Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A01
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: 115637255
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5450143 characters in sequence are not A, C, G, or T
File 1 of 349
Found at i:8727 original size:22 final size:22
Alignment explanation
Indices: 8702--8750 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 22
8692 ACTTTCGCTC
8702 AATA-ATTAAATTTAGAAT-TAAT
1 AATATATTAAA-TTA-AATATAAT
8724 AATATATTAAATTAAATATAAT
1 AATATATTAAATTAAATATAAT
8746 AATAT
1 AATAT
8751 GATATAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 3 0.12
22 16 0.64
23 6 0.24
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (22 bp):
AATATATTAAATTAAATATAAT
Found at i:13437 original size:36 final size:36
Alignment explanation
Indices: 13397--13470 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
13387 TTTTTAATAC
13397 TTGATCAAAATAGAATCCTTCTTTTGGATGACTGCA
1 TTGATCAAAATAGAATCCTTCTTTTGGATGACTGCA
13433 TTGATCAAAATAGAATCCTTCTTTTGGATGACTGCA
1 TTGATCAAAATAGAATCCTTCTTTTGGATGACTGCA
13469 TT
1 TT
13471 ATTAATTTGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (36 bp):
TTGATCAAAATAGAATCCTTCTTTTGGATGACTGCA
Found at i:16218 original size:33 final size:34
Alignment explanation
Indices: 16176--16241 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 34
16166 GTGGATGATA
16176 ATCGAGATCTTATACTTGATAC-TTGATAGTTTT
1 ATCGAGATCTTATACTTGATACTTTGATAGTTTT
16209 ATCGAGATCTTATACTTGATACTTTGATAGTTT
1 ATCGAGATCTTATACTTGATACTTTGATAGTTT
16242 GTCTTTCTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 22 0.69
34 10 0.31
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.45
Consensus pattern (34 bp):
ATCGAGATCTTATACTTGATACTTTGATAGTTTT
Found at i:24565 original size:44 final size:44
Alignment explanation
Indices: 24515--24604 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 44
24505 TTGCTAGATG
*
24515 CTGAATATTTTCAAATAGCTTATAGACTAAATTACTGTGACATA
1 CTGAATATTTTCAAATAGCTTATAGACTAAATTACAGTGACATA
24559 CTGAATATTTTCAAATAGCTTATAGACTAAATTACAGTGACATA
1 CTGAATATTTTCAAATAGCTTATAGACTAAATTACAGTGACATA
24603 CT
1 CT
24605 TTTATTGATT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (44 bp):
CTGAATATTTTCAAATAGCTTATAGACTAAATTACAGTGACATA
Found at i:40832 original size:18 final size:20
Alignment explanation
Indices: 40809--40856 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
40799 TGAAATTGCA
40809 TAATAAATTAAAATTTA-TG
1 TAATAAATTAAAATTTATTG
* *
40828 T-ATAATTTTAAGATTTATTG
1 TAATAA-ATTAAAATTTATTG
40848 TAATAAATT
1 TAATAAATT
40857 TTTTATTTAC
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
18 4 0.17
19 10 0.43
20 5 0.22
21 4 0.17
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (20 bp):
TAATAAATTAAAATTTATTG
Found at i:41326 original size:11 final size:10
Alignment explanation
Indices: 41301--41338 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
41291 GATGATTTAA
41301 TTTAAAAATT
1 TTTAAAAATT
*
41311 ATTAAATAATT
1 TTTAAA-AATT
41322 TTT-AAAATT
1 TTTAAAAATT
41331 TTTAAAAA
1 TTTAAAAA
41339 ATTTCTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
9 7 0.29
10 11 0.46
11 6 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
TTTAAAAATT
Found at i:41330 original size:20 final size:20
Alignment explanation
Indices: 41305--41342 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
41295 ATTTAATTTA
*
41305 AAAATTATTAAATAATTTTT
1 AAAATTATTAAAAAATTTTT
*
41325 AAAATTTTTAAAAAATTT
1 AAAATTATTAAAAAATTT
41343 CTTTTAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AAAATTATTAAAAAATTTTT
Found at i:46445 original size:15 final size:17
Alignment explanation
Indices: 46419--46475 Score: 57
Period size: 16 Copynumber: 3.5 Consensus size: 17
46409 TAATAAACAC
46419 AATTATTTAAAA-ATTA
1 AATTATTTAAAATATTA
46435 AATTA-TTAAAATATT-
1 AATTATTTAAAATATTA
* * *
46450 AATTGTATAAATTATTA
1 AATTATTTAAAATATTA
*
46467 AACTATTTA
1 AATTATTTA
46476 TATGGTTGGT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
15 10 0.31
16 16 0.50
17 6 0.19
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (17 bp):
AATTATTTAAAATATTA
Found at i:46449 original size:24 final size:25
Alignment explanation
Indices: 46422--46475 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
46412 TAAACACAAT
46422 TATTTAAAAAT-TAAATTATTAAAA
1 TATTTAAAAATATAAATTATTAAAA
*** *
46446 TA-TTAATTGTATAAATTATTAAAC
1 TATTTAAAAATATAAATTATTAAAA
46470 TATTTA
1 TATTTA
46476 TATGGTTGGT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
23 5 0.21
24 16 0.67
25 3 0.12
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (25 bp):
TATTTAAAAATATAAATTATTAAAA
Found at i:49739 original size:30 final size:28
Alignment explanation
Indices: 49713--49775 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
49703 TCATTTTATG
* *
49713 TGTATGATCACACTAAATCAAAATTTTA
1 TGTATAATCACAATAAATCAAAATTTTA
* *
49741 TGTATAATTACAATAAATCAAAATTTCA
1 TGTATAATCACAATAAATCAAAATTTTA
*
49769 TATATAA
1 TGTATAA
49776 AATTATATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.37
Consensus pattern (28 bp):
TGTATAATCACAATAAATCAAAATTTTA
Found at i:55596 original size:42 final size:42
Alignment explanation
Indices: 55537--55622 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
55527 ACAGTTCAAC
55537 CATCTTTTTTTCCAATTTGAAAGCCACATTTGTGGCAACTAA
1 CATCTTTTTTTCCAATTTGAAAGCCACATTTGTGGCAACTAA
55579 CATCTTTTTTTCCAATTTGAAAGCCACATTTGTGGCAACTAA
1 CATCTTTTTTTCCAATTTGAAAGCCACATTTGTGGCAACTAA
55621 CA
1 CA
55623 AGCTCGAAGG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (42 bp):
CATCTTTTTTTCCAATTTGAAAGCCACATTTGTGGCAACTAA
Found at i:57879 original size:26 final size:26
Alignment explanation
Indices: 57849--57900 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
57839 CCCCCAAAGA
57849 AAGGGAAACACTTAAATCTATTGAAG
1 AAGGGAAACACTTAAATCTATTGAAG
57875 AAGGGAAACACTTAAATCTATTGAAG
1 AAGGGAAACACTTAAATCTATTGAAG
57901 GAGAGACAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.46, C:0.12, G:0.19, T:0.23
Consensus pattern (26 bp):
AAGGGAAACACTTAAATCTATTGAAG
Found at i:59784 original size:14 final size:15
Alignment explanation
Indices: 59749--59793 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
59739 ACTCTAACTA
59749 AATTATTAATAAATTT
1 AATT-TTAATAAATTT
59765 ATATTTTAAT-AATTT
1 A-ATTTTAATAAATTT
*
59780 AATTTTAAAAAATT
1 AATTTTAATAAATT
59794 ATAAAATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 7 0.27
15 10 0.38
16 6 0.23
17 3 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
AATTTTAATAAATTT
Found at i:61119 original size:13 final size:14
Alignment explanation
Indices: 61101--61154 Score: 58
Period size: 13 Copynumber: 3.8 Consensus size: 14
61091 AGAGTAGTAT
61101 AAAGAT-AATCATG
1 AAAGATCAATCATG
*
61114 AAAGATCAATCTAGTAT
1 AAAGATCAATC-A-T-G
61131 AAAGAT-AATCATG
1 AAAGATCAATCATG
61144 AAAGATCAATC
1 AAAGATCAATC
61155 TAGTTACTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
13 12 0.35
14 9 0.26
15 2 0.06
16 5 0.15
17 6 0.18
ACGTcount: A:0.52, C:0.11, G:0.13, T:0.24
Consensus pattern (14 bp):
AAAGATCAATCATG
Found at i:61172 original size:30 final size:30
Alignment explanation
Indices: 61095--61158 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
61085 ATAGTAAGAG
61095 TAGTATAAAGATAATCATGAAAGATCAATC
1 TAGTATAAAGATAATCATGAAAGATCAATC
61125 TAGTATAAAGATAATCATGAAAGATCAATC
1 TAGTATAAAGATAATCATGAAAGATCAATC
61155 TAGT
1 TAGT
61159 TACTAACTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.48, C:0.09, G:0.14, T:0.28
Consensus pattern (30 bp):
TAGTATAAAGATAATCATGAAAGATCAATC
Found at i:61635 original size:63 final size:62
Alignment explanation
Indices: 61542--61663 Score: 167
Period size: 63 Copynumber: 2.0 Consensus size: 62
61532 AAAAAATTGC
* *
61542 CATGAATAAATCAATATGTAAATCCCACTTCGAC-CTGACTTCCAAAAATTATCTTAAAATCGG
1 CATGAAGAAATCAATATGTAAATCCCACTTCGACAC-AACTTCC-AAAATTATCTTAAAATCGG
* *
61605 CATGAAGAAATCAATACT-TAAATCCGACTTCGACACAACTTTCAAAATTATCTTAAAAT
1 CATGAAGAAATCAATA-TGTAAATCCCACTTCGACACAACTTCCAAAATTATCTTAAAAT
61664 TTGTTGACTG
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
62 16 0.30
63 35 0.66
64 2 0.04
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (62 bp):
CATGAAGAAATCAATATGTAAATCCCACTTCGACACAACTTCCAAAATTATCTTAAAATCGG
Found at i:79899 original size:60 final size:60
Alignment explanation
Indices: 79833--79952 Score: 240
Period size: 60 Copynumber: 2.0 Consensus size: 60
79823 ATCTCTTAAT
79833 TTTTTATTTGATTGAATAGGTCATCTTATTTGTTTGCTTCTGTATACTATTGTGATAAGA
1 TTTTTATTTGATTGAATAGGTCATCTTATTTGTTTGCTTCTGTATACTATTGTGATAAGA
79893 TTTTTATTTGATTGAATAGGTCATCTTATTTGTTTGCTTCTGTATACTATTGTGATAAGA
1 TTTTTATTTGATTGAATAGGTCATCTTATTTGTTTGCTTCTGTATACTATTGTGATAAGA
79953 GCACAACTTA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.23, C:0.08, G:0.17, T:0.52
Consensus pattern (60 bp):
TTTTTATTTGATTGAATAGGTCATCTTATTTGTTTGCTTCTGTATACTATTGTGATAAGA
Found at i:85078 original size:31 final size:31
Alignment explanation
Indices: 85043--85106 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
85033 TTATAAAATG
*
85043 GTTATTAAACTATTCGAAAATTTTCATTTAA
1 GTTATCAAACTATTCGAAAATTTTCATTTAA
* *
85074 GTTATCAAACTATTCGAAAGTTTTTATTTAA
1 GTTATCAAACTATTCGAAAATTTTCATTTAA
85105 GT
1 GT
85107 CATTGGGTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.45
Consensus pattern (31 bp):
GTTATCAAACTATTCGAAAATTTTCATTTAA
Found at i:87194 original size:16 final size:17
Alignment explanation
Indices: 87170--87207 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
87160 AGTACAAATA
* *
87170 ATTTAAATATTT-CTTT
1 ATTTGAATATTTGATTT
87186 ATTTGAATATTTGATTT
1 ATTTGAATATTTGATTT
87203 ATTTG
1 ATTTG
87208 TTTTAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.29, C:0.03, G:0.08, T:0.61
Consensus pattern (17 bp):
ATTTGAATATTTGATTT
Found at i:92634 original size:17 final size:17
Alignment explanation
Indices: 92614--92650 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
92604 AAATAGATTT
92614 TTAATTAAAAATTTTAA
1 TTAATTAAAAATTTTAA
**
92631 TTAATTAAACTTTTTAA
1 TTAATTAAAAATTTTAA
92648 TTA
1 TTA
92651 TTCTTTCTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (17 bp):
TTAATTAAAAATTTTAA
Found at i:95877 original size:13 final size:13
Alignment explanation
Indices: 95859--95889 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
95849 GGCACCCTGC
95859 AAAATAATTTTTA
1 AAAATAATTTTTA
