCTTGAACACTTGAATGGACAGCTTGTTAATTGATGTGCCTGTTCATATACAAAATTAC
Found at i:194751 original size:8 final size:8
Alignment explanation
Indices: 194738--194771 Score: 68
Period size: 8 Copynumber: 4.2 Consensus size: 8
194728 ATGTAATATC
194738 CTTGAATT
1 CTTGAATT
194746 CTTGAATT
1 CTTGAATT
194754 CTTGAATT
1 CTTGAATT
194762 CTTGAATT
1 CTTGAATT
194770 CT
1 CT
194772 AGTAGTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.24, C:0.15, G:0.12, T:0.50
Consensus pattern (8 bp):
CTTGAATT
Found at i:208719 original size:117 final size:117
Alignment explanation
Indices: 208541--208779 Score: 300
Period size: 117 Copynumber: 2.0 Consensus size: 117
208531 AATATTTCCA
* * ** * * * *
208541 AACAAATTCAAAATATATTAAAAAGTCTATGATTGTTGTAACTAGAATAGTAGCAAAATTAACAA
1 AACAAATTCAAAATACATTAAAAAGTCTAAGATAATTGCAACTAAAATAATAACAAAATTAACAA
* *
208606 CAAAACAAAGATTTTACAATATCCAAAC-AAAATTAAAAGCGATAGCGAAAAC
66 CAAAACAAAGATTCTACAATATCCAAACAAAAATTAAAAGCGAAAGC-AAAAC
* * *
208658 AACAGATTCAAAATACATTAAAAAGTCTAAGATAATTGCAGCTAAAATAATAACGAAATTAACAA
1 AACAAATTCAAAATACATTAAAAAGTCTAAGATAATTGCAACTAAAATAATAACAAAATTAACAA
* * * *
208723 TAAAACAAATATTCTATAATATCCAAACAAAAAATTAAAAGCGAAAGCATAAC
66 CAAAACAAAGATTCTACAATATCCAAAC-AAAAATTAAAAGCGAAAGCAAAAC
208776 AACA
1 AACA
208780 TTAAAAACAA
Statistics
Matches: 103, Mismatches: 17, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
117 78 0.76
118 8 0.08
119 17 0.17
ACGTcount: A:0.55, C:0.13, G:0.09, T:0.23
Consensus pattern (117 bp):
AACAAATTCAAAATACATTAAAAAGTCTAAGATAATTGCAACTAAAATAATAACAAAATTAACAA
CAAAACAAAGATTCTACAATATCCAAACAAAAATTAAAAGCGAAAGCAAAAC
Found at i:210982 original size:9 final size:9
Alignment explanation
Indices: 210959--210992 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
210949 AATATTATTT
210959 ATTAAGTTCG
1 ATTAA-TTCG
210969 ATTAATTCG
1 ATTAATTCG
*
210978 GTTAATTCG
1 ATTAATTCG
210987 ATTAAT
1 ATTAAT
210993 ATTTCTCAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 17 0.77
10 5 0.23
ACGTcount: A:0.32, C:0.09, G:0.15, T:0.44
Consensus pattern (9 bp):
ATTAATTCG
Found at i:228785 original size:27 final size:27
Alignment explanation
Indices: 228717--228789 Score: 64
Period size: 27 Copynumber: 2.8 Consensus size: 27
228707 ATCAAATTAT
*
228717 AATTAATTA--TTATAAAATAACTAAA
1 AATTAATTATTTTATAAATTAACTAAA
* * * *
228742 AATCAA-TATGTTAATAAATTAAGTACA
1 AATTAATTAT-TTTATAAATTAACTAAA
228769 AATTAATTATTTTAT-AATTAA
1 AATTAATTATTTTATAAATTAA
228790 ATTATATTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
24 2 0.05
25 5 0.14
26 6 0.16
27 21 0.57
28 3 0.08
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.40
Consensus pattern (27 bp):
AATTAATTATTTTATAAATTAACTAAA
Found at i:241629 original size:21 final size:21
Alignment explanation
Indices: 241605--241652 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
241595 CTGCATATTT
241605 TCTTTTCTAATCTCAAAGCAA
1 TCTTTTCTAATCTCAAAGCAA
241626 TCTTTTCTAATCTCAAAGCAA
1 TCTTTTCTAATCTCAAAGCAA
241647 TCTTTT
1 TCTTTT
241653 TCTGCAAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.29, C:0.23, G:0.04, T:0.44
Consensus pattern (21 bp):
TCTTTTCTAATCTCAAAGCAA
Found at i:244273 original size:15 final size:15
Alignment explanation
Indices: 244248--244279 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
244238 GAAAAACAAA
*
244248 AAAGAGAAAAAGAAG
1 AAAGAAAAAAAGAAG
244263 AAAGAAAAAAAGAAG
1 AAAGAAAAAAAGAAG
244278 AA
1 AA
244280 GAATAAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAAAGAAG
Found at i:247666 original size:19 final size:18
Alignment explanation
Indices: 247627--247676 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
247617 AGTGCTTTTT
* *
247627 AAAAGTACTTTCGACATA
1 AAAAATACTTTTGACATA
247645 AAAAATACTTTTGACATA
1 AAAAATACTTTTGACATA
*
247663 AAAAACACTTTTGA
1 AAAAATACTTTTGA
247677 ACCAAAAGCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.48, C:0.14, G:0.08, T:0.30
Consensus pattern (18 bp):
AAAAATACTTTTGACATA
Found at i:250575 original size:12 final size:13
Alignment explanation
Indices: 250548--250581 Score: 52
Period size: 12 Copynumber: 2.6 Consensus size: 13
250538 TGGAAGTATG
250548 GATGATAACATGGT
1 GATGATAACA-GGT
250562 GATGATAACA-GT
1 GATGATAACAGGT
250574 GATGATAA
1 GATGATAA
250582 TGCATAGTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 10 0.50
14 10 0.50
ACGTcount: A:0.41, C:0.06, G:0.26, T:0.26
Consensus pattern (13 bp):
GATGATAACAGGT
Found at i:254905 original size:24 final size:24
Alignment explanation
Indices: 254872--254926 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 24
254862 GTTAAGAGTA
254872 AAAATTGTCAGTGCAAATGTAATAC
1 AAAA-TGTCAGTGCAAATGTAATAC
* *
254897 AAAATGTCAGTGCAACTGTAATAT
1 AAAATGTCAGTGCAAATGTAATAC
254921 AAAATG
1 AAAATG
254927 AATCGATTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
24 24 0.86
25 4 0.14
ACGTcount: A:0.45, C:0.11, G:0.16, T:0.27
Consensus pattern (24 bp):
AAAATGTCAGTGCAAATGTAATAC
Found at i:257553 original size:12 final size:12
Alignment explanation
Indices: 257536--257585 Score: 57
Period size: 12 Copynumber: 3.9 Consensus size: 12
257526 GGGCAACATC
257536 TTCTTCTTCTTT
1 TTCTTCTTCTTT
