Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001162.1 Hibiscus syriacus cultivar Beakdansim tig00002317_pilon, 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: 1560963
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 9
Found at i:206778 original size:15 final size:15
Alignment explanation
Indices: 206758--206798 Score: 82
Period size: 15 Copynumber: 2.7 Consensus size: 15
206748 CTACATGAAG
206758 CGATGAAGAGGTTTC
1 CGATGAAGAGGTTTC
206773 CGATGAAGAGGTTTC
1 CGATGAAGAGGTTTC
206788 CGATGAAGAGG
1 CGATGAAGAGG
206799 AACAAGAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.29, C:0.12, G:0.37, T:0.22
Consensus pattern (15 bp):
CGATGAAGAGGTTTC
Found at i:210840 original size:24 final size:24
Alignment explanation
Indices: 210813--210893 Score: 75
Period size: 24 Copynumber: 3.5 Consensus size: 24
210803 ACACTTAACA
210813 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCATCCCTTTGAAT
* *
210837 GTGCATCGATTCAT-CATGTTG-A-
1 GTGCATCGATGCATCCCT-TTGAAT
*
210859 -TGCACCGATGCA-CGCC-TTGAAT
1 GTGCATCGATGCATC-CCTTTGAAT
210881 GTGCATCGATGCA
1 GTGCATCGATGCA
210894 CAGGGTCATG
Statistics
Matches: 45, Mismatches: 6, Indels: 13
0.70 0.09 0.20
Matches are distributed among these distances:
20 3 0.07
21 11 0.24
22 1 0.02
23 14 0.31
24 16 0.36
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.30
Consensus pattern (24 bp):
GTGCATCGATGCATCCCTTTGAAT
Found at i:212483 original size:21 final size:21
Alignment explanation
Indices: 212441--212484 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
212431 ACCCCGGGAG
* *
212441 CTAGTTCTTCACGAGCTGCTC
1 CTAGCTCTTCACGAGCTCCTC
* *
212462 CTAGCTCTTCTCGTGCTCCTC
1 CTAGCTCTTCACGAGCTCCTC
212483 CT
1 CT
212485 CCTCCTCCGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.39, G:0.16, T:0.36
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTCCTC
Found at i:212839 original size:14 final size:15
Alignment explanation
Indices: 212814--212842 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
212804 ATTATTTTGA
212814 TGTTTCTGAATTGTT
1 TGTTTCTGAATTGTT
212829 TGTTT-TGAATTGTT
1 TGTTTCTGAATTGTT
212843 AAATGTTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.14, C:0.03, G:0.21, T:0.62
Consensus pattern (15 bp):
TGTTTCTGAATTGTT
Found at i:213527 original size:20 final size:20
Alignment explanation
Indices: 213498--213535 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
213488 TTTCAAAGTG
213498 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
213518 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
213536 TATTTTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:213604 original size:45 final size:46
Alignment explanation
Indices: 213555--213645 Score: 148
Period size: 46 Copynumber: 2.0 Consensus size: 46
213545 AAACATCGAA
* * *
213555 TGCATTTTATGCATCGATGCAC-ATACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCAATGCACAAGACCATGCATCGATGCACTCAG
213600 TGCATTTGATGCATCAATGCACAAGACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCAATGCACAAGACCATGCATCGATGCACTCAG
213646 GCTTTTTTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 20 0.48
46 22 0.52
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (46 bp):
TGCATTTGATGCATCAATGCACAAGACCATGCATCGATGCACTCAG
Found at i:218073 original size:6 final size:5
Alignment explanation
Indices: 218058--218120 Score: 62
Period size: 5 Copynumber: 13.2 Consensus size: 5
218048 AAAGGAGAAA
* * *
218058 AAAAT AAAAT AGAAAT -AAAT -AAAT -AAAT CAAAG AAAA- ACAAT AAAAT
1 AAAAT AAAAT A-AAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
218105 AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT A
218121 TTTAAATTAT
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
4 15 0.29
5 32 0.63
6 4 0.08
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:218074 original size:40 final size:36
Alignment explanation
Indices: 218019--218116 Score: 119
Period size: 37 Copynumber: 2.6 Consensus size: 36
218009 CAAAAAAAAG
*
218019 AAAAATAAGA-AAAATAAAATAATAAATCAAAAGGAGAA
1 AAAAATAAAATAAAATAAAATAATAAATC-AAA-GA-AA
218057 AAAAATAAAATAGAAAT-AAATAAATAAATCAAAGAAA
1 AAAAATAAAATA-AAATAAAAT-AATAAATCAAAGAAA
*
218094 AACAATAAAATAAAATAAAATAA
1 AAAAATAAAATAAAATAAAATAA
218117 AATATTTAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
36 6 0.11
37 17 0.31
38 11 0.20
39 8 0.15
40 12 0.22
ACGTcount: A:0.76, C:0.03, G:0.06, T:0.15
Consensus pattern (36 bp):
AAAAATAAAATAAAATAAAATAATAAATCAAAGAAA
Found at i:218077 original size:15 final size:16
Alignment explanation
Indices: 218039--218080 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
218029 AAAATAAAAT
218039 AATAAATCAAAAGGAGA
1 AATAAAT-AAAAGGAGA
* *
218056 AAAAAATAAAA-TAGA
1 AATAAATAAAAGGAGA
218071 AATAAATAAA
1 AATAAATAAA
218081 TAAATCAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 12 0.55
16 4 0.18
17 6 0.27
ACGTcount: A:0.74, C:0.02, G:0.10, T:0.14
Consensus pattern (16 bp):
AATAAATAAAAGGAGA
Found at i:218079 original size:36 final size:35
Alignment explanation
Indices: 218015--218117 Score: 104
Period size: 36 Copynumber: 2.9 Consensus size: 35
218005 CATACAAAAA
* *
218015 AAAGAAAAATAAGAAAAATAAAAT-AATAAATCAAA-
1 AAAGAAAAACAA-TAAAATAAAATAAATAAAT-AAAC
*
218050 AGGAGAAAAA-AATAAAATAGAAATAAATAAATAAATC
1 A-AAGAAAAACAATAAAATA-AAATAAATAAATAAA-C
218087 AAAGAAAAACAATAAAATAAAATAAAATAAA
1 AAAGAAAAACAATAAAATAAAAT-AAATAAA
218118 ATATTTAAAT
Statistics
Matches: 58, Mismatches: 3, Indels: 12
0.79 0.04 0.16
Matches are distributed among these distances:
34 6 0.10
35 10 0.17
36 25 0.43
37 17 0.29
ACGTcount: A:0.76, C:0.03, G:0.07, T:0.15
Consensus pattern (35 bp):
AAAGAAAAACAATAAAATAAAATAAATAAATAAAC
Found at i:218485 original size:2 final size:2
Alignment explanation
Indices: 218478--218516 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
218468 AGTTTTGGTT
218478 TA TA 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 TA TA T
218517 GAAAACCAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:219476 original size:14 final size:14
Alignment explanation
Indices: 219457--219500 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
219447 ACCCAAAAAC
*
219457 AATAAAGAAAAATA
1 AATAAATAAAAATA
* *
219471 AGTAAATAAAATTA
1 AATAAATAAAAATA
219485 AATAAATAATAAATA
1 AATAAATAA-AAATA
219500 A
1 A
219501 TAATGTTAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
14 19 0.79
15 5 0.21
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.23
Consensus pattern (14 bp):
AATAAATAAAAATA
Found at i:219499 original size:21 final size:22
Alignment explanation
Indices: 219466--219526 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 22
219456 CAATAAAGAA
219466 AAATAAGTAAATAAAAT-TAAAT
1 AAATAA-TAAATAAAATGTAAAT
*
219488 AAATAATAAATAATAATGTTAAT
1 AAATAATAAATAA-AATGTAAAT
219511 ATAAT-ATATAATAAAA
1 A-AATAATA-AATAAAA
219527 AAAAATTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
21 7 0.21
22 9 0.26
23 10 0.29
24 8 0.24
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (22 bp):
AAATAATAAATAAAATGTAAAT
Found at i:219644 original size:75 final size:74
Alignment explanation
Indices: 219578--219827 Score: 366
Period size: 75 Copynumber: 3.4 Consensus size: 74
219568 AAAATAATTA
* * *
219578 TTTTCAAAACCATATA-TA-ATATA-TTTTCAAAATATTTT-AAAACTATATATTATAGATATAT
1 TTTTAAAAACTATATATTATATATATTTTTCAAAATGTTTTAAAAACTATATATTATA-ATATAT
219639 TTTCAAAATG
65 TTTCAAAATG
*
219649 TTTTAAAAACTATATATTATATATATTTTTTCAAAATGTTTTAAAAAACTATATATTAT-ATGTA
1 TTTTAAAAACTATATATTATATATA-TTTTTCAAAATGTTTT-AAAAACTATATATTATAATATA
219713 TTTTCAAAATG
64 TTTTCAAAATG
*
219724 TTTTAAAAACTATATATTATATATATTTTTTCAAAATGTTTTAAAAACTATATATTATATATACA
1 TTTTAAAAACTATATATTATATATA-TTTTTCAAAATGTTTTAAAAACTATATATTATA-ATATA
*
219789 TTTTCATAATG
64 TTTTCAAAATG
219800 TTTTAAAAACTATATATTATATATATTT
1 TTTTAAAAACTATATATTATATATATTT
219828 CGAAAATCAT
Statistics
Matches: 164, Mismatches: 7, Indels: 12
0.90 0.04 0.07
Matches are distributed among these distances:
71 14 0.09
72 2 0.01
73 5 0.03
74 16 0.10
75 74 0.45
76 38 0.23
77 15 0.09
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (74 bp):
TTTTAAAAACTATATATTATATATATTTTTCAAAATGTTTTAAAAACTATATATTATAATATATT
TTCAAAATG
Found at i:219667 original size:38 final size:38
Alignment explanation
Indices: 219590--219825 Score: 370
Period size: 38 Copynumber: 6.2 Consensus size: 38
219580 TTCAAAACCA
*
219590 TATATAATATATTTTCAAAATATTTT-AAAACTATATAT
1 TATAT-ATATATTTTCAAAATGTTTTAAAAACTATATAT
*
219628 TATAGATATATTTTCAAAATGTTTTAAAAACTATATAT
1 TATATATATATTTTCAAAATGTTTTAAAAACTATATAT
*
219666 TATATATATTTTTTCAAAATGTTTTAAAAAACTATATA-
1 TATATATATATTTTCAAAATGTTTT-AAAAACTATATAT
*
219704 T-TATATGTATTTTCAAAATGTTTTAAAAACTATATAT
1 TATATATATATTTTCAAAATGTTTTAAAAACTATATAT
*
219741 TATATATATTTTTTCAAAATGTTTTAAAAACTATATAT
1 TATATATATATTTTCAAAATGTTTTAAAAACTATATAT
* *
219779 TATATATACATTTTCATAATGTTTTAAAAACTATATAT
1 TATATATATATTTTCAAAATGTTTTAAAAACTATATAT
219817 TATATATAT
1 TATATATAT
219826 TTCGAAAATC
Statistics
Matches: 182, Mismatches: 12, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
36 12 0.07
37 41 0.23
38 117 0.64
39 12 0.07
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.48
Consensus pattern (38 bp):
TATATATATATTTTCAAAATGTTTTAAAAACTATATAT
Found at i:219672 original size:113 final size:113
Alignment explanation
Indices: 219583--219827 Score: 365
Period size: 113 Copynumber: 2.2 Consensus size: 113
219573 AATTATTTTC
219583 AAAACCATATA-TA-ATATATTTTCAAAATATTTT-AAAACTATATATTATAGATATATTTTCAA
1 AAAACCATATATTATATATATTTTCAAAATATTTTAAAAACTATATATTATAGATATATTTTCAA
*
219645 AATGTTTTAAAAACTATATATTATATATATTTTTTCAAAATGTTTTAA
66 AATGTTTTAAAAACTATATATTATATATATTTATTCAAAATGTTTTAA
* * * * *
219693 AAAACTATATATTATATGTATTTTCAAAATGTTTTAAAAACTATATATTATATATATTTTTTCAA
1 AAAACCATATATTATATATATTTTCAAAATATTTTAAAAACTATATATTATAGATATATTTTCAA
* *
219758 AATGTTTTAAAAACTATATATTATATATACATT-TTCATAATGTTTT-A
66 AATGTTTTAAAAACTATATATTATATATA-TTTATTCAAAATGTTTTAA
*
219805 AAAACTATATATTATATATATTT
1 AAAACCATATATTATATATATTT
219828 CGAAAATCAT
Statistics
Matches: 123, Mismatches: 8, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
110 10 0.08
111 2 0.02
112 41 0.33
113 68 0.55
114 2 0.02
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (113 bp):
AAAACCATATATTATATATATTTTCAAAATATTTTAAAAACTATATATTATAGATATATTTTCAA
AATGTTTTAAAAACTATATATTATATATATTTATTCAAAATGTTTTAA
Found at i:219866 original size:15 final size:15
Alignment explanation
Indices: 219842--219879 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
219832 AATCATTTGC
*
219842 AAAAAT-AAAATAAT
1 AAAAATAAAAACAAT
219856 AAAAATAAAAACAAT
1 AAAAATAAAAACAAT
*
219871 AATAATAAA
1 AAAAATAAA
219880 TAAATACGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (15 bp):
AAAAATAAAAACAAT
Found at i:222725 original size:26 final size:26
Alignment explanation
Indices: 222695--222758 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 26
222685 AGTCGAACTC
*
222695 GAATATTGATGAGTC-AAGTCGAGTTCT
1 GAATATTGATGAGTCGAA-TCGAATT-T
222722 -AATATTGATGAGTCGAATCGAATTT
1 GAATATTGATGAGTCGAATCGAATTT
222747 GAATATTGATGA
1 GAATATTGATGA
222759 ACTCGACTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
25 1 0.03
26 31 0.91
27 2 0.06
ACGTcount: A:0.34, C:0.08, G:0.23, T:0.34
Consensus pattern (26 bp):
GAATATTGATGAGTCGAATCGAATTT
Found at i:224368 original size:20 final size:20
Alignment explanation
Indices: 224339--224412 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 20
224329 ATATAATTGA
*