95872 AAAAT-ATTTTTA
1 AAAATAATTTTTA
95884 AAAATA
1 AAAATA
95890 GAAAAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
AAAATAATTTTTA
Found at i:98001 original size:23 final size:23
Alignment explanation
Indices: 97957--98000 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
97947 TTTTATATTA
97957 ATTTTAAATATATATCTTAAAAT
1 ATTTTAAATATATATCTTAAAAT
* *
97980 ATTTTAATTATA-ATTTTAAAA
1 ATTTTAAATATATATCTTAAAA
98001 AAATTATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
ATTTTAAATATATATCTTAAAAT
Found at i:102463 original size:15 final size:12
Alignment explanation
Indices: 102429--102454 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
102419 TGATTAACCG
102429 AAAAAAATTAAT
1 AAAAAAATTAAT
102441 AAAAAAATTAAT
1 AAAAAAATTAAT
102453 AA
1 AA
102455 TATATAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAAAAATTAAT
Found at i:102548 original size:18 final size:18
Alignment explanation
Indices: 102525--102562 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
102515 GATATATATT
102525 AACCCAAGTACCCAACCC
1 AACCCAAGTACCCAACCC
*
102543 AACCCAATTACCCAACCC
1 AACCCAAGTACCCAACCC
102561 AA
1 AA
102563 TTATAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.42, C:0.47, G:0.03, T:0.08
Consensus pattern (18 bp):
AACCCAAGTACCCAACCC
Found at i:102555 original size:13 final size:13
Alignment explanation
Indices: 102539--102565 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
102529 CAAGTACCCA
102539 ACCCAACCCAATT
1 ACCCAACCCAATT
102552 ACCCAACCCAATT
1 ACCCAACCCAATT
102565 A
1 A
102566 TAAAAATTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.44, G:0.00, T:0.15
Consensus pattern (13 bp):
ACCCAACCCAATT
Found at i:102630 original size:20 final size:20
Alignment explanation
Indices: 102591--102628 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
102581 ATTTAATAAA
102591 TAAAAATAAAAATCTAAAAC
1 TAAAAATAAAAATCTAAAAC
102611 TAAAAATAAAAAT-TAAAA
1 TAAAAATAAAAATCTAAAA
102629 ACATATAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (20 bp):
TAAAAATAAAAATCTAAAAC
Found at i:102683 original size:9 final size:9
Alignment explanation
Indices: 102648--102697 Score: 66
Period size: 9 Copynumber: 5.6 Consensus size: 9
102638 TTTATACAAA
*
102648 TAATTTGGT
1 TAATTCGGT
102657 TAATTCAGG-
1 TAATTC-GGT
*
102666 TAGTTCGGT
1 TAATTCGGT
102675 TAATTCGGT
1 TAATTCGGT
102684 TAATTCGGT
1 TAATTCGGT
102693 TAATT
1 TAATT
102698 TTATACTTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
8 2 0.06
9 32 0.89
10 2 0.06
ACGTcount: A:0.24, C:0.08, G:0.22, T:0.46
Consensus pattern (9 bp):
TAATTCGGT
Found at i:103120 original size:31 final size:31
Alignment explanation
Indices: 103085--103146 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
103075 CAATTTTTAT
103085 TAAGCTTTTTCATGTATTTTGAACATCTTTG
1 TAAGCTTTTTCATGTATTTTGAACATCTTTG
103116 TAAGCTTTTTCATGTATTTTGAACATCTTTG
1 TAAGCTTTTTCATGTATTTTGAACATCTTTG
103147 AATAATCATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.13, G:0.13, T:0.52
Consensus pattern (31 bp):
TAAGCTTTTTCATGTATTTTGAACATCTTTG
Found at i:105347 original size:172 final size:171
Alignment explanation
Indices: 105044--105353 Score: 489
Period size: 172 Copynumber: 1.8 Consensus size: 171
105034 TAATGTCATC
* * *
105044 AACAATACATGACATAAAATCAAATAATTCTTGTACTGAAATAAATACTAAATCTTAAAACATCC
1 AACAATACATGACATAAAATCAAAGAATTCTTGTACTGAAATAAAGACTAAATCTTAAAACAACC
*
105109 AACCATCTTTCGATTTCCCAATCTGTGAAACTAAAGAACTATGGAACTCAAACCCAAGATAACTG
66 AACCATCTTTCGATTTCCCAATCTGTGAAACTAAAGAAATATGGAACTCAAACCCAAGATAACTG
105174 CAGACATGGAGGAGAAACATGAACACAACATGTATGCCACT
131 CAGACATGGAGGAGAAACATGAACACAACATGTATGCCACT
* * * *
105215 AACAATACATGACAATACAATCAAAGAATGTC-TGTACTGAAATAAAGACTAAATCTTCAGATAA
1 AACAATACATGAC-ATAAAATCAAAGAAT-TCTTGTACTGAAATAAAGACTAAATCTTAAAACAA
* *
105279 CCAACCGTCTTTCGATTATCCCAATTTGTGAAACTAAAGAAATATGGAACTCAAACCC-AGATAA
64 CCAACCATCTTTCGATT-TCCCAATCTGTGAAACTAAAGAAATATGGAACTCAAACCCAAGATAA
105343 CTGCAGACATG
128 CTGCAGACATG
105354 TCATAGAAAC
Statistics
Matches: 126, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
171 13 0.10
172 73 0.58
173 40 0.32
ACGTcount: A:0.44, C:0.21, G:0.12, T:0.24
Consensus pattern (171 bp):
AACAATACATGACATAAAATCAAAGAATTCTTGTACTGAAATAAAGACTAAATCTTAAAACAACC
AACCATCTTTCGATTTCCCAATCTGTGAAACTAAAGAAATATGGAACTCAAACCCAAGATAACTG
CAGACATGGAGGAGAAACATGAACACAACATGTATGCCACT
Found at i:105569 original size:148 final size:147
Alignment explanation
Indices: 105226--105646 Score: 528
Period size: 148 Copynumber: 2.9 Consensus size: 147
105216 ACAATACATG
* * *
105226 ACAATACAATCAAAGAATGTCTGTACTGAAATAAAGACTAAATCTTCAGATAACCAACCGTCTTT
1 ACAATACAATCAAAGAATGTCTGTACTGAAATGAAGACTGAATCTTCACATAACCAACCGTCTTT
* * *
105291 C-GATTATCCCAATTTGTGAAACTAAAGAAATATGGAACTCAAACCCAGATAACTGCAGACATGT
66 CAG-TTATCCCAATCTGTGAAACTAAAGAAATATGGAACTCAAACCCAGATAACTACAGACATGA
*
105355 CATAGAAACACGCCACCA
130 CATACAAACACGCCACCA
* * * *
105373 ACAACACAATCAAAGAATATCTGTACTGAAATGAAGACTGTATCTTCACATAACCAACCATCTTT
1 ACAATACAATCAAAGAATGTCTGTACTGAAATGAAGACTGAATCTTCACATAACCAACCGTCTTT
* * * *
105438 CAGTTATCTCAATCTGTGAAACTAAAGAAATATGGAACCCAAACCCATATCATAGTAACACGA-A
66 CAGTTATCCCAATCTGTGAAACTAAAGAAATATGGAACTCAAACCCAGAT-A-ACT-ACA-GACA
* * *
105502 T-ACA-ACATATATGCCACCA
127 TGACATACAAACACGCCACCA
* **
105521 ACAATACAATCAAAGAATGTCTGTACTGAAATGAAGACTGCATCTTCACATAACCGCCCGTCTCT
1 ACAATACAATCAAAGAATGTCTGTACTGAAATGAAGACTGAATCTTCACATAACCAACCGTCT-T
* * * *
105586 TGA-TTATCCCAATCAGTGAAACTAAAGAAATATGGAACTCTAACCCAGATAACTGCAGACA
65 TCAGTTATCCCAATCTGTGAAACTAAAGAAATATGGAACTCAAACCCAGATAACTACAGACA
105647 ACTGAGACAA
Statistics
Matches: 235, Mismatches: 32, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
144 2 0.01
145 3 0.01
146 2 0.01
147 103 0.44
148 112 0.48
149 7 0.03
150 4 0.02
151 2 0.01
ACGTcount: A:0.41, C:0.23, G:0.12, T:0.23
Consensus pattern (147 bp):
ACAATACAATCAAAGAATGTCTGTACTGAAATGAAGACTGAATCTTCACATAACCAACCGTCTTT
CAGTTATCCCAATCTGTGAAACTAAAGAAATATGGAACTCAAACCCAGATAACTACAGACATGAC
ATACAAACACGCCACCA
Found at i:106111 original size:173 final size:171
Alignment explanation
Indices: 105685--106190 Score: 464
Period size: 164 Copynumber: 3.0 Consensus size: 171
105675 CACATGAACA
* ** * * ** * *
105685 ATGCCACCAACAATACATGACAATAAAACCAAAGAATGCCCATACTGCAATAAAGACTAAATGT-
1 ATGCCACCAACAAAACACAACAACAAAATCAAAGAAAACCTATACTACAATAAAGACTAAAT-TC
* * * * * *
105749 TCACACATCCATCTG-ACTTTCAATCAGTCAAACTAAAATACTACAGAACACAAACCCGAGACAA
65 CCATATATACAAC-GAACTTTCAATCAGTC-AACTAAAGTACTACAGAACACAAACCCGAGACAA
* * *
105813 CCAGCGACTTGTCAGAGGAACATG--A--ACACA-A---CATAT
128 CCACCGACTTGTCGGAGGAACATGACATGACATATATGCCATAT
* * * *
105849 ATGCCACCAACAATACACGACAATAAAATCAAAGAAAACCTATACTACAATAAAGACTAAATTTC
1 ATGCCACCAACAAAACACAACAACAAAATCAAAGAAAACCTATACTACAATAAAGACTAAATTCC
* *
105914 CATATATACAACGAACTTTCAATCAATCAAGCTAAAGTACTACGGAACACAAACCCGAGACAACC
66 CATATATACAACGAACTTTCAATCAGTCAA-CTAAAGTACTACAGAACACAAACCCGAGACAACC
*
105979 ACCAACTTGTCGGAGGAACATAGACATGACATATATGCCATAT
130 ACCGACTTGTCGGAGGAACAT-GACATGACATATATGCCATAT
* * * ** * *
106022 ATGCCACTAACAAAACATAACAACACAATCAAAGAATGCCTGT-GTAACAATAAAGACTAAATCT
1 ATGCCACCAACAAAACACAACAACAAAATCAAAGAAAACCTATACT-ACAATAAAGACTAAAT-T
* * * * *
106086 CCGCATATCTA-AAC-AACTTTCAATCAGTCAAATAAAGTCCTACAAAACACAAACCCAAGACAA
64 CC-CATATATACAACGAACTTTCAATCAGTCAACTAAAGTACTACAGAACACAAACCCGAGACAA
* * *
106149 CCACCGAC-TGTTTGGAGGAATATGAACATGACATATGTGCCA
128 CCACCGACTTG-TCGGAGGAACATG-ACATGACATATATGCCA
106191 CTAACAATAC
Statistics
Matches: 285, Mismatches: 40, Indels: 26
0.81 0.11 0.07
Matches are distributed among these distances:
163 4 0.01
164 127 0.45
165 1 0.00
167 1 0.00
169 4 0.01
170 1 0.00
171 3 0.01
172 61 0.21
173 71 0.25
174 5 0.02
175 7 0.02
ACGTcount: A:0.45, C:0.25, G:0.11, T:0.19
Consensus pattern (171 bp):
ATGCCACCAACAAAACACAACAACAAAATCAAAGAAAACCTATACTACAATAAAGACTAAATTCC
CATATATACAACGAACTTTCAATCAGTCAACTAAAGTACTACAGAACACAAACCCGAGACAACCA
CCGACTTGTCGGAGGAACATGACATGACATATATGCCATAT
Found at i:106535 original size:20 final size:19
Alignment explanation
Indices: 106510--106552 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
106500 TCCAAAGTTT
*
106510 AACCAAAATAAATAAAAAAA
1 AACCAAAA-AAACAAAAAAA
*
106530 AACCAAAAAACCAAAAAAA
1 AACCAAAAAAACAAAAAAA
106549 AACC
1 AACC
106553 TCAGATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.77, C:0.19, G:0.00, T:0.05
Consensus pattern (19 bp):
AACCAAAAAAACAAAAAAA
Found at i:114315 original size:31 final size:31
Alignment explanation
Indices: 114266--114325 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
114256 GCTATCATAT
**
114266 AATTAAATAAATGTTTTTAAAAATTAATTAA
1 AATTAAATAAATAATTTTAAAAATTAATTAA
* **
114297 AATTAAATACATAATTTTATTAATTAATT
1 AATTAAATAAATAATTTTAAAAATTAATT
114326 TCTATATTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (31 bp):
AATTAAATAAATAATTTTAAAAATTAATTAA
Found at i:115398 original size:4 final size:4
Alignment explanation
Indices: 115389--115428 Score: 71
Period size: 4 Copynumber: 10.0 Consensus size: 4
115379 AATACACCAG
*
115389 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAA GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
115429 CAAGGCGAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.47
Consensus pattern (4 bp):
GTAT
Found at i:121529 original size:46 final size:47
Alignment explanation
Indices: 121479--121604 Score: 195
Period size: 46 Copynumber: 2.7 Consensus size: 47
121469 TGCCATACTG
* * * *
121479 TCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTTCATATCAGGTTGCCATGGTA
121525 TCTTTCAACCATGGTCTTACACA-TTTCATATCAGGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTTCATATCAGGTTGCCATGGTA
121571 TCTTTCAACCATGGTCTTACACA-TTTCATATCAG
1 TCTTTCAACCATGGTCTTACACATTTTCATATCAG
121605 AGAGCACACT
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
45 4 0.05
46 71 0.95
ACGTcount: A:0.22, C:0.24, G:0.13, T:0.40
Consensus pattern (47 bp):
TCTTTCAACCATGGTCTTACACATTTTCATATCAGGTTGCCATGGTA
Found at i:129586 original size:24 final size:25
Alignment explanation
Indices: 129536--129586 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
129526 TAAATCAATT
* *
129536 TTTTAAATATATTTTATTTTTTGAA
1 TTTTAAATATATTTTATTTATTAAA
129561 TTTTAAATA-A-TTTATTTAATTAAA
1 TTTTAAATATATTTTATTT-ATTAAA
129585 TT
1 TT
129587 GAACTAGTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 7 0.30