257548 TTCTTCTTTCTCTT
1 TTCTTC-TTCT-TT
257562 TTACTTCTTC-TT
1 TT-CTTCTTCTTT
257574 TTCTTTCTTCTT
1 TTC-TTCTTCTT
257586 CATTTTCCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
11 1 0.03
12 16 0.48
13 5 0.15
14 7 0.21
15 4 0.12
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (12 bp):
TTCTTCTTCTTT
Found at i:257554 original size:15 final size:15
Alignment explanation
Indices: 257534--257586 Score: 65
Period size: 15 Copynumber: 3.5 Consensus size: 15
257524 CGGGGCAACA
257534 TCTTCTTCTTCTTTT
1 TCTTCTTCTTCTTTT
257549 TCTTCTT-TCTCTTTT
1 TCTTCTTCT-TCTTTT
*
257564 ACTTCTTCTT-TTCTT
1 TCTTCTTCTTCTT-TT
257579 TCTTCTTC
1 TCTTCTTC
257587 ATTTTCCTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 3 0.09
15 29 0.88
16 1 0.03
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (15 bp):
TCTTCTTCTTCTTTT
Found at i:257561 original size:18 final size:17
Alignment explanation
Indices: 257548--257592 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
257538 CTTCTTCTTT
257548 TTCTTCTTTCTCTTTTAC
1 TTCTTCTTT-TCTTTTAC
257566 TTCTTCTTTTC-TTT-C
1 TTCTTCTTTTCTTTTAC
257581 TTCTTCATTTTC
1 TTCTTC-TTTTC
257593 CTTAATACCC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 7 0.27
16 8 0.31
17 2 0.08
18 9 0.35
ACGTcount: A:0.04, C:0.27, G:0.00, T:0.69
Consensus pattern (17 bp):
TTCTTCTTTTCTTTTAC
Found at i:269151 original size:20 final size:20
Alignment explanation
Indices: 269126--269170 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
269116 CATGATTTAT
*
269126 ATTAAGAGT-AAATAGGCTTA
1 ATTAAGAGTAAAATA-GATTA
*
269146 ATTAAGATTAAAATAGATTA
1 ATTAAGAGTAAAATAGATTA
269166 ATTAA
1 ATTAA
269171 AGCTCAATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.51, C:0.02, G:0.13, T:0.33
Consensus pattern (20 bp):
ATTAAGAGTAAAATAGATTA
Found at i:277648 original size:25 final size:24
Alignment explanation
Indices: 277610--277657 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
277600 TTGTAAATCA
*
277610 GAAAAATATCTCTAGAGACTTTTT
1 GAAAAATATCTCTAGAGAATTTTT
*
277634 GAAATAATCTCTCTAGAGAATTTT
1 GAAA-AATATCTCTAGAGAATTTT
277658 CTCTCTACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (24 bp):
GAAAAATATCTCTAGAGAATTTTT
Found at i:277885 original size:11 final size:11
Alignment explanation
Indices: 277871--277946 Score: 52
Period size: 11 Copynumber: 6.8 Consensus size: 11
277861 GATAATCACT
277871 TTAATATTAAA
1 TTAATATTAAA
277882 TTAATA--AAA
1 TTAATATTAAA
*
277891 -TACTATTAAA
1 TTAATATTAAA
*
277901 ATAATATTTAAA
1 TTAATA-TTAAA
277913 TTTAAT-TTAATA
1 -TTAATATTAA-A
277925 TTAAACTATTAAA
1 TT-AA-TATTAAA
*
277938 ATAATATTA
1 TTAATATTA
277947 TTTTTGAAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 18
0.70 0.05 0.24
Matches are distributed among these distances:
8 4 0.08
9 3 0.06
10 3 0.06
11 21 0.40
12 10 0.19
13 7 0.13
14 4 0.08
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:293348 original size:3 final size:3
Alignment explanation
Indices: 293340--293495 Score: 130
Period size: 3 Copynumber: 50.7 Consensus size: 3
293330 GACTAAAACA
293340 AAT AAT AAT AAT 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 AAT AAT AAT AAT
293388 AAT AA- AGAT AAT AAAT AAAT AA- ATAT AAT -AT AAT -AT ATAT ATAT
1 AAT AAT A-AT AAT -AAT -AAT AAT A-AT AAT AAT AAT AAT A-AT A-AT
*
293432 AACA AAT AAAT AAT AA- ACA- AAT AACT AAAT AAT AAAT AAT AAT AAT
1 AA-T AAT -AAT AAT AAT A-AT AAT AA-T -AAT AAT -AAT AAT AAT AAT
*
293478 -AT AAT AAT ATT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AA
293496 CAAAAAGAAA
Statistics
Matches: 132, Mismatches: 4, Indels: 34
0.78 0.02 0.20
Matches are distributed among these distances:
2 12 0.09
3 92 0.70
4 26 0.20
5 2 0.02
ACGTcount: A:0.67, C:0.02, G:0.01, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:293406 original size:4 final size:4
Alignment explanation
Indices: 293397--293470 Score: 62
Period size: 4 Copynumber: 18.2 Consensus size: 4
293387 TAATAAAGAT
* * *
293397 AATA AATA AATA AATA TAATA TAATA TATA TATA TAACA AATA AAT- AATA
1 AATA AATA AATA AATA -AATA -AATA AATA AATA -AATA AATA AATA AATA
* *
293447 AACA AATA ACTA AAT- AATA AATA A
1 AATA AATA AATA AATA AATA AATA A
293471 TAATAATATA
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
3 6 0.10
4 41 0.71
5 11 0.19
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (4 bp):
AATA
Found at i:294189 original size:74 final size:74
Alignment explanation
Indices: 294103--294273 Score: 184
Period size: 74 Copynumber: 2.3 Consensus size: 74
294093 GATTTGGAAA
* * *
294103 ACGCCTGTGTGTCTAGGTCGTGTATCATTTCGAAACTCATTTAAAAATAAACCCAGTTG-CACAC
1 ACGCCCGTGTGTCAAGGTCGTGTATCATTTCGAAAATCATTTAAAAATAAACCCAG-TGACACAC
* *
294167 GGTTTATAAC
65 GGTCTAGAAC
* * * * **
294177 ACGCCCGTGTGTCCAGG-CTTTGTGTCGTTTCGAAAATCATTTAAAAATACGCCCAGTGATCACA
1 ACGCCCGTGTGTCAAGGTC-GTGTATCATTTCGAAAATCATTTAAAAATAAACCCAGTGA-CACA
*
294241 CGGTCTAGCAC
64 CGGTCTAGAAC
*
294252 ACGCCCGTGTGTCAAAGTCGTG
1 ACGCCCGTGTGTCAAGGTCGTG
294274 GGCCTTACTC
Statistics
Matches: 79, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
73 3 0.04
74 46 0.58
75 29 0.37
76 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (74 bp):