224339 ATTTAGGGTTTAGGGTTAAG
1 ATTTAAGGTTTAGGGTTAAG
* *
224359 ATTTAAGGTTTATGTTTAAG
1 ATTTAAGGTTTAGGGTTAAG
* * *
224379 ATTTAAAGTTTATGGTTTAG
1 ATTTAAGGTTTAGGGTTAAG
*
224399 ATTTTAGGATTTAG
1 ATTTAAGG-TTTAG
224413 TGTTCATTAC
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
20 40 0.91
21 4 0.09
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.47
Consensus pattern (20 bp):
ATTTAAGGTTTAGGGTTAAG
Found at i:224973 original size:24 final size:23
Alignment explanation
Indices: 224928--224981 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 23
224918 ATATATTTAA
224928 AATTTTATAATTATCAATAATGT
1 AATTTTATAATTATCAATAATGT
* * *
224951 ATTTTTATATATTTTTAATAATGT
1 AATTTTATA-ATTATCAATAATGT
224975 AATTTTA
1 AATTTTA
224982 AAAAATTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 8 0.31
24 18 0.69
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.56
Consensus pattern (23 bp):
AATTTTATAATTATCAATAATGT
Found at i:225132 original size:12 final size:12
Alignment explanation
Indices: 225115--225139 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
225105 ACTCACGATC
225115 TGTCACGTCTTA
1 TGTCACGTCTTA
225127 TGTCACGTCTTA
1 TGTCACGTCTTA
225139 T
1 T
225140 TTACGGCCTA
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:0.16, C:0.24, G:0.16, T:0.44
Consensus pattern (12 bp):
TGTCACGTCTTA
Found at i:226938 original size:118 final size:118
Alignment explanation
Indices: 226652--227243 Score: 538
Period size: 118 Copynumber: 5.1 Consensus size: 118
226642 AAAAAATATA
* * * * *
226652 GACGATAACATAACCGGTTAATTAATGGAAACATTATTAAACATAATAACATATTAGGTAGTGCT
1 GACGATAACAAAACCGGTTAATTATTGGAAACATTATCAAGCATAATAACATATTAGGTAGCGCT
* *
226717 TTTATAATGTAATAGGTATG-G---TTTTAAAGCTGATGGGGCTTTGGAAAAAT-A
66 TATATAATGTAATAGGTA-GCGCATTTTTAAAGCTGATGGGGCTTTGG--AAATCC
* * *** * *
226768 GACGATACCATAACTAATTAATTACTGGAAACACTATCAAGCATAATAACATATTAGGTAGCGCT
1 GACGATAACAAAACCGGTTAATTATTGGAAACATTATCAAGCATAATAACATATTAGGTAGCGCT
* * *
226833 TATATAATGTAATAGGTAGCGTATTTTTAAAGCAGATGGGGCATTGGAAATCC
66 TATATAATGTAATAGGTAGCGCATTTTTAAAGCTGATGGGGCTTTGGAAATCC
* **
226886 GACGATAACAAAACCGGTTAATTATTGGAAACATTATCGAGCATAATAACATATTAGGTAGCGAA
1 GACGATAACAAAACCGGTTAATTATTGGAAACATTATCAAGCATAATAACATATTAGGTAGCGCT
* * * *
226951 TATATAACGTAATAGGTAGCGCATTTTTAAAGCTGATTGAGCTTTGGAAATAC
66 TATATAATGTAATAGGTAGCGCATTTTTAAAGCTGATGGGGCTTTGGAAATCC
** *** * ** * *
227004 GACGATAACAAAAATAGGTTAATTACTT--AATTTGTTAT-TATTATTATCAACATATTAGGTAA
1 GACGATAAC-AAAACCGGTTAATTA-TTGGAA-ACATTATCAAGCATAAT-AACATATTAGGTAG
* ** * * * *
227066 CGCCTA-A-AATG---T---TA-C-CAAAGTTTAAA-CTGATAGAGCCTTAGAAATCC
62 CGCTTATATAATGTAATAGGTAGCGC-ATTTTTAAAGCTGATGGGGCTTTGGAAATCC
* * * *
227113 GACGATAACATAATCGGTTAATTATTGGAAACATTATTAAGCATAATAACATATTAGGTAGCGGT
1 GACGATAACAAAACCGGTTAATTATTGGAAACATTATCAAGCATAATAACATATTAGGTAGCGCT
* * * *
227178 TATGTAACGTAATAGGTAGCGCATTATTAAAGCTGATGTGGCTTTGGAAATCC
66 TATATAATGTAATAGGTAGCGCATTTTTAAAGCTGATGGGGCTTTGGAAATCC
227231 GACGATAACAAAA
1 GACGATAACAAAA
227244 TATGTTAATC
Statistics
Matches: 380, Mismatches: 72, Indels: 46
0.76 0.14 0.09
Matches are distributed among these distances:
107 2 0.01
108 34 0.09
109 34 0.09
110 11 0.03
111 2 0.01
113 1 0.00
114 1 0.00
115 1 0.00
116 76 0.20
117 14 0.04
118 147 0.39
119 55 0.14
120 2 0.01
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.30
Consensus pattern (118 bp):
GACGATAACAAAACCGGTTAATTATTGGAAACATTATCAAGCATAATAACATATTAGGTAGCGCT
TATATAATGTAATAGGTAGCGCATTTTTAAAGCTGATGGGGCTTTGGAAATCC
Found at i:227158 original size:227 final size:224
Alignment explanation
Indices: 226879--227525 Score: 932
Period size: 220 Copynumber: 2.9 Consensus size: 224
226869 TGGGGCATTG
* *
226879 GAAATCCGACGATAACAAAACCGGTTAATTATTGGAAACATTATCGAGCATAATAACATATTAGG
1 GAAATCCGACGATAACATAACCGGTTAATTATTGGAAACATTATCAAGCATAATAACATATTAGG
* * *
226944 TAGCGAATATATAACGTAATAGGTAGCGCATTTTTAAAGCTGATTGAGCTTTGGAAATACGACGA
66 TAGCGATTATGTAACGTAATAGGTAGCGCATTATTAAAGCTGATTG-GCTTTGGAAAT-CGACGA
*
227009 TAACAAAAATAGGTTAATTACTTAATTTGTTATTATTATTATCAACATATTAGGTAACGCCTAAA
129 TAAC-AAAATAGGTTAATTACTTAATTTGTTATTAGTATTATCAACATATTAGGTAACGCCTAAA
*
227074 ATGTTACCAAAGTTTAAACTGATAGAGCCTTA
193 ATATTACCAAAGTTTAAACTGATAGAGCCTTA
* *
227106 GAAATCCGACGATAACATAATCGGTTAATTATTGGAAACATTATTAAGCATAATAACATATTAGG
1 GAAATCCGACGATAACATAACCGGTTAATTATTGGAAACATTATCAAGCATAATAACATATTAGG
*
227171 TAGCGGTTATGTAACGTAATAGGTAGCGCATTATTAAAGCTGATGTGGCTTTGGAAATCCGACGA
66 TAGCGATTATGTAACGTAATAGGTAGCGCATTATTAAAGCTGAT-TGGCTTTGGAAAT-CGACGA
* * *
227236 TAACAAAATATGTTAATCACTTAA-----TA-TAGTATTATCAACATATTAGGTAATGCCTAAAA
129 TAACAAAATAGGTTAATTACTTAATTTGTTATTAGTATTATCAACATATTAGGTAACGCCTAAAA
**
227295 TATTACCAAAGTTTAAGTTGATAGAGCCTTA
194 TATTACCAAAGTTTAAACTGATAGAGCCTTA
* *
227326 GAAATCCGAC-ATTAGCATAACCGGTTAATTACTGGAAACATTATCAAGCATAATAACATATTAG
1 GAAATCCGACGA-TAACATAACCGGTTAATTATTGGAAACATTATCAAGCATAATAACATATTAG
* * * * * *
227390 GTAGCGCTTATGTAATGTAATAGGTAGCAC-TTCATTAAAGCTGATGGGGCCTTAGAAATCTGAC
65 GTAGCGATTATGTAACGTAATAGGTAGCGCATT-ATTAAAGCTGAT-TGGCTTTGGAAATC-GAC
* *
227454 GATAACAAAATAGGTTAATTACTTAATTTGTTATTAGTATTATCAACATATTAGGTAACACTTAA
127 GATAACAAAATAGGTTAATTACTTAATTTGTTATTAGTATTATCAACATATTAGGTAACGCCTAA
227519 AATATTA
192 AATATTA
227526 AGCTGATGGA
Statistics
Matches: 379, Mismatches: 31, Indels: 21
0.88 0.07 0.05
Matches are distributed among these distances:
219 4 0.01
220 194 0.51
221 2 0.01
225 2 0.01
226 53 0.14
227 122 0.32
228 2 0.01
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (224 bp):
GAAATCCGACGATAACATAACCGGTTAATTATTGGAAACATTATCAAGCATAATAACATATTAGG
TAGCGATTATGTAACGTAATAGGTAGCGCATTATTAAAGCTGATTGGCTTTGGAAATCGACGATA
ACAAAATAGGTTAATTACTTAATTTGTTATTAGTATTATCAACATATTAGGTAACGCCTAAAATA
TTACCAAAGTTTAAACTGATAGAGCCTTA
Found at i:227720 original size:2 final size:2
Alignment explanation
Indices: 227713--227738 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
227703 TAAGTATGAA
227713 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
227739 CGATACATTT
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:227811 original size:22 final size:22
Alignment explanation
Indices: 227783--227825 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
227773 ATGTGGAATT
227783 AAAGTATCGAGACAGATATAAC
1 AAAGTATCGAGACAGATATAAC
* * *
227805 AAAGTATTGATACATATATAA
1 AAAGTATCGAGACAGATATAA
227826 AAGTTTACGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.51, C:0.09, G:0.14, T:0.26
Consensus pattern (22 bp):
AAAGTATCGAGACAGATATAAC
Found at i:230835 original size:44 final size:44
Alignment explanation
Indices: 230772--230890 Score: 202
Period size: 44 Copynumber: 2.7 Consensus size: 44
230762 CACAATTATG
230772 GAAACCGATTTTGTTAATTTTTTACCTGTTAAGTTATTTATATT
1 GAAACCGATTTTGTTAATTTTTTACCTGTTAAGTTATTTATATT
230816 GAAACCGATTTTGTTAATTTTTTACCTGTTAAGTTATTTATATT
1 GAAACCGATTTTGTTAATTTTTTACCTGTTAAGTTATTTATATT
* * **
230860 GAAACCGGTTTTGTCAATTTTGAACCTGTTA
1 GAAACCGATTTTGTTAATTTTTTACCTGTTA
230891 TATTGTCATG
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 71 1.00
ACGTcount: A:0.27, C:0.11, G:0.13, T:0.49
Consensus pattern (44 bp):
GAAACCGATTTTGTTAATTTTTTACCTGTTAAGTTATTTATATT
Found at i:232393 original size:18 final size:18
Alignment explanation
Indices: 232370--232408 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
232360 GCCGAAAATG
232370 AAATTGAAATTCAAACTC
1 AAATTGAAATTCAAACTC
* *
232388 AAATTGAAATTTAAATTC
1 AAATTGAAATTCAAACTC
232406 AAA
1 AAA
232409 CTCCAACTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.54, C:0.10, G:0.05, T:0.31
Consensus pattern (18 bp):
AAATTGAAATTCAAACTC
Found at i:232396 original size:24 final size:24
Alignment explanation
Indices: 232368--232427 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
232358 GAGCCGAAAA
*
232368 TGAAATTGAAATTCAAACTCAAAT
1 TGAAATTGAAATTCAAACTCAAAC
* *
232392 TGAAATTTAAATTCAAACTCCAAC
1 TGAAATTGAAATTCAAACTCAAAC
*
232416 TAAAATTGAAAT
1 TGAAATTGAAAT
232428 GAACATGAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.50, C:0.13, G:0.07, T:0.30
Consensus pattern (24 bp):
TGAAATTGAAATTCAAACTCAAAC
Found at i:235003 original size:18 final size:18
Alignment explanation
Indices: 234964--235006 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
234954 GAATCCCTTA
*
234964 GTTGAGAAGAAGAGATTG
1 GTTGAGAAGAAGAGATTC
*
234982 GTTGAGAAGAAG-GTTTTC
1 GTTGAGAAGAAGAG-ATTC
235000 GTTGAGA
1 GTTGAGA
235007 TACCTGCACC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 1 0.05
18 21 0.95
ACGTcount: A:0.33, C:0.02, G:0.37, T:0.28
Consensus pattern (18 bp):
GTTGAGAAGAAGAGATTC
Found at i:235929 original size:200 final size:200
Alignment explanation
Indices: 235652--237516 Score: 2315
Period size: 199 Copynumber: 9.4 Consensus size: 200
235642 CATTAAACCA
* * *
235652 GTTACATTGTAAATTTACCTATTACTTTAT-ATAATCGGTTTAGATAG-TTTAAGAATGGATACT
1 GTTACATTGTAAATTTACCTATTACTTTATAATAATCGGTTTCGAT-GTTTTAAGGATCGATACT
* *
235715 TATCATACATGTATCGATACTTTATGCGTGCATCTCCTTTGGGATTCATACTGGACAAAAACTAT
65 TATCATACATGTATCGATACTTTATGCGTGCATCTCTTTTGGGATTCATACTGGACAAAAAGTAT
* * *
235780 CGATACTACTAAAACAAGTATCGATACTTTATGTTTACTTATTTTCTCATTAAATCGGTATATTT
130 CGATACTACTAAAACAAGTATCGATACTTTATGTTTACCTATTTTCTCATTAAACCGATATATTT
*
235845 TTACTG
195 TTACCG
* *
235851 GTTACATTGTAAATTTACCTAATATTTTATAATAATCGGTTTCGATGTTTTAAGGATCGATACTT
1 GTTACATTGTAAATTTACCTATTACTTTATAATAATCGGTTTCGATGTTTTAAGGATCGATACTT
* ** *
235916 ATCATATATGTATCGATACTTTATATGTGTATCTCTTTTGGGATTCATACTGGACAAAAACGTAT
66 ATCATACATGTATCGATACTTTATGCGTGCATCTCTTTTGGGATTCATACTGGACAAAAA-GTAT
* * * * *
235981 CGATACTACTAAAACAAGTATCTATACTTTACGTTTACCTATTTTCTCATTAAACTGGTATATTG
130 CGATACTACTAAAACAAGTATCGATACTTTATGTTTACCTATTTTCTCATTAAACCGATATATTT
**
236046 TTACTA
195 TTACCG
* *
236052 GTTACATTGTAAATTTACCTATT-CTTTATAATAATCGATTTCGATGTTTTAATGATCGATACTT
1 GTTACATTGTAAATTTACCTATTACTTTATAATAATCGGTTTCGATGTTTTAAGGATCGATACTT
* * *
236116 CTCATACATGTATCGATACTTTATACGTGCATCTATTTTGGGATTCATACTGGACAAAAAGTATC
66 ATCATACATGTATCGATACTTTATGCGTGCATCTCTTTTGGGATTCATACTGGACAAAAAGTATC
* * *
236181 GATACTACTAAAACAAGTATTGATACTTTATGTTTACATATTTTCTTATTAAACCGATATATTTT
131 GATACTACTAAAACAAGTATCGATACTTTATGTTTACCTATTTTCTCATTAAACCGATATATTTT
236246 TACCG
196 TACCG
* *
236251 GTTACATTGTAAATTTACCTATTACTTTATAATAACCGATTTCGATGTTTTAAGGATCG--A-TT
1 GTTACATTGTAAATTTACCTATTACTTTATAATAATCGGTTTCGATGTTTTAAGGATCGATACTT
** * *
236313 ATCATACATGTATCGATACTTTATGTATGCATCTCGTTTGGGATTCATAATGGACAAAAAGTATC
66 ATCATACATGTATCGATACTTTATGCGTGCATCTCTTTTGGGATTCATACTGGACAAAAAGTATC
* *
236378 GATACTACTAAAACAAGTATCGACACTTTATGTTTACCTATTTTCTCATTAAACCGATATAATTT
131 GATACTACTAAAACAAGTATCGATACTTTATGTTTACCTATTTTCTCATTAAACCGATATATTTT
*
236443 TAGCG
196 TACCG
* * *
236448 GTTACATTGTAAATTTACCTATTAC-TT-T-ATAATCGGTTCCAATGTTTTAAGGATGGATACTT
1 GTTACATTGTAAATTTACCTATTACTTTATAATAATCGGTTTCGATGTTTTAAGGATCGATACTT
* *
236510 ATCATATATGTATCGATACTTTAT--GTGCATCTCGTTTGGGATTCATACTGGACAAAAAAGTAT
66 ATCATACATGTATCGATACTTTATGCGTGCATCTCTTTTGGGATTCATACTGGAC-AAAAAGTAT
* *
236573 CAATACTACTAAAACAAGTATCGATA-TTTATGTTTTACCTATTTTCTCATTAAATCGATATA-T
130 CGATACTACTAAAACAAGTATCGATACTTTATG-TTTACCTATTTTCTCATTAAACCGATATATT
236636 TTTACCG
194 TTTACCG
* *
236643 GTTACATTGTAAATTTACCTATTACTTTATAATAATCGGTTTTGATGTTTTAAGAATCGATACTT
1 GTTACATTGTAAATTTACCTATTACTTTATAATAATCGGTTTCGATGTTTTAAGGATCGATACTT
* * * * *
236708 CTCACACATGTATCTATACTTTATGCGTGCATCTCTTTTGAGATTCATACTGGACAAAAAGTATT
66 ATCATACATGTATCGATACTTTATGCGTGCATCTCTTTTGGGATTCATACTGGACAAAAAGTATC
* * * *
