Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold72
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: 5928628
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 261288 characters in sequence are not A, C, G, or T
File 25 of 39
Found at i:3660891 original size:19 final size:18
Alignment explanation
Indices: 3660869--3660904 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
3660859 TTTTTAGAAA
*
3660869 AATATAAATATAAATATGT
1 AATACAAATA-AAATATGT
3660888 AATACAAATAAAATATG
1 AATACAAATAAAATATG
3660905 ATAGGAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.31
Consensus pattern (18 bp):
AATACAAATAAAATATGT
Found at i:3660976 original size:21 final size:22
Alignment explanation
Indices: 3660954--3660995 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
3660944 TAAAAATGTA
3660954 AAAT-TTAATAAT-TTTTAATT
1 AAATATTAATAATATTTTAATT
3660974 AAATATTAATAATATTTTAATT
1 AAATATTAATAATATTTTAATT
3660996 TTTAAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 4 0.20
21 8 0.40
22 8 0.40
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
AAATATTAATAATATTTTAATT
Found at i:3660993 original size:18 final size:17
Alignment explanation
Indices: 3660972--3661022 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 17
3660962 TAATTTTTAA
3660972 TTAAATATTAATAATA-TT
1 TTAAAT-TTAA-AATATTT
*
3660990 TTAATTTTTAAAATTATTT
1 TTAA-ATTTAAAA-TATTT
3661009 TTAAATTTAAAATA
1 TTAAATTTAAAATA
3661023 AAAAACACTC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
17 4 0.14
18 17 0.61
19 7 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAAATTTAAAATATTT
Found at i:3662061 original size:20 final size:20
Alignment explanation
Indices: 3662038--3662118 Score: 74
Period size: 20 Copynumber: 4.0 Consensus size: 20
3662028 ATCTATTAAA
3662038 AATTTATAAAAATTAAATTT
1 AATTTATAAAAATTAAATTT
* *
3662058 AA-TTATTAAAAAATAATTTT
1 AATTTA-TAAAAATTAAATTT
* *
3662078 ATTTTTATAAAAATTAATTTT
1 A-ATTTATAAAAATTAAATTT
* * *
3662099 AATTAATAATATTTAAATTT
1 AATTTATAAAAATTAAATTT
3662119 TTGCCTTCTT
Statistics
Matches: 49, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
19 3 0.06
20 29 0.59
21 14 0.29
22 3 0.06
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AATTTATAAAAATTAAATTT
Found at i:3662065 original size:30 final size:31
Alignment explanation
Indices: 3662006--3662074 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 31
3661996 ATATATATAT
*
3662006 AAATTAATATAAAATTTATTTAATCTATTAA
1 AAATTAATATAAAATTAATTTAATCTATTAA
*
3662037 AAATTTATA-AAAATTAAATTTAAT-TATTAA
1 AAATTAATATAAAATT-AATTTAATCTATTAA
*
3662067 AAAATAAT
1 AAATTAAT
3662075 TTTATTTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 18 0.55
31 15 0.45
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (31 bp):
AAATTAATATAAAATTAATTTAATCTATTAA
Found at i:3662071 original size:21 final size:22
Alignment explanation
Indices: 3662041--3662103 Score: 78
Period size: 19 Copynumber: 3.0 Consensus size: 22
3662031 TATTAAAAAT
3662041 TTATAAAAATTAAATTTAATTA
1 TTATAAAAATTAAATTTAATTA
* *
3662063 TTA-AAAAA-T-AATTTTATTT
1 TTATAAAAATTAAATTTAATTA
*
3662082 TTATAAAAATTAATTTTAATTA
1 TTATAAAAATTAAATTTAATTA
3662104 ATAATATTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
19 11 0.33
20 6 0.18
21 6 0.18
22 10 0.30
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TTATAAAAATTAAATTTAATTA
Found at i:3667466 original size:17 final size:18
Alignment explanation
Indices: 3667434--3667468 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
3667424 CCTCTCACTT
3667434 AAAAAATTATCACTTTTTA
1 AAAAAATTAT-ACTTTTTA
3667453 AAAAAATTAT-CTTTTT
1 AAAAAATTATACTTTTT
3667469 TTAACCTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
19 10 0.62
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.46
Consensus pattern (18 bp):
AAAAAATTATACTTTTTA
Found at i:3667496 original size:2 final size:2
Alignment explanation
Indices: 3667489--3667524 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
3667479 GCTCCATTAA
*
3667489 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3667525 TTCTTTTTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3667827 original size:28 final size:28
Alignment explanation
Indices: 3667776--3667829 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
3667766 AATAAATTAT
* * *
3667776 TTTATATTTTTAATATTTTCATAATTGA
1 TTTATATTTTTAAAAATTTAATAATTGA
3667804 TTTATATTTTTAAAAATTTAATAATT
1 TTTATATTTTTAAAAATTTAATAATT
3667830 CATATATTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (28 bp):
TTTATATTTTTAAAAATTTAATAATTGA
Found at i:3669990 original size:14 final size:14
Alignment explanation
Indices: 3669973--3670021 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
3669963 TTTAATTTTA
3669973 TAAAAATAATATAT
1 TAAAAATAATATAT
* *
3669987 TAAATATAATTTAT
1 TAAAAATAATATAT
** *
3670001 TTTAAATAATAAAT
1 TAAAAATAATATAT
3670015 TAAAAAT
1 TAAAAAT
3670022 TTAATTAATA
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TAAAAATAATATAT
Found at i:3670271 original size:33 final size:33
Alignment explanation
Indices: 3670234--3670320 Score: 124
Period size: 33 Copynumber: 2.6 Consensus size: 33
3670224 TATTATAATT
3670234 ATATTTAA-ATATTTTATATTTATATAAATTTTA
1 ATATTTAATA-ATTTTATATTTATATAAATTTTA
3670267 ATATTTTAATAATTTTATA-TTATATAAATTTTA
1 ATA-TTTAATAATTTTATATTTATATAAATTTTA
*
3670300 AAATATTAATAATTTTATATT
1 ATAT-TTAATAATTTTATATT
3670321 ATTCTATATT
Statistics
Matches: 49, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
32 1 0.02
33 33 0.67
34 14 0.29
35 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (33 bp):
ATATTTAATAATTTTATATTTATATAAATTTTA
Found at i:3670272 original size:8 final size:8
Alignment explanation
Indices: 3670234--3670320 Score: 56
Period size: 8 Copynumber: 10.6 Consensus size: 8
3670224 TATTATAATT
*
3670234 ATATTTAA
1 ATATTTTA
3670242 ATATTTT-
1 ATATTTTA
3670249 ATATTTATA
1 ATATTT-TA
*
3670258 TAAATTTTA
1 -ATATTTTA
3670267 ATATTTTA
1 ATATTTTA
3670275 ATAATTTT-
1 AT-ATTTTA
3670283 ATATTATATA
1 ATATT-T-TA
3670293 A-ATTTTA
1 ATATTTTA
* *
3670300 AAATATTA
1 ATATTTTA
3670308 ATAATTTT-
1 AT-ATTTTA
3670316 ATATT
1 ATATT
3670321 ATTCTATATT
Statistics
Matches: 64, Mismatches: 6, Indels: 19
0.72 0.07 0.21
Matches are distributed among these distances:
7 15 0.23
8 28 0.44
9 15 0.23
10 6 0.09
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (8 bp):
ATATTTTA
Found at i:3670287 original size:41 final size:42
Alignment explanation
Indices: 3670242--3670333 Score: 100
Period size: 43 Copynumber: 2.2 Consensus size: 42
3670232 TTATATTTAA
* * *
3670242 ATATTT-TATATTTATATAAATTTTAAT-ATTTTA-ATAATTTT
1 ATATTTATAAATTT-TA-AAATATTAATAATTTTATATAATTCT
*
3670283 ATATTATATAAATTTTAAAATATTAATAATTTTATATTATTCT
1 ATATT-TATAAATTTTAAAATATTAATAATTTTATATAATTCT
3670326 ATATTTAT
1 ATATTTAT
3670334 TTATTTTTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
41 14 0.33
42 12 0.28
43 17 0.40
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (42 bp):
ATATTTATAAATTTTAAAATATTAATAATTTTATATAATTCT
Found at i:3670321 original size:33 final size:33
Alignment explanation
Indices: 3670244--3670322 Score: 131
Period size: 33 Copynumber: 2.4 Consensus size: 33
3670234 ATATTTAAAT
* *
3670244 ATTTTATATTTATATAAATTTTAATATTTTAATA
1 ATTTTATA-TTATATAAATTTTAAAATATTAATA
3670278 ATTTTATATTATATAAATTTTAAAATATTAATA
1 ATTTTATATTATATAAATTTTAAAATATTAATA
3670311 ATTTTATATTAT
1 ATTTTATATTAT
3670323 TCTATATTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
33 35 0.81
34 8 0.19
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (33 bp):
ATTTTATATTATATAAATTTTAAAATATTAATA
Found at i:3670323 original size:17 final size:16
Alignment explanation
Indices: 3670232--3670320 Score: 76
Period size: 17 Copynumber: 5.4 Consensus size: 16
3670222 GATATTATAA
*
3670232 TTATATTTAAAT-ATT
1 TTATATTTTAATAATT
3670247 TTATA-TTTATATAAATT
1 TTATATTTTA-AT-AATT
3670264 TTAATATTTTAATAATT
1 TT-ATATTTTAATAATT
*
3670281 TTATATTAT-ATAAATT
1 TTATATTTTAAT-AATT
* *
3670297 TTAAAATATTAATAATT
1 TT-ATATTTTAATAATT
3670314 TTATATT
1 TTATATT
3670321 ATTCTATATT
Statistics
Matches: 59, Mismatches: 7, Indels: 15
0.73 0.09 0.19
Matches are distributed among these distances:
14 3 0.05
15 9 0.15
16 15 0.25
17 21 0.36
18 7 0.12
19 4 0.07
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTATATTTTAATAATT
Found at i:3670705 original size:30 final size:31
Alignment explanation
Indices: 3670671--3670729 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 31
3670661 AAATATAAAA
3670671 ATATAT-TAAAATTTATATA-AAATATTTTTG
1 ATATATCT-AAATTTATATATAAATATTTTTG
* *
3670701 ATATATCTTAATTTATATATTAATATTTT
1 ATATATCTAAATTTATATATAAATATTTT
3670730 AAATATAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 16 0.64
31 9 0.36
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (31 bp):
ATATATCTAAATTTATATATAAATATTTTTG
Found at i:3671408 original size:6 final size:6
Alignment explanation
Indices: 3671343--3671467 Score: 68