ACGCCCGTGTGTCAAGGTCGTGTATCATTTCGAAAATCATTTAAAAATAAACCCAGTGACACACG
GTCTAGAAC
Found at i:299948 original size:21 final size:23
Alignment explanation
Indices: 299915--299968 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 23
299905 ATATAAAAAT
*
299915 TAAATTAAAAAT-GC-AAA-TAA
1 TAAAATAAAAATGGCTAAAGTAA
299935 TAAAATAAAGAATGGCTAAAGTAA
1 TAAAATAAA-AATGGCTAAAGTAA
299959 TAAAAATAAA
1 T-AAAATAAA
299969 TTTTTCCTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 8 0.29
21 3 0.11
22 2 0.07
23 3 0.11
24 4 0.14
25 8 0.29
ACGTcount: A:0.65, C:0.04, G:0.09, T:0.22
Consensus pattern (23 bp):
TAAAATAAAAATGGCTAAAGTAA
Found at i:301449 original size:60 final size:60
Alignment explanation
Indices: 301323--301455 Score: 162
Period size: 60 Copynumber: 2.2 Consensus size: 60
301313 AAACTTTTTT
*
301323 TCCAATTTGGTACTTGAACTTAACAATTTTTCCTAATTTGGTACATAAATTTTGTTTGGA
1 TCCAATTTGGTACTTGAACTTAACAATTTTTCCTAATTTGGTACATAAATTTTGTTTAGA
* *** * *
301383 TCCAATTTGGTATTTGAACTTGGTACTTTTTCCTAATTTGGTATC-TAAGCTTTT-TTTAGA
1 TCCAATTTGGTACTTGAACTTAACAATTTTTCCTAATTTGGTA-CATAA-ATTTTGTTTAGA
*
301443 TTCAATTTGGTAC
1 TCCAATTTGGTAC
301456 CTAAATTTAT
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
60 57 0.92
61 5 0.08
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.47
Consensus pattern (60 bp):
TCCAATTTGGTACTTGAACTTAACAATTTTTCCTAATTTGGTACATAAATTTTGTTTAGA
Found at i:306075 original size:14 final size:14
Alignment explanation
Indices: 306056--306094 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
306046 TTGTTTGACT
306056 GAAAATGATTTCCA
1 GAAAATGATTTCCA
* **
306070 GAAAATGGTTTCTG
1 GAAAATGATTTCCA
306084 GAAAATGATTT
1 GAAAATGATTT
306095 ACTTTTCTGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.38, C:0.08, G:0.21, T:0.33
Consensus pattern (14 bp):
GAAAATGATTTCCA
Found at i:311751 original size:22 final size:22
Alignment explanation
Indices: 311713--311755 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
311703 TAGTAGTTTT
*
311713 GTGCTCTCTATTTAACACTTCG
1 GTGCTCTCTATTCAACACTTCG
311735 GTGCTCTCTGA-TCAACACTTC
1 GTGCTCTCT-ATTCAACACTTC
311756 AGTGTTGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.19, C:0.30, G:0.14, T:0.37
Consensus pattern (22 bp):
GTGCTCTCTATTCAACACTTCG
Found at i:316528 original size:32 final size:31
Alignment explanation
Indices: 316481--316553 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
316471 TTCAAAAACA
*
316481 TGTT-ATTTTAATCACTCTCATTATACAAAAT
1 TGTTAATTTTAATCACTCTCATTAGA-AAAAT
* * * *
316512 TGTTAATTTTAGTCACTTTTATTAGATAAAT
1 TGTTAATTTTAATCACTCTCATTAGAAAAAT
316543 TGTTAATTTTA
1 TGTTAATTTTA
316554 CTTATTTTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
31 19 0.53
32 17 0.47
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.51
Consensus pattern (31 bp):
TGTTAATTTTAATCACTCTCATTAGAAAAAT
Found at i:317006 original size:29 final size:27
Alignment explanation
Indices: 316893--317006 Score: 66
Period size: 31 Copynumber: 3.8 Consensus size: 27
316883 AATTAAATTA
* * *
316893 AAATTAAAGTTTTAAGTATACATTTGAACT
1 AAATCAAAG-TTTATGTATA-A-TTGCACT
316923 ACAATCAAAGTTTCACGTGTATAATTGCACT
1 A-AATCAAAGTTT-A--TGTATAATTGCACT
* * * *
316954 AAATTAAAATTCATGTATACAATTGTACATT
1 AAATCAAAGTTTATGTAT--AATTG--CACT
316985 AAATCAAAGTTTATGTATAATT
1 AAATCAAAGTTTATGTATAATT
317007 TTGAGATTTA
Statistics
Matches: 66, Mismatches: 10, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
27 5 0.08
29 10 0.15
30 12 0.18
31 33 0.50
32 1 0.02
33 5 0.08
ACGTcount: A:0.42, C:0.11, G:0.10, T:0.38
Consensus pattern (27 bp):
AAATCAAAGTTTATGTATAATTGCACT
Found at i:317611 original size:31 final size:30
Alignment explanation
Indices: 317576--317635 Score: 93
Period size: 31 Copynumber: 2.0 Consensus size: 30
317566 ATTTAATGGT
*
317576 AGAGTGACTAAAATTGACAACTTATCTAAAG
1 AGAGTAACTAAAATTGACAACTTAT-TAAAG
*
317607 AGAGTAACTAAAATTGATAACTTATTAAA
1 AGAGTAACTAAAATTGACAACTTATTAAA
317636 CAATAGACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 4 0.15
31 23 0.85
ACGTcount: A:0.48, C:0.10, G:0.13, T:0.28
Consensus pattern (30 bp):
AGAGTAACTAAAATTGACAACTTATTAAAG
Found at i:319906 original size:21 final size:21
Alignment explanation
Indices: 319880--319930 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
319870 GAGACAATAT
319880 TACCGATACAAGT-ATAACTTC
1 TACCGATACAAGTCAT-ACTTC
* * *
319901 TACCGAAACATGTCATGCTTC
1 TACCGATACAAGTCATACTTC
319922 TACCGATAC
1 TACCGATAC
319931 TAAAAACTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 23 0.92
22 2 0.08
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.27
Consensus pattern (21 bp):
TACCGATACAAGTCATACTTC
Found at i:320925 original size:51 final size:52
Alignment explanation
Indices: 320715--320956 Score: 342
Period size: 52 Copynumber: 4.7 Consensus size: 52
320705 ATTCCATTTA
* * * * * **
320715 ATACTCACGATGACACATAGTCATTGAACCTCTTAATTCGTGGAGGAATCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGAATCAT
*
320767 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCTTAAAGGAATCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGAATCAT
* *
320819 ATTCTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGAATCAT
* *