24 7 0.30
25 9 0.39
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (25 bp):
TTTTAAATATATTTTATTTATTAAA
Found at i:133319 original size:191 final size:191
Alignment explanation
Indices: 132938--133450 Score: 568
Period size: 191 Copynumber: 2.6 Consensus size: 191
132928 ATAAATGAAT
* * * **
132938 ATGAATATATCGATTAACAGTTCATAAAT-AGTCTGGTTTCTATTTGTTTTATGTTTGTTTATCA
1 ATGAATATATCGATAAACAGTTCATAAATCATTCTGG-TTCT-GTTCATTTATG-TTGTTTATCA
* * *
133002 AGCTAAATAAATGAACATGAACAAGATTTTGAGGCTAATTTCTT-AACTGAACCGAACAGGAACC
63 AGCTAAATAAATGAACATGAACAATATTTTGAGGCTCATTTATTAAACTGAA-C---C--GAA-C
* *
133066 TAACAAGAACAAGTTTAAAAATAAACCAATATGAACAAAGATTCCTTTGTCCAACCTCGGTTCAT
121 --ACAAGAACAAGTTTAAAAATAAACCAACATGAACAAAGATTCCTTAGTCCAACCTCGGTTCAT
133131 TCACAGCC
184 TCACAGCC
* * *
133139 GTGAATATATTGATAAACAGTTCATAAATCATTCTGGTCCTGTTCATTTATGTTCGTTTATCAA-
1 ATGAATATATCGATAAACAGTTCATAAATCATTCTGGTTCTGTTCATTTATGTT-GTTTATCAAG
* *
133203 CTAAATAAATGAATATGAACAATATTTTGAAGCTCCATTTATTAAACTGAACCGAACAC-AGAAC
65 CTAAATAAATGAACATGAACAATATTTTGAGGCT-CATTTATTAAACTGAACCGAACACAAGAAC
* * ** * * *
133267 AAGTTTAAAAATAAACTAACATGACCAGTGATTCCTTAGTTCAAGCTCGGTTCATTTACAGCC
129 AAGTTTAAAAATAAACCAACATGAACAAAGATTCCTTAGTCCAACCTCGGTTCATTCACAGCC
* * * * * * * **
133330 ATGAATATATCCATGAATAGTTCATAAATCGTCCTGTTTCAGTTTGTTTA-GCTTGTTTATCAAG
1 ATGAATATATCGATAAACAGTTCATAAATCATTCTGGTTCTGTTCATTTATG-TTGTTTATCAAG
*
133394 CTAAATAAATGAACATGAACAATATTTTGAGGCTCATTTATTAAACTGAATCGAACA
65 CTAAATAAATGAACATGAACAATATTTTGAGGCTCATTTATTAAACTGAACCGAACA
133451 TATGCAGTGA
Statistics
Matches: 269, Mismatches: 37, Indels: 23
0.82 0.11 0.07
Matches are distributed among these distances:
190 32 0.12
191 131 0.49
192 2 0.01
194 1 0.00
195 3 0.01
197 1 0.00
199 33 0.12
200 24 0.09
201 36 0.13
202 6 0.02
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (191 bp):
ATGAATATATCGATAAACAGTTCATAAATCATTCTGGTTCTGTTCATTTATGTTGTTTATCAAGC
TAAATAAATGAACATGAACAATATTTTGAGGCTCATTTATTAAACTGAACCGAACACAAGAACAA
GTTTAAAAATAAACCAACATGAACAAAGATTCCTTAGTCCAACCTCGGTTCATTCACAGCC
Found at i:135828 original size:20 final size:18
Alignment explanation
Indices: 135803--135841 Score: 60
Period size: 20 Copynumber: 2.1 Consensus size: 18
135793 ATTTTGTATT
135803 AAATATTTATATTATATTTA
1 AAATATTT-TATT-TATTTA
135823 AAATATTTTATTTATTTA
1 AAATATTTTATTTATTTA
135841 A
1 A
135842 TGTGACAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.37
19 4 0.21
20 8 0.42
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AAATATTTTATTTATTTA
Found at i:138935 original size:18 final size:20
Alignment explanation
Indices: 138912--138951 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
138902 CAATAAATTT
138912 TAAAAAATT-AT-AAAAAAA
1 TAAAAAATTCATGAAAAAAA
*
138930 TAAAAATTTCATGAAAAAAA
1 TAAAAAATTCATGAAAAAAA
138950 TA
1 TA
138952 GGAATATGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 2 0.11
20 9 0.47
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.25
Consensus pattern (20 bp):
TAAAAAATTCATGAAAAAAA
Found at i:140791 original size:197 final size:194
Alignment explanation
Indices: 140335--140796 Score: 507
Period size: 197 Copynumber: 2.4 Consensus size: 194
140325 AAATTATAAA
**
140335 TCCCAAAGATGAAAAAAAA-TCAGTTTAATACTTTTAAAATTCTAAAATAA-ATA-C-ATAAAA-
1 TCCCAAAGAT-AAAAAAAATTCAGTTTAAT-CCCTTAAAATTCTAAAATAACA-AGCTATAAAAG
** * *
140395 ATAAAATTGTACTTTTGACCCCTTTAAATTTTCATAATATACTTTTGGCCCCTCAAAAGGCAAAT
63 ATAAAATTACACTTTTGACCCCATTAAATTTTCATAATATACTTTTAGCCCCTCAAAAGGCAAAT
* *
140460 TATCAATTTAGTCCCTTGAAGTTTTTAATATTAAATTTTAATTTAATAGTAAAAATACACTTTGA
128 TATCAATTTAGTCCCTTGAAGTTTTTAAAATTAAATGTTAATTTAATAGTAAAAATACACTTTGA
140525 CC
193 CC
* * * * *
140527 TCCATAAAGAT-GAAAAATTTCAGTTTAATTCCCTTAAAATTCGAAAATAACAAGCTTAAACAAA
1 TCC-CAAAGATAAAAAAAATTCAGTTTAA-TCCCTTAAAATTCTAAAATAACAAGC-TATA-AAA
* * *
140591 GATAAAATTACACTTATTGA-CCCATTAAAGTTTT-ATAATTTATTTTTAG-CCC-CAAAAGAGG
62 GATAAAATTACACTT-TTGACCCCATTAAA-TTTTCATAATATACTTTTAGCCCCTCAAAAG-GC
* * *
140652 AAATTATCATTTTAGTCCCTTTAAGTTTTTAAAATTATAA-GTTAATTTAAATGGTAAAAATACA
124 AAATTATCAATTTAGTCCCTTGAAGTTTTTAAAATTA-AATGTTAATTT-AATAGTAAAAATACA
*
140716 CTTT-AGCAT
187 CTTTGA-C-C
*
140725 TCCCAAAGATAAAAAAAATTCAGTTTAACCCCTTAAAAATTCTAAAATAACAAGCATATAAAAGA
1 TCCCAAAGATAAAAAAAATTCAGTTTAATCCCTT-AAAATTCTAAAATAACAAGC-TATAAAAGA
140790 TAAAATT
64 TAAAATT
140797 GTATTTTGAC
Statistics
Matches: 225, Mismatches: 27, Indels: 31
0.80 0.10 0.11
Matches are distributed among these distances:
191 5 0.02
192 30 0.13
193 9 0.04
195 8 0.04
196 49 0.22
197 76 0.34
198 48 0.21
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.34
Consensus pattern (194 bp):
TCCCAAAGATAAAAAAAATTCAGTTTAATCCCTTAAAATTCTAAAATAACAAGCTATAAAAGATA
AAATTACACTTTTGACCCCATTAAATTTTCATAATATACTTTTAGCCCCTCAAAAGGCAAATTAT
CAATTTAGTCCCTTGAAGTTTTTAAAATTAAATGTTAATTTAATAGTAAAAATACACTTTGACC
Found at i:145851 original size:19 final size:20
Alignment explanation
Indices: 145804--145854 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
145794 TTTGTGATTA
*
145804 AAAAAATTTAAATTTTTTTT
1 AAAAAATTTAAATTTATTTT
* * *
145824 GAAAGATTT-TATTTATTTT
1 AAAAAATTTAAATTTATTTT
145843 AAAAAATTTAAA
1 AAAAAATTTAAA
145855 GAAAACAATA
Statistics
Matches: 23, Mismatches: 7, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (20 bp):
AAAAAATTTAAATTTATTTT
Found at i:148323 original size:22 final size:21
Alignment explanation
Indices: 148287--148353 Score: 72
Period size: 22 Copynumber: 3.4 Consensus size: 21
148277 CGTTGATGTT
148287 ATTTTAATTTAATATTTAATA
1 ATTTTAATTTAATATTTAATA
* *
148308 ATTTTATATTTTATATTTATTA
1 ATTTTA-ATTTAATATTTAATA
148330 ATTTT--TTT-ATA--TAATA
1 ATTTTAATTTAATATTTAATA
148346 ATTTTAAT
1 ATTTTAAT
148354 ATATTTTAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
16 9 0.22
18 4 0.10
19 3 0.08
21 6 0.15
22 18 0.45
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
ATTTTAATTTAATATTTAATA
Found at i:148363 original size:16 final size:16
Alignment explanation
Indices: 148294--148363 Score: 56
Period size: 16 Copynumber: 4.4 Consensus size: 16
148284 GTTATTTTAA
148294 TTTAATATTTAATA-AT
1 TTTAAT-TTTAATATAT
148310 TTTATATTTT-ATAT-T
1 TTTA-ATTTTAATATAT
**
148325 TATTAATTTTTTTATAT
1 T-TTAATTTTAATATAT
**
148342 AATAATTTTAATATAT
1 TTTAATTTTAATATAT
148358 TTTAAT
1 TTTAAT
148364 ACTTATTTAT
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
15 10 0.24
16 29 0.69
17 3 0.07
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTAATTTTAATATAT
Found at i:152167 original size:35 final size:36
Alignment explanation
Indices: 152096--152167 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
152086 CGTCAAGTCT
*
152096 AATAGATTTTATCCATAATATTTGAGTGTTGGATAA
1 AATAGATTTTATCCATAAGATTTGAGTGTTGGATAA
* *
152132 AATAGATTTTATCCGTAAGA-TTGAGTGTTGTATAA
1 AATAGATTTTATCCATAAGATTTGAGTGTTGGATAA
152167 A
1 A
152168 GATCGTGAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 15 0.45
36 18 0.55
ACGTcount: A:0.36, C:0.06, G:0.18, T:0.40
Consensus pattern (36 bp):
AATAGATTTTATCCATAAGATTTGAGTGTTGGATAA
Found at i:153226 original size:30 final size:30
Alignment explanation
Indices: 153192--153253 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
153182 CATCAACTAA
153192 AAAAATATAAATCATTTTATAAAAAAGTTC
1 AAAAATATAAATCATTTTATAAAAAAGTTC
153222 AAAAATATAAATCATTTTATAAAAAAGTTC
1 AAAAATATAAATCATTTTATAAAAAAGTTC
153252 AA
1 AA
153254 GTGATGAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.32
Consensus pattern (30 bp):
AAAAATATAAATCATTTTATAAAAAAGTTC
Found at i:172698 original size:58 final size:59
Alignment explanation
Indices: 172589--172704 Score: 164
Period size: 58 Copynumber: 2.0 Consensus size: 59
172579 CAAAATTGAG
* * * *
172589 TAGTTGAGTGATCATTTTGTAACTTTTCATAATTAGATTATCAAAAAAAATT-TACTAA
1 TAGTTAAGTGATCATTTTATAACTTTTCATAATTAGATCAGCAAAAAAAATTATACTAA
*
172647 TAGTTAAGTGATCATTTTATAACTTTTCATAATTAGA-CGGCAAAAAGAAATTATACTA
1 TAGTTAAGTGATCATTTTATAACTTTTCATAATTAGATCAGCAAAAA-AAATTATACTA
172705 GATTAAGGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
57 6 0.12
58 40 0.78
59 5 0.10
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (59 bp):
TAGTTAAGTGATCATTTTATAACTTTTCATAATTAGATCAGCAAAAAAAATTATACTAA
Found at i:176649 original size:18 final size:18
Alignment explanation
Indices: 176628--176669 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
176618 AACCTTAAGG
176628 TCTGTTTGAACTTTAAAT
1 TCTGTTTGAACTTTAAAT
176646 TCTGTTTGAACTTTAAAT
1 TCTGTTTGAACTTTAAAT
*
176664 TATGTT
1 TCTGTT
176670 ACTTGTTGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.26, C:0.10, G:0.12, T:0.52
Consensus pattern (18 bp):
TCTGTTTGAACTTTAAAT
Found at i:181267 original size:12 final size:12
Alignment explanation
Indices: 181250--181276 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
181240 TTTGAATGAG
181250 TTTTAATTGAAT
1 TTTTAATTGAAT
181262 TTTTAATTGAAT
1 TTTTAATTGAAT
181274 TTT
1 TTT
181277 AACATAAAAT
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:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (12 bp):
TTTTAATTGAAT
Found at i:181276 original size:11 final size:11
Alignment explanation
Indices: 181237--181278 Score: 50
Period size: 12 Copynumber: 3.8 Consensus size: 11
181227 TTGAACAAAC
*
181237 GAATTTGAA-T
1 GAATTTTAATT
*
181247 GAGTTTTAATT
1 GAATTTTAATT
181258 GAATTTTTAATT
1 GAA-TTTTAATT
181270 GAATTTTAA
1 GAATTTTAA
181279 CATAAAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 7 0.26
11 9 0.33
12 11 0.41
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (11 bp):
GAATTTTAATT
Found at i:191494 original size:12 final size:12
Alignment explanation
Indices: 191477--191503 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
191467 AATGTTATTA
191477 TTTCATACAAAC
1 TTTCATACAAAC
191489 TTTCATACAAAC
1 TTTCATACAAAC
191501 TTT
1 TTT
191504 TTTTCGTGAT
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:0.22, G:0.00, T:0.41
Consensus pattern (12 bp):
TTTCATACAAAC
Found at i:207950 original size:19 final size:19
Alignment explanation
Indices: 207926--207966 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
207916 AACATAATAT
207926 TTTATCATGGGTCAAGAGA
1 TTTATCATGGGTCAAGAGA
207945 TTTATCATGGGTCAAGAGA
1 TTTATCATGGGTCAAGAGA
207964 TTT
1 TTT
207967 TTGAAATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.29, C:0.10, G:0.24, T:0.37
Consensus pattern (19 bp):
TTTATCATGGGTCAAGAGA