Period size: 6 Copynumber: 20.8 Consensus size: 6
3671333 AAATAATTGA
* * *
3671343 TATATT TTTATT ATATTTT TATATT T-TATT T-TA-T TATAAT TATATT
1 TATATT TATATT -TATATT TATATT TATATT TATATT TATATT TATATT
* * *
3671389 TA-AAT TAT-TT TATATT TATATA AAT-TT TAATATAT TAATAATT TATATTTT
1 TATATT TATATT TATATT TATATT TATATT T-ATAT-T T-AT-ATT TATA--TT
3671440 TAATATT T-TATT TATA-T TATATT TATAT
1 T-ATATT TATATT TATATT TATATT TATAT
3671468 AATGACCTAA
Statistics
Matches: 94, Mismatches: 11, Indels: 28
0.71 0.08 0.21
Matches are distributed among these distances:
4 2 0.02
5 28 0.30
6 39 0.41
7 10 0.11
8 10 0.11
9 5 0.05
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
TATATT
Found at i:3671442 original size:16 final size:15
Alignment explanation
Indices: 3671356--3671452 Score: 58
Period size: 14 Copynumber: 6.3 Consensus size: 15
3671346 ATTTTTATTA
3671356 TATTTTT-AT-ATTT
1 TATTTTTAATAATTT
* *
3671369 TATTTTATTATAATTA
1 TATTTT-TAATAATTT
* *
3671385 TA-TTTAAATTATTT
1 TATTTTTAATAATTT
*
3671399 TATATTTATATAAATTT
1 TATTTTTA-AT-AATTT
*
3671416 TAATATATTAATAATTT
1 T-AT-TTTTAATAATTT
3671433 ATATTTTTAAT-ATTT
1 -TATTTTTAATAATTT
3671448 TATTT
1 TATTT
3671453 ATATTATATT
Statistics
Matches: 64, Mismatches: 11, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
13 6 0.09
14 13 0.20
15 12 0.19
16 13 0.20
17 12 0.19
18 5 0.08
19 3 0.05
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TATTTTTAATAATTT
Found at i:3671450 original size:43 final size:45
Alignment explanation
Indices: 3671334--3671450 Score: 100
Period size: 43 Copynumber: 2.6 Consensus size: 45
3671324 ATTCATCAGA
** *
3671334 AATAATTGATATATTTTTATTATATTTTTATATTTTATTTTATTATAATT
1 AATAATT--TATATTTTTA--ATA-TTTTATATTAAATTTTAATATAATT
* *
3671384 -AT-ATTTAAATTATTTTATA-TTTATA-TAAATTTTAATAT-ATT
1 AATAATTTATATT-TTTAATATTTTATATTAAATTTTAATATAATT
3671425 AATAATTTATATTTTTAATATTTTAT
1 AATAATTTATATTTTTAATATTTTAT
3671451 TTATATTATA
Statistics
Matches: 56, Mismatches: 7, Indels: 15
0.72 0.09 0.19
Matches are distributed among these distances:
41 3 0.05
42 18 0.32
43 19 0.34
45 3 0.05
46 5 0.09
47 3 0.05
48 3 0.05
49 2 0.04
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.62
Consensus pattern (45 bp):
AATAATTTATATTTTTAATATTTTATATTAAATTTTAATATAATT
Found at i:3671456 original size:33 final size:31
Alignment explanation
Indices: 3671392--3671467 Score: 86
Period size: 33 Copynumber: 2.4 Consensus size: 31
3671382 TTATATTTAA
3671392 ATTAT-TTTATATTTATATAAATTTTAATAT
1 ATTATATTTATATTTATATAAATTTTAATAT
*
3671422 ATTAATAATTTATATTT-T-TAATATTTTATTTAT
1 ATT-AT-ATTTATATTTATATAA-ATTTTA-ATAT
3671455 ATTATATTTATAT
1 ATTATATTTATAT
3671468 AATGACCTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
30 3 0.08
31 13 0.32
32 9 0.22
33 15 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (31 bp):
ATTATATTTATATTTATATAAATTTTAATAT
Found at i:3671461 original size:16 final size:16
Alignment explanation
Indices: 3671361--3671463 Score: 74
Period size: 16 Copynumber: 6.5 Consensus size: 16
3671351 TATTATATTT
3671361 TTATATTTTATTT-TA
1 TTATATTTTATTTATA
* *
3671376 TTATAATTATATTTAAA
1 TTAT-ATTTTATTTATA
3671393 TTAT-TTTATATTTATA
1 TTATATTT-TATTTATA
* *
3671409 -TAAATTTTA-ATATA
1 TTATATTTTATTTATA
3671423 TTAATAATTTATATTT-T-
1 TT-AT-ATTT-TATTTATA
*
3671440 TAATATTTTATTTATA
1 TTATATTTTATTTATA
3671456 TTATATTT
1 TTATATTT
3671464 ATATAATGAC
Statistics
Matches: 67, Mismatches: 10, Indels: 21
0.68 0.10 0.21
Matches are distributed among these distances:
14 9 0.13
15 16 0.24
16 28 0.42
17 10 0.15
18 3 0.04
19 1 0.01
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTATATTTTATTTATA
Found at i:3671462 original size:11 final size:11
Alignment explanation
Indices: 3671343--3671467 Score: 72
Period size: 11 Copynumber: 12.0 Consensus size: 11
3671333 AAATAATTGA
*
3671343 TATATTTTTAT
1 TATATTTATAT
3671354 TATA-TT-T-T
1 TATATTTATAT
3671362 TATATTT-TAT
1 TATATTTATAT
*
3671372 TTTA-TTATAAT
1 TATATTTAT-AT
*
3671383 TATATTTAAAT
1 TATATTTATAT
3671394 TAT-TTTATAT
1 TATATTTATAT
* *
3671404 T-TATATAAAT
1 TATATTTATAT
* *
3671414 TTTA-ATATAT
1 TATATTTATAT
3671424 TAATAATTTATAT
1 T-AT-ATTTATAT
*
3671437 T-T-TTAATAT
1 TATATTTATAT
*
3671446 TTTATTTATAT
1 TATATTTATAT
3671457 TATATTTATAT
1 TATATTTATAT
3671468 AATGACCTAA
Statistics
Matches: 90, Mismatches: 12, Indels: 24
0.71 0.10 0.19
Matches are distributed among these distances:
8 5 0.06
9 14 0.16
10 27 0.30
11 34 0.38
12 4 0.04
13 6 0.07
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TATATTTATAT
Found at i:3671470 original size:27 final size:27
Alignment explanation
Indices: 3671345--3671470 Score: 76
Period size: 27 Copynumber: 4.9 Consensus size: 27
3671335 ATAATTGATA
*
3671345 TATTTTTATTATATTT-T-T-ATATTT
1 TATTTATATTATATTTATATAATATTT
3671369 TATTT-TATTATA---AT-T-ATATTT
1 TATTTATATTATATTTATATAATATTT
* * *
3671390 AAATTATTTTATATTTATATAA-ATTT
1 TATTTATATTATATTTATATAATATTT
*
3671416 TA-ATATATTAATAATTTATATTTTTAATATTT
1 TATTTATATT-AT-ATTTATA----TAATATTT
3671448 TATTTATATTATATTTATATAAT
1 TATTTATATTATATTTATATAAT
3671471 GACCTAAGAA
Statistics
Matches: 80, Mismatches: 7, Indels: 27
0.70 0.06 0.24
Matches are distributed among these distances:
21 11 0.14
22 6 0.08
23 7 0.09
24 5 0.06
25 7 0.09
26 8 0.10
27 12 0.15
31 10 0.12
32 8 0.10
33 6 0.08
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (27 bp):
TATTTATATTATATTTATATAATATTT
Found at i:3680653 original size:2 final size:2
Alignment explanation
Indices: 3680646--3680680 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3680636 CATCTCTTGC
3680646 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
3680681 CTGGAGCTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3685537 original size:13 final size:13
Alignment explanation
Indices: 3685521--3685547 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3685511 GGAGAAATCC
3685521 AAAAAAGAAAAAA
1 AAAAAAGAAAAAA
3685534 AAAAAAGAAAAAA
1 AAAAAAGAAAAAA
3685547 A
1 A
3685548 TGCAGATAGT
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:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAA
Found at i:3687845 original size:23 final size:23
Alignment explanation
Indices: 3687819--3687886 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 23
3687809 TAATATTTAA
3687819 TAATTAAAAAAATTATTTAAATT
1 TAATTAAAAAAATTATTTAAATT
* *
3687842 TAATT-ATAAAA-TATATAAATAT
1 TAATTAAAAAAATTATTTAAAT-T
*
3687864 TAA-TATAAAATATT-TTTAAATT
1 TAATTA-AAAAAATTATTTAAATT
3687886 T
1 T
3687887 TTATTAATTA
Statistics
Matches: 36, Mismatches: 5, Indels: 9
0.72 0.10 0.18
Matches are distributed among these distances:
21 9 0.25
22 11 0.31
23 15 0.42
24 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
TAATTAAAAAAATTATTTAAATT
Found at i:3687870 original size:21 final size:21
Alignment explanation
Indices: 3687827--3687876 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
3687817 AATAATTAAA
*
3687827 AAAATTATTTAAATTTAATTAT
1 AAAA-TATATAAATTTAATTAT
3687849 AAAATATATAAATATTAA-TAT
1 AAAATATATAAAT-TTAATTAT
3687870 AAAATAT
1 AAAATAT
3687877 TTTTAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 18 0.69
22 8 0.31
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AAAATATATAAATTTAATTAT
Found at i:3688587 original size:12 final size:13
Alignment explanation
Indices: 3688554--3688587 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
3688544 TAAATTTAAT
3688554 TATAATATAAAAA
1 TATAATATAAAAA
3688567 TACTAATATAAAAA
1 TA-TAATATAAAAA
3688581 T-TAATAT
1 TATAATAT
3688588 TTTAATAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 6 0.30
13 2 0.10
14 12 0.60
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (13 bp):
TATAATATAAAAA
Found at i:3691950 original size:13 final size:13
Alignment explanation
Indices: 3691931--3691962 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
3691921 CCTTTAGGAT
3691931 CTTTTTTTTTT--
1 CTTTTTTTTTTAA
3691942 CTTTTTTTTTTAA
1 CTTTTTTTTTTAA
3691955 CTTTTTTT
1 CTTTTTTT
3691963 CGGTATTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.58
13 8 0.42
ACGTcount: A:0.06, C:0.09, G:0.00, T:0.84
Consensus pattern (13 bp):
CTTTTTTTTTTAA
Found at i:3692656 original size:23 final size:22
Alignment explanation
Indices: 3692599--3692656 Score: 55
Period size: 23 Copynumber: 2.5 Consensus size: 22
3692589 AAATATAATT
* * *
3692599 ATATAAATATGTTACATATATT
1 ATATAAATATATAACATATATA
3692621 ATCATTAAA-ATATAACATAATATA
1 AT-A-TAAATATATAACAT-ATATA
3692645 ATATAAATATAT
1 ATATAAATATAT
3692657 TATTAAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
22 6 0.21
23 13 0.45
24 10 0.34
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (22 bp):
ATATAAATATATAACATATATA
Found at i:3692852 original size:21 final size:21
Alignment explanation
Indices: 3692826--3692868 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
3692816 TAAATTCAGT
3692826 TTTAATTTAATTTT-TATTGAA
1 TTTAATTTAATTTTAT-TTGAA
*