236773 GATACTACTAAAACAAGTATCGAT-CTTTATGTTTACATATTTTCTCATTAAGCAGGTATATTTT
131 GATACTACTAAAACAAGTATCGATACTTTATGTTTACCTATTTTCTCATTAAACCGATATATTTT
236837 TACCG
196 TACCG
*
236842 GTTACATTGTAAATTTACCTATTACTTTATAATAATCGGTTTTGATGTTTTAAGGATCGATACTT
1 GTTACATTGTAAATTTACCTATTACTTTATAATAATCGGTTTCGATGTTTTAAGGATCGATACTT
* * * * * *
236907 CTCACACATGTATCTATACTTTATGTGTGCATCTCTTTTGGGATTCATACTGGACAAAACGTATT
66 ATCATACATGTATCGATACTTTATGCGTGCATCTCTTTTGGGATTCATACTGGACAAAAAGTATC
* **
236972 GATACTACTAAAACAAGTATCGATACTTTATGCTTACCTATTTTCAAATTAAA-CGAATATATTT
131 GATACTACTAAAACAAGTATCGATACTTTATGTTTACCTATTTTCTCATTAAACCG-ATATATTT
237036 TTACCG
195 TTACCG
* *
237042 GTT--ATTGTAAATTTACCTATTACTTTATAATAATCAGATTCGATGTTTTAAGGATCGATACTT
1 GTTACATTGTAAATTTACCTATTACTTTATAATAATCGGTTTCGATGTTTTAAGGATCGATACTT
* * * *
237105 ATCATATATG--TCGATACTTTATGCATGTATCTCGTTTGGGATTC--A-TGGACAAAAAGTATC
66 ATCATACATGTATCGATACTTTATGCGTGCATCTCTTTTGGGATTCATACTGGACAAAAAGTATC
* *
237165 GACACTACT-AAACAAGTATCGATACTTTATGGTTTGCCTATTTTCTCATT-AACCGATATATTT
131 GATACTACTAAAACAAGTATCGATACTTTAT-GTTTACCTATTTTCTCATTAAACCGATATATTT
237228 TTACCG
195 TTACCG
* * * ** * ** *
237234 GTTACATTATAAATTTACCGATTACCTTCA-AATAATCAATTTCGATGTTTTAAGAATTAAAACT
1 GTTACATTGTAAATTTACCTATTA-CTTTATAATAATCGGTTTCGATGTTTTAAGGATCGATACT
* * * * * *** * * * ** * *
237298 T-TTA-ATATTTCTCGATACTTTCTTTTTACTAACT-TAAGTTTGGTAAGCATAATGGACATAAA
65 TATCATACATGTATCGATACTTTATGCGTGC-ATCTCT---TTTGGGATTCATACTGGACAAAAA
* * * * *
237360 GTATCGATACATA-TAAAA-AAGTATCGATACGTTATGTTAACGTATTTTATCA-T-AACCG--G
126 GTATCGATAC-TACTAAAACAAGTATCGATACTTTATGTTTACCTATTTTCTCATTAAACCGATA
* *
237419 TATTTTTAACT
190 TATTTTTACCG
* * * * ** * * *
237430 GCTAAATTGTAAATTTACCTATTACTTTA-AGTTAATTGGTTTTAAAGTTTTAAGAATCTATACT
1 GTTACATTGTAAATTTACCTATTACTTTATA-ATAATCGGTTTCGATGTTTTAAGGATCGATACT
* *
237494 TTTCATACTTGTATCGATACTTT
65 TATCATACATGTATCGATACTTT
237517 CTTTCTTATT
Statistics
Matches: 1466, Mismatches: 163, Indels: 75
0.86 0.10 0.04
Matches are distributed among these distances:
192 44 0.03
193 40 0.03
194 82 0.06
195 78 0.05
196 148 0.10
197 184 0.13
198 157 0.11
199 328 0.22
200 311 0.21
201 94 0.06
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (200 bp):
GTTACATTGTAAATTTACCTATTACTTTATAATAATCGGTTTCGATGTTTTAAGGATCGATACTT
ATCATACATGTATCGATACTTTATGCGTGCATCTCTTTTGGGATTCATACTGGACAAAAAGTATC
GATACTACTAAAACAAGTATCGATACTTTATGTTTACCTATTTTCTCATTAAACCGATATATTTT
TACCG
Found at i:235946 original size:19 final size:21
Alignment explanation
Indices: 235906--235948 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
235896 TGTTTTAAGG
235906 ATCGATACTTATCATATATGT
1 ATCGATACTTATCATATATGT
*
235927 ATCGATACTT-T-ATATGTGT
1 ATCGATACTTATCATATATGT
235946 ATC
1 ATC
235949 TCTTTTGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.48
20 1 0.05
21 10 0.48
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (21 bp):
ATCGATACTTATCATATATGT
Found at i:237051 original size:592 final size:594
Alignment explanation
Indices: 235377--237290 Score: 2643
Period size: 592 Copynumber: 3.3 Consensus size: 594
235367 TATCGTTGTT
*
235377 TTCATACTAGACAAAAAA-TATCGATACTACTAAAACAAGTATCGATACTTTATGTTTACCTATT
1 TTCATACTGGACAAAAAAGTATCGATACTACTAAAACAAGTATCGATACTTTATGTTTACCTATT
* *
235441 TTCTCATTAAACCGTTATAGTTTTACCGGTTACATTGTAAATTTACCTATTACTTTATAATAACC
66 TTCTCATTAAACCGATATAGTTTTACCGGTTACATTGTAAATTTACCTATTACTTTATAATAATC
* * * * *
235506 GGTTT-GATG-TTTAAGGATCGATACTTATAATACATGTAT-TGATACTTTATGCGTGCATCACT
131 GATTTCGATGTTTTAAGAATCGATACTTCTCATACATGTATCT-ATACTTTATGCGTGCATCTCT
* * * *
235568 TTTGAGATTCATACTTGAC-AAAACTATCAATACTACTAAAACAAGTATCAATACTTTATGTTTA
195 TTTGAGATTCATACTGGACAAAAAGTATCGATACTACTAAAACAAGTATCGATACTTTATGTTTA
* * *
235632 CCTA--TTCTC--T--CA-T-TA----AACCAGTTACATTGTAAATTTACCTATTACTTTAT-AT
260 CATATTTTCTCATTAACAGTATATTTTTACCGGTTACATTGTAAATTTACCTATTACTTTATAAT
* * *
235684 AATCGGTTTAGATAG-TTTAAGAATGGATACTTATCATACATGTATCGATACTTTATGCGTGCAT
325 AATCGGTTTAGAT-GTTTTAAGGATCGATACTTATCATACATGTATCGATACTTTATGTGTGCAT
235748 CTCCTTTGGGATTCATACTGGACAAAAAC-TATCGATACTACTAAAACAAGTATCGATACTTTAT
389 CTCCTTTGGGATTCATACTGGAC-AAAACGTATCGATACTACTAAAACAAGTATCGATACTTTAT
* * * * * *
235812 GTTTACTTATTTTCTCATTAAATCGGTATATTTTTACTGGTTACATTGTAAATTTACCTAATATT
453 GTTTACCTATTTTCTCATTAAACCGATATATTTTTACCGGTTA-ATTGTAAATTTACCTATTA-C
235877 TTATAATAATCGGTTTCGATGTTTTAAGGATCGATACTTATCATATATGTATCGATACTTTATAT
516 TTATAATAATCGG-TTCGATGTTTTAAGGATCGATACTTATCATATATGTATCGATAC-TT-TAT
*
235942 GTGTATCTCTTTTGGGA
578 GTGTATCTCGTTTGGGA
* * *
235959 TTCATACTGGACAAAAACGTATCGATACTACTAAAACAAGTATCTATACTTTACGTTTACCTATT
1 TTCATACTGGACAAAAAAGTATCGATACTACTAAAACAAGTATCGATACTTTATGTTTACCTATT
* * **
236024 TTCTCATTAAACTGGTATA-TTGTTACTAGTTACATTGTAAATTTACCTATT-CTTTATAATAAT
66 TTCTCATTAAACCGATATAGTT-TTACCGGTTACATTGTAAATTTACCTATTACTTTATAATAAT
* * *
236087 CGATTTCGATGTTTTAATG-ATCGATACTTCTCATACATGTATCGATACTTTATACGTGCATCTA
130 CGATTTCGATGTTTTAA-GAATCGATACTTCTCATACATGTATCTATACTTTATGCGTGCATCTC
* *
236151 TTTTGGGATTCATACTGGACAAAAAGTATCGATACTACTAAAACAAGTATTGATACTTTATGTTT
194 TTTTGAGATTCATACTGGACAAAAAGTATCGATACTACTAAAACAAGTATCGATACTTTATGTTT
* *
236216 ACATATTTTCTTATTAAACCGATATATTTTTACCGGTTACATTGTAAATTTACCTATTACTTTAT
259 ACATATTTTCTCATT-AACAG-TATATTTTTACCGGTTACATTGTAAATTTACCTATTACTTTAT
* * * *
236281 AATAACCGATTTCGATGTTTTAAGGATCG--A-TTATCATACATGTATCGATACTTTATGTATGC
322 AATAATCGGTTTAGATGTTTTAAGGATCGATACTTATCATACATGTATCGATACTTTATGTGTGC
* * * *
236343 ATCTCGTTTGGGATTCATAATGGACAAAAAGTATCGATACTACTAAAACAAGTATCGACACTTTA
387 ATCTCCTTTGGGATTCATACTGGACAAAACGTATCGATACTACTAAAACAAGTATCGATACTTTA
* *
236408 TGTTTACCTATTTTCTCATTAAACCGATATAATTTTAGCGGTTACATTGTAAATTTACCTATTAC
452 TGTTTACCTATTTTCTCATTAAACCGATATATTTTTACCGGTTA-ATTGTAAATTTACCTATTAC
* *
236473 TT-T-ATAATCGGTTCCAATGTTTTAAGGATGGATACTTATCATATATGTATCGATACTTTATGT
516 TTATAATAATCGGTT-CGATGTTTTAAGGATCGATACTTATCATATATGTATCGATACTTTATGT
*
236536 GCATCTCGTTTGGGA
580 GTATCTCGTTTGGGA
*
236551 TTCATACTGGACAAAAAAGTATCAATACTACTAAAACAAGTATCGATA-TTTATGTTTTACCTAT
1 TTCATACTGGACAAAAAAGTATCGATACTACTAAAACAAGTATCGATACTTTATG-TTTACCTAT
*
236615 TTTCTCATTAAATCGATATA-TTTTACCGGTTACATTGTAAATTTACCTATTACTTTATAATAAT
65 TTTCTCATTAAACCGATATAGTTTTACCGGTTACATTGTAAATTTACCTATTACTTTATAATAAT
* * *
236679 CGGTTTTGATGTTTTAAGAATCGATACTTCTCACACATGTATCTATACTTTATGCGTGCATCTCT
130 CGATTTCGATGTTTTAAGAATCGATACTTCTCATACATGTATCTATACTTTATGCGTGCATCTCT
*
236744 TTTGAGATTCATACTGGACAAAAAGTATTGATACTACTAAAACAAGTATCGAT-CTTTATGTTTA
195 TTTGAGATTCATACTGGACAAAAAGTATCGATACTACTAAAACAAGTATCGATACTTTATGTTTA
236808 CATATTTTCTCATTAAGCAGGTATATTTTTACCGGTTACATTGTAAATTTACCTATTACTTTATA
260 CATATTTTCTCATTAA-CA-GTATATTTTTACCGGTTACATTGTAAATTTACCTATTACTTTATA
* * * *
236873 ATAATCGGTTTTGATGTTTTAAGGATCGATACTTCTCACACATGTATCTATACTTTATGTGTGCA
323 ATAATCGGTTTAGATGTTTTAAGGATCGATACTTATCATACATGTATCGATACTTTATGTGTGCA
* *
236938 TCTCTTTTGGGATTCATACTGGACAAAACGTATTGATACTACTAAAACAAGTATCGATACTTTAT
388 TCTCCTTTGGGATTCATACTGGACAAAACGTATCGATACTACTAAAACAAGTATCGATACTTTAT
* **
237003 GCTTACCTATTTTCAAATTAAA-CGAATATATTTTTACCGGTT-ATTGTAAATTTACCTATTACT
453 GTTTACCTATTTTCTCATTAAACCG-ATATATTTTTACCGGTTAATTGTAAATTTACCTATTAC-
*
237066 TTATAATAATCAGATTCGATGTTTTAAGGATCGATACTTATCATATATG--TCGATACTTTATGC
516 TTATAATAATC-GGTTCGATGTTTTAAGGATCGATACTTATCATATATGTATCGATACTTTATG-
237129 ATGTATCTCGTTTGGGA
579 -TGTATCTCGTTTGGGA
* *
237146 TTC--A-TGGAC-AAAAAGTATCGACACTACT-AAACAAGTATCGATACTTTATGGTTTGCCTAT
1 TTCATACTGGACAAAAAAGTATCGATACTACTAAAACAAGTATCGATACTTTAT-GTTTACCTAT
* * * *
237206 TTTCTCATT-AACCGATATATTTTTACCGGTTACATTATAAATTTACCGATTACCTTCA-AATAA
65 TTTCTCATTAAACCGATATAGTTTTACCGGTTACATTGTAAATTTACCTATTA-CTTTATAATAA
*
237269 TCAATTTCGATGTTTTAAGAAT
129 TCGATTTCGATGTTTTAAGAAT
237291 TAAAACTTTT
Statistics
Matches: 1187, Mismatches: 101, Indels: 79
0.87 0.07 0.06
Matches are distributed among these distances:
582 34 0.03
583 92 0.08
584 61 0.05
585 45 0.04
587 4 0.00
589 1 0.00
590 26 0.02
591 220 0.19
592 242 0.20
593 23 0.02
594 173 0.15
595 58 0.05
596 9 0.01
597 143 0.12
598 1 0.00
599 34 0.03
600 21 0.02
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (594 bp):
TTCATACTGGACAAAAAAGTATCGATACTACTAAAACAAGTATCGATACTTTATGTTTACCTATT
TTCTCATTAAACCGATATAGTTTTACCGGTTACATTGTAAATTTACCTATTACTTTATAATAATC
GATTTCGATGTTTTAAGAATCGATACTTCTCATACATGTATCTATACTTTATGCGTGCATCTCTT
TTGAGATTCATACTGGACAAAAAGTATCGATACTACTAAAACAAGTATCGATACTTTATGTTTAC
ATATTTTCTCATTAACAGTATATTTTTACCGGTTACATTGTAAATTTACCTATTACTTTATAATA
ATCGGTTTAGATGTTTTAAGGATCGATACTTATCATACATGTATCGATACTTTATGTGTGCATCT
CCTTTGGGATTCATACTGGACAAAACGTATCGATACTACTAAAACAAGTATCGATACTTTATGTT
TACCTATTTTCTCATTAAACCGATATATTTTTACCGGTTAATTGTAAATTTACCTATTACTTATA
ATAATCGGTTCGATGTTTTAAGGATCGATACTTATCATATATGTATCGATACTTTATGTGTATCT
CGTTTGGGA
Found at i:240127 original size:27 final size:27
Alignment explanation
Indices: 240089--240140 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
240079 TACGTCTTAG
*
240089 GACAACGCTGACATTTGGAATAATGTA
1 GACAACGATGACATTTGGAATAATGTA
240116 GACAACGATGACATTTGGAATAATG
1 GACAACGATGACATTTGGAATAATG
240141 CAAGTCTCGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.25
Consensus pattern (27 bp):
GACAACGATGACATTTGGAATAATGTA
Found at i:247201 original size:24 final size:25
Alignment explanation
Indices: 247174--247221 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
247164 ATTAAAATAA
**
247174 TTATTAATTAATAATAT-TTATTAT
1 TTATTAAAAAATAATATATTATTAT
247198 TTATTAAAAAATAATATATTATTA
1 TTATTAAAAAATAATATATTATTA
247222 ACTTATTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
TTATTAAAAAATAATATATTATTAT
Found at i:247260 original size:41 final size:41
Alignment explanation
Indices: 247169--247262 Score: 104
Period size: 41 Copynumber: 2.3 Consensus size: 41
247159 TATTTATTAA
*
247169 AATAATTATTAATTAATAATATTTATTATTTATTAAAAAAT
1 AATAATTATTAATTAATAATATTTACTATTTATTAAAAAAT
* *
247210 AATATATTATTAACTT-ATTAT-TTTACTATTT-TATAATAAATT
1 AATA-ATTATTAA-TTAATAATATTTACTATTTAT-TAA-AAAAT
247252 AATAATTATTA
1 AATAATTATTA
247263 TTTAGATTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
40 1 0.02
41 23 0.50
42 20 0.43
43 2 0.04
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (41 bp):
AATAATTATTAATTAATAATATTTACTATTTATTAAAAAAT
Found at i:260588 original size:12 final size:11
Alignment explanation
Indices: 260578--260619 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 11
260568 GAAAAATAAC
260578 AAAATAAATAA-
1 AAAATAAA-AAT
260589 ATAAATAAAAAT
1 A-AAATAAAAAT
260601 AAAATGAAAAAT
1 AAAAT-AAAAAT
260613 AAAATAA
1 AAAATAA
260620 TATATATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 9 0.32
12 19 0.68
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:260601 original size:18 final size:18
Alignment explanation
Indices: 260569--260616 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
260559 ATTGGAGCCG
260569 AAAAATAACAAA-ATAAATA
1 AAAAATAA-AAATA-AAATA
*
260588 AATAAATAAAAATAAAATG
1 AA-AAATAAAAATAAAATA
260607 AAAAATAAAA
1 AAAAATAAAA
260617 TAATATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 8 0.31
19 11 0.42
20 7 0.27
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (18 bp):
AAAAATAAAAATAAAATA
Found at i:260648 original size:15 final size:16
Alignment explanation
Indices: 260628--260660 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
260618 AATATATATA
260628 TTTCAAAA-AATATGT
1 TTTCAAAACAATATGT
*
260643 TTTCAAAACTATATGT
1 TTTCAAAACAATATGT
260659 TT
1 TT
260661 AAAAAAAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.45