Found at i:208271 original size:6 final size:7
Alignment explanation
Indices: 208258--208298 Score: 55
Period size: 7 Copynumber: 5.7 Consensus size: 7
208248 TAGAATATAG
*
208258 TAAAAAA
1 TAAAAAT
208265 TAAAAAT
1 TAAAAAT
208272 TAAAAAT
1 TAAAAAT
208279 TAAAAAT
1 TAAAAAT
*
208286 TATGAAAT
1 TA-AAAAT
208294 TAAAA
1 TAAAA
208299 CATTTCATTC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
7 24 0.80
8 6 0.20
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (7 bp):
TAAAAAT
Found at i:208565 original size:20 final size:20
Alignment explanation
Indices: 208537--208576 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
208527 TTTTTATAAA
208537 TATTAAAAAAGTTAAATTTT
1 TATTAAAAAAGTTAAATTTT
*
208557 TATTTAAAAAGTTAAATTTT
1 TATTAAAAAAGTTAAATTTT
208577 AAGTAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (20 bp):
TATTAAAAAAGTTAAATTTT
Found at i:208583 original size:19 final size:20
Alignment explanation
Indices: 208542--208583 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
208532 ATAAATATTA
**
208542 AAAAAGTTAAATTTTTATTT
1 AAAAAGTTAAATTTTTAAGT
208562 AAAAAGTTAAA-TTTTAAGT
1 AAAAAGTTAAATTTTTAAGT
208581 AAA
1 AAA
208584 TTAAAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.40
Consensus pattern (20 bp):
AAAAAGTTAAATTTTTAAGT
Found at i:208646 original size:32 final size:32
Alignment explanation
Indices: 208586--208648 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
208576 TAAGTAAATT
*
208586 AAAAATTATAAATCTTATAAAATATATTTTTA
1 AAAAATTATAAATATTATAAAATATATTTTTA
* *
208618 AAAAATTATATAATATTTTAATAT-TATTTTT
1 AAAAATTATA-AATATTATAAAATATATTTTT
208649 CAATATAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 17 0.63
33 10 0.37
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (32 bp):
AAAAATTATAAATATTATAAAATATATTTTTA
Found at i:217130 original size:142 final size:140
Alignment explanation
Indices: 216958--217212 Score: 372
Period size: 142 Copynumber: 1.8 Consensus size: 140
216948 TTCTATTATG
* *
216958 TTAATTTAAAATATTGTTTATATCATTATATTTTTAATGGTTGAA-TTTTTACAT-AAATAAATA
1 TTAATTTAAAATACTGTTTATATCATTATATTTTTAATGGTTAAATTTTTTACATAAAATAAATA
* *
217021 ATTTTAAAAAATTAAATTATTATTTCAAAC-TTGAAATACATTATTTAATTTATGTCAATAAAAC
66 A--TT-AAAAATTAAA-T-TTATTACAAACTTTAAAATACATTATTTAATTTATGTCAATAAAAC
217085 AAATAAAATTGTATA
126 AAATAAAATTGTATA
*
217100 TTAATTTAAAATACTGTTTATTTCATTATATTTTTAATGGTTAAATTTTTTACATAAAATAAATA
1 TTAATTTAAAATACTGTTTATATCATTATATTTTTAATGGTTAAATTTTTTACATAAAATAAATA
* * *
217165 ATTAAAATTTTAATTTATTACAAACTTTAAAATACATTATTTTATTTA
66 ATTAAAAATTAAATTTATTACAAACTTTAAAATACATTATTTAATTTA
217213 CGTAAGTAAC
Statistics
Matches: 102, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
139 10 0.10
140 21 0.21
141 8 0.08
142 44 0.43
143 9 0.09
144 10 0.10
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (140 bp):
TTAATTTAAAATACTGTTTATATCATTATATTTTTAATGGTTAAATTTTTTACATAAAATAAATA
ATTAAAAATTAAATTTATTACAAACTTTAAAATACATTATTTAATTTATGTCAATAAAACAAATA
AAATTGTATA
Found at i:219833 original size:29 final size:31
Alignment explanation
Indices: 219801--219863 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 31
219791 TCAACAATTT
*
219801 AAAATTTAGTCTCTTTA-TTTTTAT-TATAA
1 AAAATTTAATCTCTTTACTTTTTATATATAA
* *
219830 AAAATTTAATCTTTTTACTTTTTATATTTAA
1 AAAATTTAATCTCTTTACTTTTTATATATAA
219861 AAA
1 AAA
219864 TATAAATCCA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 15 0.52
30 7 0.24
31 7 0.24
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (31 bp):
AAAATTTAATCTCTTTACTTTTTATATATAA
Found at i:220415 original size:15 final size:15
Alignment explanation
Indices: 220395--220423 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
220385 TATGAAAACT
220395 CTAATTTTTGAGAGA
1 CTAATTTTTGAGAGA
220410 CTAATTTTTGAGAG
1 CTAATTTTTGAGAG
220424 GCCATTATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.07, G:0.21, T:0.41
Consensus pattern (15 bp):
CTAATTTTTGAGAGA
Found at i:220448 original size:12 final size:12
Alignment explanation
Indices: 220431--220465 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
220421 GAGGCCATTA
220431 TAGAATTTTTCT
1 TAGAATTTTTCT
*
220443 TAGAATTTTACT
1 TAGAATTTTTCT
*
220455 TAGTATTTTTC
1 TAGAATTTTTC
220466 ATTAAGCTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.26, C:0.09, G:0.09, T:0.57
Consensus pattern (12 bp):
TAGAATTTTTCT
Found at i:232982 original size:7 final size:7
Alignment explanation
Indices: 232967--232998 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
232957 AGGGTGGGGA
*
232967 GTTGGGC
1 GTTGAGC
232974 GTTGAGC
1 GTTGAGC
232981 GTTGAGC
1 GTTGAGC
232988 GTTGAGC
1 GTTGAGC
232995 GTTG
1 GTTG
232999 GGTATTTCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.09, C:0.12, G:0.47, T:0.31
Consensus pattern (7 bp):
GTTGAGC
Found at i:233774 original size:31 final size:31
Alignment explanation
Indices: 233737--233832 Score: 113
Period size: 31 Copynumber: 3.1 Consensus size: 31
233727 GGTCTAATTA
*
233737 AAATTTTTTAAAAAATTTAAAAGATTTAATG
1 AAATTTTTTAAAAAAATTAAAAGATTTAATG
* * *
233768 ATATTTTTTTAAAAAAAATAAAA-ATTTAATT
1 A-AATTTTTTAAAAAAATTAAAAGATTTAATG
* * *
233799 AAAATTTTTAAAAAAATTGAAAGGTTTAATG
1 AAATTTTTTAAAAAAATTAAAAGATTTAATG
233830 AAA
1 AAA
233833 AGTTGTGAAA
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
30 17 0.32
31 18 0.34
32 18 0.34
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (31 bp):
AAATTTTTTAAAAAAATTAAAAGATTTAATG
Found at i:249858 original size:19 final size:19
Alignment explanation
Indices: 249834--249871 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
249824 CCATTTAGTG
249834 AAGTAT-TATAACATGATTT
1 AAGTATGTATAA-ATGATTT
*
249853 AAGTATGTCTAAATGATTT
1 AAGTATGTATAAATGATTT
249872 CAATATCCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.39, C:0.05, G:0.13, T:0.42
Consensus pattern (19 bp):
AAGTATGTATAAATGATTT
Found at i:255218 original size:20 final size:20
Alignment explanation
Indices: 255193--255237 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
255183 TTGGTTGCAT
255193 GAAAA-AGTGAAAGGTTGAAAA
1 GAAAAGAGTGAAA-G-TGAAAA
255214 GAAAAGAGTGAAAGTGAAAA
1 GAAAAGAGTGAAAGTGAAAA
255234 GAAA
1 GAAA
255238 TAAATTTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 10 0.43
21 6 0.26
22 7 0.30
ACGTcount: A:0.60, C:0.00, G:0.29, T:0.11
Consensus pattern (20 bp):
GAAAAGAGTGAAAGTGAAAA
Found at i:258865 original size:32 final size:32
Alignment explanation
Indices: 258782--258847 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
258772 GAGAATTAAA
258782 TCAAAATATATTTACCTTTTTGCACATGCTTT
1 TCAAAATATATTTACCTTTTTGCACATGCTTT
258814 TCAAAATATATTTACCTTTTTGCACATGCTTT
1 TCAAAATATATTTACCTTTTTGCACATGCTTT
258846 TC
1 TC
258848 GAAGTCTTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.27, C:0.20, G:0.06, T:0.47
Consensus pattern (32 bp):
TCAAAATATATTTACCTTTTTGCACATGCTTT
Found at i:273128 original size:39 final size:39
Alignment explanation
Indices: 273080--273323 Score: 373
Period size: 39 Copynumber: 6.3 Consensus size: 39
273070 CAGGACTTTA
* *
273080 AGCCCGGATATAATACCAACACGAATGCCTTCGGGACTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
273119 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
* * *
273158 AGCCTGGATATAGCACCAGCACAAATGCCTTCGGGACTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
* *
273197 AGCCCGGATATAATACCAGCACGAATGCCTTCAGGACTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
* * *
273236 AGCCCGGATATAATACCAGTACGAATGCCTTCAGGACTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
* *
273275 AGTCCGGATATAACACCAGCACGAATGCTTTCGGGACTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
273314 A-CCCGGATAT
1 AGCCCGGATAT
273324 TTTTCCAGCA
Statistics
Matches: 188, Mismatches: 17, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
38 8 0.04
39 180 0.96
ACGTcount: A:0.30, C:0.28, G:0.22, T:0.21
Consensus pattern (39 bp):
AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
Found at i:273368 original size:39 final size:39
Alignment explanation
Indices: 273316--273447 Score: 194
Period size: 39 Copynumber: 3.4 Consensus size: 39
273306 CGGGACTTAC
* * *
273316 CCGGATATTTTTCCAGCACT-TAGCCTGCGGACTTTAAGT
1 CCGGATATATTTCCAGCA-TAAAGCCTGCGGACTTCAAGT
*
273355 CTGGATATATTTCCAGCATAAAGCCTGCGGACTTCAAGT
1 CCGGATATATTTCCAGCATAAAGCCTGCGGACTTCAAGT
*
273394 CCGAATATATTTCCAGCATAAAGCCTGCGGACTTCAAGT
1 CCGGATATATTTCCAGCATAAAGCCTGCGGACTTCAAGT
*
273433 CCGGATATTTTTCCA
1 CCGGATATATTTCCA
273448 ATACCATGCA
Statistics
Matches: 84, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
38 1 0.01
39 83 0.99
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (39 bp):
CCGGATATATTTCCAGCATAAAGCCTGCGGACTTCAAGT
Found at i:275552 original size:30 final size:29
Alignment explanation
Indices: 275518--275607 Score: 83
Period size: 31 Copynumber: 3.0 Consensus size: 29
275508 AAAAATTTTG
* * *
275518 AAAATTGGATCAAATCAAAATTTCATGTAT
1 AAAATTGCATAAAATCAAAATTT-ATATAT
*
275548 AAAATT-CATAAAATCAAACTTTATATAT
1 AAAATTGCATAAAATCAAAATTTATATAT
** *
275576 AAAATTGCACATCGAATCAAAATTCATATAT
1 AAAATTG--CATAAAATCAAAATTTATATAT
275607 A
1 A
275608 GTTTTGAGAT
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
28 11 0.22
29 13 0.27
30 6 0.12
31 19 0.39
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.32
Consensus pattern (29 bp):
AAAATTGCATAAAATCAAAATTTATATAT
Found at i:277252 original size:22 final size:23
Alignment explanation
Indices: 277216--277259 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 23
277206 TTTATTTTTC
277216 AGTTAAACTTATTTTTTTAACAG
1 AGTTAAACTTATTTTTTTAACAG
277239 AGTTAAA-TTATTTTTTTAACA
1 AGTTAAACTTATTTTTTTAACA
277260 AAAATATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.50
Consensus pattern (23 bp):
AGTTAAACTTATTTTTTTAACAG
Found at i:279276 original size:12 final size:12
Alignment explanation
Indices: 279238--279285 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
279228 ATAGGTCAGT
279238 TATACATACACA
1 TATACATACACA
*
279250 TACACATACACA
1 TATACATACACA
* *
279262 TATACATATATA
1 TATACATACACA
*
279274 TATATATACACA
1 TATACATACACA
279286 AAAGCCTTCT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (12 bp):
TATACATACACA
Found at i:285050 original size:18 final size:18
Alignment explanation
Indices: 285027--285062 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
285017 TTTTTTTCTC
285027 TTTATTGGTGCTAACAAT
1 TTTATTGGTGCTAACAAT
*