3692847 TTTAATTTTATTTTATTTGAA
1 TTTAATTTAATTTTATTTGAA
3692868 T
1 T
3692869 AATCATTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (21 bp):
TTTAATTTAATTTTATTTGAA
Found at i:3693952 original size:13 final size:12
Alignment explanation
Indices: 3693903--3693953 Score: 57
Period size: 12 Copynumber: 3.9 Consensus size: 12
3693893 ACCTTCACTG
3693903 TTTCAAATTGAA
1 TTTCAAATTGAA
*
3693915 TTTCAACATTTACTA
1 TTTCAA-ATTGA--A
3693930 TTTCAAATTGAA
1 TTTCAAATTGAA
3693942 TTTCAAAATTGA
1 TTTC-AAATTGA
3693954 CGGCACAGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
12 11 0.33
13 11 0.33
14 4 0.12
15 7 0.21
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.43
Consensus pattern (12 bp):
TTTCAAATTGAA
Found at i:3695737 original size:89 final size:89
Alignment explanation
Indices: 3695586--3695767 Score: 364
Period size: 89 Copynumber: 2.0 Consensus size: 89
3695576 TTCTTGCATG
3695586 GCTTTAATCCAACAATCTTTATCTTTGTGAAATTGTACTTCTTCGAAGCTTTCTGGCTCCCCCTC
1 GCTTTAATCCAACAATCTTTATCTTTGTGAAATTGTACTTCTTCGAAGCTTTCTGGCTCCCCCTC
3695651 ATCAGCAATTAAGATATATTCAGA
66 ATCAGCAATTAAGATATATTCAGA
3695675 GCTTTAATCCAACAATCTTTATCTTTGTGAAATTGTACTTCTTCGAAGCTTTCTGGCTCCCCCTC
1 GCTTTAATCCAACAATCTTTATCTTTGTGAAATTGTACTTCTTCGAAGCTTTCTGGCTCCCCCTC
3695740 ATCAGCAATTAAGATATATTCAGA
66 ATCAGCAATTAAGATATATTCAGA
3695764 GCTT
1 GCTT
3695768 GGATATCTTG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 93 1.00
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (89 bp):
GCTTTAATCCAACAATCTTTATCTTTGTGAAATTGTACTTCTTCGAAGCTTTCTGGCTCCCCCTC
ATCAGCAATTAAGATATATTCAGA
Found at i:3698736 original size:14 final size:13
Alignment explanation
Indices: 3698686--3698737 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
3698676 ATTTTTACTG
3698686 TTTCAAATTGAAT
1 TTTCAAATTGAAT
* *
3698699 TTT-AACATTTACT
1 TTTCAA-ATTGAAT
3698712 ATTTCAAATTGAAT
1 -TTTCAAATTGAAT
3698726 TTTCAAAATTGA
1 TTTC-AAATTGA
3698738 CGGCGCCTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
12 2 0.06
13 12 0.39
14 15 0.48
15 2 0.06
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (13 bp):
TTTCAAATTGAAT
Found at i:3700538 original size:19 final size:19
Alignment explanation
Indices: 3700514--3700551 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
3700504 CAAAGATTAA
3700514 ATCTTAATCTTTAACAATT
1 ATCTTAATCTTTAACAATT
3700533 ATCTTAATCTTTAACAATT
1 ATCTTAATCTTTAACAATT
3700552 TCCTATGCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.16, G:0.00, T:0.47
Consensus pattern (19 bp):
ATCTTAATCTTTAACAATT
Found at i:3704709 original size:11 final size:11
Alignment explanation
Indices: 3704695--3704747 Score: 63
Period size: 11 Copynumber: 4.8 Consensus size: 11
3704685 TAAAATAAAG
3704695 GAAAAAAATGA
1 GAAAAAAATGA
*
3704706 GAAAAAAATTA
1 GAAAAAAATGA
**
3704717 -AAATAAAAAAA
1 GAAA-AAAATGA
3704728 GAAAAAAATGA
1 GAAAAAAATGA
3704739 GAAAAAAAT
1 GAAAAAAAT
3704748 TGAAAAAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
10 3 0.09
11 29 0.83
12 3 0.09
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.11
Consensus pattern (11 bp):
GAAAAAAATGA
Found at i:3704737 original size:33 final size:36
Alignment explanation
Indices: 3704681--3704753 Score: 125
Period size: 33 Copynumber: 2.1 Consensus size: 36
3704671 TGCTTTGAAA
3704681 AAAATAAAATAAAGGAAAAAAATGAGAAAAAAATT-
1 AAAATAAAATAAAGGAAAAAAATGAGAAAAAAATTG
3704716 AAAATAAAA-AAA-GAAAAAAATGAGAAAAAAATTG
1 AAAATAAAATAAAGGAAAAAAATGAGAAAAAAATTG
3704750 AAAA
1 AAAA
3704754 AATTATTTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
33 21 0.57
34 7 0.19
35 9 0.24
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.12
Consensus pattern (36 bp):
AAAATAAAATAAAGGAAAAAAATGAGAAAAAAATTG
Found at i:3704754 original size:11 final size:10
Alignment explanation
Indices: 3704678--3704755 Score: 52
Period size: 11 Copynumber: 7.5 Consensus size: 10
3704668 ATTTGCTTTG
3704678 AAAAAAAT-A
1 AAAAAAATGA
* *
3704687 AAATAAA-GG
1 AAAAAAATGA
3704696 AAAAAAATGA
1 AAAAAAATGA
*
3704706 GAAAAAAATTA
1 -AAAAAAATGA
**
3704717 AAATAAAAAAA
1 AAA-AAAATGA
3704728 GAAAAAAATGA
1 -AAAAAAATGA
3704739 GAAAAAAATTGA
1 -AAAAAAA-TGA
3704751 AAAAA
1 AAAAA
3704756 TTATTTAAGC
Statistics
Matches: 54, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
9 12 0.22
10 4 0.07
11 32 0.59
12 6 0.11
ACGTcount: A:0.78, C:0.00, G:0.10, T:0.12
Consensus pattern (10 bp):
AAAAAAATGA
Found at i:3709280 original size:15 final size:16
Alignment explanation
Indices: 3709260--3709385 Score: 76
Period size: 16 Copynumber: 7.9 Consensus size: 16
3709250 GTTCAGGCAG
*
3709260 GTTCGGGTT-TGGCTC
1 GTTCGGGTTCGGGCTC
3709275 GTTCGGGTTCGGGCTC
1 GTTCGGGTTCGGGCTC
* *
3709291 ATTCGGGTTCGGGCTT
1 GTTCGGGTTCGGGCTC
* ** * *
3709307 TTTCTAGTTCAGGCTTA
1 GTTCGGGTTCGGGC-TC
* *
3709324 G-TCGGGTTCAGGCTT
1 GTTCGGGTTCGGGCTC
*
3709339 GTTCGGGTTTGGGCTC
1 GTTCGGGTTCGGGCTC
* * * * *
3709355 TTTCGAGTTTGGGTTT
1 GTTCGGGTTCGGGCTC
*
3709371 TTTCGGGTTCGGGCT
1 GTTCGGGTTCGGGCT
3709386 TATTCAAGTT
Statistics
Matches: 86, Mismatches: 22, Indels: 5
0.76 0.19 0.04
Matches are distributed among these distances:
15 11 0.13
16 74 0.86
17 1 0.01
ACGTcount: A:0.05, C:0.18, G:0.37, T:0.40
Consensus pattern (16 bp):
GTTCGGGTTCGGGCTC
Found at i:3709295 original size:16 final size:16
Alignment explanation
Indices: 3709276--3709390 Score: 97
Period size: 16 Copynumber: 7.2 Consensus size: 16
3709266 GTTTGGCTCG
*
3709276 TTCGGGTTCGGGCTCA
1 TTCGGGTTCGGGCTTA
*
3709292 TTCGGGTTCGGGCTTT
1 TTCGGGTTCGGGCTTA
** *
3709308 TTCTAGTTCAGGCTTA
1 TTCGGGTTCGGGCTTA
* * *
3709324 GTCGGGTTCAGGCTTG
1 TTCGGGTTCGGGCTTA
*
3709340 TTCGGGTTTGGGCTCT-
1 TTCGGGTTCGGGCT-TA
* * * *
3709356 TTCGAGTTTGGGTTTT
1 TTCGGGTTCGGGCTTA
3709372 TTCGGGTTCGGGCTTA
1 TTCGGGTTCGGGCTTA
3709388 TTC
1 TTC
3709391 AAGTTCGGGT
Statistics
Matches: 78, Mismatches: 19, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
15 1 0.01
16 76 0.97
17 1 0.01
ACGTcount: A:0.06, C:0.18, G:0.34, T:0.42
Consensus pattern (16 bp):
TTCGGGTTCGGGCTTA
Found at i:3709331 original size:48 final size:48
Alignment explanation
Indices: 3709277--3709399 Score: 129
Period size: 48 Copynumber: 2.6 Consensus size: 48
3709267 TTTGGCTCGT
* * *
3709277 TCGGGTTCGGGCTCATTCGGGTTCGGGCTTTTTCTAGTTCAGGCTTAG
1 TCGGGTTCGGGCTTATTCGGGTTCGGGCTCTTTCGAGTTCAGGCTTAG
* * * ** * **
3709325 TCGGGTTCAGGCTTGTTCGGGTTTGGGCTCTTTCGAGTTTGGGTTTTT
1 TCGGGTTCGGGCTTATTCGGGTTCGGGCTCTTTCGAGTTCAGGCTTAG
**
3709373 TCGGGTTCGGGCTTATTCAAGTTCGGG
1 TCGGGTTCGGGCTTATTCGGGTTCGGG
3709400 TTCAGGTTCA
Statistics
Matches: 59, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
48 59 1.00
ACGTcount: A:0.07, C:0.18, G:0.35, T:0.40
Consensus pattern (48 bp):
TCGGGTTCGGGCTTATTCGGGTTCGGGCTCTTTCGAGTTCAGGCTTAG
Found at i:3709401 original size:32 final size:32
Alignment explanation
Indices: 3709276--3709399 Score: 115
Period size: 32 Copynumber: 3.9 Consensus size: 32
3709266 GTTTGGCTCG
* *
3709276 TTCGGGTTCGGGCTCATTCGGGTTCGGGCTTT
1 TTCGGGTTCGGGCTTATTCGAGTTCGGGCTTT
** * * * * *
3709308 TTCTAGTTCAGGCTTAGTCGGGTTCAGGCTTG
1 TTCGGGTTCGGGCTTATTCGAGTTCGGGCTTT
* * *
3709340 TTCGGGTTTGGGCTCT-TTCGAGTTTGGGTTTT
1 TTCGGGTTCGGGCT-TATTCGAGTTCGGGCTTT
*
3709372 TTCGGGTTCGGGCTTATTCAAGTTCGGG
1 TTCGGGTTCGGGCTTATTCGAGTTCGGG
3709400 TTCAGGTTCA
Statistics
Matches: 70, Mismatches: 20, Indels: 4
0.74 0.21 0.04
Matches are distributed among these distances:
31 1 0.01
32 68 0.97
33 1 0.01
ACGTcount: A:0.07, C:0.18, G:0.35, T:0.40
Consensus pattern (32 bp):
TTCGGGTTCGGGCTTATTCGAGTTCGGGCTTT
Found at i:3709611 original size:17 final size:17
Alignment explanation
Indices: 3709589--3709627 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
3709579 TTGAAATCTA
3709589 TATTTA-TATATAAAATT
1 TATTTATTATATAAAA-T
*
3709606 TATTTATTGTATAAAAT
1 TATTTATTATATAAAAT
3709623 TATTT
1 TATTT
3709628 TTTCAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
TATTTATTATATAAAAT
Found at i:3710181 original size:38 final size:38
Alignment explanation
Indices: 3710139--3710219 Score: 117
Period size: 38 Copynumber: 2.1 Consensus size: 38
3710129 TCCTTAAAGA
*
3710139 ACTATTGAATGTAGCTCTTGATTGTGATTTTTAAACTT
1 ACTATTAAATGTAGCTCTTGATTGTGATTTTTAAACTT
* * * *
3710177 ACTATTAAATGTAGTTGTTGATTGTGCTTTTTAAATTT
1 ACTATTAAATGTAGCTCTTGATTGTGATTTTTAAACTT
3710215 ACTAT
1 ACTAT
3710220 AACTTTTTCA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.27, C:0.09, G:0.15, T:0.49
Consensus pattern (38 bp):
ACTATTAAATGTAGCTCTTGATTGTGATTTTTAAACTT
Found at i:3710337 original size:16 final size:15
Alignment explanation
Indices: 3710310--3710339 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
3710300 ATGTTAACTT
3710310 TATATTCTATTCTAC
1 TATATTCTATTCTAC
3710325 TATATTGCTATTCTA
1 TATATT-CTATTCTA
3710340 AGTGTAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.27, C:0.17, G:0.03, T:0.53
Consensus pattern (15 bp):
TATATTCTATTCTAC
Found at i:3713859 original size:24 final size:23