Consensus pattern (16 bp):
TTTCAAAACAATATGT
Found at i:260705 original size:38 final size:36
Alignment explanation
Indices: 260664--260909 Score: 193
Period size: 37 Copynumber: 6.6 Consensus size: 36
260654 TATGTTTAAA
260664 AAAAACCATTTTTAAAAACTATATATTATATGTTTTC
1 AAAAACCATTTTT-AAAACTATATATTATATGTTTTC
*
260701 AAAAAACA-TTTTAAAA--AT-TA-TATATGTTTTC
1 AAAAACCATTTTTAAAACTATATATTATATGTTTTC
*
260732 AAAAA-TATTTTTCAAAACTATATATTATATGTTTTC
1 AAAAACCATTTTT-AAAACTATATATTATATGTTTTC
* ** * *
260768 CAAAACCGATTTTTTAAAAAAGAAATATATATATATATATTC
1 AAAAACC-A-TTTTT--AAAA-CTATATAT-TATATGTTTTC
**
260810 AAAAACCAATTTTTTAAAAACTATATATTATATACTTTC
1 AAAAACC-A-TTTTT-AAAACTATATATTATATGTTTTC
* * *
260849 AAAAACCGGTTTCTAAAATTATATATTATATGTTTTTTC
1 AAAAACC-ATTTTTAAAACTATATATTATATG--TTTTC
260888 AAAAA--ATATTTTAAAACTATAT
1 AAAAACCAT-TTTTAAAACTATAT
260910 TATATTATTA
Statistics
Matches: 170, Mismatches: 24, Indels: 30
0.76 0.11 0.13
Matches are distributed among these distances:
30 1 0.01
31 20 0.12
32 6 0.04
33 2 0.01
34 2 0.01
35 6 0.04
36 20 0.12
37 35 0.21
38 5 0.03
39 30 0.18
40 10 0.06
41 11 0.06
42 22 0.13
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.42
Consensus pattern (36 bp):
AAAAACCATTTTTAAAACTATATATTATATGTTTTC
Found at i:260754 original size:31 final size:31
Alignment explanation
Indices: 260690--260756 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
260680 AACTATATAT
*
260690 TATATGTTTTCAAAAAACATTTTAAAAATTA
1 TATATGTTTTCAAAAAACATTTTAAAAACTA
* *
260721 TATATGTTTTCAAAAATA-TTTTTCAAAACTA
1 TATATGTTTTCAAAAA-ACATTTTAAAAACTA
260752 TATAT
1 TATAT
260757 TATATGTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
31 31 0.97
32 1 0.03
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (31 bp):
TATATGTTTTCAAAAAACATTTTAAAAACTA
Found at i:262637 original size:29 final size:29
Alignment explanation
Indices: 262593--262662 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
262583 AAAAAATCGG
262593 TTAATTC-GTTCCGTTAATAATTTTCAAA
1 TTAATTCGGTTCCGTTAATAATTTTCAAA
* *
262621 TTAATTCGGTTCGGTTACTAATTTTCAAA
1 TTAATTCGGTTCCGTTAATAATTTTCAAA
*
262650 TAAATTCTGGTTC
1 TTAATTC-GGTTC
262663 AATTAACTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
28 7 0.19
29 25 0.68
30 5 0.14
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.46
Consensus pattern (29 bp):
TTAATTCGGTTCCGTTAATAATTTTCAAA
Found at i:262765 original size:29 final size:29
Alignment explanation
Indices: 262732--262803 Score: 82
Period size: 24 Copynumber: 2.6 Consensus size: 29
262722 AAAAATTCGG
262732 TTAATTCGGTTCGATTAATAATTTTCAAA
1 TTAATTCGGTTCGATTAATAATTTTCAAA
262761 TTAATTC-G---GA-TAATAATTTTCAAA
1 TTAATTCGGTTCGATTAATAATTTTCAAA
* *
262785 TAAATTTTGGTTCGATTAA
1 TTAA-TTCGGTTCGATTAA
262804 ACCGAACCGA
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
24 17 0.49
25 4 0.11
26 1 0.03
28 1 0.03
29 9 0.26
30 3 0.09
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.44
Consensus pattern (29 bp):
TTAATTCGGTTCGATTAATAATTTTCAAA
Found at i:262778 original size:135 final size:132
Alignment explanation
Indices: 262531--262832 Score: 353
Period size: 135 Copynumber: 2.2 Consensus size: 132
262521 ATGAATTTTT
* * * *
262531 AACCGAACCAAATTAACTGAATTTTTGCTTCGATTAATTCGATTAATAATTAAAAAAATCGGTTA
1 AACCGAAACGAATTAACCGAA-TTTTGTTTCGATTAATTCGATTAATAATTAAAAAAATCGGTTA
* *
262596 ATTCGTTCCGTTAATAATTTTCAAATTAATTCGGTTCGGTTACTAATTTTCAAATAAATTCTGGT
65 ATTCGTTCCGTTAATAATTTTCAAATTAA----GTTCGGATAATAATTTTCAAATAAATTCTGGT
262661 TCAATT-
126 TCAATTA
* *
262667 AACTGAAACGAATTAACCGAATTTTGTTTCGATTAATT-GGTTAATAATTTTCAAAAAAAATTCG
1 AACCGAAACGAATTAACCGAATTTTGTTTCGATTAATTCGATTAATAA--TT--AAAAAAA-TCG
*
262731 GTTAATTCGGTT-CGATTAATAATTTTCAAATTAA-TTCGGATAATAATTTTCAAATAAATTTTG
61 GTTAATTC-GTTCCG-TTAATAATTTTCAAATTAAGTTCGGATAATAATTTTCAAATAAATTCTG
*
262794 GTTCGATTA
124 GTTCAATTA
*
262803 AACCGAACCGAATTAACCGAAATTTT-TTTC
1 AACCGAAACGAATTAACCG-AATTTTGTTTC
262833 TTTAACCTTT
Statistics
Matches: 145, Mismatches: 12, Indels: 18
0.83 0.07 0.10
Matches are distributed among these distances:
134 8 0.06
135 49 0.34
136 40 0.28
137 6 0.04
138 7 0.05
139 13 0.09
140 22 0.15
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.39
Consensus pattern (132 bp):
AACCGAAACGAATTAACCGAATTTTGTTTCGATTAATTCGATTAATAATTAAAAAAATCGGTTAA
TTCGTTCCGTTAATAATTTTCAAATTAAGTTCGGATAATAATTTTCAAATAAATTCTGGTTCAAT
TA
Found at i:277119 original size:22 final size:22
Alignment explanation
Indices: 277094--277154 Score: 86
Period size: 22 Copynumber: 2.8 Consensus size: 22
277084 CACTAGTGCT
* *
277094 AAAGTGCCTTAGTACTGATACG
1 AAAGTGCCTTAGCACTAATACG
* *
277116 AAAGTGCATTAGCACTAATACT
1 AAAGTGCCTTAGCACTAATACG
277138 AAAGTGCCTTAGCACTA
1 AAAGTGCCTTAGCACTA
277155 CTGGGGATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (22 bp):
AAAGTGCCTTAGCACTAATACG
Found at i:282359 original size:20 final size:20
Alignment explanation
Indices: 282322--282360 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
282312 AGATTGAGTG
* * *
282322 GATTTTGATGTTGTTTGCAC
1 GATTTTAATGATGATTGCAC
282342 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
282361 AGTTTAGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAC
Found at i:282547 original size:21 final size:22
Alignment explanation
Indices: 282516--282596 Score: 87
Period size: 21 Copynumber: 3.7 Consensus size: 22
282506 TCAGAACCCA
*
282516 GGGGGATATCGATTCCCCT-ATG
1 GGGGGA-ATCGATTCCCCTCAAG
* *
282538 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGATTCCCC-TCAAG
*
282561 GGGGGAATCGGTT-CCCTCAAG
1 GGGGGAATCGATTCCCCTCAAG
282582 GGGGG-ATCGATTCCC
1 GGGGGAATCGATTCCC
282597 TCTGCACCAA
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
20 6 0.12
21 21 0.41
22 10 0.20
23 14 0.27
ACGTcount: A:0.19, C:0.25, G:0.35, T:0.22
Consensus pattern (22 bp):
GGGGGAATCGATTCCCCTCAAG
Found at i:282584 original size:20 final size:21
Alignment explanation
Indices: 282538--282598 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
282528 TTCCCCTATG
282538 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
282561 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
282581 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
282599 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:287208 original size:40 final size:40
Alignment explanation
Indices: 287148--287228 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
287138 TTGAAAATCT
287148 ATCCGTCATAGCTTTAATATCTTCATTTGGTTTCATCCTG
1 ATCCGTCATAGCTTTAATATCTTCATTTGGTTTCATCCTG
* *
287188 ATCCGTTATAGCTTTGATATCTTCATTTGGTTTCATCCTG
1 ATCCGTCATAGCTTTAATATCTTCATTTGGTTTCATCCTG
287228 A
1 A
287229 AATTTTCATA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.20, C:0.21, G:0.14, T:0.46
Consensus pattern (40 bp):
ATCCGTCATAGCTTTAATATCTTCATTTGGTTTCATCCTG
Found at i:289386 original size:16 final size:16
Alignment explanation
Indices: 289365--289397 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
289355 TAATAAATAA
*
289365 ACGAACATAAGCGAAC
1 ACGAACATAAACGAAC
289381 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
289397 A
1 A
289398 AATTTTTTTT
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:0.24, G:0.15, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:289493 original size:16 final size:16
Alignment explanation
Indices: 289472--289518 Score: 76
Period size: 16 Copynumber: 2.9 Consensus size: 16
289462 ATAAACGAAC
*
289472 GAACACAAACATAAAT
1 GAACACGAACATAAAT
289488 GAACACGAACATAAAT
1 GAACACGAACATAAAT
*
289504 GAACATGAACATAAA
1 GAACACGAACATAAA
289519 CGTTAGAGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.60, C:0.17, G:0.11, T:0.13
Consensus pattern (16 bp):
GAACACGAACATAAAT
Found at i:291457 original size:3 final size:3
Alignment explanation
Indices: 291449--291492 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
291439 CGACCTTCTA
291449 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
291493 GCTAATTAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:292086 original size:29 final size:29
Alignment explanation
Indices: 292053--292137 Score: 82
Period size: 29 Copynumber: 2.9 Consensus size: 29
292043 AAATTTTGGG
* *
292053 TAGTGAACAAAATATAAGTTTTAAAAGTT
1 TAGTGACCAAAATATAAATTTTAAAAGTT
* **
292082 TAGTGGCCAAGGTATAAATTTTAAAAAGTT
1 TAGTGACCAAAATATAAATTTT-AAAAGTT
* *
292112 TAAG-GACCAAAATGTAATTTTTAAAA
1 T-AGTGACCAAAATATAAATTTTAAAA
292138 ATTATAAATT
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
29 21 0.48
30 21 0.48
31 2 0.05
ACGTcount: A:0.46, C:0.06, G:0.15, T:0.33
Consensus pattern (29 bp):
TAGTGACCAAAATATAAATTTTAAAAGTT
Found at i:294567 original size:16 final size:16
Alignment explanation
Indices: 294546--294579 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
294536 AGAGTCGTAG
294546 TGCACTTGACATGCCT
1 TGCACTTGACATGCCT
*
294562 TGCACTTGATATGCCT
1 TGCACTTGACATGCCT
294578 TG
1 TG
294580 AAGTTGAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.26, G:0.21, T:0.35
Consensus pattern (16 bp):
TGCACTTGACATGCCT
Found at i:294822 original size:7 final size:7
Alignment explanation
Indices: 294806--294836 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
294796 TATTTGAAAA
294806 GAAA-AT
1 GAAATAT
294812 GAAATAT
1 GAAATAT
294819 GAAATAT
1 GAAATAT
294826 GAAATAT
1 GAAATAT
294833 GAAA
1 GAAA
294837 GTTTTGAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.17
7 20 0.83
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (7 bp):
GAAATAT
Found at i:299475 original size:31 final size:30
Alignment explanation
Indices: 299399--299484 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 30
299389 TTAGGGTATT
*
299399 GACCAAAATGTAAGTTTTG-AAAGTTTAGCG
1 GACCAAAATATAA-TTTTGAAAAGTTTAGCG
*
299429 G-CCAAAGTATAAATTTTGAAAAGTTTATG-G
1 GACCAAAATAT-AATTTTGAAAAGTTTA-GCG
*
299459 GACCAAAAATATAATTTTTAAAAGTT
1 GACC-AAAATATAATTTTGAAAAGTT
299485 AAATATTTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
29 12 0.26
30 13 0.28
31 16 0.34
32 6 0.13
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.33
Consensus pattern (30 bp):
GACCAAAATATAATTTTGAAAAGTTTAGCG
Found at i:301401 original size:21 final size:21
Alignment explanation
Indices: 301377--301417 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
301367 CAATTATGAG
* *
301377 TATTCAATGTTGAATTTTAAT
1 TATTAAATGCTGAATTTTAAT
*
301398 TATTAAATGCTGGATTTTAA
1 TATTAAATGCTGAATTTTAA
301418 GTTAGAATGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.05, G:0.12, T:0.49
Consensus pattern (21 bp):
TATTAAATGCTGAATTTTAAT
Found at i:304519 original size:18 final size:18
Alignment explanation
Indices: 304496--304540 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
304486 TTTAGATTAC
*
304496 TTATTTAATTATTTTCTT
1 TTATTTAATTATTATCTT
*
304514 TTATTTAATTCTTATCTT
1 TTATTTAATTATTATCTT
304532 TTAATTTAA
1 TT-ATTTAA
304541 AAACAACTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 18 0.75
19 6 0.25
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.67
Consensus pattern (18 bp):
TTATTTAATTATTATCTT
Found at i:304628 original size:20 final size:20
Alignment explanation
Indices: 304605--304671 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
304595 TATATGTCCC
304605 TTTTATTT-ATTATTATTTTA
1 TTTTATTTAATT-TTATTTTA
* *
304625 TTTTGTTTAATTTTATTTTC
1 TTTTATTTAATTTTATTTTA
* *
304645 TTTT-TTAAATTTT-TATTA
1 TTTTATTTAATTTTATTTTA
304663 TTTTTATTT
1 -TTTTATTT
304672 TATGAAATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
18 3 0.08
19 12 0.32
20 20 0.53
21 3 0.08