320871 ATACTCATGATGACACATAGTCATCGGACC-TTTAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGAATCAT
* *
320922 ATACTCACAATGACACATAGTCATCAGACCCTTTT
1 ATACTCACGATGACACATAGTCATCGGA-CCTTTT
320957 TTTATTTACA
Statistics
Matches: 173, Mismatches: 15, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
51 46 0.27
52 124 0.72
53 3 0.02
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGAATCAT
Found at i:330866 original size:17 final size:17
Alignment explanation
Indices: 330819--330868 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
330809 CCCTAATACC
330819 ATTAATATATTT-T-AA
1 ATTAATATATTTCTAAA
*
330834 ATTAA-ATATCTCCTAAA
1 ATTAATATAT-TTCTAAA
330851 ATTAATATATTTCTAAA
1 ATTAATATATTTCTAAA
330868 A
1 A
330869 GCAATAATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
14 4 0.14
15 6 0.21
16 1 0.03
17 14 0.48
18 4 0.14
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTAATATATTTCTAAA
Found at i:334127 original size:13 final size:13
Alignment explanation
Indices: 334109--334133 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
334099 GTGCATCTTA
334109 ATTATTAATATTC
1 ATTATTAATATTC
334122 ATTATTAATATT
1 ATTATTAATATT
334134 AGAATTGTGT
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:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (13 bp):
ATTATTAATATTC
Found at i:336521 original size:19 final size:19
Alignment explanation
Indices: 336499--336535 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
336489 TAAATTGTGA
**
336499 TAATATATTTAAAATATAC
1 TAATATATGAAAAATATAC
336518 TAATATATGAAAAATATA
1 TAATATATGAAAAATATA
336536 TTATTTTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (19 bp):
TAATATATGAAAAATATAC
Found at i:337586 original size:20 final size:19
Alignment explanation
Indices: 337558--337617 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 19
337548 TCTCTCAACA
*
337558 AATTATAAAAAGTTCAAAAT
1 AATTTTAAAAA-TTCAAAAT
337578 AATTTTAAAAAATTCAAAAT
1 AATTTT-AAAAATTCAAAAT
337598 -ATTTATAAAAATTCTAAAAT
1 AATTT-TAAAAATTC-AAAAT
337618 TTATATATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
19 12 0.33
20 19 0.53
21 5 0.14
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (19 bp):
AATTTTAAAAATTCAAAAT
Found at i:337587 original size:19 final size:20
Alignment explanation
Indices: 337560--337622 Score: 78
Period size: 19 Copynumber: 3.2 Consensus size: 20
337550 TCTCAACAAA
*
337560 TTATAAAAAGTTCAAAATAAT
1 TTATAAAAAATTCAAAAT-AT
337581 TT-TAAAAAATTCAAAATAT
1 TTATAAAAAATTCAAAATAT
*
337600 TTAT-AAAAATTCTAAA-AT
1 TTATAAAAAATTCAAAATAT
337618 TTATA
1 TTATA
337623 TATATATTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
18 6 0.16
19 15 0.39
20 15 0.39
21 2 0.05
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.38
Consensus pattern (20 bp):
TTATAAAAAATTCAAAATAT
Found at i:337638 original size:22 final size:24
Alignment explanation
Indices: 337613--337661 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
337603 TAAAAATTCT
337613 AAAATT-T-ATATATATATTTAAA
1 AAAATTATAATATATATATTTAAA
*
337635 AAAATTATAATATATATTTTTAAA
1 AAAATTATAATATATATATTTAAA
337659 AAA
1 AAA
337662 TTTCTAAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 6 0.25
23 1 0.04
24 17 0.71
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
AAAATTATAATATATATATTTAAA
Found at i:339496 original size:27 final size:27
Alignment explanation
Indices: 339434--339500 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 27
339424 ATTGCTAGTT
* * *
339434 GGGTTCGCCAGATGGTTTGGTGAGTTA
1 GGGTTCGCTAGTTGGTTTGGTGAGCTA
*
339461 GGGTTCGCTAGTTGGTTTGGTGAGCTG
1 GGGTTCGCTAGTTGGTTTGGTGAGCTA
339488 GGGTTCGCTAGTT
1 GGGTTCGCTAGTT
339501 TAGTTATGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.10, C:0.12, G:0.42, T:0.36
Consensus pattern (27 bp):
GGGTTCGCTAGTTGGTTTGGTGAGCTA
Found at i:354025 original size:18 final size:18
Alignment explanation
Indices: 354002--354045 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
353992 TACTCAGATG
354002 AGCCACAAGTTCAAATGC
1 AGCCACAAGTTCAAATGC
*
354020 AGCCACAGGTTCAAATGC
1 AGCCACAAGTTCAAATGC
*
354038 AACCACAA
1 AGCCACAA
354046 CAAACTGTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.41, C:0.30, G:0.16, T:0.14
Consensus pattern (18 bp):
AGCCACAAGTTCAAATGC
Found at i:360173 original size:3 final size:3
Alignment explanation
Indices: 360157--360202 Score: 51
Period size: 3 Copynumber: 15.3 Consensus size: 3
360147 GGCAGAGGAG
*
360157 GAA GAAA GAA -AA GAA GAA GAA GAA GAA G-A GAA GGAA GAA AAA GAA
1 GAA G-AA GAA GAA GAA GAA GAA GAA GAA GAA GAA -GAA GAA GAA GAA
360202 G
1 G
360203 CAGATGTTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
2 4 0.11
3 27 0.73
4 6 0.16
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:360183 original size:21 final size:21
Alignment explanation
Indices: 360157--360202 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
360147 GGCAGAGGAG
*
360157 GAAGAA-AGAAAAGAAGAAGAA
1 GAAGAAGAG-AAAGAAGAAAAA
*
360178 GAAGAAGAGAAGGAAGAAAAA
1 GAAGAAGAGAAAGAAGAAAAA
360199 GAAG
1 GAAG
360203 CAGATGTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (21 bp):
GAAGAAGAGAAAGAAGAAAAA