Alignment explanation
Indices: 3713813--3713874 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 23
3713803 TGTTATATCT
* *
3713813 ATTTTTGTATTGTATTTTAATTAA
1 ATTTTTATATTTTATTTTAATT-A
3713837 ATTTTTATATTTTATTTGT-ATTA
1 ATTTTTATATTTTATTT-TAATTA
*
3713860 TTTTTTATATATTTA
1 ATTTTTATAT-TTTA
3713875 AAGTATTAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 10 0.30
24 22 0.67
25 1 0.03
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (23 bp):
ATTTTTATATTTTATTTTAATTA
Found at i:3714686 original size:20 final size:19
Alignment explanation
Indices: 3714661--3714707 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
3714651 TTATCCTCAA
*
3714661 TTTATTTTATAT-TTTTATAT
1 TTTATTTTA-ATGATTTA-AT
*
3714681 TTTATTATAATGATTTAAT
1 TTTATTTTAATGATTTAAT
3714700 TTTATTTT
1 TTTATTTT
3714708 CAAATTCAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (19 bp):
TTTATTTTAATGATTTAAT
Found at i:3716593 original size:15 final size:16
Alignment explanation
Indices: 3716570--3716606 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
3716560 TGGAAAGAAA
3716570 AAAAAAAAAGAAAG-G
1 AAAAAAAAAGAAAGAG
*
3716585 AAAAGAAAAGAAAGAG
1 AAAAAAAAAGAAAGAG
3716601 AAAAAA
1 AAAAAA
3716607 CGAAACATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAGAAAGAG
Found at i:3716602 original size:6 final size:5
Alignment explanation
Indices: 3716563--3716604 Score: 52
Period size: 5 Copynumber: 8.6 Consensus size: 5
3716553 GTAGATATGG
*
3716563 AAAGA AAA-A AAA-A AAAGA AAGGA AAAGA AAAGA AAGAGA AAA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AA-AGA AAA
3716605 AACGAAACAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 8 0.24
5 20 0.61
6 5 0.15
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:3718629 original size:202 final size:202
Alignment explanation
Indices: 3718283--3718699 Score: 834
Period size: 202 Copynumber: 2.1 Consensus size: 202
3718273 CGAGTCTATG
3718283 TAGGATGCGCTGACATCATCAGTGTATCCTACGTGTCAACGCTATGTAGGATTGCAAATCTTTCG
1 TAGGATGCGCTGACATCATCAGTGTATCCTACGTGTCAACGCTATGTAGGATTGCAAATCTTTCG
3718348 TGGATGTGCTAGATGGGTTAGCGCATCCACATAGGATTCGCGTCCTAGGTCAACGTTTCCTGCTA
66 TGGATGTGCTAGATGGGTTAGCGCATCCACATAGGATTCGCGTCCTAGGTCAACGTTTCCTGCTA
3718413 GTTTTTCTGTACTGACCGGTCAAAGGTCGATTGGGCTACGATGGCGTGGATGCGCTGACATGACG
131 GTTTTTCTGTACTGACCGGTCAAAGGTCGATTGGGCTACGATGGCGTGGATGCGCTGACATGACG
3718478 TGCCACT
196 TGCCACT
3718485 TAGGATGCGCTGACATCATCAGTGTATCCTACGTGTCAACGCTATGTAGGATTGCAAATCTTTCG
1 TAGGATGCGCTGACATCATCAGTGTATCCTACGTGTCAACGCTATGTAGGATTGCAAATCTTTCG
3718550 TGGATGTGCTAGATGGGTTAGCGCATCCACATAGGATTCGCGTCCTAGGTCAACGTTTCCTGCTA
66 TGGATGTGCTAGATGGGTTAGCGCATCCACATAGGATTCGCGTCCTAGGTCAACGTTTCCTGCTA
3718615 GTTTTTCTGTACTGACCGGTCAAAGGTCGATTGGGCTACGATGGCGTGGATGCGCTGACATGACG
131 GTTTTTCTGTACTGACCGGTCAAAGGTCGATTGGGCTACGATGGCGTGGATGCGCTGACATGACG
3718680 TGCCACT
196 TGCCACT
3718687 TAGGATGCGCTGA
1 TAGGATGCGCTGA
3718700 AGCGGGTAGC
Statistics
Matches: 215, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
202 215 1.00
ACGTcount: A:0.21, C:0.22, G:0.28, T:0.29
Consensus pattern (202 bp):
TAGGATGCGCTGACATCATCAGTGTATCCTACGTGTCAACGCTATGTAGGATTGCAAATCTTTCG
TGGATGTGCTAGATGGGTTAGCGCATCCACATAGGATTCGCGTCCTAGGTCAACGTTTCCTGCTA
GTTTTTCTGTACTGACCGGTCAAAGGTCGATTGGGCTACGATGGCGTGGATGCGCTGACATGACG
TGCCACT
Found at i:3719090 original size:32 final size:33
Alignment explanation
Indices: 3719061--3719121 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 33
3719051 TTATTATTTT
* *
3719061 TGTGTAATTA-GTTGATAGTAATT-GTTTATTA
1 TGTGGAATTAGGTTGACAGTAATTAGTTTATTA
*
3719092 TGTGGAATTAGGTTTACAGTAATTAGTTTA
1 TGTGGAATTAGGTTGACAGTAATTAGTTTA
3719122 GGGGTAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 9 0.36
32 11 0.44
33 5 0.20
ACGTcount: A:0.30, C:0.02, G:0.21, T:0.48
Consensus pattern (33 bp):
TGTGGAATTAGGTTGACAGTAATTAGTTTATTA
Found at i:3719167 original size:7 final size:7
Alignment explanation
Indices: 3719155--3719192 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
3719145 AAAATGTTTG
3719155 TATTGAT
1 TATTGAT
3719162 TATTGAT
1 TATTGAT
3719169 TATTGAT
1 TATTGAT
*
3719176 TATTTAT
1 TATTGAT
3719183 T-TTG-T
1 TATTGAT
3719188 TATTG
1 TATTG
3719193 TTTAGGGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
5 2 0.07
6 5 0.18
7 21 0.75
ACGTcount: A:0.24, C:0.00, G:0.13, T:0.63
Consensus pattern (7 bp):
TATTGAT
Found at i:3725108 original size:21 final size:21
Alignment explanation
Indices: 3725075--3725119 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3725065 TTGCAAGTTG
*
3725075 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
3725097 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
3725117 AAA
1 AAA
3725120 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:3726943 original size:15 final size:15
Alignment explanation
Indices: 3726923--3726953 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3726913 TAAAAATGTC
*
3726923 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
3726938 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
3726953 C
1 C
3726954 CAAACAAAAT
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:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:3729046 original size:20 final size:20
Alignment explanation
Indices: 3728967--3729046 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
3728957 AATGTCCAAA
*
3728967 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
3728987 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
3729012 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
3729032 TTGTATCGATACATT
1 ATGTATCGATACATT
3729047 GTATCGATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:3729050 original size:13 final size:13
Alignment explanation
Indices: 3729032--3729070 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
3729022 ACATTTTTCT
3729032 TTGTATCGATACA
1 TTGTATCGATACA
3729045 TTGTATCGATACA
1 TTGTATCGATACA
*
3729058 CTGTATCGATACA
1 TTGTATCGATACA
3729071 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3729234 original size:20 final size:20
Alignment explanation
Indices: 3729191--3729236 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
3729181 AAATCTTTTG
3729191 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
3729212 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
3729232 CAAAA
1 CAAAA
3729237 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:3731631 original size:13 final size:13
Alignment explanation
Indices: 3731613--3731638 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3731603 TACAGCAAGT
3731613 ATGTATCGATACA
1 ATGTATCGATACA
3731626 ATGTATCGATACA
1 ATGTATCGATACA
3731639 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3734142 original size:27 final size:27
Alignment explanation
Indices: 3734106--3734190 Score: 152
Period size: 27 Copynumber: 3.1 Consensus size: 27
3734096 CACCATATTT
* *
3734106 TCCTACTCAATCTCCATACCCGTCATA
1 TCCTACTCAACCTCCATACCCATCATA
3734133 TCCTACTCAACCTCCATACCCATCATA
1 TCCTACTCAACCTCCATACCCATCATA
3734160 TCCTACTCAACCTCCATACCCATCATA
1 TCCTACTCAACCTCCATACCCATCATA
3734187 TCCT
1 TCCT
3734191 GCCACGACCC
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 56 1.00
ACGTcount: A:0.27, C:0.44, G:0.01, T:0.28
Consensus pattern (27 bp):
TCCTACTCAACCTCCATACCCATCATA
Found at i:3734593 original size:39 final size:38
Alignment explanation
Indices: 3734550--3734662 Score: 97
Period size: 36 Copynumber: 3.0 Consensus size: 38
3734540 GAAACATTTG
3734550 TTGATTGTAGTTATCGTGCAGATTATCTCGGATTAGTTA
1 TTGATTGTAGTTATCGTG-AGATTATCTCGGATTAGTTA
* * * * * ** * *
3734589 TTGATAGTAG-TATTGTGA-AATATAC-AGAAACATTTG
1 TTGATTGTAGTTATCGTGAGATTAT-CTCGGATTAGTTA
3734625 TTGATTGTAGTTATCGTGTAGATTATCTCGGATTAGTT
1 TTGATTGTAGTTATCGTG-AGATTATCTCGGATTAGTT
3734663 GATAGTAGTA
Statistics
Matches: 52, Mismatches: 17, Indels: 10
0.66 0.22 0.13
Matches are distributed among these distances:
36 18 0.35
37 8 0.15
38 8 0.15
39 18 0.35
ACGTcount: A:0.27, C:0.08, G:0.22, T:0.42
Consensus pattern (38 bp):
TTGATTGTAGTTATCGTGAGATTATCTCGGATTAGTTA
Found at i:3734595 original size:75 final size:75
Alignment explanation
Indices: 3734491--3734785 Score: 443
Period size: 75 Copynumber: 4.0 Consensus size: 75
3734481 ATGTAAAATA
* * *
3734491 TGCAGATTATCTCGGATTAGTTGTTGATAGTAGTAATATAAAATATGCAGAAACATTTGTTGATT
1 TGCAGATTATCTCGGATTAGTTATTGATAGTAGTAATGTGAAATATGCAGAAACATTTGTTGATT
*
3734556 GTAGTTATCG
66 GTAATTATCG
* *
3734566 TGCAGATTATCTCGGATTAGTTATTGATAGTAGTATTGTGAAATATACAGAAACATTTGTTGATT
1 TGCAGATTATCTCGGATTAGTTATTGATAGTAGTAATGTGAAATATGCAGAAACATTTGTTGATT
*
3734631 GTAGTTATCG
66 GTAATTATCG
* *
3734641 TGTAGATTATCTCGGATTAG---TTGATAGTAGTAATGTGAAATATGCAAAAACATTTGTTGATT
1 TGCAGATTATCTCGGATTAGTTATTGATAGTAGTAATGTGAAATATGCAGAAACATTTGTTGATT
3734703 GTAATTATCG
66 GTAATTATCG
* * * * *
3734713 TACAGATTATCTCGAATTAGTTATTGATAGTAGTACTGTGAAATATGCATAAATATTTGTTGATT
1 TGCAGATTATCTCGGATTAGTTATTGATAGTAGTAATGTGAAATATGCAGAAACATTTGTTGATT