ACGTcount: A:0.21, C:0.01, G:0.01, T:0.76
Consensus pattern (20 bp):
TTTTATTTAATTTTATTTTA
Found at i:304706 original size:25 final size:25
Alignment explanation
Indices: 304678--304731 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
304668 ATTTTATGAA
304678 ATTTATTATTTTCTACATTT-A-TTTT
1 ATTTATTATTTT-TA-ATTTAATTTTT
* *
304703 ATTTTTTCTTTTTAATTTAATTTTT
1 ATTTATTATTTTTAATTTAATTTTT
304728 ATTT
1 ATTT
304732 GATATTTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
23 4 0.16
24 3 0.12
25 18 0.72
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (25 bp):
ATTTATTATTTTTAATTTAATTTTT
Found at i:308618 original size:45 final size:45
Alignment explanation
Indices: 308569--308654 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
308559 TAAAGAAATA
* * *
308569 AAAAAAGGAAC-AATTGTTCACTGTTTCGAATAGCAAAAAAATCG
1 AAAAAAGGAACAAATTGTTCACTATTTCGAACAACAAAAAAATCG
308613 AAAAAAGGAACAAATTGTTCACTATTTCGAACAACAAAAAAA
1 AAAAAAGGAACAAATTGTTCACTATTTCGAACAACAAAAAAA
308655 GGGAAGAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
44 11 0.29
45 27 0.71
ACGTcount: A:0.52, C:0.14, G:0.13, T:0.21
Consensus pattern (45 bp):
AAAAAAGGAACAAATTGTTCACTATTTCGAACAACAAAAAAATCG
Found at i:309637 original size:85 final size:86
Alignment explanation
Indices: 309397--309690 Score: 439
Period size: 86 Copynumber: 3.4 Consensus size: 86
309387 AGAGTCACTC
* * *
309397 GAAGAATAT-CTCACATAACTTTCCCGTGAAGGGGAGTCCTCCAAAGATAATCTCACCTGGTTCA
1 GAAGAATATAC-CACATGACTTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTCACCTGGTTCA
309461 AACCCGCAAAGGGGAACCACCT
65 AACCCGCAAAGGGGAACCACCT
* *
309483 GAAGAATATACCACATGACTTTCCCGTGAAGGGGAGTCATCCAAATATCATCTCACCTGGTTCAG
1 GAAGAATATACCACATGACTTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTCACCTGGTTCAA
*
309548 ACCCGCAAAAGGGAACCACCT
66 ACCCGCAAAGGGGAACCACCT
* * *
309569 GAAGAATATACCACATGA-TTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTCTCTTTGTTCAA
1 GAAGAATATACCACATGACTTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTCACCTGGTTCAA
* *
309633 ACCCGCGAAGGGGAACAACCT
66 ACCCGCAAAGGGGAACCACCT
* * *
309654 GAAGAATATACCACTTGGCTTTCCCATGAAGGGGAGT
1 GAAGAATATACCACATGACTTTCCCGTGAAGGGGAGT
309691 TAACTAAAGA
Statistics
Matches: 189, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
85 75 0.40
86 113 0.60
87 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (86 bp):
GAAGAATATACCACATGACTTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTCACCTGGTTCAA
ACCCGCAAAGGGGAACCACCT
Found at i:310107 original size:200 final size:199
Alignment explanation
Indices: 309762--310343 Score: 783
Period size: 200 Copynumber: 2.9 Consensus size: 199
309752 CCGTTTATAG
* * *
309762 CATAGCTCAAGGTGAGAAGGGTTATCTATCAACAAAACTTTTGAGTTCGATTCCATTCAGCTCGA
1 CATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAACTTTTGAGTTCGATTCCATTCAGCTCGA
* * * *
309827 AGGCATATCAACCGCATGGTAGTAA-GGAGGAACTACTTTCCAGTTGAAGTTTAAATCAAGGTCT
66 AGGCATTTCAACCGCATGGTAGCAACGG-GGAACTACTTTCTAGTTGAAGTTTAAAT-GAGGTCT
* * **
309891 TTAAGTCAAGAAGAAGACCTAGGTTGGGTGCGATTTAGCAATAAGGAACTATCTCCCAGTCGAAT
129 TTAAGTCAAGAAGAAGACCTAGGTTGGCTGCGATTTAGCAACAAGGAACTATCTCCCAACCGAAT
309956 TTACAA
194 TTACAA
* * * *
309962 TATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAACTTTCGAGTTCGATTTCATTCTGCTCGA
1 CATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAACTTTTGAGTTCGATTCCATTCAGCTCGA
* *
310027 AGGCATTTCAACCGCATGGTAACAACGGGGAACTACTTTCTGGTTGAAGTTTAAACTGAGGTCTT
66 AGGCATTTCAACCGCATGGTAGCAACGGGGAACTACTTTCTAGTTGAAGTTTAAA-TGAGGTCTT
* * *
310092 TAAGTCAATAAGAAGACCTAGGTTGGCTGCGATTTAGCAACAATGAACTATCTCCTAACCGAATT
130 TAAGTCAAGAAGAAGACCTAGGTTGGCTGCGATTTAGCAACAAGGAACTATCTCCCAACCGAATT
*
310157 TATAA
195 TACAA
* *
310162 CATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAACTTTTGAGTTCGATTCCATTCAGGTCGA
1 CATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAACTTTTGAGTTCGATTCCATTCAGCTCGA
* * * * *
310227 AGGCATATT-AAACGCATTGTAGCAACGAGGAACTATTTTCTTGTTGAAGTTTAAAATGAGGTCT
66 AGGCAT-TTCAACCGCATGGTAGCAACGGGGAACTACTTTCTAGTTGAAGTTT-AAATGAGGTCT
* * * * * * *
310291 TTAAGTCGAGAAGAAGACCAAGGTTGACTACGATTTGGAAACAA-GAACCATCT
129 TTAAGTCAAGAAGAAGACCTAGGTTGGCTGCGATTTAGCAACAAGGAACTATCT
310344 TCTGATTCAA
Statistics
Matches: 337, Mismatches: 41, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
199 8 0.02
200 321 0.95
201 8 0.02
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.27
Consensus pattern (199 bp):
CATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAACTTTTGAGTTCGATTCCATTCAGCTCGA
AGGCATTTCAACCGCATGGTAGCAACGGGGAACTACTTTCTAGTTGAAGTTTAAATGAGGTCTTT
AAGTCAAGAAGAAGACCTAGGTTGGCTGCGATTTAGCAACAAGGAACTATCTCCCAACCGAATTT
ACAA
Found at i:311238 original size:17 final size:18
Alignment explanation
Indices: 311216--311257 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
311206 CTTTAGATTA
*
311216 TTTATTTAATTATTAT-T
1 TTTATTTAAGTATTATCT
*
311233 TTTATTTAAGTCTTATCT
1 TTTATTTAAGTATTATCT
311251 TTTATTT
1 TTTATTT
311258 TAAAAACAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.69
Consensus pattern (18 bp):
TTTATTTAAGTATTATCT
Found at i:311308 original size:3 final size:3
Alignment explanation
Indices: 311302--311360 Score: 52
Period size: 3 Copynumber: 19.7 Consensus size: 3
311292 CTACTACTAT
*
311302 TTA TTA TT- TTA TTA -TA TTTA TCTT TTA TTTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA T-TA TTA -TTA TTA TTA TTA TTA TTA
*
311348 TT- TTA TTT TTA TT
1 TTA TTA TTA TTA TT
311361 TTCTCTTTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
2 6 0.13
3 33 0.72
4 7 0.15
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (3 bp):
TTA
Found at i:311321 original size:17 final size:17
Alignment explanation
Indices: 311299--311354 Score: 66
Period size: 16 Copynumber: 3.5 Consensus size: 17
311289 TTACTACTAC
311299 TATTTATTATTTTATTA
1 TATTTATTATTTTATTA
*
311316 TATTTA-TCTTTTATT-
1 TATTTATTATTTTATTA
311331 TA-TTATTATTATTATTA
1 TATTTATTATT-TTATTA
311348 T-TTTATT
1 TATTTATT
311355 TTTATTTTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
14 3 0.09
15 5 0.15
16 13 0.39
17 12 0.36
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (17 bp):
TATTTATTATTTTATTA
Found at i:311342 original size:20 final size:20
Alignment explanation
Indices: 311302--311360 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
311292 CTACTACTAT
311302 TTATTATTTTATTA-TATTTA
1 TTATTATTTTATTATTA-TTA
*
311322 TCTTTTA-TTTATTATTATTA
1 T-TATTATTTTATTATTATTA
*
311342 TTATTATTTTATTTTTATT
1 TTATTATTTTATTATTATT
311361 TTCTCTTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
19 4 0.12
20 23 0.70
21 6 0.18
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (20 bp):
TTATTATTTTATTATTATTA
Found at i:311359 original size:17 final size:17
Alignment explanation
Indices: 311302--311392 Score: 55
Period size: 17 Copynumber: 5.3 Consensus size: 17
311292 CTACTACTAT
*
311302 TTATTATTTTA-TTATA
1 TTATTATTTTATTTTTA
*
311318 TT-TATCTTTTATTTATTA
1 TTAT-TATTTTATTT-TTA
311336 TTATTATTATTA-TTTTA
1 TTATTATT-TTATTTTTA
* *
311353 TTTTTATTTTCTCTTTTA
1 TTATTATTTTAT-TTTTA
**
311371 ACATT-TTTTATATTTTA
1 TTATTATTTTAT-TTTTA
311388 TTATT
1 TTATT
311393 TTTCTTTTCT
Statistics
Matches: 56, Mismatches: 12, Indels: 13
0.69 0.15 0.16
Matches are distributed among these distances:
15 1 0.02
16 10 0.18
17 25 0.45
18 16 0.29
19 4 0.07
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (17 bp):
TTATTATTTTATTTTTA
Found at i:311395 original size:17 final size:18
Alignment explanation
Indices: 311329--311392 Score: 58
Period size: 17 Copynumber: 3.5 Consensus size: 18
311319 TTATCTTTTA
311329 TTTATTATTATTATTATTAT
1 TTTATTATTATT-TTA-TAT
* * *
311349 TTTATTTTTATTTTCTCT
1 TTTATTATTATTTTATAT
**
311367 TTTAACATT-TTTTATAT
1 TTTATTATTATTTTATAT
311384 TTTATTATT
1 TTTATTATT
311393 TTTCTTTTCT
Statistics
Matches: 34, Mismatches: 10, Indels: 3
0.72 0.21 0.06
Matches are distributed among these distances:
17 13 0.38
18 8 0.24
19 2 0.06
20 11 0.32
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTATTATTTTATAT
Found at i:311534 original size:39 final size:39
Alignment explanation
Indices: 311462--311558 Score: 92
Period size: 39 Copynumber: 2.5 Consensus size: 39
311452 ATATAATAAT
* *
311462 TTTTTTAATTTAATATTTCTTCTTTGATTTATTT-TTTTC
1 TTTTTTAATTTAATATTTCTTATTTGA-TTATTTCTTTTA
311501 TTTTTTAATTTAATTTAATTT-TTATTTGA-TATTTCTTTTA
1 TTTTTTAATTTAA--T-ATTTCTTATTTGATTATTTCTTTTA
* * *
311541 TTTTATAATCTAACATTT
1 TTTTTTAATTTAATATTT
311559 TTAACTTTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
37 4 0.08
39 18 0.37
40 15 0.31
41 8 0.16
42 4 0.08
ACGTcount: A:0.24, C:0.06, G:0.02, T:0.68
Consensus pattern (39 bp):
TTTTTTAATTTAATATTTCTTATTTGATTATTTCTTTTA
Found at i:311631 original size:12 final size:12
Alignment explanation
Indices: 311614--311640 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
311604 GAATCAGGTC
311614 TTTAAATTTTAA
1 TTTAAATTTTAA
311626 TTTAAATTTTAA
1 TTTAAATTTTAA
311638 TTT
1 TTT
311641 TTGCAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TTTAAATTTTAA
Found at i:320354 original size:29 final size:29
Alignment explanation
Indices: 320312--320386 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 29
320302 ATTTTAAAAC
* *
320312 TTGCAATACAGTCCCCAACATTTGGTCCAT
1 TTGCAATA-TGTCCCCAACATTTAGTCCAT
**
320342 TTGCAATATGTCCCCAACATTTAGTCTGT
1 TTGCAATATGTCCCCAACATTTAGTCCAT
320371 TTGCAATATGGTCCCC
1 TTGCAATAT-GTCCCC
320387 GACCGTTTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 26 0.65
30 14 0.35
ACGTcount: A:0.24, C:0.28, G:0.15, T:0.33
Consensus pattern (29 bp):
TTGCAATATGTCCCCAACATTTAGTCCAT
Found at i:322355 original size:31 final size:31
Alignment explanation
Indices: 322320--322386 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
322310 TCAAACGGCC
*
322320 GGGGACCATAGTACAAATAGA-TAAAATGTTG
1 GGGGACCATAGTACAAATAGACT-AAATATTG
* * *
322351 GGGGACCATATTGCAAATGGACTAAATATTG
1 GGGGACCATAGTACAAATAGACTAAATATTG
322382 GGGGA
1 GGGGA
322387 TTTTTACAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 30 0.97
32 1 0.03
ACGTcount: A:0.37, C:0.10, G:0.30, T:0.22
Consensus pattern (31 bp):
GGGGACCATAGTACAAATAGACTAAATATTG
Found at i:323113 original size:30 final size:31
Alignment explanation
Indices: 323066--323141 Score: 102
Period size: 30 Copynumber: 2.5 Consensus size: 31
323056 TTTCTAAAAC
*
323066 TTACAATACAG-CCCCCAACATTTAGTCCGT
1 TTACAATATAGTCCCCCAACATTTAGTCCGT
** *
323096 TTGTAATAT-GTCCCCCAACATTTAGTCTGT
1 TTACAATATAGTCCCCCAACATTTAGTCCGT
323126 TTACAATATAGTCCCC
1 TTACAATATAGTCCCC
323142 GACCGTTTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 1 0.03
30 31 0.82
31 6 0.16
ACGTcount: A:0.28, C:0.29, G:0.11, T:0.33
Consensus pattern (31 bp):
TTACAATATAGTCCCCCAACATTTAGTCCGT
Found at i:325135 original size:31 final size:29
Alignment explanation
Indices: 325071--325136 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
325061 TCAAATGGTT
*
325071 GGGGACCATATTACAAATATAAAATGTTG
1 GGGGACCATATTACAAATATAAAATATTG
*
325100 GGGGACCATATTGCAAATGGACT-AAATATTG
1 GGGGACCATATTACAAAT--A-TAAAATATTG
325131 GGGGAC
1 GGGGAC
325137 TGTTTTGCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 17 0.53
31 14 0.44
32 1 0.03
ACGTcount: A:0.36, C:0.12, G:0.27, T:0.24
Consensus pattern (29 bp):
GGGGACCATATTACAAATATAAAATATTG
Found at i:325893 original size:30 final size:30
Alignment explanation
Indices: 325859--325916 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
325849 TACAATACAA
*
325859 CCCCCAACATTTAGTCTGTTTGCAATATAT