Found at i:369111 original size:17 final size:18
Alignment explanation
Indices: 369089--369190 Score: 86
Period size: 17 Copynumber: 5.8 Consensus size: 18
369079 TAATACGTAT
369089 TAAAAATATATAAAG-AA
1 TAAAAATATATAAAGTAA
*
369106 TAAAAATATA-AGATGTAA
1 TAAAAATATATA-AAGTAA
* *
369124 TAGAAATATAT-ATGTAA
1 TAAAAATATATAAAGTAA
369141 TAAAAATATATAAAG-AA
1 TAAAAATATATAAAGTAA
* * * * *
369158 TAAAGATAAACAAAATAC
1 TAAAAATATATAAAGTAA
*
369176 TTAAAATATATAAAG
1 TAAAAATATATAAAG
369191 AGCAAAAATA
Statistics
Matches: 66, Mismatches: 14, Indels: 9
0.74 0.16 0.10
Matches are distributed among these distances:
16 1 0.02
17 41 0.62
18 24 0.36
ACGTcount: A:0.64, C:0.02, G:0.08, T:0.26
Consensus pattern (18 bp):
TAAAAATATATAAAGTAA
Found at i:369202 original size:35 final size:33
Alignment explanation
Indices: 369143--369258 Score: 101
Period size: 35 Copynumber: 3.4 Consensus size: 33
369133 ATATGTAATA
369143 AAAATATATAAAGAATAAAGATAAACAAAATACTT
1 AAAATATATAAAGAA-AAA-ATAAACAAAATACTT
* * *
369178 AAAATATATAAAGAGCAAAAATAAACTAATTACGGT
1 AAAATATATAAAGA--AAAAATAAACAAAATAC-TT
* * *
369214 AAATAGAAATATAAGAAAAAA-ATA-AAAATACTT
1 AAA-ATATATA-AAGAAAAAATAAACAAAATACTT
369247 AAAATATATAAA
1 AAAATATATAAA
369259 TGCTGTAAAT
Statistics
Matches: 65, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
31 2 0.03
32 5 0.08
33 4 0.06
34 5 0.08
35 27 0.42
36 12 0.18
37 6 0.09
38 4 0.06
ACGTcount: A:0.66, C:0.05, G:0.07, T:0.22
Consensus pattern (33 bp):
AAAATATATAAAGAAAAAATAAACAAAATACTT
Found at i:369417 original size:30 final size:28
Alignment explanation
Indices: 369362--369417 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 28
369352 TTGAGAAAAG
*
369362 TAAATGCATAAATTTAAAGGCAAGAATT
1 TAAATGCATAAATTTAAAGGAAAGAATT
369390 TAAATTGCAATAAA-TTAAAGTGAAAGAA
1 TAAA-TGC-ATAAATTTAAAG-GAAAGAA
369418 AGTAAAGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 4 0.17
29 9 0.38
30 11 0.46
ACGTcount: A:0.54, C:0.05, G:0.14, T:0.27
Consensus pattern (28 bp):
TAAATGCATAAATTTAAAGGAAAGAATT
Found at i:374264 original size:59 final size:59
Alignment explanation
Indices: 374172--374289 Score: 191
Period size: 59 Copynumber: 2.0 Consensus size: 59
374162 CAAAAAGATC
*
374172 GTTTTATTATCTTTAAGGCCGATTGAGGCCTAAAGGTTAGTTAACGTACTTCGTGAGTG
1 GTTTTATTATCTTTAAGGCCGATTGAGGCCTAAAGGTTAGCTAACGTACTTCGTGAGTG
* * * *
374231 GTTTTATTGTCTTTTAGGCCTATTGAGGCCTAAAGGTTAGCTAACGTACTTTGTGAGTG
1 GTTTTATTATCTTTAAGGCCGATTGAGGCCTAAAGGTTAGCTAACGTACTTCGTGAGTG
374290 TGCATGAGAC
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 54 1.00
ACGTcount: A:0.22, C:0.14, G:0.25, T:0.39
Consensus pattern (59 bp):
GTTTTATTATCTTTAAGGCCGATTGAGGCCTAAAGGTTAGCTAACGTACTTCGTGAGTG
Found at i:383934 original size:87 final size:87
Alignment explanation
Indices: 383788--383996 Score: 321
Period size: 87 Copynumber: 2.4 Consensus size: 87
383778 GTCCAGAACT
* *
383788 TTTACGCTTGTCAG-ATAATCAGAATCAAAATGATCGTGTCTCATAATAACCCGAGTCCGCAACA
1 TTTACGCTTGTCAGCA-AATCAGAATTAGAATGATCGTGTCTCATAATAACCCGAGTCCGCAACA
383852 CATGCAGGAGCTCGGTCAAAATG
65 CATGCAGGAGCTCGGTCAAAATG
* * *
383875 TTTACGCTTGTCAGCAAATCAGAATTAGAATGATTGTGTCTGATAATAACTCGAGTCCGCAACAC
1 TTTACGCTTGTCAGCAAATCAGAATTAGAATGATCGTGTCTCATAATAACCCGAGTCCGCAACAC
* * *
383940 ATGCAGGAGTTTGGTCAGAATG
66 ATGCAGGAGCTCGGTCAAAATG
*
383962 TTTACGCTTGTCAGCAAATCAAAATTAGAATGATC
1 TTTACGCTTGTCAGCAAATCAGAATTAGAATGATC
383997 CTATCAGGTT
Statistics
Matches: 111, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
87 110 0.99
88 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (87 bp):
TTTACGCTTGTCAGCAAATCAGAATTAGAATGATCGTGTCTCATAATAACCCGAGTCCGCAACAC
ATGCAGGAGCTCGGTCAAAATG
Found at i:398126 original size:20 final size:20
Alignment explanation
Indices: 398096--398137 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
398086 TAAGTGCTTA
398096 AAAGTGAGATTAATTAAGGTT
1 AAAGTGAGATTAATT-AGGTT
398117 AAAGTG-GATTAATTAGGTT
1 AAAGTGAGATTAATTAGGTT
398136 AA
1 AA
398138 TTATAAAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 7 0.33
20 8 0.38
21 6 0.29
ACGTcount: A:0.43, C:0.00, G:0.24, T:0.33
Consensus pattern (20 bp):
AAAGTGAGATTAATTAGGTT
Found at i:398614 original size:52 final size:52
Alignment explanation
Indices: 398550--398725 Score: 219
Period size: 52 Copynumber: 3.4 Consensus size: 52
398540 GTACTTGGTA
* * *
398550 TGAGTAAGTGAATTCTTTAAGGATTTTGAGGTCCGATGACTAAGTGTCATCG
1 TGAGTAAATGAATCCTTTAAGGATTATGAGGTCCGATGACTAAGTGTCATCG
* * * *
398602 TGAGTAAATGAATCCTTTACGGATTATAAGGTCTGATGGCTAAGTGTCATCG
1 TGAGTAAATGAATCCTTTAAGGATTATGAGGTCCGATGACTAAGTGTCATCG
* ** *
398654 TGAGTATATGAATCCTTTACA-GATGGTGAGGTGCGATGACTAAGTGTCATCG
1 TGAGTAAATGAATCCTTTA-AGGATTATGAGGTCCGATGACTAAGTGTCATCG
*
398706 TGAGTACATGAATTCCTTTA
1 TGAGTAAATGAA-TCCTTTA
398726 CGAAACAGGA
Statistics
Matches: 106, Mismatches: 16, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
52 99 0.93
53 7 0.07
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.34
Consensus pattern (52 bp):
TGAGTAAATGAATCCTTTAAGGATTATGAGGTCCGATGACTAAGTGTCATCG
Found at i:404873 original size:20 final size:20
Alignment explanation
Indices: 404843--404884 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