3734778 GTAATTAT
66 GTAATTAT
3734786 TGTAAACATT
Statistics
Matches: 201, Mismatches: 16, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
72 65 0.32
75 136 0.68
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (75 bp):
TGCAGATTATCTCGGATTAGTTATTGATAGTAGTAATGTGAAATATGCAGAAACATTTGTTGATT
GTAATTATCG
Found at i:3734693 original size:147 final size:148
Alignment explanation
Indices: 3734494--3734785 Score: 460
Period size: 147 Copynumber: 2.0 Consensus size: 148
3734484 TAAAATATGC
*
3734494 AGATTATCTCGGATTAGTTGTTGATAGTAGTAATATAAAATATGCAGAAACATTTGTTGATTGTA
1 AGATTATCTCGGATTA--TGTTGATAGTAGTAATATAAAATATGCAAAAACATTTGTTGATTGTA
* * * *
3734559 GTTATCGTGCAGATTATCTCGGATTAGTTATTGATAGTAGTATTGTGAAATATACAGAAACATTT
64 ATTATCGTACAGATTATCTCGAATTAGTTATTGATAGTAGTACTGTGAAATATACAGAAACATTT
*
3734624 GTTGATTGTAGTTATCGTGT
129 GTTGATTGTAATTATCGTGT
* *
3734644 AGATTATCTCGGATTA-GTTGATAGTAGTAATGTGAAATATGCAAAAACATTTGTTGATTGTAAT
1 AGATTATCTCGGATTATGTTGATAGTAGTAATATAAAATATGCAAAAACATTTGTTGATTGTAAT
* * *
3734708 TATCGTACAGATTATCTCGAATTAGTTATTGATAGTAGTACTGTGAAATATGCATAAATATTTGT
66 TATCGTACAGATTATCTCGAATTAGTTATTGATAGTAGTACTGTGAAATATACAGAAACATTTGT
3734773 TGATTGTAATTAT
131 TGATTGTAATTAT
3734786 TGTAAACATT
Statistics
Matches: 131, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
147 115 0.88
150 16 0.12
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (148 bp):
AGATTATCTCGGATTATGTTGATAGTAGTAATATAAAATATGCAAAAACATTTGTTGATTGTAAT
TATCGTACAGATTATCTCGAATTAGTTATTGATAGTAGTACTGTGAAATATACAGAAACATTTGT
TGATTGTAATTATCGTGT
Found at i:3734798 original size:26 final size:26
Alignment explanation
Indices: 3734762--3734811 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
3734752 GAAATATGCA
*
3734762 TAAATATTTGTTGATTGTAATTATTG
1 TAAACATTTGTTGATTGTAATTATTG
*
3734788 TAAACATTTGTTGATTGTAGTTAT
1 TAAACATTTGTTGATTGTAATTAT
3734812 CGTGCATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.30, C:0.02, G:0.16, T:0.52
Consensus pattern (26 bp):
TAAACATTTGTTGATTGTAATTATTG
Found at i:3734868 original size:101 final size:100
Alignment explanation
Indices: 3734688--3734886 Score: 267
Period size: 101 Copynumber: 2.0 Consensus size: 100
3734678 AAATATGCAA
* * *
3734688 AAACATTTGTTGATTGTAATTATCGTACAGATTATCTCGAATTAGTTATTGATAGTAGTACTGTG
1 AAACATTTGTTGATTGTAATTATCGTACAGATTATCTCGAATTAGTTATTAATAATAGTACTATG
*
3734753 AAATATGCATAAATATTTGTTGATTGTAATTATTGT
66 AAATAT-CATAAATATTTGTTGATTATAATTATTGT
* * * *
3734789 AAACATTTGTTGATTGTAGTTATCGTGCATATTATCTC-AGATTAGTTATTAATAATAGTATTAT
1 AAACATTTGTTGATTGTAATTATCGTACAGATTATCTCGA-ATTAGTTATTAATAATAGTACTAT
*
3734853 TAAATAT-ATCGAAATATTTGTTGATTATAATTAT
65 GAAATATCAT--AAATATTTGTTGATTATAATTAT
3734887 CATGCAGATT
Statistics
Matches: 86, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
99 2 0.02
100 1 0.01
101 83 0.97
ACGTcount: A:0.34, C:0.07, G:0.15, T:0.45
Consensus pattern (100 bp):
AAACATTTGTTGATTGTAATTATCGTACAGATTATCTCGAATTAGTTATTAATAATAGTACTATG
AAATATCATAAATATTTGTTGATTATAATTATTGT
Found at i:3734919 original size:75 final size:75
Alignment explanation
Indices: 3734793--3734982 Score: 204
Period size: 75 Copynumber: 2.5 Consensus size: 75
3734783 TATTGTAAAC
* * * * * *
3734793 ATTTGTTGATTGTAGTTATCGTGCATATTATCTCAGATTAGTTATTAATAATAGTATTATTAAAT
1 ATTTGTTGATTATAATTATCATGCAGATTATCTCAGATTAGTTATTAATAATAGTACTATAAAAT
*
3734858 ATATC-GAAAT
66 ATA-CAAAAAT
* * * * *
3734868 ATTTGTTGATTATAATTATCATGCAGATTATTTCGGATTAGTTGTTGATAATAGTACTGTAAAAT
1 ATTTGTTGATTATAATTATCATGCAGATTATCTCAGATTAGTTATTAATAATAGTACTATAAAAT
3734933 ATACAAAAAT
66 ATACAAAAAT
* * * *
3734943 ATTTGTTGA-TAGTAGTTATTATACAGATTATCTCATATTA
1 ATTTGTTGATTA-TAATTATCATGCAGATTATCTCAGATTA
3734983 TCCTTTCATT
Statistics
Matches: 95, Mismatches: 18, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
74 3 0.03
75 92 0.97
ACGTcount: A:0.35, C:0.07, G:0.14, T:0.44
Consensus pattern (75 bp):
ATTTGTTGATTATAATTATCATGCAGATTATCTCAGATTAGTTATTAATAATAGTACTATAAAAT
ATACAAAAAT
Found at i:3734927 original size:176 final size:173
Alignment explanation
Indices: 3734616--3734962 Score: 444
Period size: 176 Copynumber: 2.0 Consensus size: 173
3734606 AAATATACAG
* * * * *
3734616 AAACATTTGTTGATTGTAGTTATCGTGTAGATTATCTCGGATTAGTTGATAGTAGTAATGTGAAA
1 AAACATTTGTTGATTGTAGTTATCGTGCAGATTATCTCAGATTAGTTAATAATAGTAATATGAAA
* * *
3734681 TATGCAAAAACATTTGTTGATTGTAATTATCGTACAGATTATCTCGAATTAGTTATTGATAGTAG
66 TATGCAAAAACATTTGTTGATTATAATTATCATACAGATTATCTCGAATTAGTTATTGATAATAG
* * * *
3734746 TACTGTGAAATATGCATAAATATTTGTTGATTGTAATTATTGT
131 TACTGTAAAATATACAAAAATATTTGTTGATAGTAATTATTGT
* * *
3734789 AAACATTTGTTGATTGTAGTTATCGTGCATATTATCTCAGATTAGTTATTAATAATAGTATTATT
1 AAACATTTGTTGATTGTAGTTATCGTGCAGATTATCTCAGATTAG---TTAATAATAGTAATATG
* * * * * * *
3734854 AAATATATC-GAAATATTTGTTGATTATAATTATCATGCAGATTATTTCGGATTAGTTGTTGATA
63 AAATAT-GCAAAAACATTTGTTGATTATAATTATCATACAGATTATCTCGAATTAGTTATTGATA
*
3734918 ATAGTACTGTAAAATATACAAAAATATTTGTTGATAGTAGTTATT
127 ATAGTACTGTAAAATATACAAAAATATTTGTTGATAGTAATTATT
3734963 ATACAGATTA
Statistics
Matches: 147, Mismatches: 23, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
173 42 0.29
176 104 0.71
177 1 0.01
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.43
Consensus pattern (173 bp):
AAACATTTGTTGATTGTAGTTATCGTGCAGATTATCTCAGATTAGTTAATAATAGTAATATGAAA
TATGCAAAAACATTTGTTGATTATAATTATCATACAGATTATCTCGAATTAGTTATTGATAATAG
TACTGTAAAATATACAAAAATATTTGTTGATAGTAATTATTGT
Found at i:3735520 original size:30 final size:29
Alignment explanation
Indices: 3735486--3735546 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
3735476 AGACATTTAA
3735486 ATCAAAATACT-ATTAAAATTAAAATAAATT
1 ATCAAAATA-TAATT-AAATTAAAATAAATT
* *
3735516 ATCAAAATATAATTTATTTAAAATAAATT
1 ATCAAAATATAATTAAATTAAAATAAATT
3735545 AT
1 AT
3735547 TAAATTATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 16 0.57
30 12 0.43
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (29 bp):
ATCAAAATATAATTAAATTAAAATAAATT
Found at i:3735541 original size:14 final size:14
Alignment explanation
Indices: 3735504--3735547 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
3735494 ACTATTAAAA
3735504 TTAAAATAAATTA-
1 TTAAAATAAATTAT
*
3735517 TCAAAATATAATTTAT
1 TTAAAATA-AA-TTAT
3735533 TTAAAATAAATTAT
1 TTAAAATAAATTAT
3735547 T
1 T
3735548 AAATTATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 7 0.27
14 7 0.27
15 5 0.19
16 7 0.27
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAATAAATTAT
Found at i:3736069 original size:5 final size:5
Alignment explanation
Indices: 3736059--3736109 Score: 52
Period size: 5 Copynumber: 10.2 Consensus size: 5
3736049 GATAATTTTA
* *
3736059 AATAT AATAT ATATAT AAT-T ATTA- AATAT AACAT AATAT AATAT AAATAT
1 AATAT AATAT A-ATAT AATAT AATAT AATAT AATAT AATAT AATAT -AATAT
3736109 A
1 A
3736110 TCATTTAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
4 6 0.16
5 22 0.58
6 10 0.26
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (5 bp):
AATAT
Found at i:3736163 original size:20 final size:18
Alignment explanation
Indices: 3736063--3736166 Score: 54
Period size: 18 Copynumber: 5.4 Consensus size: 18
3736053 ATTTTAAATA
3736063 TAATATATATATAA-TTAT
1 TAATATA-ATATAATTTAT
*
3736081 TAAATATAACATAA--TA-
1 T-AATATAATATAATTTAT
3736097 TAATATAAATATATCATTTAAAAT
1 TAATAT-AATATA--ATTT---AT
*
3736121 TTATATAATATAATTTAT
1 TAATATAATATAATTTAT
* *
3736139 TAATATATTATATTTTAT
1 TAATATAATATAATTTAT
3736157 ATAAATATAA
1 -T-AATATAA
3736167 AATATTTCAA
Statistics
Matches: 67, Mismatches: 7, Indels: 22
0.70 0.07 0.23
Matches are distributed among these distances:
15 5 0.07
16 6 0.09
17 2 0.03
18 24 0.36
19 7 0.10
20 7 0.10
21 4 0.06
23 7 0.10
24 5 0.07
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (18 bp):
TAATATAATATAATTTAT
Found at i:3743156 original size:16 final size:16
Alignment explanation
Indices: 3743135--3743165 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3743125 CCCAAGTATT
3743135 AAATTCAAAATGATTC
1 AAATTCAAAATGATTC
3743151 AAATTCAAAATGATT
1 AAATTCAAAATGATT
3743166 TAACATTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.32
Consensus pattern (16 bp):
AAATTCAAAATGATTC
Found at i:3743230 original size:16 final size:15
Alignment explanation
Indices: 3743204--3743307 Score: 75
Period size: 16 Copynumber: 6.6 Consensus size: 15
3743194 TAATTAATCT
*
3743204 AAATCTAAAATGAGTTC
1 AAAT-TAAAAT-AATTC
*
3743221 AAATTAAAATAACTC
1 AAATTAAAATAATTC
*
3743236 AAACTCAAAATAAATT-
1 AAA-TTAAAAT-AATTC
* *
3743252 AAATTTAAAATATTTT
1 AAA-TTAAAATAATTC
* *
3743268 AAATTAAAATGACTC
1 AAATTAAAATAATTC
*
3743283 GAAATTAAAATAATTA
1 -AAATTAAAATAATTC
3743299 AAATTAAAA
1 AAATTAAAA
3743308 AATAATGTAA
Statistics
Matches: 69, Mismatches: 14, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
15 26 0.38
16 36 0.52
17 7 0.10
ACGTcount: A:0.58, C:0.08, G:0.04, T:0.31
Consensus pattern (15 bp):
AAATTAAAATAATTC
Found at i:3743273 original size:47 final size:47