1 CCCCCAACATTTAGTCTATTTGCAATATAT
325889 CCCCCAACATTTAGTCTATTTGCAATAT
1 CCCCCAACATTTAGTCTATTTGCAATAT
325917 GGTCCCCGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.36
Consensus pattern (30 bp):
CCCCCAACATTTAGTCTATTTGCAATATAT
Found at i:330562 original size:20 final size:20
Alignment explanation
Indices: 330537--330579 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
330527 CCCAATAAGA
330537 CTTAATAAATACTTTACAAC
1 CTTAATAAATACTTTACAAC
330557 CTTAATAAATACTTTACAAC
1 CTTAATAAATACTTTACAAC
330577 CTT
1 CTT
330580 TAAGGGTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.42, C:0.21, G:0.00, T:0.37
Consensus pattern (20 bp):
CTTAATAAATACTTTACAAC
Found at i:332032 original size:18 final size:19
Alignment explanation
Indices: 332009--332054 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
331999 TGTCCTGGAT
*
332009 ATAGAGGAAATGAGTAT-A
1 ATAGAGGAAATGAGGATCA
*
332027 ATAGAGGATATGAGGATCA
1 ATAGAGGAAATGAGGATCA
332046 ATA-AGGAAA
1 ATAGAGGAAA
332055 CCTTATTTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.50, C:0.02, G:0.28, T:0.20
Consensus pattern (19 bp):
ATAGAGGAAATGAGGATCA
Found at i:337808 original size:18 final size:18
Alignment explanation
Indices: 337787--337833 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 18
337777 TAAAATTGAC
*
337787 ATCGATACTAAAGCCATT
1 ATCGATACTAAAGCCAAT
*
337805 ATCGATACCCTAAGGCCAAT
1 ATCGATA--CTAAAGCCAAT
337825 ATCGATACT
1 ATCGATACT
337834 GATGCCCTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 9 0.36
20 16 0.64
ACGTcount: A:0.36, C:0.26, G:0.13, T:0.26
Consensus pattern (18 bp):
ATCGATACTAAAGCCAAT
Found at i:337822 original size:20 final size:20
Alignment explanation
Indices: 337794--337832 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
337784 GACATCGATA
*
337794 CTAAAGCCATTATCGATACC
1 CTAAAGCCAATATCGATACC
*
337814 CTAAGGCCAATATCGATAC
1 CTAAAGCCAATATCGATAC
337833 TGATGCCCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (20 bp):
CTAAAGCCAATATCGATACC
Found at i:338579 original size:21 final size:21
Alignment explanation
Indices: 338553--338602 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
338543 CGTTTTGTAA
338553 ACTTAAATTTTATACTTAATT
1 ACTTAAATTTTATACTTAATT
338574 ACTTAAATTTTATACTTAATT
1 ACTTAAATTTTATACTTAATT
*
338595 GCTTAAAT
1 ACTTAAAT
338603 GCGATGGATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (21 bp):
ACTTAAATTTTATACTTAATT
Found at i:345204 original size:14 final size:14
Alignment explanation
Indices: 345185--345212 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
345175 ATCAATTCAT
345185 GCCCAACTATCTTC
1 GCCCAACTATCTTC
345199 GCCCAACTATCTTC
1 GCCCAACTATCTTC
345213 CTATCACTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.43, G:0.07, T:0.29
Consensus pattern (14 bp):
GCCCAACTATCTTC
Found at i:350367 original size:449 final size:450
Alignment explanation
Indices: 349528--350376 Score: 1253
Period size: 449 Copynumber: 1.9 Consensus size: 450
349518 AATAGTAGTT
** *
349528 TTATTGGGTTATAGGGTCCAATGATCACCCTTAGGGATTCTATCGTGTATGGACGCGATATCAGG
1 TTATTGGGTTATAGGGTCCAACAATCAACCTTAGGGATTCTATCGTGTATGGACGCGATATCAGG
* *
349593 TGCTTGACAGCCCAACCTGCCAAGGCACACGTGTGCCTTGCGAAGCCCATAGGCCCGCCCGCAAC
66 TGCTTGACAGCCCAACCTGCCAAGGCACACGTGTGCATTGCGAAGCCCATAGGCCCGCCCACAAC
* * *
349658 ACGCTATAGATGTGAGGCTCTGCAATGCTGTGGTGAATTGTGGGGGCTGCCCTACAAGAATCCAC
131 ACGCTATAGATGCGAGGCTCTGCAATGCTGTGATGAATTGTAGGGGCTGCCCTACAAGAATCCAC
** * *
349723 CTTGGCTTGGGGGAAACCAGTATCACTCGCTATAAAGATATGAGGTTAAAATGGCCCACCTGCTT
196 CTTAACTTGGGGGAAACCAGTATCACTCGCTACAAAGATATGAGGTTAAAATGGCCCACCTACTT
* *
349788 ATCACTAATTGGTTTTAAGAAGGAATGGTGACCATTCAATTCAAAACTCTGTAGTTAACCGTGTT
261 ATCACCAATTGGTTTTAAGAAGGAATGGTGACCATTCAATTCAAAACTCTGTAGTTAACCGTGCT
*
349853 TGAACCAGAGTAATCCAAGGATGGGTGACCCACTGGGAAGTTGTTCAAAAATTGAATGACTCGAT
326 TGAACCAGAGTAATCCAAGGATGGGTGACCCACTGGAAAGTTGTTCAAAAATTGAATGACTCGAT
349918 CCTATCAAGTGGTATCAGAGTAGGTTGTAGGTTCGAATCCCCCAGTTATTGCTGGGGTGA
391 CCTATCAAGTGGTATCAGAGTAGGTTGTAGGTTCGAATCCCCCAGTTATTGCTGGGGTGA
* * *
349978 TTATTGGGTTATGGGGTCCAGCAATCAACCTTAGGGATTCTATCGTGTATGGGCGCGATATCAGG
1 TTATTGGGTTATAGGGTCCAACAATCAACCTTAGGGATTCTATCGTGTATGGACGCGATATCAGG
* * * * *
350043 TGCTTGACAGCCCAACCTGTCGAGGC-CAATGTGTGCATTGCGAATCCTC-TAGGCCCGCCCATA
66 TGCTTGACAGCCCAACCTGCCAAGGCAC-ACGTGTGCATTGCGAAGCC-CATAGGCCCGCCCACA
* * * **
350106 GCACGCTATATATGCGGGGCTCTTTAATG-TCGTGATGAATTGTAGGGG-TG-CCTCACAAGAAT
129 ACACGCTATAGATGCGAGGCTCTGCAATGCT-GTGATGAATTGTAGGGGCTGCCCT-ACAAGAAT
* * *
350168 CCACCTTAACTT-GGGGAAACTAGTGATCAC-CTGTTACAAAGATATGAGGTTAAAATGTCCCAC
192 CCACCTTAACTTGGGGGAAACCAGT-ATCACTC-GCTACAAAGATATGAGGTTAAAATGGCCCAC
* * * * *
350231 GTACTTATCACCAATTGGTTTTAAGAAGGAATGGTGATCATTCACTTCAGAACTCTGTAGTTAAG
255 CTACTTATCACCAATTGGTTTTAAGAAGGAATGGTGACCATTCAATTCAAAACTCTGTAGTTAAC
* *
350296 CGTGCTTGAACCAGAGTAATCTAAGGATGGGTGACCCATTGGAAAGTTGTTCAAAAATTGAATGA
320 CGTGCTTGAACCAGAGTAATCCAAGGATGGGTGACCCACTGGAAAGTTGTTCAAAAATTGAATGA
350361 CTCGATCCTATCAAGT
385 CTCGATCCTATCAAGT
350377 TTAACAAGGG
Statistics
Matches: 355, Mismatches: 38, Indels: 13
0.87 0.09 0.03
Matches are distributed among these distances:
448 15 0.04
449 190 0.54
450 149 0.42
451 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (450 bp):
TTATTGGGTTATAGGGTCCAACAATCAACCTTAGGGATTCTATCGTGTATGGACGCGATATCAGG
TGCTTGACAGCCCAACCTGCCAAGGCACACGTGTGCATTGCGAAGCCCATAGGCCCGCCCACAAC
ACGCTATAGATGCGAGGCTCTGCAATGCTGTGATGAATTGTAGGGGCTGCCCTACAAGAATCCAC
CTTAACTTGGGGGAAACCAGTATCACTCGCTACAAAGATATGAGGTTAAAATGGCCCACCTACTT
ATCACCAATTGGTTTTAAGAAGGAATGGTGACCATTCAATTCAAAACTCTGTAGTTAACCGTGCT
TGAACCAGAGTAATCCAAGGATGGGTGACCCACTGGAAAGTTGTTCAAAAATTGAATGACTCGAT
CCTATCAAGTGGTATCAGAGTAGGTTGTAGGTTCGAATCCCCCAGTTATTGCTGGGGTGA
Found at i:355770 original size:2 final size:2
Alignment explanation
Indices: 355763--355806 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
355753 ATGAGTGATA
355763 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
355805 AT
1 AT
355807 TTAGAAGTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:363746 original size:2 final size:2
Alignment explanation
Indices: 363739--363767 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
363729 TCTATCTATC
363739 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 T
363768 TAAAAAGCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:365372 original size:15 final size:16
Alignment explanation
Indices: 365354--365384 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
365344 TATAAGTTCA
365354 AATTCTCCT-ATATTT
1 AATTCTCCTCATATTT
365369 AATTCTCCTCATATTT
1 AATTCTCCTCATATTT
365385 TCACGTTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.26, C:0.23, G:0.00, T:0.52
Consensus pattern (16 bp):
AATTCTCCTCATATTT
Found at i:366801 original size:69 final size:67
Alignment explanation
Indices: 366686--366821 Score: 218
Period size: 69 Copynumber: 2.0 Consensus size: 67
366676 ATAAAGATTA
* * * *
366686 ATCTCTCAAAAAGGTATAATTTTTGCTTGGTTATAAGCTAATGGGTCACTGTTTTTTTAACTTAG
1 ATCTCTCAAAAAGGTATAATCTTTGCTTGATTATAAGCTAACGGGTCACAG-TTTTTTAACTT-G
366751 CTTT
64 CTTT
366755 ATCTCTCAAAAAGGTATAATCTTTGCTTGATTATAAGCTAACGGGTCACAGTTTTTTAACTTGCT
1 ATCTCTCAAAAAGGTATAATCTTTGCTTGATTATAAGCTAACGGGTCACAGTTTTTTAACTTGCT
366820 TT
66 TT
366822 TTCATTTTCT
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
67 5 0.08
68 11 0.17
69 47 0.75
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (67 bp):
ATCTCTCAAAAAGGTATAATCTTTGCTTGATTATAAGCTAACGGGTCACAGTTTTTTAACTTGCT
TT
Found at i:372244 original size:14 final size:14
Alignment explanation
Indices: 372196--372244 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
372186 TTATAACATT
*
372196 TCACGTAGCTTATA
1 TCACATAGCTTATA
* * *
372210 TCACATAGATCATTG
1 TCACATAGCTTA-TA
372225 TCACATAGCTTATA
1 TCACATAGCTTATA
372239 TCACAT
1 TCACAT
372245 TTTCATATAA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
14 16 0.59
15 11 0.41
ACGTcount: A:0.33, C:0.22, G:0.10, T:0.35
Consensus pattern (14 bp):
TCACATAGCTTATA
Found at i:372320 original size:45 final size:45
Alignment explanation
Indices: 372209--372323 Score: 149
Period size: 45 Copynumber: 2.6 Consensus size: 45
372199 CGTAGCTTAT
* * * *
372209 ATCACATAGATCATTGTCACATAGCTTATATCACATTTTCATATA
1 ATCACATAGGTCAATATCATATAGCTTATATCACATTTTCATATA
* * ** *
372254 ATCATATAGGTCGATCCCATATAGCTTATATCACATTTTCATGTA
1 ATCACATAGGTCAATATCATATAGCTTATATCACATTTTCATATA
372299 ATCACATAGGTCAATATCATATAGC
1 ATCACATAGGTCAATATCATATAGC
372324 ATGAAATATA
Statistics
Matches: 58, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 58 1.00
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.36
Consensus pattern (45 bp):
ATCACATAGGTCAATATCATATAGCTTATATCACATTTTCATATA
Found at i:374366 original size:23 final size:23
Alignment explanation
Indices: 374339--374382 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
374329 GCCTCATAGG
374339 GAGCCATATTAATGCTCGACTGA
1 GAGCCATATTAATGCTCGACTGA
374362 GAGCCATATTAATGCTCGACT
1 GAGCCATATTAATGCTCGACT
374383 TTGAGATTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (23 bp):
GAGCCATATTAATGCTCGACTGA
Found at i:379007 original size:23 final size:23
Alignment explanation
Indices: 378981--379040 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
378971 CACGTATAAA
* *
378981 TGTCCTGAAGGACCATATAGATT
1 TGTCCCGAAGGACCACATAGATT
* *
379004 TGTCCCGGAGGACCACATAGAAT
1 TGTCCCGAAGGACCACATAGATT
* *
379027 TATCCCAAAGGACC
1 TGTCCCGAAGGACC
379041 GCGTAGAACC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.22
Consensus pattern (23 bp):
TGTCCCGAAGGACCACATAGATT
Found at i:379159 original size:16 final size:14
Alignment explanation
Indices: 379125--379234 Score: 62
Period size: 15 Copynumber: 7.4 Consensus size: 14
379115 TTATAACATT
*
379125 TCACATAGCTTATA
1 TCACATAGCATATA
379139 TCACATAGACATATAA
1 TCACATAG-CATAT-A
*
379155 TCACATAG-ATCATTG
1 TCACATAGCAT-A-TA
*
379170 TCACATAGCTTATA
1 TCACATAGCATATA
**
379184 TCACATTTTCATATAA
1 TCACA-TAGCATAT-A
*
379200 TCACATAGGTCA-ATG
1 TCACATA-G-CATATA
* *
379215 CCACATAGCTTATA
1 TCACATAGCATATA
379229 TCACAT
1 TCACAT
379235 TTTCATGTGA
Statistics
Matches: 72, Mismatches: 14, Indels: 20
0.68 0.13 0.19
Matches are distributed among these distances:
13 1 0.01
14 24 0.33
15 26 0.36
16 19 0.26
17 2 0.03
ACGTcount: A:0.37, C:0.22, G:0.08, T:0.33
Consensus pattern (14 bp):
TCACATAGCATATA
Found at i:379235 original size:45 final size:45
Alignment explanation
Indices: 379126--379254 Score: 186
Period size: 45 Copynumber: 2.9 Consensus size: 45
379116 TATAACATTT
*** * * *
379126 CACATAGCTTATATCACATAGACATATAATCACATAGATCATTGT
1 CACATAGCTTATATCACATTTTCATATAATCACATAGGTCAATGC
379171 CACATAGCTTATATCACATTTTCATATAATCACATAGGTCAATGC
1 CACATAGCTTATATCACATTTTCATATAATCACATAGGTCAATGC
* *
379216 CACATAGCTTATATCACATTTTCATGTGATCACATAGGT
1 CACATAGCTTATATCACATTTTCATATAATCACATAGGT
379255 AATATCATAT
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 76 1.00
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (45 bp):
CACATAGCTTATATCACATTTTCATATAATCACATAGGTCAATGC
Found at i:383970 original size:29 final size:29
Alignment explanation
Indices: 383928--384008 Score: 135
Period size: 29 Copynumber: 2.8 Consensus size: 29
383918 AACTAAATTA
*
383928 ATGTCATTGCTTACATCATTTAAGTAAAG
1 ATGTCATTGCTTACATCATTTAAATAAAG
*
383957 ATGTCATTGCTTACATCATTTAAATAATG
1 ATGTCATTGCTTACATCATTTAAATAAAG
383986 ATGTCATTGCTTACATCAATTTA
1 ATGTCATTGCTTACATC-ATTTA
384009 GTTAGGTGAG
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (29 bp):