404833 TAAGTGCTTA
404843 AAAGTGAGATTAATTAAGGTT
1 AAAGTGAGATTAATT-AGGTT
404864 AAAGTG-GATTAATTAGGTT
1 AAAGTGAGATTAATTAGGTT
404883 AA
1 AA
404885 TTATAAAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 7 0.33
20 8 0.38
21 6 0.29
ACGTcount: A:0.43, C:0.00, G:0.24, T:0.33
Consensus pattern (20 bp):
AAAGTGAGATTAATTAGGTT
Found at i:405844 original size:52 final size:52
Alignment explanation
Indices: 405744--406016 Score: 289
Period size: 52 Copynumber: 5.2 Consensus size: 52
405734 AAATGAAAAG
* * **
405744 GGTCCAATGATTAAGTGTCATTGTGAGTAAATGAA-TCATTTACGGATTATGA
1 GGTCCGATGACTAAGTGTCATCATGAGTAAATGAATTC-TTTACGGATTATGA
* * **
405796 GGTCTGATGACTAAGTGTCATTATGAGTAAATGAATTCTTTATAGATTATGA
1 GGTCCGATGACTAAGTGTCATCATGAGTAAATGAATTCTTTACGGATTATGA
* * *
405848 GGTCCGATGACTAAGTGTCATCATGAGTAAAT-AATCCTTTATGGATTATAA
1 GGTCCGATGACTAAGTGTCATCATGAGTAAATGAATTCTTTACGGATTATGA
* * * * * ** *
405899 GGTCCGCTGGCTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATGGTTA
1 GGTCCGATGACTAAGTGTCATCATGAGTAAATGAATTCTTTACGGATTATGA
** ** *
405951 GGTCCGATGACTAAGTGTCATCATGAGTACTTGAATTCCTTTACGGAACAGGA
1 GGTCCGATGACTAAGTGTCATCATGAGTAAATGAATT-CTTTACGGATTATGA
*
406004 GGTCCGACGACTA
1 GGTCCGATGACTA
406017 TATGTTTTTG
Statistics
Matches: 187, Mismatches: 31, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
51 44 0.24
52 119 0.64
53 24 0.13
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (52 bp):
GGTCCGATGACTAAGTGTCATCATGAGTAAATGAATTCTTTACGGATTATGA
Found at i:405926 original size:103 final size:104
Alignment explanation
Indices: 405744--405997 Score: 294
Period size: 103 Copynumber: 2.4 Consensus size: 104
405734 AAATGAAAAG
* * ** * *
405744 GGTCCAATGATTAAGTGTCATTGTGAGTAAATGAATCATTTACGGATTATGAGGTCTGATGACTA
1 GGTCCGATGACTAAGTGTCATCATGAGTAAATGAATCATTTACGGATTATAAGGTCCGATGACTA
* * * *
405809 AGTGTCATTATGAGTAAATGAATTCTTTATAGATTATGA
66 AGTGTCATCATGAGTAAATGAATCCTTTACAGATGATGA
* * * *
405848 GGTCCGATGACTAAGTGTCATCATGAGTAAAT-AATCCTTTATGGATTATAAGGTCCGCTGGCTA
1 GGTCCGATGACTAAGTGTCATCATGAGTAAATGAATCATTTACGGATTATAAGGTCCGATGACTA
* * * * *
405912 AGTGTCATCGTGAGTATATGAATCCTTTACGGATGGTTA
66 AGTGTCATCATGAGTAAATGAATCCTTTACAGATGATGA
** *
405951 GGTCCGATGACTAAGTGTCATCATGAGTACTTGAATTCCTTTACGGA
1 GGTCCGATGACTAAGTGTCATCATGAGTAAATGAA-TCATTTACGGA
405998 ACAGGAGGTC
Statistics
Matches: 126, Mismatches: 22, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
103 86 0.68
104 30 0.24
105 10 0.08
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.34
Consensus pattern (104 bp):
GGTCCGATGACTAAGTGTCATCATGAGTAAATGAATCATTTACGGATTATAAGGTCCGATGACTA
AGTGTCATCATGAGTAAATGAATCCTTTACAGATGATGA
Found at i:409732 original size:24 final size:24
Alignment explanation
Indices: 409699--409773 Score: 71
Period size: 24 Copynumber: 3.1 Consensus size: 24
409689 ATACTGTTTA
*
409699 AACTCTATCTGGGTTCGAATGAGCT
1 AACT-TATCTGGGCTCGAATGAGCT
* *
409724 AACTTATCTAGGCTCGTAA-GAGCC
1 AACTTATCTGGGCTCG-AATGAGCT
* * *
409748 AACCTATCTGGGCTCGTATGGGCT
1 AACTTATCTGGGCTCGAATGAGCT
409772 AA
1 AA
409774 TTTTGTTCTG
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
23 1 0.03
24 33 0.82
25 6 0.15
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.28
Consensus pattern (24 bp):
AACTTATCTGGGCTCGAATGAGCT
Found at i:414199 original size:24 final size:24
Alignment explanation
Indices: 414172--414229 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
414162 TTAAACTCTG
*
414172 TTTGGGCTC-AAATGAGCTAACTTA
1 TTTGGGCTCGAAA-GAGCTAACCTA
*
414196 TTTGGGCTCGTAAGAGCTAACCTA
1 TTTGGGCTCGAAAGAGCTAACCTA
*
414220 TCTGGGCTCG
1 TTTGGGCTCG
414230 TATGGGCTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
24 28 0.93
25 2 0.07
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.31
Consensus pattern (24 bp):
TTTGGGCTCGAAAGAGCTAACCTA
Found at i:414239 original size:24 final size:24
Alignment explanation
Indices: 414185--414231 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
414175 GGGCTCAAAT
* *
414185 GAGCTAACTTATTTGGGCTCGTAA
1 GAGCTAACCTATCTGGGCTCGTAA
414209 GAGCTAACCTATCTGGGCTCGTA
1 GAGCTAACCTATCTGGGCTCGTA
414232 TGGGCTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (24 bp):
GAGCTAACCTATCTGGGCTCGTAA
Found at i:417515 original size:24 final size:24
Alignment explanation
Indices: 417488--417576 Score: 99
Period size: 24 Copynumber: 3.7 Consensus size: 24
417478 ACTCTGTCTA
*
417488 GGCTCGAATGAGCTAACTTATCTG
1 GGCTCGTATGAGCTAACTTATCTG
*
417512 GGCTCGT-TAGAGCTAACCTATCTG
1 GGCTCGTAT-GAGCTAACTTATCTG
* * *
417536 GGCTCGTATGGGCTAATTTTGTCTG
1 GGCTCGTATGAGCTAA-CTTATCTG
*
417561 GGTTCGTATGAGCTAA
1 GGCTCGTATGAGCTAA
417577 ATTTCTTGAA
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
23 1 0.02
24 33 0.61
25 20 0.37
ACGTcount: A:0.20, C:0.19, G:0.28, T:0.33
Consensus pattern (24 bp):
GGCTCGTATGAGCTAACTTATCTG
Found at i:428877 original size:20 final size:20
Alignment explanation
Indices: 428852--428903 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 20
428842 AGGTGGTAAA
428852 AATTTTATTTTCTAA-TTTTT
1 AATTTTATTTT-TAACTTTTT
428872 AATTTTAATTTATTAACTTTTT
1 AATTTT-ATTT-TTAACTTTTT
428894 AA-TTTATTTT
1 AATTTTATTTT