Alignment explanation
Indices: 3743198--3743307 Score: 125
Period size: 47 Copynumber: 2.3 Consensus size: 47
3743188 TAAACTTAAT
*
3743198 TAATCTAAATCTAAAATGAGTTCAAATTAAAATAACTC-AAACTCAAAA
1 TAAT-TAAATTTAAAATGAGTTCAAATTAAAATAACTCGAAA-TCAAAA
* * * *
3743246 TAAATTAAATTTAAAAT-ATTTTAAATTAAAATGACTCGAAATTAAAA
1 T-AATTAAATTTAAAATGAGTTCAAATTAAAATAACTCGAAATCAAAA
*
3743293 TAATTAAAATTAAAA
1 TAATTAAATTTAAAA
3743308 AATAATGTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
46 13 0.24
47 23 0.43
48 15 0.28
49 3 0.06
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.32
Consensus pattern (47 bp):
TAATTAAATTTAAAATGAGTTCAAATTAAAATAACTCGAAATCAAAA
Found at i:3743924 original size:29 final size:29
Alignment explanation
Indices: 3743892--3743959 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
3743882 TTTATCATTA
3743892 TATTAATATTA-A-AAATAATATTTTAAATT
1 TATTAA-ATTACATAAATAA-ATTTTAAATT
* *
3743921 TATTAAATTACATAATTAAATTTTTAATT
1 TATTAAATTACATAAATAAATTTTAAATT
3743950 TCATTAAATT
1 T-ATTAAATT
3743960 TTGAAAAGGC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 4 0.12
29 17 0.50
30 13 0.38
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (29 bp):
TATTAAATTACATAAATAAATTTTAAATT
Found at i:3744189 original size:22 final size:22
Alignment explanation
Indices: 3744146--3744190 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
3744136 GTGAAATAAA
*
3744146 ATTTAAAGTATAAATATGTTAT
1 ATTTAAAGTATAAATATCTTAT
*
3744168 ATTTAAATTAT-AATATTCTTAT
1 ATTTAAAGTATAAATA-TCTTAT
3744190 A
1 A
3744191 ACATATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.49
Consensus pattern (22 bp):
ATTTAAAGTATAAATATCTTAT
Found at i:3744529 original size:23 final size:23
Alignment explanation
Indices: 3744494--3744543 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
3744484 AGATTGATTT
3744494 AATAAAAATTTTAATATTTAAA-A
1 AATAAAAATTTTAATA-TTAAATA
3744517 AATAAATAA-TTTAATATTAAATA
1 AATAAA-AATTTTAATATTAAATA
3744540 AATA
1 AATA
3744544 TTAATTATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 5 0.20
23 18 0.72
24 2 0.08
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
AATAAAAATTTTAATATTAAATA
Found at i:3744859 original size:22 final size:22
Alignment explanation
Indices: 3744830--3744876 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
3744820 AATTTAATAA
3744830 AAATAATATATTTAATATAATTTTT
1 AAATAATA-A-TTAA-ATAATTTTT
*
3744855 AAATAATAATTAAATTATTTTT
1 AAATAATAATTAAATAATTTTT
3744877 TATTAATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 8 0.38
23 4 0.19
24 1 0.05
25 8 0.38
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AAATAATAATTAAATAATTTTT
Found at i:3744884 original size:25 final size:25
Alignment explanation
Indices: 3744830--3744878 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 25
3744820 AATTTAATAA
*
3744830 AAATAATATATTTAATATAATTTTT
1 AAATAATATATTAAATATAATTTTT
*
3744855 AAATAATA-ATTAAAT-TATTTTTT
1 AAATAATATATTAAATATAATTTTT
3744878 A
1 A
3744879 TTAATATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 8 0.36
24 6 0.27
25 8 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
AAATAATATATTAAATATAATTTTT
Found at i:3745057 original size:27 final size:27
Alignment explanation
Indices: 3744983--3745070 Score: 88
Period size: 27 Copynumber: 3.1 Consensus size: 27
3744973 TTTTTTAATT
*
3744983 TTTTTAATATATTTAAATTATAAATTTAA
1 TTTTTAACAT-TTTAAATT-TAAATTTAA
* **
3745012 TCTTTCAAACAAATTAAATTTAAATTTAA
1 T-TTT-TAACATTTTAAATTTAAATTTAA
3745041 TTTTTAACATTTTAAA-TTATAATTTAA
1 TTTTTAACATTTTAAATTTA-AATTTAA
3745068 TTT
1 TTT
3745071 AAATAAATTT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
26 3 0.06
27 19 0.39
28 3 0.06
29 11 0.22
30 10 0.20
31 3 0.06
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (27 bp):
TTTTTAACATTTTAAATTTAAATTTAA
Found at i:3745081 original size:27 final size:28
Alignment explanation
Indices: 3744988--3745082 Score: 83
Period size: 27 Copynumber: 3.4 Consensus size: 28
3744978 TAATTTTTTT
*
3744988 AATATATTTAAATTATAAATTTAATCTTTCA
1 AATAAATTTAAATTATAAATTTAA--TTT-A
*
3745019 AACAAA-TTAAATT-TAAATTTAATTT-
1 AATAAATTTAAATTATAAATTTAATTTA
*
3745044 -TTAACATTTTAAATTAT-AATTTAATTTA
1 AATAA-A-TTTAAATTATAAATTTAATTTA
3745072 AATAAATTTAA
1 AATAAATTTAA
3745083 TAACGAAGTG
Statistics
Matches: 53, Mismatches: 5, Indels: 16
0.72 0.07 0.22
Matches are distributed among these distances:
24 2 0.04
25 1 0.02
27 25 0.47
28 2 0.04
29 12 0.23
30 7 0.13
31 4 0.08
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.47
Consensus pattern (28 bp):
AATAAATTTAAATTATAAATTTAATTTA
Found at i:3747243 original size:14 final size:14
Alignment explanation
Indices: 3747224--3747251 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3747214 TTATTTATAA
3747224 AATATAAAAATATT
1 AATATAAAAATATT
3747238 AATATAAAAATATT
1 AATATAAAAATATT
3747252 TTTATTATTT
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AATATAAAAATATT
Found at i:3747814 original size:22 final size:22
Alignment explanation
Indices: 3747759--3747815 Score: 87
Period size: 22 Copynumber: 2.5 Consensus size: 22
3747749 TTATTTATTT
* *
3747759 AATAAAAATAAGTTATAATTTAA
1 AATAAAAA-AATTTAAAATTTAA
3747782 AATAAAAAAATTTAAAATTTAA
1 AATAAAAAAATTTAAAATTTAA
3747804 AATAAAAAAATT
1 AATAAAAAAATT
3747816 ATTTTACTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 24 0.75
23 8 0.25
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (22 bp):
AATAAAAAAATTTAAAATTTAA
Found at i:3748754 original size:2 final size:2
Alignment explanation
Indices: 3748733--3748770 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
3748723 TACTTTAACT
* *
3748733 TA TA T- TA TT TA TA TA CA 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
3748771 GTAAATCGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3750490 original size:27 final size:28
Alignment explanation
Indices: 3750438--3750490 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
3750428 AAAATAAAAA
*
3750438 ATATGAAAATTTTTATTTTTATTATTTG
1 ATATGAAAATTTTAATTTTTATTATTTG
* *
3750466 ATATTAAAA-TTTAATTTTTTTTATT
1 ATATGAAAATTTTAATTTTTATTATT
3750491 GAATTGATGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 14 0.64
28 8 0.36
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (28 bp):
ATATGAAAATTTTAATTTTTATTATTTG
Found at i:3750836 original size:2 final size:2
Alignment explanation
Indices: 3750829--3750863 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3750819 CATAAATAAT
3750829 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3750864 CAATGAAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3751371 original size:74 final size:74
Alignment explanation
Indices: 3751234--3751382 Score: 169
Period size: 74 Copynumber: 2.0 Consensus size: 74
3751224 TTTGATTCAA
* ** *
3751234 AATATTATTTATAAATTAAAATAATATATTTTTATTTATATTTAATTATAAAATTAATATAAAAA
1 AATATTATTTATAAAATAAAATAATATATTTAAATTTATAATTAA-TATAAAATTAATATAAAAA
3751299 ATAAAATTTT
65 ATAAAATTTT
* *
3751309 AATATT-TTTAATAAAATAAAA-AATATATTTAAATTTATAAATTAA-ATTAAATTAAATTTAAA
1 AATATTATTT-ATAAAATAAAATAATATATTTAAATTTAT-AATTAATATAAAATT-AATATAAA
**
3751371 ATTTAAAATTTT
63 AAATAAAATTTT
3751383 TTAAATAACT
Statistics
Matches: 63, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
73 7 0.11
74 35 0.56
75 21 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (74 bp):
AATATTATTTATAAAATAAAATAATATATTTAAATTTATAATTAATATAAAATTAATATAAAAAA
TAAAATTTT
Found at i:3754639 original size:10 final size:10
Alignment explanation
Indices: 3754626--3754698 Score: 58
Period size: 10 Copynumber: 7.0 Consensus size: 10
3754616 AATTGATTTA
3754626 AATTTAAAAT
1 AATTTAAAAT
3754636 AA-TTAAAATTT
1 AATTTAAAA--T
3754647 AATTTAAAAT
1 AATTTAAAAT
*
3754657 AATATTAAATT
1 AAT-TTAAAAT
* **
3754668 AAATTAATCT
1 AATTTAAAAT
*
3754678 GAATTTTAAAT
1 -AATTTAAAAT
3754689 AATTTAAAAT
1 AATTTAAAAT
3754699 TTTAATGATA
Statistics
Matches: 49, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
9 6 0.12
10 20 0.41
11 17 0.35
12 6 0.12
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (10 bp):
AATTTAAAAT
Found at i:3754664 original size:16 final size:15
Alignment explanation
Indices: 3754642--3754695 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 15
3754632 AAATAATTAA
3754642 AATTTAATTTAAAAT
1 AATTTAATTTAAAAT
* *
3754657 AATATTAAATTAAATT
1 AAT-TTAATTTAAAAT
* *
3754673 AATCTGAATTTTAAAT
1 AAT-TTAATTTAAAAT
3754689 AATTTAA
1 AATTTAA
3754696 AATTTTAATG
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
15 6 0.20
16 24 0.80
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (15 bp):
AATTTAATTTAAAAT
Found at i:3754669 original size:21 final size:20
Alignment explanation
Indices: 3754626--3754698 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 20
3754616 AATTGATTTA
*
3754626 AATTTAAAATAATTAAAATTT
1 AATTTAAAATAATTTAAA-TT
3754647 AATTTAAAATAATATTAAATT
1 AATTTAAAATAAT-TTAAATT
* **
3754668 AAATTAATCTGAATTTTAAA-T
1 AATTTAAAAT-AA-TTTAAATT