ATGTCATTGCTTACATCATTTAAATAAAG
Found at i:388708 original size:29 final size:29
Alignment explanation
Indices: 388666--388747 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
388656 AAACTAAATT
*
388666 GATGTCATTGCTTACATCATTTAAGTAAA
1 GATGTCATTGCTTACATCATTTAAATAAA
*
388695 GATGTCATTGCTTACATCATTTAAATAAT
1 GATGTCATTGCTTACATCATTTAAATAAA
*
388724 GATGTAATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
388748 GTTAGGTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.40
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAATAAA
Found at i:393087 original size:27 final size:27
Alignment explanation
Indices: 393034--393087 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
393024 AATCAATTTT
*
393034 TTGAAAAATATAAAATTAAGAACTAAA
1 TTGAAAAATATAAAATTAACAACTAAA
* *
393061 TTGAACAAATATGAAATT-ACAAGTAAA
1 TTGAA-AAATATAAAATTAACAACTAAA
393088 AATTTAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.59, C:0.06, G:0.09, T:0.26
Consensus pattern (27 bp):
TTGAAAAATATAAAATTAACAACTAAA
Found at i:393486 original size:22 final size:20
Alignment explanation
Indices: 393461--393508 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 20
393451 GCATATAAAC
393461 TATATAGTTTATTAATACAAAT
1 TATATAGTTTA-T-ATACAAAT
*
393483 TATATAGTTTATATATAAAT
1 TATATAGTTTATATACAAAT
393503 TATATA
1 TATATA
393509 TGAATTATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 13 0.52
21 1 0.04
22 11 0.44
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (20 bp):
TATATAGTTTATATACAAAT
Found at i:393499 original size:11 final size:11
Alignment explanation
Indices: 393491--393529 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
393481 ATTATATAGT
393491 TTATATATAAA
1 TTATATATAAA
*
393502 TTATATATGAA
1 TTATATATAAA
*
393513 TTATATTTAAA
1 TTATATATAAA
393524 -TATATA
1 TTATATA
393530 CAGCTTATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
10 5 0.21
11 19 0.79
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (11 bp):
TTATATATAAA
Found at i:393502 original size:20 final size:22
Alignment explanation
Indices: 393453--393508 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
393443 TAAACTACGC
*
393453 ATATAAACTATATAGTTTATTA
1 ATATAAATTATATAGTTTATTA
*
393475 ATACAAATTATATAGTTTA-T-
1 ATATAAATTATATAGTTTATTA
393495 ATATAAATTATATA
1 ATATAAATTATATA
393509 TGAATTATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 13 0.42
21 1 0.03
22 17 0.55
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.45
Consensus pattern (22 bp):
ATATAAATTATATAGTTTATTA
Found at i:393509 original size:22 final size:21
Alignment explanation
Indices: 393453--393539 Score: 63
Period size: 22 Copynumber: 4.1 Consensus size: 21
393443 TAAACTACGC
*
393453 ATATAAA-CTATATAGTTTATT
1 ATATAAATATATATAGTTTA-T
*
393474 AATACAAAT-TATATAGTTTAT
1 -ATATAAATATATATAGTTTAT
*
393495 ATATAAAT-TATATATGAATTAT
1 ATATAAATATATATA-G-TTTAT
* * *
393517 ATTTAAATATATACAGCTTAT
1 ATATAAATATATATAGTTTAT
393538 AT
1 AT
393540 TTATATTTAA
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
20 13 0.24
21 8 0.15
22 29 0.53
23 5 0.09
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.45
Consensus pattern (21 bp):
ATATAAATATATATAGTTTAT
Found at i:395662 original size:31 final size:31
Alignment explanation
Indices: 395624--395690 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
395614 CAAACGGTCA
395624 GGGACCATATTACAAATAG-ACTAAATGTTGG
1 GGGACCATATTACAAA-AGAACTAAATGTTGG
* *
395655 GGGACCATTTTACAAACGAACTAAATGTTGG
1 GGGACCATATTACAAAAGAACTAAATGTTGG
395686 GGGAC
1 GGGAC
395691 TGTATTGCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 1 0.03
31 32 0.97
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.24
Consensus pattern (31 bp):
GGGACCATATTACAAAAGAACTAAATGTTGG
Found at i:395794 original size:17 final size:17
Alignment explanation
Indices: 395769--395810 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
395759 TACTTTACCC
* * *
395769 TATATTTATATATTATT
1 TATAATTATAAATTATA
395786 TATAATTATAAATTATA
1 TATAATTATAAATTATA
395803 TAT-ATTAT
1 TATAATTAT
395811 GTAAAATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TATAATTATAAATTATA
Found at i:395818 original size:26 final size:26
Alignment explanation
Indices: 395775--395899 Score: 73
Period size: 26 Copynumber: 4.9 Consensus size: 26
395765 ACCCTATATT
* *
395775 TATATATTATTTATAATTATAAATTA
1 TATATATTATGTAAAATTATAAATTA
* *
395801 TATATATTATGTAAAATTTTATAGTT-
1 TATATATTATGTAAAATTATA-AATTA
* *
395827 TATATAGT-T-TAAAA--ATAAAGTA
1 TATATATTATGTAAAATTATAAATTA
* *
395849 TATA-AGTATATATATAAACTATAAATTA
1 TATATA-T-TATGTA-AAATTATAAATTA
* * *
395877 TATATATAAAGTATAATTATAAA
1 TATATATTATGTAAAATTATAAA
395900 GACTAAAGTA
Statistics
Matches: 74, Mismatches: 15, Indels: 20
0.68 0.14 0.18
Matches are distributed among these distances:
21 3 0.04
22 6 0.08
23 1 0.01
24 6 0.08
25 3 0.04
26 36 0.49
27 6 0.08
28 12 0.16
29 1 0.01
ACGTcount: A:0.50, C:0.01, G:0.05, T:0.45
Consensus pattern (26 bp):
TATATATTATGTAAAATTATAAATTA
Found at i:395852 original size:20 final size:20
Alignment explanation
Indices: 395827--395935 Score: 71
Period size: 20 Copynumber: 5.3 Consensus size: 20
395817 TTTTATAGTT
*
395827 TATATAGTTTAAAAATAAAG
1 TATATAGTTTAAATATAAAG
* * *
395847 TATATAAGTATATATATAAAC
1 TATAT-AGTTTAAATATAAAG
* *
395868 TATA-AATTATATATATAAAG
1 TATATAGTT-TAAATATAAAG
*
395888 TATA-A-TTATAAAGACTAAAG
1 TATATAGTT-TAAATA-TAAAG
*
395908 TATATAAGTATATAATATAAAG
1 TATAT-AGTTTA-AATATAAAG
395930 TATATA
1 TATATA
395936 AGTATATATA
Statistics
Matches: 71, Mismatches: 11, Indels: 13
0.75 0.12 0.14
Matches are distributed among these distances:
19 9 0.13
20 29 0.41
21 16 0.23
22 13 0.18
23 4 0.06
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (20 bp):
TATATAGTTTAAATATAAAG
Found at i:395873 original size:7 final size:6
Alignment explanation
Indices: 395848--396214 Score: 53
Period size: 7 Copynumber: 54.8 Consensus size: 6
395838 AAAATAAAGT
* * * *
395848 ATATAA GTATAT ATATAA ACTATAA ATTATAT ATATAA AGTATAA TTATAA
1 ATATAA ATATAA ATATAA A-TATAA A-TATAA ATATAA A-TATAA ATATAA
* * *
395899 AGACTAA AGTATATA AGTATATA ATATAA AGTATATA AGTATATA TACATAT
1 ATA-TAA A-TATA-A A-TATA-A ATATAA A-TATA-A A-TATA-A -ATATAA
* *
395951 ATATAA ACTATAA CGTA-AA AGTATAT ATATAA ATTATAA AGTATATA
1 ATATAA A-TATAA -ATATAA A-TATAA ATATAA A-TATAA A-TATA-A
* * * * *
395998 TATATAA AGTTTTA GTAGAA CATAT-- ATATAC ATATATA AT-T-A ATATAA
1 -ATATAA A-TATAA ATATAA -ATATAA ATATAA ATATA-A ATATAA ATATAA
* *
396046 A-ATAA GTATATTAT ATATAA AGTACATAA GTATATA ATATAA AGTATATA
1 ATATAA --ATA-TAA ATATAA A-T--ATAA ATATA-A ATATAA A-TATA-A
* * * *
396096 AGTATTAA ATATGAGT ATATAA GTATTGA ATATAA AGTATATA AGTATAT
1 A-TA-TAA ATAT-A-A ATATAA ATA-TAA ATATAA A-TATA-A A-TATAA
* * * * *
396146 ATATAA ACTATAA TATATAT ATATAT ATATAA AGTATAA GTATAT CTATAA
1 ATATAA A-TATAA -ATATAA ATATAA ATATAA A-TATAA ATATAA ATATAA
* *
396197 AGTATAT ATATAT ATATA
1 A-TATAA ATATAA ATATA
396215 TACACTCTAT
Statistics
Matches: 270, Mismatches: 49, Indels: 84
0.67 0.12 0.21
Matches are distributed among these distances:
4 7 0.03
5 5 0.02
6 96 0.36
7 103 0.38
8 49 0.18
9 10 0.04
ACGTcount: A:0.52, C:0.03, G:0.07, T:0.38
Consensus pattern (6 bp):
ATATAA
Found at i:395919 original size:22 final size:21
Alignment explanation
Indices: 395827--396204 Score: 183
Period size: 22 Copynumber: 18.3 Consensus size: 21
395817 TTTTATAGTT
* *
395827 TATAT-AGTTTAAAAATAAAG
1 TATATAAGTATAAATATAAAG
* *
395847 TATATAAGTATATATATAAAC
1 TATATAAGTATAAATATAAAG
* *
395868 TATA-AATTATATATATAAAG
1 TATATAAGTATAAATATAAAG
* *
395888 --TATAATTATAAAGACTAAAG
1 TATATAAGTATAAATA-TAAAG
395908 TATATAAGTATATAATATAAAG
1 TATATAAGTATA-AATATAAAG
* * *
395930 TATATAAGTATATATACATA-
1 TATATAAGTATAAATATAAAG
* *
395950 TATATAAACTATAACGTA-AAAG
1 TATAT-AAGTATAA-ATATAAAG
395972 TATAT-A-TATAAATTATAAAG
1 TATATAAGTATAAA-TATAAAG
**
395992 TATATATA-TATAAAGT-TTTAG
1 TATATA-AGTATAAA-TATAAAG
* *
396013 TAGA-ACA-TAT--ATATACA-
1 TATATA-AGTATAAATATAAAG
* *
396030 TATATAATTAATATAAAAT-AAG
1 TATATAAGT-ATA-AATATAAAG
396052 TATAT---TAT--ATATAAAG
1 TATATAAGTATAAATATAAAG
*
396068 TACATAAGTATATAATATAAAG
1 TATATAAGTATA-AATATAAAG
*
396090 TATATAAGTATTAAATAT-GAG
1 TATATAAGTA-TAAATATAAAG
*
396111 TATATAAGTATTGAATATAAAG
1 TATATAAGTA-TAAATATAAAG
* *
396133 TATATAAGTATATATATAAAC
1 TATATAAGTATAAATATAAAG
*
396154 TATAATATATATATATATATATAAAG
1 TAT-ATA-A-GTATA-A-ATATAAAG
**
396180 --TATAAGTATATCTATAAAG
1 TATATAAGTATAAATATAAAG
396199 TATATA
1 TATATA
396205 TATATATATA
Statistics
Matches: 278, Mismatches: 43, Indels: 73
0.71 0.11 0.19
Matches are distributed among these distances:
15 3 0.01
16 7 0.03
17 5 0.02
18 9 0.03
19 29 0.10
20 44 0.16
21 73 0.26
22 87 0.31
23 9 0.03
24 5 0.02
26 7 0.03
ACGTcount: A:0.52, C:0.03, G:0.08, T:0.37
Consensus pattern (21 bp):
TATATAAGTATAAATATAAAG
Found at i:395997 original size:16 final size:15
Alignment explanation
Indices: 395836--396210 Score: 90
Period size: 15 Copynumber: 25.5 Consensus size: 15
395826 TTATATAGTT
*
395836 TAAAAATAAAGTATA
1 TAAATATAAAGTATA
*
395851 TAAGTAT--A-TATA
1 TAAATATAAAGTATA
395863 TAAACTATAAA-T-TA
1 TAAA-TATAAAGTATA
*
395877 TATATATAAAG--TA
1 TAAATATAAAGTATA
*
395890 TAATTATAAAG-ACTA
1 TAAATATAAAGTA-TA
*
395905 -AAGTATATAAGTATA
1 TAAATATA-AAGTATA
395920 T-AATATAAAGTATA
1 TAAATATAAAGTATA
* * *
395934 TAAGTATATA-TACA
1 TAAATATAAAGTATA
* *
395948 TATATATAAACTATAA
1 TAAATATAAAGTAT-A
*
395964 CGTAAA-AGTATA-TATA
1 --TAAATA-TAAAGTATA
395980 TAAATTATAAAGTATA
1 TAAA-TATAAAGTATA
* *
395996 TATATATAAAGTTTTA
1 TAAATATAAAG-TATA
*
396012 GTAGAACAT--A-TATA
1 -TA-AATATAAAGTATA
* *
396026 TACATATATAATTAATA
1 TAAATATA-AAGT-ATA
396043 TAAA-AT-AAGTATA
1 TAAATATAAAGTATA
* *
396056 TTATATATAAAGTACA
1 -TAAATATAAAGTATA
*
396072 TAAGTATATAA-TATA
1 TAAATATA-AAGTATA
*
396087 -AAGTATATAAGTAT-
1 TAAATATA-AAGTATA
*
396101 TAAATAT-GAGTATA
1 TAAATATAAAGTATA
* *
396115 TAAGTATTGAA-TATA
1 TAAATA-TAAAGTATA
*
396130 -AAGTATATAAGTATA
1 TAAATATA-AAGTATA
*
396145 T--ATATAAACTATAA
1 TAAATATAAAGTAT-A
*
396159 TATATATATATA-TATA
1 TA-A-ATATAAAGTATA
396175 TAAAGTAT-AAGTATA
1 TAAA-TATAAAGTATA
*
396190 T--CTATAAAGTATA
1 TAAATATAAAGTATA
*
396203 TATATATA
1 TAAATATA
396211 TATATACACT
Statistics
Matches: 269, Mismatches: 43, Indels: 96
0.66 0.11 0.24
Matches are distributed among these distances:
12 13 0.05
13 45 0.17
14 72 0.27
15 79 0.29
16 30 0.11
17 15 0.06
18 15 0.06
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.37
Consensus pattern (15 bp):
TAAATATAAAGTATA
Found at i:396096 original size:9 final size:8
Alignment explanation
Indices: 396047--396146 Score: 92
Period size: 8 Copynumber: 13.4 Consensus size: 8
396037 TTAATATAAA
396047 ATAAGTAT
1 ATAAGTAT
*
396055 ATTA-TAT
1 ATAAGTAT
*
396062 ATAAAGTAC
1 AT-AAGTAT
396071 ATAAGTAT
1 ATAAGTAT
396079 ATAA-TAT
1 ATAAGTAT
396086 A-AAGTAT
1 ATAAGTAT
396093 ATAAGTAT
1 ATAAGTAT
396101 -TAA--AT
1 ATAAGTAT
*
396106 ATGAGTAT
1 ATAAGTAT
396114 ATAAGTAT
1 ATAAGTAT
396122 -TGAA-TAT
1 AT-AAGTAT
396129 A-AAGTAT
1 ATAAGTAT
396136 ATAAGTAT
1 ATAAGTAT
396144 ATA
1 ATA
396147 TATAAACTAT
Statistics
Matches: 75, Mismatches: 6, Indels: 22
0.73 0.06 0.21
Matches are distributed among these distances:
5 2 0.03
6 6 0.08
7 24 0.32
8 39 0.52
9 4 0.05
ACGTcount: A:0.51, C:0.01, G:0.11, T:0.37
Consensus pattern (8 bp):
ATAAGTAT
Found at i:396146 original size:2 final size:2
Alignment explanation
Indices: 396141--396267 Score: 77