285045 TTTATTGGTGCTACCAAT
1 TTTATTGGTGCTAACAAT
285063 AAATTTTGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.44
Consensus pattern (18 bp):
TTTATTGGTGCTAACAAT
Found at i:291524 original size:21 final size:23
Alignment explanation
Indices: 291491--291533 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
291481 GCAAAAAATA
*
291491 AAAATTGA-TTTTTCTTTTATTT
1 AAAATTGATTTTTTATTTTATTT
291513 AAAATT-ATTTTTTATTTTATT
1 AAAATTGATTTTTTATTTTATT
291534 AATTTTTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (23 bp):
AAAATTGATTTTTTATTTTATTT
Found at i:295245 original size:1 final size:1
Alignment explanation
Indices: 295239--295263 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
295229 TCCCTAATTC
295239 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
295264 GCGTTTGACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:299428 original size:14 final size:14
Alignment explanation
Indices: 299409--299436 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
299399 GTTTTCAAAG
299409 TATATGTGTGTATA
1 TATATGTGTGTATA
299423 TATATGTGTGTATA
1 TATATGTGTGTATA
299437 GCACAGTGAT
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:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (14 bp):
TATATGTGTGTATA
Found at i:310705 original size:38 final size:38
Alignment explanation
Indices: 310654--310777 Score: 185
Period size: 38 Copynumber: 3.3 Consensus size: 38
310644 ATATTCGATG
* *
310654 TATATCCGGGTTAAATCCCACAGGCTTCGTACTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
310692 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
* * * *
310730 TATATTCGGGATAAATCCCGCAGGCCTAGTGCTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
*
310768 TATATTCGGG
1 TATATCCGGG
310778 CCTTCGTGCC
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 80 1.00
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (38 bp):
TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
Found at i:310847 original size:43 final size:43
Alignment explanation
Indices: 310770--310851 Score: 128
Period size: 43 Copynumber: 1.9 Consensus size: 43
310760 GCTGGTATTA
* * **
310770 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGGGCCTAGCAGGCGTAATGCCGGTGATGTG
310813 TATTCGGGCCTTCGGGCCTAGCAGGCGTAATGCCGGTGA
1 TATTCGGGCCTTCGGGCCTAGCAGGCGTAATGCCGGTGA
310852 AATGATATGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.12, C:0.26, G:0.35, T:0.27
Consensus pattern (43 bp):
TATTCGGGCCTTCGGGCCTAGCAGGCGTAATGCCGGTGATGTG
Found at i:312673 original size:3 final size:3
Alignment explanation
Indices: 312665--312696 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
312655 TATTTTTAAA
312665 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
312697 ATAAGCCATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:314053 original size:3 final size:3
Alignment explanation
Indices: 314045--314070 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
314035 GAAACTTCAA
314045 CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CA
314071 ATCTAATCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:314719 original size:17 final size:17
Alignment explanation
Indices: 314697--314730 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
314687 TTAAAAGAAT
314697 GGTCATATACTGCATGC
1 GGTCATATACTGCATGC
314714 GGTCATATACTGCATGC
1 GGTCATATACTGCATGC
314731 TAATTACAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (17 bp):
GGTCATATACTGCATGC
Found at i:320226 original size:74 final size:74
Alignment explanation
Indices: 320141--320288 Score: 278
Period size: 74 Copynumber: 2.0 Consensus size: 74
320131 AAGTCCACTC
*
320141 AACTTTTAAATAATTTTACGGTGATTTTATAATATTTTAAAATTAAATGACTAATAATTTAATAA
1 AACTTTCAAATAATTTTACGGTGATTTTATAATATTTTAAAATTAAATGACTAATAATTTAATAA
320206 ACCAATTTA
66 ACCAATTTA
*
320215 AACTTTCAAATAATTTTATGGTGATTTTATAATATTTTAAAATTAAATGACTAATAATTTAATAA
1 AACTTTCAAATAATTTTACGGTGATTTTATAATATTTTAAAATTAAATGACTAATAATTTAATAA
320280 ACCAATTTA
66 ACCAATTTA
320289 CACTAATTAT
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 72 1.00
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (74 bp):
AACTTTCAAATAATTTTACGGTGATTTTATAATATTTTAAAATTAAATGACTAATAATTTAATAA
ACCAATTTA
Found at i:324344 original size:18 final size:18
Alignment explanation
Indices: 324323--324361 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
324313 GATTGAGAGT
* *
324323 GAAAAGGAATGTGAAACA
1 GAAAAGAAATGTGAAAAA
*
324341 GAAAAGAAATTTGAAAAA
1 GAAAAGAAATGTGAAAAA
324359 GAA
1 GAA
324362 GTTGAAGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.62, C:0.03, G:0.23, T:0.13
Consensus pattern (18 bp):
GAAAAGAAATGTGAAAAA
Found at i:327486 original size:23 final size:23
Alignment explanation
Indices: 327460--327507 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
327450 ACATAGTTTG
*
327460 TATCATATAGAAAAATATGCTTT
1 TATCATATAGAAAAACATGCTTT
*
327483 TATCATATGGAAAAACATGCTTT
1 TATCATATAGAAAAACATGCTTT
327506 TA
1 TA
327508 GTATTTCTCG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (23 bp):
TATCATATAGAAAAACATGCTTT
Found at i:332596 original size:31 final size:32
Alignment explanation
Indices: 332560--332651 Score: 102
Period size: 31 Copynumber: 3.0 Consensus size: 32
332550 CTATTTAGTG
*
332560 CTTGAGTTTGATTTTAATGTTTGATTTGGTAT
1 CTTGAGTTTGATTTTAATGTTTAATTTGGTAT
* *
332592 -TTGAGTTTTATTTT--TGTTTCAAATTGGTAT
1 CTTGAGTTTGATTTTAATGTTT-AATTTGGTAT
* *
332622 CTT-AGTTTGGTTTTAATGTTCAATTTGGTA
1 CTTGAGTTTGATTTTAATGTTTAATTTGGTA
332652 CCTAGGCCAA
Statistics
Matches: 49, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
29 5 0.10
30 17 0.35
31 23 0.47
32 4 0.08
ACGTcount: A:0.20, C:0.04, G:0.20, T:0.57
Consensus pattern (32 bp):
CTTGAGTTTGATTTTAATGTTTAATTTGGTAT
Found at i:334129 original size:23 final size:23
Alignment explanation
Indices: 334086--334129 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
334076 TCCGCCTCTT
* *
334086 CCGCCCTCTTTCCCGCTCTCAAA
1 CCGCCCTCTTTCCCCCCCTCAAA
334109 CCGCCCT-TTTCCGCCCCCTCA
1 CCGCCCTCTTTCC-CCCCCTCA
334130 CCCGTCGCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.09, C:0.57, G:0.09, T:0.25
Consensus pattern (23 bp):
CCGCCCTCTTTCCCCCCCTCAAA
Found at i:335093 original size:193 final size:192
Alignment explanation
Indices: 334840--335388 Score: 712
Period size: 194 Copynumber: 2.8 Consensus size: 192
334830 GAAATTTCCT
* **
334840 AAGCTATGAAA-CTTTGATTCCTTACTGATTCTGCTATGTTGTGTTTATGATTGTTGATATATGC
1 AAGCTATAAAATC-TTGATTCCTTACTGATTCTGCTAAATTGTGTTTATGATTGTTGATATATGC
* *
334904 TGTTTGTTGCTGTATATTGC-TTTGAGTTTTTCAAAAATCGAAGAGAAATGTCTTTGAAAAATGG
65 TGTTTGTTGCTGTATATTGCTTTTGAGTTTTTCAAAAGTCGAAGAGAAATGTCTTT-AAGAATGG
* * *
334968 GAATACGGGTTTTGTTTAACTGTCTGAATTGCTTCTCGACAAAA-CCCAGTTTACAACATTTCCG
129 GAAT-CGGGTGTTGTTTAACTGTCTGAATTGCTTCTCAACAAAACCCCAGTTTACAACATATCCG
* * *
335032 ACGTTATAAAATCTTGATTTCTTACTGATTCTGCTAAAATTGTGTTTATGATTGTTGATATATGC
1 AAGCTATAAAATCTTGATTCCTTACTGATTCTGCT-AAATTGTGTTTATGATTGTTGATATATGC
335097 TGTTTGTTGCTGTATATTGCTTTTGAGTTTTTCAAAAGTCGAAGAGAAGCAT-T-TTTAAGAATG
65 TGTTTGTTGCTGTATATTGCTTTTGAGTTTTTCAAAAGTCGAAGAGAA--ATGTCTTTAAGAATG
* * **
335160 GGAATTCGGGTGTTGTTTAACTGTCCGAATTGCTTCTCAACAAAACCCCATTTTATGACATATCC
128 GGAA-TCGGGTGTTGTTTAACTGTCTGAATTGCTTCTCAACAAAACCCCAGTTTACAACATATCC
335225 G
192 G
* * * *
335226 AAGCTATGAAATCTTGATTCCTTAATGATTCTGCTGGATTTGTGTTTATGATTGTTGATATATGC
1 AAGCTATAAAATCTTGATTCCTTACTGATTCTGCT-AAATTGTGTTTATGATTGTTGATATATGC
* * * * * * *
335291 TGTATGTTGCTATATATTGCTTTTGAGTTTTTCAAGAGTCGAAGAAAAACGACTTTTAAGAACGG
65 TGTTTGTTGCTGTATATTGCTTTTGAGTTTTTCAAAAGTCGAAGAGAAATGTC-TTTAAGAATGG
* **
335356 GAATCTGTGTGTTGTTTAACCATCTGAATTGCT
129 GAATC-GGGTGTTGTTTAACTGTCTGAATTGCT
335389 GCTCTGGTCG
Statistics
Matches: 312, Mismatches: 34, Indels: 19
0.85 0.09 0.05
Matches are distributed among these distances:
192 30 0.10
193 94 0.30
194 149 0.48
195 37 0.12
196 2 0.01
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.41
Consensus pattern (192 bp):
AAGCTATAAAATCTTGATTCCTTACTGATTCTGCTAAATTGTGTTTATGATTGTTGATATATGCT
GTTTGTTGCTGTATATTGCTTTTGAGTTTTTCAAAAGTCGAAGAGAAATGTCTTTAAGAATGGGA
ATCGGGTGTTGTTTAACTGTCTGAATTGCTTCTCAACAAAACCCCAGTTTACAACATATCCG
Found at i:337362 original size:72 final size:72
Alignment explanation
Indices: 337279--337417 Score: 224
Period size: 72 Copynumber: 1.9 Consensus size: 72
337269 CGATTCCGAT
* * *
337279 GAAAAGGGTTCTTCTGATTGTAGCGAAGACGTTAATCCATAAGGCTTACACAAGTAAAAGTGCCA
1 GAAAAGGGTTCTTCCGATTATAGCGAAGACGATAATCCATAAGGCTTACACAAGTAAAAGTGCCA
337344 TTGAAAA
66 TTGAAAA
* * *
337351 GAAAAGTGTTCTTCCGATTATAGCGAAGATGATAATCCATATGGCTTACACAAGTAAAAGTGCCA
1 GAAAAGGGTTCTTCCGATTATAGCGAAGACGATAATCCATAAGGCTTACACAAGTAAAAGTGCCA
337416 TT
66 TT
337418 CTTTGGTATA
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
72 61 1.00
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.27
Consensus pattern (72 bp):
GAAAAGGGTTCTTCCGATTATAGCGAAGACGATAATCCATAAGGCTTACACAAGTAAAAGTGCCA
TTGAAAA
Found at i:337607 original size:16 final size:16
Alignment explanation
Indices: 337582--337634 Score: 88
Period size: 16 Copynumber: 3.3 Consensus size: 16
337572 TTGGTTCGCT
*
337582 GTAATAGAATAGAGGC
1 GTAATGGAATAGAGGC
*
337598 GTAATGGAATAGAGAC
1 GTAATGGAATAGAGGC
337614 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
337630 GTAAT
1 GTAAT
337635 AGTAATTCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.42, C:0.06, G:0.32, T:0.21
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:337704 original size:39 final size:43
Alignment explanation
Indices: 337614--337720 Score: 134
Period size: 45 Copynumber: 2.5 Consensus size: 43
337604 GAATAGAGAC
337614 GTAATGGAATAGAGGCGTAATAGTAATTCAATTGTTTGGTTAAAT
1 GTAATGGAATAGAGGCGTAATAGTAATTCAATTGTTTGGTT--AT
*
337659 GTAATGGAATAGAGGCGTAATAGT-ATTC-TTGTGTTTGG-T-T
1 GTAATGGAATAGAGGCGTAATAGTAATTCAAT-TGTTTGGTTAT
*
337699 G-AATGGAATAGAAGCGTAATAG
1 GTAATGGAATAGAGGCGTAATAG
337721 CAGAAGGAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 8
0.86 0.03 0.12
Matches are distributed among these distances:
39 20 0.34
40 2 0.03
43 2 0.03
44 11 0.19
45 24 0.41
ACGTcount: A:0.34, C:0.05, G:0.28, T:0.34
Consensus pattern (43 bp):
GTAATGGAATAGAGGCGTAATAGTAATTCAATTGTTTGGTTAT
Found at i:337840 original size:21 final size:20
Alignment explanation
Indices: 337816--337902 Score: 53
Period size: 19 Copynumber: 4.5 Consensus size: 20