428904 AAATTGTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
19 1 0.03
20 10 0.34
21 10 0.34
22 8 0.28
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (20 bp):
AATTTTATTTTTAACTTTTT
Found at i:429822 original size:18 final size:18
Alignment explanation
Indices: 429801--429841 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
429791 AAATTCTGAA
*
429801 GAAGAAGAGGATCCCGAG
1 GAAGAAGAAGATCCCGAG
*
429819 GAAGAAGAAGATCCTGAG
1 GAAGAAGAAGATCCCGAG
429837 GAAGA
1 GAAGA
429842 CCTTGAAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.44, C:0.12, G:0.37, T:0.07
Consensus pattern (18 bp):
GAAGAAGAAGATCCCGAG
Found at i:433529 original size:21 final size:21
Alignment explanation
Indices: 433481--433529 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
433471 AAAACCAATT
* **
433481 GAACCAAAACCAGTTTTACCA
1 GAACCAGAACCAAATTTACCA
*
433502 GAACCAGAACCAAATTTGCCA
1 GAACCAGAACCAAATTTACCA
433523 GAACCAG
1 GAACCAG
433530 TTTTACCAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.43, C:0.29, G:0.14, T:0.14
Consensus pattern (21 bp):
GAACCAGAACCAAATTTACCA
Found at i:435677 original size:127 final size:128
Alignment explanation
Indices: 435450--435708 Score: 421
Period size: 127 Copynumber: 2.0 Consensus size: 128
435440 ATTCTGGCTT
* * * *
435450 AGCTCATGAAGATGCAAGAGAACATTTAAAATCATTTTTGCTTGTTTGTCGTATCTTGTAGCCAG
1 AGCTCATGAAGATGCAAGAGAACATTTAAAATCATTTTTGCTTGATTGCCGCATCTTGTAGCCAA
* * * *
435515 CATGGTGTCCTTGATGATGCTTTAAAAATGCAATTATTTCCTTATTCGTTGTAGGGAAGAGCC
66 CACGGTGTCCTTGATGATGCTTTAAAAATGAAATTATTTCCTTATTCATTGCAGGGAAGAGCC
* *
435578 AGCTCATGAAGATGTAAGAGAACATTTAAAGTCATTTTTGCTT-ATTGCCGCATCTTGTAGCCAA
1 AGCTCATGAAGATGCAAGAGAACATTTAAAATCATTTTTGCTTGATTGCCGCATCTTGTAGCCAA
435642 CACGGTGTCCTTGATGATGCTTTAAAAATGAAATTATTTCCTTATTCATTGCAGGGAAGAGCC
66 CACGGTGTCCTTGATGATGCTTTAAAAATGAAATTATTTCCTTATTCATTGCAGGGAAGAGCC
435705 AGCT
1 AGCT
435709 GGATCTATTA
Statistics
Matches: 121, Mismatches: 10, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
127 80 0.66
128 41 0.34
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (128 bp):
AGCTCATGAAGATGCAAGAGAACATTTAAAATCATTTTTGCTTGATTGCCGCATCTTGTAGCCAA
CACGGTGTCCTTGATGATGCTTTAAAAATGAAATTATTTCCTTATTCATTGCAGGGAAGAGCC
Found at i:445250 original size:3 final size:3
Alignment explanation
Indices: 445242--445268 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
445232 GTTTATTTTC
445242 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
445269 TAGGCTATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:452073 original size:16 final size:16
Alignment explanation
Indices: 452054--452086 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
452044 TTTGTAGAGT
452054 ATTAATCTAAATTAAA
1 ATTAATCTAAATTAAA
*
452070 ATTAATCTAAGTTAAA
1 ATTAATCTAAATTAAA
452086 A
1 A
452087 AGATAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.36
Consensus pattern (16 bp):
ATTAATCTAAATTAAA
Found at i:455189 original size:16 final size:16
Alignment explanation
Indices: 455168--455200 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
455158 TGATTAAATA
455168 TTAATTTTATTTGTTC
1 TTAATTTTATTTGTTC
455184 TTAATTTTATTTGTTC
1 TTAATTTTATTTGTTC
455200 T
1 T
455201 CAAAAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.70
Consensus pattern (16 bp):
TTAATTTTATTTGTTC
Found at i:455210 original size:23 final size:23
Alignment explanation
Indices: 455192--455659 Score: 393
Period size: 23 Copynumber: 20.4 Consensus size: 23
455182 TCTTAATTTT
* * *
455192 ATTTGTTCTCAAAAATTAATGTG
1 ATTTGTGCTCAAATATTAATATG
*
455215 ATTTGTGCTTAAATATTAATATG
1 ATTTGTGCTCAAATATTAATATG
*
455238 ATTTGTGCTCAAATATTAATGTG
1 ATTTGTGCTCAAATATTAATATG
* * **
455261 ATTTATGCTTAAATATTAATGGG
1 ATTTGTGCTCAAATATTAATATG
* *
455284 ATTTGTGCTTAAATATTAATGTG
1 ATTTGTGCTCAAATATTAATATG
* * *
455307 ATTTGTGCTTAAATAATAATGTG
1 ATTTGTGCTCAAATATTAATATG
* *
455330 ATTTGCGCTTAAATATTAATATG
1 ATTTGTGCTCAAATATTAATATG
* * *
455353 ATTTATGCTTAAATATTAATGTG
1 ATTTGTGCTCAAATATTAATATG
* * * *
455376 ATTTATGATTAAATATTAATGTG
1 ATTTGTGCTCAAATATTAATATG
* * *
455399 ATTTTTGCTTAAATATTAATTTG
1 ATTTGTGCTCAAATATTAATATG
* * *
455422 ATTTATGCTTAAATATTAATGTG
1 ATTTGTGCTCAAATATTAATATG
* * * *
455445 ATTTCTACTTAAATATT-ATGTG
1 ATTTGTGCTCAAATATTAATATG
** * * *
455467 ATTTGTATTGAAATATTAATCTC
1 ATTTGTGCTCAAATATTAATATG
* * *
455490 ATTTGTGTTAAAATATTAATTTG
1 ATTTGTGCTCAAATATTAATATG
*
455513 ATTTGTGCTTAAATATTAATATG
1 ATTTGTGCTCAAATATTAATATG
* * * *
455536 ATTTGTACTGAAATATTAATGTA
1 ATTTGTGCTCAAATATTAATATG
*
455559 ATTTGTGCTTAAATATTAA-ATTG
1 ATTTGTGCTCAAATATTAATA-TG
* * *
455582 ATTTATGCTTAAATATTAATGTG
1 ATTTGTGCTCAAATATTAATATG
* * *
455605 ATTTGTGCTTAAATATTAATTTC
1 ATTTGTGCTCAAATATTAATATG
* * *
455628 ATTTATGATAAAATATTAA-AGTG
1 ATTTGTGCTCAAATATTAATA-TG
455651 ATTTGTGCT
1 ATTTGTGCT
455660 TAAAGAATTA
Statistics
Matches: 383, Mismatches: 58, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
22 19 0.05
23 364 0.95
ACGTcount: A:0.34, C:0.05, G:0.13, T:0.47
Consensus pattern (23 bp):
ATTTGTGCTCAAATATTAATATG
Found at i:455242 original size:46 final size:46
Alignment explanation
Indices: 455192--455663 Score: 592