Period size: 2 Copynumber: 64.0 Consensus size: 2
396131 AGTATATAAG
* *
396141 TA TA TA TA TA AA CTA TA -A TA TA TA TA TA TA TA TA TA AA GTA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * * *
396184 -A GTA TA TC TA TA AA GTA TA TA TA TA TA TA TA TA CA CTC TA T-
1 TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * * *
396225 TC TT TA TA -A T- TA TA -A TC TA TC TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
396264 TA TA
1 TA TA
396268 ACAATAAAGT
Statistics
Matches: 96, Mismatches: 18, Indels: 22
0.71 0.13 0.16
Matches are distributed among these distances:
1 6 0.06
2 86 0.90
3 4 0.04
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.45
Consensus pattern (2 bp):
TA
Found at i:396209 original size:19 final size:19
Alignment explanation
Indices: 395841--396318 Score: 162
Period size: 20 Copynumber: 24.6 Consensus size: 19
395831 TAGTTTAAAA
395841 ATAAAGTATATAAGTATATAT
1 ATAAAGTATAT-A-TATATAT
* *
395862 ATAAACTATAAATTATATAT
1 ATAAAGTATATA-TATATAT
* *
395882 ATAAAGTATA-ATTATAAAG
1 ATAAAGTATATA-TATATAT
395901 ACTAAAGTATATAAGTATATAAT
1 A-TAAAGTATAT-A-TATAT-AT
395924 ATAAAGTATATA-AGTATAT
1 ATAAAGTATATATA-TATAT
* *
395943 ATACA-TATATATAAACTAT
1 ATAAAGTATATATATA-TAT
*
395962 AACGTAAAAGTATATATATAAATT
1 -A--T-AAAGTATATATATATA-T
*
395986 ATAAAGTATATATATATAA
1 ATAAAGTATATATATATAT
** * *
396005 AGTTTTAGTAGA-ACATATAT
1 A--TAAAGTATATATATATAT
*
396025 ATACA-TATATA-AT-TAAT
1 ATAAAGTATATATATAT-AT
*
396042 ATAAAATA-AGTATATTATAT
1 ATAAAGTATA-TATA-TATAT
*
396062 ATAAAGTACATAAGTATATAAT
1 ATAAAGTATAT-A-TATAT-AT
*
396084 ATAAAGTATATA-A-GTAT
1 ATAAAGTATATATATATAT
396101 -TAAA-TATGAGTATATA-AGT
1 ATAAAGTAT-A-TATATATA-T
* *
396120 ATTGAA-TATA-A-A-GTAT
1 A-TAAAGTATATATATATAT
*
396136 AT-AAGTATATATATAAACT
1 ATAAAGTATATATATATA-T
396155 ATAATA-TATATATATATAT
1 ATAA-AGTATATATATATAT
*
396174 ATAAAGTATA-AGTATATCT
1 ATAAAGTATATA-TATATAT
396193 ATAAAGTATATATATATAT
1 ATAAAGTATATATATATAT
* * * *
396212 ATATACACTCTATTCTTTATAATT
1 ATA-A-AGTATA-TATATAT-A-T
** *
396236 ATAATCTATCTATATATAT
1 ATAAAGTATATATATATAT
* *
396255 ATATA-TATATATA-ACA-
1 ATAAAGTATATATATATAT
*
396271 ATAAAGTATGA-GTATAT-T
1 ATAAAGTAT-ATATATATAT
*
396289 AT-AAGTATATATATAAACT
1 ATAAAGTATATATATATA-T
396308 ATAAAGTATAT
1 ATAAAGTATAT
396319 GTTGAGTTAA
Statistics
Matches: 346, Mismatches: 54, Indels: 115
0.67 0.10 0.22
Matches are distributed among these distances:
14 2 0.01
15 8 0.02
16 14 0.04
17 36 0.10
18 32 0.09
19 67 0.19
20 87 0.25
21 40 0.12
22 38 0.11
23 8 0.02
24 14 0.04
ACGTcount: A:0.51, C:0.04, G:0.07, T:0.38
Consensus pattern (19 bp):
ATAAAGTATATATATATAT
Found at i:396297 original size:11 final size:12
Alignment explanation
Indices: 396246--396304 Score: 50
Period size: 12 Copynumber: 4.9 Consensus size: 12
396236 ATAATCTATC
396246 TATATATATATA-
1 TATATATATA-AG
*
396258 TATATATATAAC
1 TATATATATAAG
* * *
396270 AATAAAGTATGAG
1 TATATA-TATAAG
396283 TATAT-TATAAG
1 TATATATATAAG
396294 TATATATATAA
1 TATATATATAA
396305 ACTATAAAGT
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
11 11 0.30
12 19 0.51
13 7 0.19
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.41
Consensus pattern (12 bp):
TATATATATAAG
Found at i:397276 original size:90 final size:92
Alignment explanation
Indices: 397123--397308 Score: 340
Period size: 90 Copynumber: 2.0 Consensus size: 92
397113 GGTACCATTG
397123 GTTATGGTATCGGTACTACTATATATAAGGGTATCGGTACCGTGTAGGGTATTGGTACCCAAATT
1 GTTATGGTATCGGTACTACTATATATAAGGGTATCGGTACCGTGTAGGGTATTGGTACCCAAATT
*
397188 GCATTCGGTGTTC-GGGTA-CGATACT
66 GCATTCGATGTTCGGGGTATCGATACT
397213 GTTATGGTATCGGTACTACTATATATAAGGGTATCGGTACCGTGTAGGGTATTGGTACCCAAATT
1 GTTATGGTATCGGTACTACTATATATAAGGGTATCGGTACCGTGTAGGGTATTGGTACCCAAATT
*
397278 GTATTCGATGTTCGGGGTATCGATACT
66 GCATTCGATGTTCGGGGTATCGATACT
397305 GTTA
1 GTTA
397309 AATGCAGTAT
Statistics
Matches: 92, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
90 76 0.83
91 5 0.05
92 11 0.12
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.34
Consensus pattern (92 bp):
GTTATGGTATCGGTACTACTATATATAAGGGTATCGGTACCGTGTAGGGTATTGGTACCCAAATT
GCATTCGATGTTCGGGGTATCGATACT
Found at i:397733 original size:2 final size:2
Alignment explanation
Indices: 397728--397767 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
397718 ATGTGTGTGC
397728 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
397768 CTACTAAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:399928 original size:21 final size:21
Alignment explanation
Indices: 399902--399975 Score: 55
Period size: 21 Copynumber: 3.5 Consensus size: 21
399892 TTTTACAAGG
399902 GTATCGATACTCGTTGAAGTA
1 GTATCGATACTCGTTGAAGTA
* *
399923 GTATCGGTACT-GTT-AAGAACA
1 GTATCGATACTCGTTGAAG--TA
* * *
399944 ATATTGATAC-CTATTGAAGTA
1 GTATCGATACTC-GTTGAAGTA
399965 GTATCGATACT
1 GTATCGATACT
399976 ATGACTGGGT
Statistics
Matches: 38, Mismatches: 9, Indels: 11
0.66 0.16 0.19
Matches are distributed among these distances:
19 3 0.08
20 3 0.08
21 27 0.71
22 2 0.05
23 3 0.08
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (21 bp):
GTATCGATACTCGTTGAAGTA
Found at i:406226 original size:22 final size:21
Alignment explanation
Indices: 406171--406242 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 21
406161 TTTTCAATAG
*
406171 TATATATATATAAAGT-GTAAT
1 TATATA-ATATAAAGTAGTAAA
*
406192 TATA-AAGACTAAAGTACGTAAA
1 TATATAATA-TAAAGTA-GTAAA
406214 TATATAATATAAAGTA-TATAA
1 TATATAATATAAAGTAGTA-AA
406235 GTATATAA
1 -TATATAA
406243 GTTTTAGTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
19 2 0.05
20 9 0.21
21 6 0.14
22 22 0.52
23 3 0.07
ACGTcount: A:0.53, C:0.03, G:0.10, T:0.35
Consensus pattern (21 bp):
TATATAATATAAAGTAGTAAA
Found at i:406395 original size:20 final size:20
Alignment explanation
Indices: 406372--406422 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
406362 ATGTACATTA
406372 TATAATATATATACATGT-AT
1 TATAATATATATACAT-TCAT
*
406392 TATATTATCATA-ACATTCAT
1 TATAATAT-ATATACATTCAT
406412 TAT-ATATATAT
1 TATAATATATAT
406423 TAGAATTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
18 3 0.12
19 4 0.15
20 16 0.62
21 3 0.12
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.47
Consensus pattern (20 bp):
TATAATATATATACATTCAT
Found at i:406894 original size:14 final size:14
Alignment explanation
Indices: 406877--406919 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
406867 AAACTATAAA
406877 GTATAAGTATATAT
1 GTATAAGTATATAT
*
406891 GTATATGTATATAT
1 GTATAAGTATATAT
*
406905 ATA-AAGTATA-AT
1 GTATAAGTATATAT
406917 GTA
1 GTA
406920 CATTTATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
12 4 0.16
13 6 0.24
14 15 0.60
ACGTcount: A:0.44, C:0.00, G:0.14, T:0.42
Consensus pattern (14 bp):
GTATAAGTATATAT
Found at i:407385 original size:561 final size:564
Alignment explanation
Indices: 406419--407448 Score: 1784
Period size: 561 Copynumber: 1.8 Consensus size: 564
406409 CATTATATAT
**
406419 ATATTAGAATTGTTTTAATTTTTCCACAACTTTTGAAATTAATGCAATTCAATTTATTTTACAAT
1 ATATTAGAATTGTTTTAATTTTTCCACAACTTTTGAAATTAATGCAATTCAATCCATTTTACAAT
* *
406484 TTTTCCTCACATTTTAGAATTTTTTGATTTGATCCTTTTATGTTGTTGTTTATTTTTATTTAAAT
66 TTTTCCTCACATTTTACAATTTTTTGATTTGATCCTTTTA--TTGTTGTTTATTTGTATTTAAAT
* *
406549 TTTAATTTGTAATTTCTCATTTGTTCAATTTAGTCCTTCAAATTATTTTCGTATCTGAAATTAAC
129 TTTAATTTGTAATTTCTCATTTGTTCAATTTAGTCATTCAAATTATATTCGTATCTGAAATTAAC
406614 CCATACTTATTTATATTTTTGTAATTTACTTAAAACAAACCCTATAAAATGTAAATCACATAATA
194 CCATACTTATTTATATTTTTGTAATTTACTTAAAACAAACCCTATAAAATGTAAATCACATAATA
* * * *
406679 AATTTCTTTTCAAATTATGTTCAGCAACTTTTTAATTGTATGCAATTTAGTCCATTTTTATATTA
259 AATTTCTTTTCAAATTATGTTCACCAACTTTTTAAATGTATACAACTTAGTCCATTTTTATATTA
* * *
406744 ATATCATCTTCACATTTTAGAATTAATTCAATTTTATCCCTCATCAATGTGTGTTGCATAATTTA
324 ATATCAGCATCACATTTTAGAATTAATTCAATTTCATCCCTCATCAATGTGTGTTGCATAATTTA
406809 TTCAATTTTTTATTTCCAATTTCATGTTTGTTCAATTTGGCACTTTATATACATATATAAACTAT
389 TTCAATTTTTTATTTCCAATTTCATGTTTGTTCAATTTGGCACTTTATATACATATATAAACTAT
406874 AAAGTATAAGTATATATGTATATGTATATATATAAAGTATAATGTACATTTATATACATGCATCA
454 AAAGTATAAGTATATATGTATATGTATATATATAAAGTATAATGTACATTTATATACATGCATCA
406939 TATTATCATAACATTCATTATACATATTATTCACACACACACACAC
519 TATTATCATAACATTCATTATACATATTATTCACACACACACACAC
* *
406985 ATATTATAATTGTTTTAA-TTTTCCCCAACTTTTGAAATTAATGCAATTCAATCCA-TTTACAAT
1 ATATTAGAATTGTTTTAATTTTTCCACAACTTTTGAAATTAATGCAATTCAATCCATTTTACAAT
*
407048 TTTTCCTCACATTTTACAATTTTTTTGATTTGATCCTTTTA-TGTTGTTTA-TTGTATTTAAGTT
66 TTTTCCTCACATTTTACAA-TTTTTTGATTTGATCCTTTTATTGTTGTTTATTTGTATTTAAATT
* *
407111 TTAATTTGTAATTTCTTATTTGTTCAATTTAGTCATTCAAATTATATTCGTATCTGAAATTGACC
130 TTAATTTGTAATTTCTCATTTGTTCAATTTAGTCATTCAAATTATATTCGTATCTGAAATTAACC
407176 CATACTTATTTATATTTTTGTAATTTACTTAAAAACAAACCCTATAAAATGTAAATCACATAAT-
195 CATACTTATTTATATTTTTGTAATTTACTT-AAAACAAACCCTATAAAATGTAAATCACATAATA
407240 AATTTCTTTTCAAATTATGTTTC-CCAACTTTTTAAATGTATACAACTTAGTCCATTTTTATATT
259 AATTTCTTTTCAAATTATG-TTCACCAACTTTTTAAATGTATACAACTTAGTCCATTTTTATATT
* *
407304 AATATCAGCATCACATTTTATAATTAATTCAATTTCATCCCTCATCAATGTGTGTTGCTTAATTT
323 AATATCAGCATCACATTTTAGAATTAATTCAATTTCATCCCTCATCAATGTGTGTTGCATAATTT
*
407369 ATTCAATTTTTTATTTCCAATTTCATGTTTGTTCAATTTGGTACTTTATATACATATATAAACTA
388 ATTCAATTTTTTATTTCCAATTTCATGTTTGTTCAATTTGGCACTTTATATACATATATAAACTA
407434 TAAAGTATAAGTATA
453 TAAAGTATAAGTATA
407449 CATTCCATAA
Statistics
Matches: 440, Mismatches: 21, Indels: 11
0.93 0.04 0.02
Matches are distributed among these distances:
561 297 0.68
562 45 0.10
564 26 0.06
565 55 0.12
566 17 0.04
ACGTcount: A:0.33, C:0.14, G:0.07, T:0.47
Consensus pattern (564 bp):
ATATTAGAATTGTTTTAATTTTTCCACAACTTTTGAAATTAATGCAATTCAATCCATTTTACAAT
TTTTCCTCACATTTTACAATTTTTTGATTTGATCCTTTTATTGTTGTTTATTTGTATTTAAATTT
TAATTTGTAATTTCTCATTTGTTCAATTTAGTCATTCAAATTATATTCGTATCTGAAATTAACCC
ATACTTATTTATATTTTTGTAATTTACTTAAAACAAACCCTATAAAATGTAAATCACATAATAAA
TTTCTTTTCAAATTATGTTCACCAACTTTTTAAATGTATACAACTTAGTCCATTTTTATATTAAT
ATCAGCATCACATTTTAGAATTAATTCAATTTCATCCCTCATCAATGTGTGTTGCATAATTTATT
CAATTTTTTATTTCCAATTTCATGTTTGTTCAATTTGGCACTTTATATACATATATAAACTATAA
AGTATAAGTATATATGTATATGTATATATATAAAGTATAATGTACATTTATATACATGCATCATA
TTATCATAACATTCATTATACATATTATTCACACACACACACAC
Found at i:407534 original size:20 final size:20
Alignment explanation
Indices: 407509--407564 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
407499 CAATTCATTC
*
407509 CATTTTACAATCTTTCTTCA
1 CATTTTACAATCTTGCTTCA
407529 CATTTTACAATCTTGCTTCA
1 CATTTTACAATCTTGCTTCA
407549 CATTTTACAATCTTGC
1 CATTTTACAATCTTGC
407565 ATTCCATAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.25, C:0.25, G:0.04, T:0.46
Consensus pattern (20 bp):
CATTTTACAATCTTGCTTCA
Found at i:407758 original size:14 final size:13
Alignment explanation
Indices: 407721--407749 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
407711 TGTTTATTGT
407721 ATTTAAATTTA-A
1 ATTTAAATTTATA
407733 ATTTAAATTTATA
1 ATTTAAATTTATA
407746 ATTT
1 ATTT
407750 CATATTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATTTAAATTTATA
Found at i:407962 original size:24 final size:24
Alignment explanation
Indices: 407917--407962 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
407907 TTAGTCCATT
*
407917 TTTTATATTAATATCAGCTTCACA
1 TTTTATATTAATATCAACTTCACA
*
407941 TTTTATAATTAAT-TCAATTTCA
1 TTTTAT-ATTAATATCAACTTCA
407963 TCCCTCATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 13 0.68
25 6 0.32
ACGTcount: A:0.35, C:0.13, G:0.02, T:0.50
Consensus pattern (24 bp):
TTTTATATTAATATCAACTTCACA
Done.