337806 AATAAGATTA
337816 TTAATATAAATAATAAATAAT
1 TTAATATAAATAA-AAATAAT
* *
337837 TTAATAATAATTTAAAATAA-
1 TTAAT-ATAAATAAAAATAAT
* *
337857 TT-AT-T-ATTAAATATAAT
1 TTAATATAAATAAAAATAAT
*
337874 TTAATA-AAA-AATATATAAT
1 TTAATATAAATAA-AAATAAT
337893 TTAATA-AAAT
1 TTAATATAAAT
337903 TCTTAATATA
Statistics
Matches: 54, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
16 9 0.17
17 3 0.06
18 4 0.07
19 19 0.35
20 2 0.04
21 11 0.20
22 6 0.11
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TTAATATAAATAAAAATAAT
Found at i:337845 original size:11 final size:11
Alignment explanation
Indices: 337826--337858 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
337816 TTAATATAAA
337826 TAATAAATAATT
1 TAAT-AATAATT
337838 TAATAATAATT
1 TAATAATAATT
337849 TAA-AATAATT
1 TAATAATAATT
337859 ATTATTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 7 0.33
11 10 0.48
12 4 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
TAATAATAATT
Found at i:337879 original size:24 final size:21
Alignment explanation
Indices: 337803--337915 Score: 79
Period size: 21 Copynumber: 5.1 Consensus size: 21
337793 GTTATTAAAT
337803 TTTAATAAGATTATTAATATAA
1 TTTAATAA-ATTATTAATATAA
* *
337825 -ATAATAAATAATTTAATAATAA
1 TTTAATAAATTA-TTAAT-ATAA
337847 TTTAAAATAATTATTATTAAATATAA
1 TTT--AATAA--ATTATT-AATATAA
* *
337873 TTTAATAAA-AAAT-ATATAA
1 TTTAATAAATTATTAATATAA
*
337892 TTTAATAAAATTCTTAATATAA
1 TTTAAT-AAATTATTAATATAA
337914 TT
1 TT
337916 ATTCTTATAT
Statistics
Matches: 71, Mismatches: 9, Indels: 22
0.70 0.09 0.22
Matches are distributed among these distances:
19 12 0.17
20 6 0.08
21 14 0.20
22 13 0.18
23 1 0.01
24 5 0.07
25 5 0.07
26 9 0.13
27 6 0.08
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (21 bp):
TTTAATAAATTATTAATATAA
Found at i:337882 original size:29 final size:28
Alignment explanation
Indices: 337849--337939 Score: 71
Period size: 29 Copynumber: 3.2 Consensus size: 28
337839 AATAATAATT
337849 TAAAATAATTATTATTAAATATAATTTAA
1 TAAAATAATTATTATTAAATATAATTT-A
* * *
337878 TAAAA-AATATATAATTTAATAAAATTCT-
1 TAAAATAAT-TATTATTAAATATAATT-TA
* * *
337906 TAATATAATTATTCTTATAT-TAATTTA
1 TAAAATAATTATTATTAAATATAATTTA
337933 CTAAAAT
1 -TAAAAT
337940 CATAATATAT
Statistics
Matches: 47, Mismatches: 10, Indels: 11
0.69 0.15 0.16
Matches are distributed among these distances:
26 1 0.02
27 4 0.09
28 19 0.40
29 22 0.47
30 1 0.02
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (28 bp):
TAAAATAATTATTATTAAATATAATTTA
Found at i:337892 original size:56 final size:57
Alignment explanation
Indices: 337816--337944 Score: 156
Period size: 56 Copynumber: 2.3 Consensus size: 57
337806 AATAAGATTA
337816 TTAATATAAATAATAAATAATTTAATAATAA-T-TTAAAATAATTATTATTAAATATAAT
1 TTAATA-AAATAATAAATAATTTAATAA-AATTCTTAAAATAATTATTATTAAAT-TAAT
* * * *
337874 TTAATAAAA-AATATATAATTTAATAAAATTCTTAATATAATTATTCTTATATTAAT
1 TTAATAAAATAATAAATAATTTAATAAAATTCTTAAAATAATTATTATTAAATTAAT
* *
337930 TTACTAAAATCATAA
1 TTAATAAAATAATAA
337945 TATATAATAA
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
55 2 0.03
56 29 0.48
57 24 0.39
58 6 0.10
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (57 bp):
TTAATAAAATAATAAATAATTTAATAAAATTCTTAAAATAATTATTATTAAATTAAT
Found at i:338357 original size:77 final size:77
Alignment explanation
Indices: 338230--338381 Score: 295
Period size: 77 Copynumber: 2.0 Consensus size: 77
338220 TTTTTGTCCA
338230 CTTTAATAATTGAACTTGACAATTAGATATATTTTAATCTTTGAACTTGAAATATATAAAATTTT
1 CTTTAATAATTGAACTTGACAATTAGATATATTTTAATCTTTGAACTTGAAATATATAAAATTTT
338295 ATTGACATAACT
66 ATTGACATAACT
*
338307 CTTTAATAATTGAACTTGACAATTAGATATATTTTAATCTTTGAACTTGAAATGTATAAAATTTT
1 CTTTAATAATTGAACTTGACAATTAGATATATTTTAATCTTTGAACTTGAAATATATAAAATTTT
338372 ATTGACATAA
66 ATTGACATAA
338382 AACTTTAAGA
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 74 1.00
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.43
Consensus pattern (77 bp):
CTTTAATAATTGAACTTGACAATTAGATATATTTTAATCTTTGAACTTGAAATATATAAAATTTT
ATTGACATAACT
Found at i:340941 original size:53 final size:54
Alignment explanation
Indices: 340857--340963 Score: 207
Period size: 53 Copynumber: 2.0 Consensus size: 54
340847 GCAGTGAATT
340857 TCAAAAACCACAACAAAATGACAGGGAAAAAATGAAAAAAGAGACCGAGAGAGA
1 TCAAAAACCACAACAAAATGACAGGGAAAAAATGAAAAAAGAGACCGAGAGAGA
340911 TCAAAAACCACAAC-AAATGACAGGGAAAAAATGAAAAAAGAGACCGAGAGAGA
1 TCAAAAACCACAACAAAATGACAGGGAAAAAATGAAAAAAGAGACCGAGAGAGA
340964 GAATAGGTAA
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
53 39 0.74
54 14 0.26
ACGTcount: A:0.59, C:0.15, G:0.21, T:0.06
Consensus pattern (54 bp):
TCAAAAACCACAACAAAATGACAGGGAAAAAATGAAAAAAGAGACCGAGAGAGA
Found at i:344804 original size:16 final size:16
Alignment explanation
Indices: 344783--344820 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
344773 AATCACTTTT
344783 AAGTTCAAG-TCATTTC
1 AAGTTCAAGCT-ATTTC
*
344799 AAGTTCATGCTATTTC
1 AAGTTCAAGCTATTTC
344815 AAGTTC
1 AAGTTC
344821 TGATCATTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 19 0.95
17 1 0.05
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.39
Consensus pattern (16 bp):
AAGTTCAAGCTATTTC
Found at i:357861 original size:17 final size:18
Alignment explanation
Indices: 357839--357881 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
357829 TATAAAAAAA
357839 TTATTTTAATTT-TTTAT
1 TTATTTTAATTTATTTAT
*
357856 TTATTTT-ATTTATTTGT
1 TTATTTTAATTTATTTAT
*
357873 CTATTTTAA
1 TTATTTTAA
357882 CTCTTAAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 4 0.18
17 17 0.77
18 1 0.05
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (18 bp):
TTATTTTAATTTATTTAT
Found at i:362393 original size:8 final size:8
Alignment explanation
Indices: 362293--362392 Score: 128
Period size: 8 Copynumber: 12.5 Consensus size: 8
362283 CATTCAACAG
362293 GGCAGTTT
1 GGCAGTTT
362301 GGCAGTTT
1 GGCAGTTT
362309 GGCAGTTT
1 GGCAGTTT
362317 GGCAGTTT
1 GGCAGTTT
*
362325 GGTAGTTT
1 GGCAGTTT
362333 GGCAGTTT
1 GGCAGTTT
*
362341 GGTAGTTT
1 GGCAGTTT
*
362349 GGCAGCTT
1 GGCAGTTT
*
362357 GGCAATTT
1 GGCAGTTT
*
362365 GGTAGTTT
1 GGCAGTTT
* *
362373 GACATTTT
1 GGCAGTTT
*
362381 GGCATTTT
1 GGCAGTTT
362389 GGCA
1 GGCA
362393 TGACAATCGA
Statistics
Matches: 79, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 79 1.00
ACGTcount: A:0.15, C:0.11, G:0.34, T:0.40
Consensus pattern (8 bp):
GGCAGTTT
Found at i:384661 original size:16 final size:16
Alignment explanation
Indices: 384640--384673 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
384630 ATCAAAGTCA
*
384640 AATATATTATGCTAAT
1 AATATATCATGCTAAT
*
384656 AATATATCATTCTAAT
1 AATATATCATGCTAAT
384672 AA
1 AA
384674 ATGCTAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (16 bp):
AATATATCATGCTAAT
Found at i:384686 original size:24 final size:24
Alignment explanation
Indices: 384656--384706 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
384646 TTATGCTAAT
* *
384656 AATATATCATTCTAATAAATGCTA
1 AATATATCATACTAATAAATACTA
* *
384680 AATATATTATACTTATAAATACTA
1 AATATATCATACTAATAAATACTA
384704 AAT
1 AAT
384707 CTTCTAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.49, C:0.10, G:0.02, T:0.39
Consensus pattern (24 bp):
AATATATCATACTAATAAATACTA
Found at i:386653 original size:17 final size:17
Alignment explanation
Indices: 386631--386663 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
386621 TTTTAAAAAT
386631 TATAAA-ATATAAATTAA
1 TATAAAGATA-AAATTAA
386648 TATAAAGATAAAATTA
1 TATAAAGATAAAATTA
386664 CATTATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
TATAAAGATAAAATTAA
Found at i:387546 original size:143 final size:136
Alignment explanation
Indices: 387375--389000 Score: 781
Period size: 120 Copynumber: 11.8 Consensus size: 136
387365 ATGACAAAAT
387375 TATATATTTTGTTGTTTGGTTA-GTTAGAAAGTAAATTGAAGTGGATTAAGCTTAATTTAGCTAT
1 TATATATTTTGTTGTTTGGTTACG-TAGAAAGTAAATT-AAGTGGATTAAGCTTAATTTAGCTAT
* * * *
387439 TTTAATTGTCTAAATTTGGTCATTTAGCTG-AAAATTTTAGTGTTCTTTTGTTATTAATAAGTTT
64 TTTAATTGTCTAAATTTCGTAATTTAGCTGAAAAAATTTAGTGTTC---T-TT-TTAAT--GGTT
*
387503 CTTTATGAATATATG
122 CTTTATGAATATAAG
* * * *
387518 TATATATTTTATTGTTTGGTTACGTAGAAAGTAAATTAAAGTGGATTAAGTTTAATTTAACCATT
1 TATATATTTTGTTGTTTGGTTACGTAGAAAGTAAATT-AAGTGGATTAAGCTTAATTTAGCTATT
* * **
387583 TTAATTGTCTCAATTTCGTAATTTAGGTGAAAAAATTTAGTGTTCTTTTTGGTGGTTCTTTATGA
65 TTAATTGTCTAAATTTCGTAATTTAGCTGAAAAAATTTAGTGTTCTTTTTAATGGTTCTTTATGA
387648 ATATAAG
130 ATATAAG
* * * *
387655 TATATATTTTGTTCTTTGGTTACTTAGAAAGTAAATTATAGTGGATTAAGCTTAATATAGCTACT
1 TATATATTTTGTTGTTTGGTTACGTAGAAAGTAAATTA-AGTGGATTAAGCTTAATTTAGCTATT
* * ***** *
387720 TTAGTTGTCGTGAAA-----AAATTTAG-TG-TTCTTTTTGGTGGTTC---TT--T--------A
65 TTAATTGTC-T-AAATTTCGTAATTTAGCTGAAAAAATTTAGT-GTTCTTTTTAATGGTTCTTTA
387765 TGAATATAAG
127 TGAATATAAG
* * * * *
387775 TATATATTTTGTTCTTTGGTTACTTAGAAAGTAAATTATAGTGGATTAAGCTTAATATAGATACT
1 TATATATTTTGTTGTTTGGTTACGTAGAAAGTAAATTA-AGTGGATTAAGCTTAATTTAGCTATT
* * * ** ** *
387840 TTAGTTGTCGGGAAA-----AAATTTAG-TG-TTATTTTTGGTGGTTC---TT--T--------A
65 TTAATTGTC--TAAATTTCGTAATTTAGCTGAAAAAATTTAGT-GTTCTTTTTAATGGTTCTTTA
387885 TGAATATAAG
127 TGAATATAAG
* * * *
387895 TATATTTTTTGTTGTTTGGTTACTTAGAAAGTAAATTTTAGTGGATTAAGCTTAATTTAGCTACT
1 TATATATTTTGTTGTTTGGTTACGTAGAAAGTAAA-TTAAGTGGATTAAGCTTAATTTAGCTATT
* * * * * * **
387960 TTAATCGTCTCAATTTCGTCATTTAGGTGAAAAATTTTAGTGTTCATTTTGGTGGTTCTTTATGA
65 TTAATTGTCTAAATTTCGTAATTTAGCTGAAAAAATTTAGTGTTCTTTTTAATGGTTCTTTATGA
388025 ATATAAG
130 ATATAAG
* * * * * *
388032 TATATAATTTGTTGTTGGGTTACTTAGAAAGTAAATTATAATGGAATAAGCTT-ATGTTAGCTAC
1 TATATATTTTGTTGTTTGGTTACGTAGAAAGTAAATTA-AGTGGATTAAGCTTAAT-TTAGCTAT
* * * * *
388096 TTTAATT-TCTAAGTTTGGTCATTTAGGTGAAAAACA-TTAGTGTTCTTCTGCTTTTTTTTTTTA
64 TTTAATTGTCTAAATTTCGTAATTTAGCTGAAAAA-ATTTAGTG----T-T-C-----TTTTTAA
*
388159 TGGTTCTTTATGAATATATG
117 TGGTTCTTTATGAATATAAG
* * * *
388179 TATATAATTTGTTGTTTGTTTACTTAGAAAGTAAATTATAGTGGGA-TAAGCTTAATTTACACTA
1 TATATATTTTGTTGTTTGGTTACGTAGAAAGTAAATTA-AGT-GGATTAAGCTTAATTTA-GCTA
* * * * ** *
388243 CTTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAAA--T--TGTTATTAGTAA-GTTTCTTTAT
63 TTTTAATTGTCTAAATTTCGTAATTTAGCTGAAAAAATTTAGTGTTCTTTTTAATGGTTCTTTAT
**
388303 GAAT-TGATC
128 GAATAT-AAG
* * **
388312 TATATGTTTTGTTGTTTGGTTACTTAGAAAGTAAATGGT-AGTGGGA-TAAGCTTAA-GAATGCT
1 TATATATTTTGTTGTTTGGTTACGTAGAAAGTAAAT--TAAGT-GGATTAAGCTTAATTTA-GCT