Period size: 46 Copynumber: 10.3 Consensus size: 46
455182 TCTTAATTTT
* * * * *
455192 ATTTGTTCTCAAAAATTAATGTGATTTGTGCTTAAATATTAATATG
1 ATTTGTGCTTAAATATTAATGTGATTTATGCTTAAATATTAATGTG
* *
455238 ATTTGTGCTCAAATATTAATGTGATTTATGCTTAAATATTAATGGG
1 ATTTGTGCTTAAATATTAATGTGATTTATGCTTAAATATTAATGTG
* *
455284 ATTTGTGCTTAAATATTAATGTGATTTGTGCTTAAATAATAATGTG
1 ATTTGTGCTTAAATATTAATGTGATTTATGCTTAAATATTAATGTG
* *
455330 ATTTGCGCTTAAATATTAATATGATTTATGCTTAAATATTAATGTG
1 ATTTGTGCTTAAATATTAATGTGATTTATGCTTAAATATTAATGTG
* * * *
455376 ATTTATGATTAAATATTAATGTGATTTTTGCTTAAATATTAATTTG
1 ATTTGTGCTTAAATATTAATGTGATTTATGCTTAAATATTAATGTG
* * *
455422 ATTTATGCTTAAATATTAATGTGATTTCTACTTAAATATT-ATGTG
1 ATTTGTGCTTAAATATTAATGTGATTTATGCTTAAATATTAATGTG
* * * * *
455467 ATTTGT-ATTGAAATATTAATCTCATTTGTG-TTAAAATATTAATTTG
1 ATTTGTGCTT-AAATATTAATGTGATTTATGCTT-AAATATTAATGTG
* * * * *
455513 ATTTGTGCTTAAATATTAATATGATTTGTACTGAAATATTAATGTA
1 ATTTGTGCTTAAATATTAATGTGATTTATGCTTAAATATTAATGTG
455559 ATTTGTGCTTAAATATTAAAT-TGATTTATGCTTAAATATTAATGTG
1 ATTTGTGCTTAAATATT-AATGTGATTTATGCTTAAATATTAATGTG
* * * * *
455605 ATTTGTGCTTAAATATTAATTTCATTTATGATAAAATATTAAAGTG
1 ATTTGTGCTTAAATATTAATGTGATTTATGCTTAAATATTAATGTG
455651 ATTTGTGCTTAAA
1 ATTTGTGCTTAAA
455664 GAATTAAGAT
Statistics
Matches: 374, Mismatches: 45, Indels: 14
0.86 0.10 0.03
Matches are distributed among these distances:
44 4 0.01
45 35 0.09
46 329 0.88
47 6 0.02
ACGTcount: A:0.35, C:0.05, G:0.13, T:0.47
Consensus pattern (46 bp):
ATTTGTGCTTAAATATTAATGTGATTTATGCTTAAATATTAATGTG
Found at i:455279 original size:69 final size:69
Alignment explanation
Indices: 455192--455663 Score: 567
Period size: 69 Copynumber: 6.9 Consensus size: 69
455182 TCTTAATTTT
* * * *
455192 ATTTGTTCTCAAAAATTAATGTGATTTGTGCTTAAATATTAATATGATTTGTGCTCAAATATTAA
1 ATTTGTGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATATGATTTGTGCTTAAATATTAA
455257 TGTG
66 TGTG
* * * *
455261 ATTTATGCTTAAATATTAATGGGATTTGTGCTTAAATATTAATGTGATTTGTGCTTAAATAATAA
1 ATTTGTGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATATGATTTGTGCTTAAATATTAA
455326 TGTG
66 TGTG
* * * * * *
455330 ATTTGCGCTTAAATATTAATATGATTTATGCTTAAATATTAATGTGATTTATGATTAAATATTAA
1 ATTTGTGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATATGATTTGTGCTTAAATATTAA
455395 TGTG
66 TGTG
* * * * * *
455399 ATTTTTGCTTAAATATTAATTTGATTTATGCTTAAATATTAATGTGATTTCTACTTAAATATT-A
1 ATTTGTGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATATGATTTGTGCTTAAATATTAA
455463 TGTG
66 TGTG
* * * *
455467 ATTTGT-ATTGAAATATTAATCTCATTTGTG-TTAAAATATTAATTTGATTTGTGCTTAAATATT
1 ATTTGTGCTT-AAATATTAATGTGATTTGTGCTT-AAATATTAATATGATTTGTGCTTAAATATT
*
455530 AATATG
64 AATGTG
* * * *
455536 ATTTGTACTGAAATATTAATGTAATTTGTGCTTAAATATTAA-ATTGATTTATGCTTAAATATTA
1 ATTTGTGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATA-TGATTTGTGCTTAAATATTA
455600 ATGTG
65 ATGTG
* * * * *
455605 ATTTGTGCTTAAATATTAATTTCATTTATGATAAAATATTAA-AGTGATTTGTGCTTAAA
1 ATTTGTGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATA-TGATTTGTGCTTAAA
455664 GAATTAAGAT
Statistics
Matches: 350, Mismatches: 47, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
67 4 0.01
68 54 0.15
69 289 0.83
70 3 0.01
ACGTcount: A:0.35, C:0.05, G:0.13, T:0.47
Consensus pattern (69 bp):
ATTTGTGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATATGATTTGTGCTTAAATATTAA
TGTG
Found at i:459159 original size:23 final size:23
Alignment explanation
Indices: 459133--459600 Score: 598
Period size: 23 Copynumber: 20.3 Consensus size: 23
459123 CTTATATCTA
*
459133 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATGTGATTTG
* **
459156 TGCTCATTTATTAATGTGATTTTG
1 TGCTTAAATATTAATGTGA-TTTG
*
459180 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
459203 TGCTCAAATATTAATGTGATTTA
1 TGCTTAAATATTAATGTGATTTG
459226 TGCTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
**
459249 TGCTTAAATATTGCTGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
*
459272 TTCTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
*
459295 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
459318 TGC-TAAATTAATAATGTGATTTA
1 TGCTTAAA-TATTAATGTGATTTG
* *
459341 TGCTTAGATATTAATGTGATTTA
1 TGCTTAAATATTAATGTGATTTG
459364 TGCTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
459387 TGCTTAAATATTAATGTGACTTA
1 TGCTTAAATATTAATGTGATTTG
459410 TGCTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
*
459433 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATGTGATTTG
* * *
459456 CGCTCAAATATTATTGTG-TTTG
1 TGCTTAAATATTAATGTGATTTG
* * *
459478 TTCTTAAATATTAATATGGTTTG
1 TGCTTAAATATTAATGTGATTTG
* *
459501 TGCTCAAATATTAATGTGATTTA
1 TGCTTAAATATTAATGTGATTTG
**
459524 TGCTTAAATATTAATGAAATTTG
1 TGCTTAAATATTAATGTGATTTG
* * * *
459547 TGCTTAAATATTAATATGGTATA
1 TGCTTAAATATTAATGTGATTTG
* *
459570 TGATTAAATATTAATATGATTTG
1 TGCTTAAATATTAATGTGATTTG
459593 TGCTTAAA
1 TGCTTAAA
459601 GAATTAAGAT
Statistics
Matches: 380, Mismatches: 61, Indels: 8
0.85 0.14 0.02
Matches are distributed among these distances:
22 21 0.06
23 337 0.89
24 22 0.06
ACGTcount: A:0.32, C:0.06, G:0.15, T:0.47
Consensus pattern (23 bp):
TGCTTAAATATTAATGTGATTTG
Done.