3754689 AATTTAAAAT
1 AATTTAAAAT
3754699 TTTAATGATA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
21 30 0.71
22 11 0.26
23 1 0.02
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (20 bp):
AATTTAAAATAATTTAAATT
Found at i:3755410 original size:14 final size:13
Alignment explanation
Indices: 3755384--3755408 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3755374 AACCAATTTA
3755384 AAAAAATTTAAAT
1 AAAAAATTTAAAT
3755397 AAAAAATTTAAA
1 AAAAAATTTAAA
3755409 ATTTTTTAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAAAATTTAAAT
Found at i:3759667 original size:25 final size:25
Alignment explanation
Indices: 3759639--3759738 Score: 71
Period size: 25 Copynumber: 3.8 Consensus size: 25
3759629 GACCAAAAGC
3759639 AATTATATAAATATAATAAATACAA
1 AATTATATAAATATAATAAATACAA
* *
3759664 AATTATAAAAAT-TGATATAATACAA
1 AATTATATAAATATAATA-AATACAA
*
3759689 TAATAATATAATCACTATAA-AATTATA-AA
1 -AATTATATAA--A-TATAATAA--ATACAA
3759718 AATTATGATATAATATAATAA
1 AATTAT-ATA-AATATAATAA
3759739 TAATATAATT
Statistics
Matches: 58, Mismatches: 6, Indels: 19
0.70 0.07 0.23
Matches are distributed among these distances:
24 4 0.07
25 18 0.31
26 8 0.14
27 5 0.09
28 10 0.17
29 7 0.12
30 6 0.10
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (25 bp):
AATTATATAAATATAATAAATACAA
Found at i:3759697 original size:45 final size:47
Alignment explanation
Indices: 3759648--3759747 Score: 150
Period size: 45 Copynumber: 2.2 Consensus size: 47
3759638 CAATTATATA
3759648 AATATAATAAATACAAAATTATAAAAA-T-TGATATAATACAATAAT
1 AATATAATAAATACAAAATTATAAAAATTATGATATAATACAATAAT
* * * *
3759693 AATATAATCACTATAAAATTATAAAAATTATGATATAATATAATAAT
1 AATATAATAAATACAAAATTATAAAAATTATGATATAATACAATAAT
3759740 AATATAAT
1 AATATAAT
3759748 TTTAAAATTT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
45 24 0.49
46 1 0.02
47 24 0.49
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (47 bp):
AATATAATAAATACAAAATTATAAAAATTATGATATAATACAATAAT
Found at i:3759731 original size:36 final size:33
Alignment explanation
Indices: 3759691--3759768 Score: 86
Period size: 36 Copynumber: 2.3 Consensus size: 33
3759681 TAATACAATA
*
3759691 ATAATATAATCACT-ATAAAATTATAAAAATTATGAT
1 ATAATATAAT-AATAATAAAATT-TAAAAATT-T-AT
* *
3759727 ATAATATAATAATAATATAATTTTAAAATTTAT
1 ATAATATAATAATAATAAAATTTAAAAATTTAT
3759760 ATAATATAA
1 ATAATATAA
3759769 ATTATATATA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
33 11 0.29
34 1 0.03
35 9 0.24
36 17 0.45
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (33 bp):
ATAATATAATAATAATAAAATTTAAAAATTTAT
Found at i:3759763 original size:47 final size:43
Alignment explanation
Indices: 3759662--3759756 Score: 129
Period size: 47 Copynumber: 2.1 Consensus size: 43
3759652 TAATAAATAC
3759662 AAAATTATAAAAATTGATATAATACAATAATAATATAATCACTAT
1 AAAATTATAAAAATTGATATAATACAATAATAATATAAT--CTAT
* *
3759707 AAAATTATAAAAATTATGATATAATATAATAATAATATAAT-TTT
1 AAAATTATAAAAA-T-TGATATAATACAATAATAATATAATCTAT
3759751 AAAATT
1 AAAATT
3759757 TATATAATAT
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
44 8 0.17
45 13 0.28
46 1 0.02
47 24 0.52
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (43 bp):
AAAATTATAAAAATTGATATAATACAATAATAATATAATCTAT
Found at i:3759767 original size:33 final size:32
Alignment explanation
Indices: 3759716--3759813 Score: 107
Period size: 32 Copynumber: 3.1 Consensus size: 32
3759706 TAAAATTATA
3759716 AAAATTATGATATAATATAATAATAATATAATTTT
1 AAAATT-T-ATATAATATAA-AATAATATAATTTT
*
3759751 AAAATTTATATAATAT-AAATTATATATATTTT
1 AAAATTTATATAATATAAAATAATATA-ATTTT
*
3759783 AAAATTAATATAA-ATAAAA-AA-AT-ATTTT
1 AAAATTTATATAATATAAAATAATATAATTTT
3759811 AAA
1 AAA
3759814 TATAATTATT
Statistics
Matches: 58, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
28 8 0.14
30 2 0.03
31 11 0.19
32 21 0.36
33 9 0.16
34 1 0.02
35 6 0.10
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (32 bp):
AAAATTTATATAATATAAAATAATATAATTTT
Found at i:3759776 original size:16 final size:16
Alignment explanation
Indices: 3759717--3759880 Score: 69
Period size: 16 Copynumber: 10.1 Consensus size: 16
3759707 AAAATTATAA
3759717 AAATTATGATATAATAT
1 AAATTAT-ATATAATAT
* *
3759734 -AATAATAATATAATTTT
1 AAATTAT-ATATAA-TAT
3759751 AAAATT-TATATAATAT
1 -AAATTATATATAATAT
* *
3759767 AAATTATATATATTTT
1 AAATTATATATAATAT
3759783 AAAATTA-ATATAA-AT
1 -AAATTATATATAATAT
** *
3759798 AAAAAAATATTTTAA-AT
1 -AAATTATA-TATAATAT
3759815 ATAATTATTATATGATATAT
1 A-AATTA-TATAT-A-ATAT
*
3759835 AAAATATAT-TAAT-T
1 AAATTATATATAATAT
3759849 ATAATTATAATATAATA-
1 A-AATTAT-ATATAATAT
3759866 AAA-TATATA-AATAT
1 AAATTATATATAATAT
3759880 A
1 A
3759881 TTATTGATAT
Statistics
Matches: 113, Mismatches: 17, Indels: 37
0.68 0.10 0.22
Matches are distributed among these distances:
13 4 0.04
14 6 0.05
15 21 0.19
16 33 0.29
17 31 0.27
18 7 0.06
19 8 0.07
20 3 0.03
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (16 bp):
AAATTATATATAATAT
Found at i:3759776 original size:47 final size:46
Alignment explanation
Indices: 3759672--3759776 Score: 106
Period size: 47 Copynumber: 2.2 Consensus size: 46
3759662 AAAATTATAA
3759672 AAATTGATATAATACAATAATAATATAATCACTATAAAATTATAAAAAT
1 AAATT-ATATAATACAATAATAATATAAT--CTATAAAATTATAAAAAT
* * * * *
3759721 -TATGATATAATATAATAATAATATAAT-TTTAAAATTTATATAATAT
1 AAATTATATAATACAATAATAATATAATCTATAAAA-TTATA-AAAAT
3759767 AAATTATATA
1 AAATTATATA
3759777 TATTTTAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
44 6 0.13
45 5 0.11
46 4 0.09
47 29 0.63
48 2 0.04
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (46 bp):
AAATTATATAATACAATAATAATATAATCTATAAAATTATAAAAAT
Found at i:3759819 original size:28 final size:27
Alignment explanation
Indices: 3759758--3759819 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 27
3759748 TTTAAAATTT
* * *
3759758 ATATAATATAAATTATATATATTTTAA
1 ATATAATATAAATAAAAAATATTTTAA
3759785 A-ATTAATATAAATAAAAAAATATTTTAA
1 ATA-TAATATAAAT-AAAAAATATTTTAA
3759813 ATATAAT
1 ATATAAT
3759820 TATTATATGA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
26 1 0.03
27 11 0.38
28 16 0.55
29 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (27 bp):
ATATAATATAAATAAAAAATATTTTAA
Found at i:3759840 original size:34 final size:32
Alignment explanation
Indices: 3759785--3759891 Score: 105
Period size: 34 Copynumber: 3.4 Consensus size: 32
3759775 TATATTTTAA
* * *
3759785 AATTAATATAAATAAAAAAATATTTTAAATAT
1 AATTATTATATATAATAAAATATTTTAAATAT
* *
3759817 AATTATTATATGATATATAAAATATATTAATTAT
1 AATTATTATAT-ATA-ATAAAATATTTTAAATAT
*
3759851 AATTA-TA-ATATAATAAAATA-TATAAATAT
1 AATTATTATATATAATAAAATATTTTAAATAT
3759880 -ATTATTGATATA
1 AATTATT-ATATA
3759892 CAGGTTACCA
Statistics
Matches: 62, Mismatches: 8, Indels: 11
0.77 0.10 0.14
Matches are distributed among these distances:
28 4 0.06
29 7 0.11
30 9 0.15
31 6 0.10
32 11 0.18
33 5 0.08
34 20 0.32
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (32 bp):
AATTATTATATATAATAAAATATTTTAAATAT
Found at i:3760318 original size:35 final size:35
Alignment explanation
Indices: 3760244--3760318 Score: 91
Period size: 35 Copynumber: 2.1 Consensus size: 35
3760234 TAATTCAATG
* *
3760244 TTAATCAAATAAAATTATATTTTAATTATTTTATA
1 TTAATCAAATAAAATTATATTTTAAATATTTAATA
*
3760279 TTAAT-AAATAAAAATTATATTTTAAA-ATATTAATT
1 TTAATCAAAT-AAAATTATATTTTAAATAT-TTAATA
3760314 TTAAT
1 TTAAT
3760319 TTTTTATAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
34 6 0.17
35 29 0.83
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (35 bp):
TTAATCAAATAAAATTATATTTTAAATATTTAATA
Found at i:3760969 original size:11 final size:11
Alignment explanation
Indices: 3760953--3761020 Score: 59
Period size: 11 Copynumber: 6.0 Consensus size: 11
3760943 TGATATTTAT
3760953 TATTAAAATTA
1 TATTAAAATTA
3760964 TATTAAAATTA
1 TATTAAAATTA
*
3760975 T-TAAAAATTA
1 TATTAAAATTA
*
3760985 -ATTAAAAAATA
1 TATT-AAAATTA
*
3760996 TATGATAAAATTT
1 TAT--TAAAATTA
3761009 TATGTAAAATTA
1 TAT-TAAAATTA
3761021 AAAAAAATAT
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
10 9 0.20
11 18 0.40
12 9 0.20
13 8 0.18
14 1 0.02
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (11 bp):
TATTAAAATTA
Found at i:3760976 original size:20 final size:20
Alignment explanation
Indices: 3760951--3760991 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
3760941 AGTGATATTT
3760951 ATTATT-AAAATTATATTAAA
1 ATTATTAAAAATTA-ATTAAA
3760971 ATTATTAAAAATTAATTAAA
1 ATTATTAAAAATTAATTAAA
3760991 A
1 A
3760992 AATATATGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
ATTATTAAAAATTAATTAAA
Found at i:3761473 original size:4 final size:4
Alignment explanation
Indices: 3761464--3761491 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
3761454 GTCAAAAATA
3761464 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
3761492 CTTAAATGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:3761752 original size:17 final size:16
Alignment explanation