* * * * * * * * *
388374 ACTTTAGTTTTCTAAATTTCGTTACTTAGGTGACAAAAGTTAGTGTTCTTATGCTATTTTTTATG
62 ATTTTAATTGTCTAAATTTCGTAATTTAGCTGAAAAAATTTAGTG----T-T-C--TTTTTAATG
* *
388439 GTTCATTATGAATATATG
119 GTTCTTTATGAATATAAG
* * * * * *
388457 TATATAATTTATTGTTTGGTTACCTACAAAGTAAATTACAGTGGGA-TAACCTTAATTTAGCTAC
1 TATATATTTTGTTGTTTGGTTACGTAGAAAGTAAATTA-AGT-GGATTAAGCTTAATTTAGCTAT
* * * * * * * *
388521 TTTACTTTTCTAAATTTCTTCATTTAGGTGAAAAAATTTAGTGTCTTTTGTTTTTTTTTTATAGT
64 TTTAATTGTCTAAATTTCGTAATTTAGCTGAAAAAATTTA--G-----TG-TTCTTTTTAATGGT
*
388586 TCTTTATGAATAT--C
121 TCTTTATGAATATAAG
* * * *
388600 TTTATA-TTTGTTGTTTGGTTACTTAGAAAGTAAATTATAATGGATTGAGCTTAATTTAGCTACT
1 TATATATTTTGTTGTTTGGTTACGTAGAAAGTAAATTA-AGTGGATTAAGCTTAATTTAGCTA-T
* * ** * *
388664 TTT-ATTGTCTAAATTTCGTCATTTAGGTGAAAACTTTTTGTGTTCTTTTGTTATTAGCAAGTTT
64 TTTAATTGTCTAAATTTCGTAATTTAGCTGAAAAAATTTAGTGTTC-TTT-TTAAT-G---G-TT
**
388728 CTTTATGAATATGTG
122 CTTTATGAATATAAG
* * * * * *
388743 TATATATTTTGTTGTTTGGTTTCTTAGAAAGCAAATTGTAGTGGGA-TAAGCTTAATTTAACTAC
1 TATATATTTTGTTGTTTGGTTACGTAGAAAGTAAATT-AAGT-GGATTAAGCTTAATTTAGCTAT
** * * * * * **
388807 TTTAATTGTCTAAATTTCGTCGTTTAGGTAAAAAAATTTCGTGTTTCTTTTGTTATTAGTAAGTT
64 TTTAATTGTCTAAATTTCGTAATTTAGCTGAAAAAATTTAGTG-TTC-TTT-TTAATGGT-TCTT
* *
388872 TATGCACAAACATATG
125 TATG----AATATAAG
* * * * *
388888 TATATA--TTGCTT-TTTGGTTGCTTAGAAAGTAAATTATGGTGGAATAAGCTTAATTTAGCTAC
1 TATATATTTTG-TTGTTTGGTTACGTAGAAAGTAAATTA-AGTGGATTAAGCTTAATTTAGCTAT
* * * *
388950 TTTAATTGTCCAAATTTCGTTATTTAGGTG-AAAAATTTAAATGTTCTTTTT
64 TTTAATTGTCTAAATTTCGTAATTTAGCTGAAAAAATTT-AGTGTTCTTTTT
389001 GTTTTTTTGG
Statistics
Matches: 1223, Mismatches: 162, Indels: 199
0.77 0.10 0.13
Matches are distributed among these distances:
118 2 0.00
120 190 0.16
121 3 0.00
123 6 0.00
124 6 0.00
125 7 0.01
127 2 0.00
128 1 0.00
129 1 0.00
130 2 0.00
132 42 0.03
133 70 0.06
134 14 0.01
135 6 0.00
136 40 0.03
137 149 0.12
138 1 0.00
139 5 0.00
140 10 0.01
141 31 0.03
142 90 0.07
143 171 0.14
144 100 0.08
145 151 0.12
146 2 0.00
147 74 0.06
148 18 0.01
149 27 0.02
152 2 0.00
ACGTcount: A:0.29, C:0.07, G:0.17, T:0.47
Consensus pattern (136 bp):
TATATATTTTGTTGTTTGGTTACGTAGAAAGTAAATTAAGTGGATTAAGCTTAATTTAGCTATTT
TAATTGTCTAAATTTCGTAATTTAGCTGAAAAAATTTAGTGTTCTTTTTAATGGTTCTTTATGAA
TATAAG
Found at i:388564 original size:145 final size:143
Alignment explanation
Indices: 387877--388281 Score: 384
Period size: 137 Copynumber: 2.8 Consensus size: 143
387867 ATTTTTGGTG
* * * *
387877 GTTCTTTATGAATATAAGTATATTTTTTGTTGTTTGGTTACTTAGAAAGTAAATTTTAGT-GGAT
1 GTTCATTATGAATATATGTATA-TATTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGTGGGA-
* * * *
387941 TAAGCTTAATTTAGCTACTTTAATCGTCTCAATTTCGTCATTTAGGTGAAAAATTTTAGTGTTCA
64 TAAGCTTAATTTAGCTACTTTAATTGTCTAAATTTCTTCATTTAGGTGAAAAAATTTAGTGTTC-
*
388006 TTTTG------G--TG
128 TTTTGTTATTAGTATA
* * * * *
388014 GTTCTTTATGAATATAAGTATATAATTTGTTGTTGGGTTACTTAGAAAGTAAATTATAATGGAAT
1 GTTCATTATGAATATATGTATAT-ATTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGTGGGAT
* **
388079 AAGCTT-ATGTTAGCTACTTTAATT-TCTAAGTTTGGTCATTTAGGTGAAAAACA-TTAGTGTTC
65 AAGCTTAAT-TTAGCTACTTTAATTGTCTAAATTTCTTCATTTAGGTGAAAAA-ATTTAGTGTTC
* * ** *
388141 TTCTGCTTTTTTTTTTTATG
128 -T-T--TTGTTATTAGTATA
* *
388161 GTTCTTTATGAATATATGTATATAATTTGTTGTTTGTTTACTTAGAAAGTAAATTATAGTGGGAT
1 GTTCATTATGAATATATGTATAT-ATTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGTGGGAT
* *
388226 AAGCTTAATTTACACTACTTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAAATT
65 AAGCTTAATTTA-GCTACTTTAATTGTCTAAATTTCTTCATTTAGGTGAAAAAATT
388282 GTTATTAGTA
Statistics
Matches: 228, Mismatches: 21, Indels: 26
0.83 0.08 0.09
Matches are distributed among these distances:
136 37 0.16
137 76 0.33
138 2 0.01
139 2 0.01
147 71 0.31
148 14 0.06
149 26 0.11
ACGTcount: A:0.29, C:0.08, G:0.17, T:0.46
Consensus pattern (143 bp):
GTTCATTATGAATATATGTATATATTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGTGGGATA
AGCTTAATTTAGCTACTTTAATTGTCTAAATTTCTTCATTTAGGTGAAAAAATTTAGTGTTCTTT
TGTTATTAGTATA
Found at i:388579 original size:145 final size:145
Alignment explanation
Indices: 388319--389008 Score: 658
Period size: 145 Copynumber: 4.8 Consensus size: 145
388309 ATCTATATGT
** ** *
388319 TTTGTTGTTTGGTTACTTAGAAAGTAAATGGTAGTGGGATAAGCTTAA-GAATGCTACTTTAGTT
1 TTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGTGGGATAAGCTTAATTTA-GCTACTTTAATT
* * * * * * * *
388383 TTCTAAATTTCGTT-ACTTAGGTGACAAAAGTTAGTGTTCTTATGCTATTTT-TTATGGTTCATT
65 GTCTAAATTTC-TTCATTTAGGTGAAAAAATTTAGTGTTCTTTTGTTTTTTTATTATAGTTCATT
388446 ATGAATATATGTATATAA
129 ATGAATATATGTATAT-A
* * * * * * *
388464 TTTATTGTTTGGTTACCTACAAAGTAAATTACAGTGGGATAACCTTAATTTAGCTACTTTACTTT
1 TTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGTGGGATAAGCTTAATTTAGCTACTTTAATTG
* *
388529 TCTAAATTTCTTCATTTAGGTGAAAAAATTTAGTG-TCTTTTGTTTTTTTTTTATAGTTCTTTAT
66 TCTAAATTTCTTCATTTAGGTGAAAAAATTTAGTGTTCTTTTGTTTTTTTATTATAGTTCATTAT
*
388593 GAATATCT-T-TATA
131 GAATATATGTATATA
* * *
388606 TTTGTTGTTTGGTTACTTAGAAAGTAAATTATAAT-GGATTGAGCTTAATTTAGCTACTTTTATT
1 TTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGTGGGA-TAAGCTTAATTTAGCTACTTTAATT
* ** * * ** *
388670 GTCTAAATTTCGTCATTTAGGTGAAAACTTTTTGTGTTCTTTTG--TTATTAGCA-AGTTTCTTT
65 GTCTAAATTTCTTCATTTAGGTGAAAAAATTTAGTGTTCTTTTGTTTTTTTATTATAG-TTCATT
*
388732 ATGAATATGTGTATATA
129 ATGAATATATGTATATA
* * * *
388749 TTTTGTTGTTTGGTTTCTTAGAAAGCAAATTGTAGTGGGATAAGCTTAATTTAACTACTTTAATT
1 -TTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGTGGGATAAGCTTAATTTAGCTACTTTAATT
* * * * * * *
388814 GTCTAAATTTCGTCGTTTAGGTAAAAAAATTTCGTGTTTCTTTTG--TTATTAGTA-AGTTTATG
65 GTCTAAATTTCTTCATTTAGGTGAAAAAATTTAGTG-TTCTTTTGTTTTTTTATTATAGTTCAT-
* ** *
388876 CACAAACATATGTATATA
128 TATGAATATATGTATATA
* * *
388894 -TTGCTT-TTTGGTTGCTTAGAAAGTAAATTATGGTGGAATAAGCTTAATTTAGCTACTTTAATT
1 TTTG-TTGTTTGGTTACTTAGAAAGTAAATTATAGTGGGATAAGCTTAATTTAGCTACTTTAATT
* *
388957 GTCCAAATTTCGTT-ATTTAGGTG-AAAAATTTAAATGTTCTTTTTGTTTTTTT
65 GTCTAAATTTC-TTCATTTAGGTGAAAAAATTT-AGTGTTC-TTTTGTTTTTTT
389009 GGGTGTTTCT
Statistics
Matches: 456, Mismatches: 71, Indels: 36
0.81 0.13 0.06
Matches are distributed among these distances:
140 2 0.00
141 23 0.05
142 95 0.21
143 92 0.20
144 104 0.23
145 139 0.30
146 1 0.00
ACGTcount: A:0.28, C:0.09, G:0.16, T:0.47
Consensus pattern (145 bp):
TTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGTGGGATAAGCTTAATTTAGCTACTTTAATTG
TCTAAATTTCTTCATTTAGGTGAAAAAATTTAGTGTTCTTTTGTTTTTTTATTATAGTTCATTAT
GAATATATGTATATA
Found at i:388835 original size:286 final size:284
Alignment explanation
Indices: 388280--388984 Score: 733
Period size: 287 Copynumber: 2.4 Consensus size: 284
388270 GGTGAAAAAA
*
388280 TTGTTATTAGTAAGTTTCTTTATGAATTGATCTATATGTTTTGTTGTTTGGTTACTTAGAAAGTA
1 TTGTTATTAGTAAG-TTCTTTATGAA-T-ATCTATAT-ATTTGTTGTTTGGTTACTTAGAAAGTA
** ** * *
388345 AATGGTAGTGGGATAAGCTTAA-GAATGCTAC-TTTAGTTTTCTAAATTTCGTTACTTAGGTGAC
62 AATTATAGT-GGATAAGCTTAATTTA-GCTACTTTTA-TTGTCTAAATTTCGTTATTTAGGTGA-
*** *
388408 AAAAGTTAGTGTTCTTATGCTATTTTTTATGGTTCATTATGAATATATGTATATAATTTATTGTT
123 AAAAGTTAGTGTTCTTATGCTATTTAGCAAGGTTCATTATGAATATATGTATATAATTTATTGTT
* * * *
388473 TGGTTACCTACAAAGTAAATTACAGTGGGATAACCTTAATTTAGCTACTTTACTTTTCTAAATTT
188 TGGTTACCTACAAAGCAAATTACAGTGGGATAACCTTAATTTAACTACTTTAATTGTCTAAATTT
* *
388538 CTTCATTTAGGTGAAAAAATTTAGTG--TCTT
253 CGTCATTTAGGTAAAAAAATTTAGTGTTTCTT
* ** *
388568 TTGTTTTTTTTTTATAGTTCTTTATGAATATCTTTATATTTGTTGTTTGGTTACTTAGAAAGTAA
1 TTG--TTATTAGTA-AGTTCTTTATGAATATCTATATATTTGTTGTTTGGTTACTTAGAAAGTAA
* * *
388633 ATTATAATGGATTGAGCTTAATTTAGCTACTTTTATTGTCTAAATTTCGTCATTTAGGTGAAAAC
63 ATTATAGTGGA-TAAGCTTAATTTAGCTACTTTTATTGTCTAAATTTCGTTATTTAGGTGAAAA-
** * * * * * * * *
388698 TTTTTGTGTTCTTTTGTTA-TTAGCAAGTTTCTTTATGAATATGTGTATATATTTTGTTGTTTGG
126 AGTTAGTGTTCTTATGCTATTTAGCAAGGTTCATTATGAATATATGTATATAATTTATTGTTTGG
* * * ** *
388762 TTTCTTAGAAAGCAAATTGTAGTGGGATAAGCTTAATTTAACTACTTTAATTGTCTAAATTTCGT
191 TTACCTACAAAGCAAATTACAGTGGGATAACCTTAATTTAACTACTTTAATTGTCTAAATTTCGT
* *
388827 CGTTTAGGTAAAAAAATTTCGTGTTTCTT
256 CATTTAGGTAAAAAAATTTAGTGTTTCTT
* ** * *
388856 TTGTTATTAGTAAGTT-TATGCACAAACATATGTATATA-TTGCTT-TTTGGTTGCTTAGAAAGT
1 TTGTTATTAGTAAGTTCT-T-TA-TGA-ATATCTATATATTTG-TTGTTTGGTTACTTAGAAAGT
* * *
388918 AAATTATGGTGGAATAAGCTTAATTTAGCTACTTTAATTGTCCAAATTTCGTTATTTAGGTGAAA
61 AAATTATAGTGG-ATAAGCTTAATTTAGCTACTTTTATTGTCTAAATTTCGTTATTTAGGTGAAA
388983 AA
125 AA
388985 TTTAAATGTT
Statistics
Matches: 344, Mismatches: 58, Indels: 32
0.79 0.13 0.07
Matches are distributed among these distances:
284 1 0.00
285 5 0.01
286 123 0.36
287 161 0.47
288 34 0.10
289 1 0.00
290 17 0.05
291 2 0.01
ACGTcount: A:0.28, C:0.09, G:0.16, T:0.47
Consensus pattern (284 bp):
TTGTTATTAGTAAGTTCTTTATGAATATCTATATATTTGTTGTTTGGTTACTTAGAAAGTAAATT
ATAGTGGATAAGCTTAATTTAGCTACTTTTATTGTCTAAATTTCGTTATTTAGGTGAAAAAGTTA
GTGTTCTTATGCTATTTAGCAAGGTTCATTATGAATATATGTATATAATTTATTGTTTGGTTACC
TACAAAGCAAATTACAGTGGGATAACCTTAATTTAACTACTTTAATTGTCTAAATTTCGTCATTT
AGGTAAAAAAATTTAGTGTTTCTT
Found at i:389003 original size:431 final size:416
Alignment explanation
Indices: 387878--389008 Score: 1202
Period size: 431 Copynumber: 2.7 Consensus size: 416
387868 TTTTTGGTGG
** * *
387878 TTCTTTATGAATATAAGTATATTTTTTGTTGTTTGGTTACTTAGAAAGTAAATTTTAGT-GGATT
1 TTCTTTATGAATATGTGTATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTGTAGTGGGA-T
* * * *
387942 AAGCTTAATTTAGCTACTTTAATCGTCTCAATTTCGTCATTTAGGTGAAAAATTTTAGTGTTCAT
65 AAGCTTAATTTAACTACTTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAAATTTAGTGTTC-T
* * ** * *
388007 TTTG--GTGGT-TCTTTATG-AATATAAGTATATAATTTGTTGTTGGGTTACTTAGAAAGTAAAT
129 TTTGTATTAGTAAGTTTATGAAATATATGTATATAA-TTGTTGTTTGGTTACTTAGAAAGTAAAT
* * * * *
388068 TATAATGGAATAAGCTT-ATGTTAGCTACTTTAATTTCTAAGTTTGGTCATTTAGGTGAAAAACA
193 TATAGTGGAATAAGCTTAAT-TTAGCTACTTTAATTTCTAAATTTCGTTATTTAGGTGAAAAA-T
* *
388132 TTAGTGTTCTTCTGCTTTTTTTTTTTATGGTTCTTTATGAATATATGTATATAATTTGTTGTTTG
256 TTAGTGTTCTTTTG--TTTTTTTTTTATAGTTCTTTATGAATATATGTATATAATTTGTTGTTTG
* *
388197 TTTACTTAGAAAGTAAATTATAGTGGGATAAGCTTAATTTACACTACTTTAATTGTCTAAATTTC
319 GTTACTTAGAAAGTAAATTATAATGGGATAAGCTTAATTTACACTACTTTAATTGTCTAAATTTC
*
388262 GTCATTTAGGTGAAAAAATTGTTATTAGTAAGT
384 GTCATTTAGGTGAAAAAATTGTTATTAGCAAGT
* * *
388295 TTCTTTATGAAT-TGATCTATATGTTTTGTTGTTTGGTTACTTAGAAAGTAAATGGTAGTGGGAT