Indices: 3761696--3761764 Score: 74
Period size: 17 Copynumber: 4.4 Consensus size: 16
3761686 AATATTTAAT
3761696 TTTATTAAATTT-AATA
1 TTTA-TAAATTTAAATA
3761712 TTT-T-AATTTAAATA
1 TTTATAAATTTAAATA
*
3761726 -TTATATATTTAAATAA
1 TTTATAAATTTAAAT-A
3761742 TTTATAAATTTAAATA
1 TTTATAAATTTAAATA
3761758 TATTATA
1 T-TTATA
3761765 TTTATTATTA
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
13 7 0.16
14 6 0.13
15 8 0.18
16 6 0.13
17 18 0.40
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTTATAAATTTAAATA
Found at i:3762522 original size:14 final size:14
Alignment explanation
Indices: 3762503--3762533 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
3762493 TTTGCTAGTT
3762503 TTATCATGATACTG
1 TTATCATGATACTG
3762517 TTATCATGATACTG
1 TTATCATGATACTG
3762531 TTA
1 TTA
3762534 ACTACTTGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (14 bp):
TTATCATGATACTG
Found at i:3769913 original size:8 final size:8
Alignment explanation
Indices: 3769900--3769924 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
3769890 TAATAAAATT
3769900 AAAATATA
1 AAAATATA
3769908 AAAATATA
1 AAAATATA
3769916 AAAATATA
1 AAAATATA
3769924 A
1 A
3769925 TATTAAGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AAAATATA
Found at i:3769918 original size:21 final size:22
Alignment explanation
Indices: 3769883--3769927 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
3769873 TTTAAATCAA
* *
3769883 ATAAAATTAATAAAATTAAAAT
1 ATAAAAATAATAAAAATAAAAT
*
3769905 ATAAAAAT-ATAAAAATATAAT
1 ATAAAAATAATAAAAATAAAAT
3769926 AT
1 AT
3769928 TAAGAGTACT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
ATAAAAATAATAAAAATAAAAT
Found at i:3770634 original size:2 final size:2
Alignment explanation
Indices: 3770627--3770656 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3770617 CCATTTCAAC
3770627 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
3770657 TTCCAAAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3771366 original size:37 final size:37
Alignment explanation
Indices: 3771292--3771367 Score: 116
Period size: 37 Copynumber: 2.1 Consensus size: 37
3771282 AATCAAAATC
*
3771292 TTAGAAAATAATGGAATTAGATAAATGTTACAAATTT
1 TTAGAAAATAATGGAATTAGATAAATATTACAAATTT
* * *
3771329 TTAGAAAATAATGTAATTAGATAAATATTATATATTT
1 TTAGAAAATAATGGAATTAGATAAATATTACAAATTT
3771366 TT
1 TT
3771368 TTTATTGAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.47, C:0.01, G:0.11, T:0.41
Consensus pattern (37 bp):
TTAGAAAATAATGGAATTAGATAAATATTACAAATTT
Found at i:3772130 original size:21 final size:22
Alignment explanation
Indices: 3772085--3772134 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
3772075 TTTTAAAAAA
* * *
3772085 TATGGTAATATATTTTTTATTT
1 TATGTTAATATATTTTTAATAT
3772107 TATGTTAAT-TATTTTTAATAT
1 TATGTTAATATATTTTTAATAT
3772128 TAT-TTAA
1 TATGTTAA
3772135 AAATTAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.16
21 13 0.52
22 8 0.32
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (22 bp):
TATGTTAATATATTTTTAATAT
Found at i:3772942 original size:173 final size:170
Alignment explanation
Indices: 3772515--3772856 Score: 432
Period size: 172 Copynumber: 2.0 Consensus size: 170
3772505 AATATATTAA
* * ** * * * ** * *
3772515 ATTTTGATAAATTAAAAAATAATTTTATAAAAATCTTTCTCTCTACTAAAATATTTTAATTAAAT
1 ATTTT-ATAAATT-AAAAATTATTTTATAAAATTAATACTCTCTTCTAAAAGATTAAAAATGAAT
* * *
3772580 TTGACTCAATTATATATTTAAACTTTATTTTTCTAGCCTCAAAAAAATTAAAATTCTAAGAGTTT
64 ATGACT-AATTATATATTTAAACTTTATTTTTCTAGCCTCAAAAAAATTAAAATACTAAAAGTTT
*
3772645 TTTATTTTGAATTTCAAGCTTCATCTTCGCAATTTAGTCAAAT
128 TTTATTTTGAATTTCAAGCTTCATCTTCACAATTTAGTCAAAT
* * ** * *
3772688 ATTTTATAAATTAAAAATTAATTTTATAAAATTATTTCTCTCTTCTAAAAGATTTTAATTGAATT
1 ATTTTATAAATTAAAAATT-ATTTTATAAAATTAATACTCTCTTCTAAAAGATTAAAAATGAATA
*
3772753 TGACTCAATTATATATTTAAACTTTATTTTTACTGGCCTCAAAAAAATTAAAATACTAAAAGTTT
65 TGACT-AATTATATATTTAAACTTTATTTTT-CTAGCCTCAAAAAAATTAAAATACTAAAAGTTT
3772818 TTTATTTTGAATTTCAAGCTTCATCTTCACAATTTAGTC
128 TTTATTTTGAATTTCAAGCTTCATCTTCACAATTTAGTC
3772857 TTCAATTTTA
Statistics
Matches: 157, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
171 6 0.04
172 78 0.50
173 73 0.46
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.45
Consensus pattern (170 bp):
ATTTTATAAATTAAAAATTATTTTATAAAATTAATACTCTCTTCTAAAAGATTAAAAATGAATAT
GACTAATTATATATTTAAACTTTATTTTTCTAGCCTCAAAAAAATTAAAATACTAAAAGTTTTTT
ATTTTGAATTTCAAGCTTCATCTTCACAATTTAGTCAAAT
Found at i:3774048 original size:38 final size:38
Alignment explanation
Indices: 3774006--3774111 Score: 92
Period size: 38 Copynumber: 2.8 Consensus size: 38
3773996 TAATTTTTTA
3774006 ATTTTTTTAAAAAATAATATATTAAATTATAAAAATTG
1 ATTTTTTTAAAAAATAATATATTAAATTATAAAAATTG
* * * * *
3774044 ATTTTTTTCAAATAAA-AATGTA-AAAATTATTTATAATTT
1 ATTTTTTT-AAA-AAATAATATATTAAATTA-TAAAAATTG
* * *
3774083 A-TTTTCTGAAAAATAATTTATTAAATTAT
1 ATTTTTTTAAAAAATAATATATTAAATTAT
3774112 TTTTCAAATA
Statistics
Matches: 54, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
36 3 0.06
37 8 0.15
38 25 0.46
39 15 0.28
40 3 0.06
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (38 bp):
ATTTTTTTAAAAAATAATATATTAAATTATAAAAATTG
Found at i:3774158 original size:31 final size:30
Alignment explanation
Indices: 3774077--3774166 Score: 96
Period size: 31 Copynumber: 3.0 Consensus size: 30
3774067 AAATTATTTA
*
3774077 TAATTTATTTTCTGAAAAATAAT-T--TAT
1 TAATTTATTTTCTTAAAAATAATATAATAT
* *
3774104 TAAATTATTTTTCAAATAAAAATAATATAATATT
1 TAATTTA-TTTTC--TTAAAAATAATATAATA-T
3774138 TAATTTATTTTCTTAAAAATAATATAATA
1 TAATTTATTTTCTTAAAAATAATATAATA
3774167 ACTTATAAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
27 6 0.12
28 5 0.10
30 9 0.18
31 17 0.33
33 7 0.14
34 7 0.14
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (30 bp):
TAATTTATTTTCTTAAAAATAATATAATAT
Found at i:3774221 original size:26 final size:28
Alignment explanation
Indices: 3774172--3774223 Score: 81
Period size: 26 Copynumber: 1.9 Consensus size: 28
3774162 TAATAACTTA
3774172 TAAAAATTGATTTTTTTCAAATAAAATG
1 TAAAAATTGATTTTTTTCAAATAAAATG
*
3774200 TAAAAATT-A-TTTTTTCACATAAAA
1 TAAAAATTGATTTTTTTCAAATAAAA
3774224 AATAGATTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 14 0.61
27 1 0.04
28 8 0.35
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (28 bp):
TAAAAATTGATTTTTTTCAAATAAAATG
Found at i:3774322 original size:18 final size:17
Alignment explanation
Indices: 3774289--3774325 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
3774279 AATACGTGAA
*
3774289 TATTTTAATTTTATATT
1 TATTTTAATATTATATT
3774306 TATTTTAAATATTATATT
1 TATTTT-AATATTATATT
3774324 TA
1 TA
3774326 AGCTATGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TATTTTAATATTATATT
Found at i:3775190 original size:25 final size:22
Alignment explanation
Indices: 3775143--3775199 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 22
3775133 GATATGAATT
3775143 AAATT-AA-TAAAATTATTTAA
1 AAATTAAATTAAAATTATTTAA
3775163 AAATTAAATTAAAATTAATTTAA
1 AAATTAAATTAAAATT-ATTTAA
*
3775186 TAAAATAAACTTAA
1 -AAATTAAA-TTAA
3775200 GGAGATTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
20 5 0.16
21 2 0.06
22 7 0.23
23 6 0.19
24 7 0.23
25 4 0.13
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (22 bp):
AAATTAAATTAAAATTATTTAA
Found at i:3775282 original size:17 final size:16
Alignment explanation
Indices: 3775255--3775291 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 16
3775245 AACTACTTAC
3775255 TTATACAAAAAAATAT
1 TTATACAAAAAAATAT
3775271 TTATATCAAAAAAATAT
1 TTATA-CAAAAAAATAT
3775288 TTAT
1 TTAT
3775292 TTATTATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (16 bp):
TTATACAAAAAAATAT
Found at i:3775626 original size:7 final size:7
Alignment explanation
Indices: 3775611--3775645 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
3775601 TTTTCATATT
3775611 TTATTTA
1 TTATTTA
*
3775618 TTATATA
1 TTATTTA
3775625 TTATTTAA
1 TTATTT-A
3775633 TTATTTA
1 TTATTTA
3775640 TTATTT
1 TTATTT
3775646 CATCGAATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
TTATTTA
Found at i:3775641 original size:15 final size:14
Alignment explanation
Indices: 3775606--3775645 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
3775596 AAAAATTTTC
*
3775606 ATATTTTATTTATT
1 ATATATTATTTATT
3775620 ATATATTATTTAATT
1 ATATATTATTT-ATT
*
3775635 ATTTATTATTT
1 ATATATTATTT
3775646 CATCGAATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
ATATATTATTTATT
Found at i:3775888 original size:14 final size:14
Alignment explanation
Indices: 3775860--3775906 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
3775850 TTCCACCATA
3775860 ATTATATTA--TAT
1 ATTATATTATTTAT
3775872 ATTATATTATTTAT
1 ATTATATTATTTAT
*
3775886 ATTATATAATTT-T
1 ATTATATTATTTAT
*
3775899 AATATATT
1 ATTATATT
3775907 TATGTATTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
12 9 0.30
13 7 0.23
14 14 0.47
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
ATTATATTATTTAT
Done.