1 TTCTTTATGAATATG-TGTATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTGTAGTGGGAT
* * * * * * *
388359 AAGCTTAA--GAATGCTACTTTAGTTTTCTAAATTTCGTTACTTAGGTGACAAAAGTTAGTGTTC
65 AAGCTTAATTTAA--CTACTTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAAATTTAGTGTTC
* ** * * * *
388422 TTATGCTATTTTTTATGGTTCATTATG-AATATATGTATATAATTTATTGTTTGGTTACCTACAA
128 TTTTG-TA-TTAGTA-AG-T--TTATGAAATATATGTATATAA-TTGTTGTTTGGTTACTTAGAA
* * * *
388486 AGTAAATTACAGTGGGATAACCTTAATTTAGCTACTTTACTTTTCTAAATTTC-TTCATTTAGGT
186 AGTAAATTATAGTGGAATAAGCTTAATTTAGCTACTTTA-ATTTCTAAATTTCGTT-ATTTAGGT
*
388550 GAAAAAATTTAGTG-TCTTTTGTTTTTTTTTTATAGTTCTTTATGAATATCT-T-TAT-ATTTGT
249 G-AAAAATTTAGTGTTCTTTTGTTTTTTTTTTATAGTTCTTTATGAATATATGTATATAATTTGT
* * *
388611 TGTTTGGTTACTTAGAAAGTAAATTATAAT-GGATTGAGCTTAATTTA-GCTACTTTTATTGTCT
313 TGTTTGGTTACTTAGAAAGTAAATTATAATGGGA-TAAGCTTAATTTACACTACTTTAATTGTCT
**
388674 AAATTTCGTCATTTAGGTGAAAACTTTTTGTGTTCTTTTGTTATTAGCAAGT
377 AAATTTCGTCATTTAGGTGAAAA------------AATTGTTATTAGCAAGT
* *
388726 TTCTTTATGAATATGTGTATATATTTTGTTGTTTGGTTTCTTAGAAAGCAAATTGTAGTGGGATA
1 TTCTTTATGAATATGTGTATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTGTAGTGGGATA
* * *
388791 AGCTTAATTTAACTACTTTAATTGTCTAAATTTCGTCGTTTAGGTAAAAAAATTTCGTGTTTCTT
66 AGCTTAATTTAACTACTTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAAATTTAGTG-TTCTT
* *
388856 TTGTTATTAGTAAGTTTATGCACAAACATATGTATAT-ATTGCTT-TTTGGTTGCTTAGAAAGTA
130 TTG-TATTAGTAAGTTTATG---AAATATATGTATATAATTG-TTGTTTGGTTACTTAGAAAGTA
* *
388919 AATTATGGTGGAATAAGCTTAATTTAGCTACTTTAATTGTCCAAATTTCGTTATTTAGGTGAAAA
190 AATTATAGTGGAATAAGCTTAATTTAGCTACTTTAATT-TCTAAATTTCGTTATTTAGGTGAAAA
*
388984 ATTTAAATGTTCTTTTTGTTTTTTT
254 ATTT-AGTGTTC-TTTTGTTTTTTT
389009 GGGTGTTTCT
Statistics
Matches: 590, Mismatches: 80, Indels: 74
0.79 0.11 0.10
Matches are distributed among these distances:
415 1 0.00
416 5 0.01
417 101 0.17
418 3 0.01
419 40 0.07
420 48 0.08
421 3 0.01
422 1 0.00
423 29 0.05
425 76 0.13
426 27 0.05
427 10 0.02
428 10 0.02
429 71 0.12
430 8 0.01
431 144 0.24
432 11 0.02
433 2 0.00
ACGTcount: A:0.28, C:0.08, G:0.16, T:0.47
Consensus pattern (416 bp):
TTCTTTATGAATATGTGTATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTGTAGTGGGATA
AGCTTAATTTAACTACTTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAAATTTAGTGTTCTTT
TGTATTAGTAAGTTTATGAAATATATGTATATAATTGTTGTTTGGTTACTTAGAAAGTAAATTAT
AGTGGAATAAGCTTAATTTAGCTACTTTAATTTCTAAATTTCGTTATTTAGGTGAAAAATTTAGT
GTTCTTTTGTTTTTTTTTTATAGTTCTTTATGAATATATGTATATAATTTGTTGTTTGGTTACTT
AGAAAGTAAATTATAATGGGATAAGCTTAATTTACACTACTTTAATTGTCTAAATTTCGTCATTT
AGGTGAAAAAATTGTTATTAGCAAGT
Found at i:392433 original size:4 final size:4
Alignment explanation
Indices: 392424--392500 Score: 57
Period size: 4 Copynumber: 19.0 Consensus size: 4
392414 TGCATAGGAT
* * ** * *
392424 TGTA TGTA TGTA TGTA TGTA TGTA TTTT TGGTA -AAA TGTA TGTA TATG
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA T-GTA TGTA TGTA TGTA TGTA
* *
392472 TGTTA TGTA TGTA TGCA TGCA TGTA TGTA
1 TG-TA TGTA TGTA TGTA TGTA TGTA TGTA
392501 CATAAGAGGA
Statistics
Matches: 56, Mismatches: 14, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
3 1 0.02
4 51 0.91
5 4 0.07
ACGTcount: A:0.26, C:0.03, G:0.23, T:0.48
Consensus pattern (4 bp):
TGTA
Found at i:394322 original size:16 final size:16
Alignment explanation
Indices: 394297--394342 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
394287 ATTTAACTCC
*
394297 AAAAGTGGAAGAAACAA
1 AAAAGAGGAAGAAA-AA
394314 AAAAG-GGAAGAAAAA
1 AAAAGAGGAAGAAAAA
*
394329 AAGAGAGGAAGAAA
1 AAAAGAGGAAGAAA
394343 TGCTTTTCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 6 0.22
16 16 0.59
17 5 0.19
ACGTcount: A:0.67, C:0.02, G:0.28, T:0.02
Consensus pattern (16 bp):
AAAAGAGGAAGAAAAA
Found at i:394860 original size:189 final size:178
Alignment explanation
Indices: 394513--394861 Score: 450
Period size: 189 Copynumber: 1.9 Consensus size: 178
394503 CTGTCTCTCC
*
394513 AAAACAGAGGATAAGCTCTCTCAAGGTCCCTCCTCCTCTTATATACACATTCATCATATCTACAT
1 AAAACAGAGGATAAGCTCTCTCAAGCTCCCTCCTCCTCTTATATA-ACATTCATCATATCTACAT
* *
394578 ACTTATACACATCACATAATACATAAGCATCATCATCCATATGTTCCATGTATCTTTGAGAAGTA
65 AATTATACACATCACATAATACATAAGCATCATCATCCATATGTTCCATGTATCTTTGAGAAGCA
*
394643 TACTCAAAGCTTGTAATCTGTTTCTTTTTTATTTTCTTGGGTTATATCA
130 TACCCAAAGCTTGTAATCTGTTTCTTTTTTATTTTCTTGGGTTATATCA
* * * **
394692 AAAACAGAGGATAAGCTTTCTCAAGCTCTCT-TTTTTCTTATAT-ACATTCATCATGTATACGTA
1 AAAACAGAGGATAAGCTCTCTCAAGCTCCCTCCTCCTCTTATATAACATTCATCA--TAT-C-TA
* *
394755 CATATATATATACACATCACATAATACATAAGCATCATCATCGTCCATTTGTTCTATGTATGCAT
62 CATA-AT-TATACACATCACATAATACATAAGCATCATCA---TCCATATGTTCCATGTAT-C-T
*
394820 GGTTTAGAAGCATACCCAAAGCTTGTAATCTGTTTCTTTTTT
120 --TTGAGAAGCATACCCAAAGCTTGTAATCTGTTTCTTTTTT
394862 TCTTTGTTTT
Statistics
Matches: 145, Mismatches: 12, Indels: 16
0.84 0.07 0.09
Matches are distributed among these distances:
176 10 0.07
178 12 0.08
179 29 0.20
180 6 0.04
181 1 0.01
182 32 0.22
185 16 0.11
186 1 0.01
187 1 0.01
189 37 0.26
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.38
Consensus pattern (178 bp):
AAAACAGAGGATAAGCTCTCTCAAGCTCCCTCCTCCTCTTATATAACATTCATCATATCTACATA
ATTATACACATCACATAATACATAAGCATCATCATCCATATGTTCCATGTATCTTTGAGAAGCAT
ACCCAAAGCTTGTAATCTGTTTCTTTTTTATTTTCTTGGGTTATATCA
Found at i:395182 original size:4 final size:4
Alignment explanation
Indices: 395173--395210 Score: 69
Period size: 4 Copynumber: 9.8 Consensus size: 4
395163 TTCCTCTTTT
395173 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA- ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
395211 AGCATCATCA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.09
4 30 0.91
ACGTcount: A:0.53, C:0.21, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:395527 original size:30 final size:31
Alignment explanation
Indices: 395487--395545 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
395477 CAATACGGTG
395487 GGTACTCGAGCTCGGGTGTAAATATCGGAAA
1 GGTACTCGAGCTCGGGTGTAAATATCGGAAA
* *
395518 GGTAC-CGAGCTCGTGTGTAAATTTCGGA
1 GGTACTCGAGCTCGGGTGTAAATATCGGA
395546 TACAGGTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.25, C:0.17, G:0.32, T:0.25
Consensus pattern (31 bp):
GGTACTCGAGCTCGGGTGTAAATATCGGAAA
Found at i:401278 original size:34 final size:34
Alignment explanation
Indices: 401240--401309 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
401230 AGATATCAAA
401240 AGTTTGGTGCAGAGAAGAATTAATTAAAGAAAAG
1 AGTTTGGTGCAGAGAAGAATTAATTAAAGAAAAG
401274 AGTTTGGTGCAGAGAAGAATTAATTAAAGAAAAG
1 AGTTTGGTGCAGAGAAGAATTAATTAAAGAAAAG
401308 AG
1 AG
401310 AAAACAAATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.47, C:0.03, G:0.27, T:0.23
Consensus pattern (34 bp):
AGTTTGGTGCAGAGAAGAATTAATTAAAGAAAAG
Found at i:405672 original size:23 final size:23
Alignment explanation
Indices: 405646--405690 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
405636 CTAAAACCAT
405646 ATTA-TCCCTAAAAAATAGGTTTC
1 ATTATTCCCTAAAAAA-AGGTTTC
* *
405669 ATTATTCTCTATAAAAAGGTTT
1 ATTATTCCCTAAAAAAAGGTTT
405691 AATTTTGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (23 bp):
ATTATTCCCTAAAAAAAGGTTTC
Found at i:408506 original size:22 final size:22
Alignment explanation
Indices: 408494--408536 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
408484 TGCTGTTGTT
*
408494 TTGCTAATATTTTGTTATTATA
1 TTGCTAATATTTTGTTGTTATA
*
408516 TTGCTAATTTTTTGTTGTTAT
1 TTGCTAATATTTTGTTGTTAT
408537 TATTTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.05, G:0.12, T:0.63
Consensus pattern (22 bp):
TTGCTAATATTTTGTTGTTATA
Found at i:410806 original size:12 final size:12
Alignment explanation
Indices: 410781--410814 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
410771 TCTCATACAC
*
410781 AAAAAA-AAAGA
1 AAAAAAGAAAAA
410792 AAAAAAGAAAAA
1 AAAAAAGAAAAA
410804 AAAAAAGAAAA
1 AAAAAAGAAAA
410815 CAGCAACAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 6 0.29
12 15 0.71
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAAA
Found at i:413208 original size:15 final size:14
Alignment explanation
Indices: 413186--413216 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
413176 TAATATATTT
*
413186 GGAAAATTTTTAGA
1 GGAAAAATTTTAGA
413200 GGAAAAATTTTAGA
1 GGAAAAATTTTAGA
413214 GGA
1 GGA
413217 TCATATTCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.26, T:0.29
Consensus pattern (14 bp):
GGAAAAATTTTAGA
Found at i:414325 original size:17 final size:18
Alignment explanation
Indices: 414300--414339 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
414290 ATTAATGTGG
*
414300 AAAAATGTTCTC-AATAT
1 AAAATTGTTCTCTAATAT
*
414317 AAAATTGTTCTCTCATAT
1 AAAATTGTTCTCTAATAT
414335 AAAAT
1 AAAAT
414340 CAAAAGCTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (18 bp):
AAAATTGTTCTCTAATAT
Found at i:417898 original size:15 final size:15
Alignment explanation
Indices: 417888--417917 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
417878 TCCCTTCTTG
417888 ACCACGACCTTTTCC
1 ACCACGACCTTTTCC
*
417903 ACCACGACCATTTCC
1 ACCACGACCTTTTCC
417918 TCGATCTCCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.47, G:0.07, T:0.23
Consensus pattern (15 bp):
ACCACGACCTTTTCC
Found at i:418681 original size:17 final size:18
Alignment explanation
Indices: 418656--418695 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
418646 CAAATTGTGG
*
418656 AAAAATGTTCTC-AATAT
1 AAAATTGTTCTCTAATAT
*
418673 AAAATTGTTCTCTCATAT
1 AAAATTGTTCTCTAATAT
418691 AAAAT
1 AAAAT
418696 CAAAAGCTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (18 bp):
AAAATTGTTCTCTAATAT
Found at i:418874 original size:15 final size:15
Alignment explanation
Indices: 418854--418884 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
418844 AAAACAATAT
*
418854 AACTCTTGACCTTTC
1 AACTCTTGACATTTC
418869 AACTCTTGACATTTC
1 AACTCTTGACATTTC
418884 A
1 A
418885 CTTACATGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.29, G:0.06, T:0.39
Consensus pattern (15 bp):
AACTCTTGACATTTC
Found at i:424505 original size:7 final size:8
Alignment explanation
Indices: 424476--424502 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
424466 GATCCATTGA
424476 AAAATTAT
1 AAAATTAT
424484 AAAATTAT
1 AAAATTAT
424492 AAAATTAT
1 AAAATTAT
424500 AAA
1 AAA
424503 TTAGCCCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
AAAATTAT
Done.