Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167937.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_2, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 35885061
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 165000 characters in sequence are not A, C, G, or T
File 14 of 195
Found at i:3193350 original size:9 final size:9
Alignment explanation
Indices: 3193338--3193401 Score: 69
Period size: 9 Copynumber: 7.1 Consensus size: 9
3193328 AAATTATATT
3193338 TTTATTTTA
1 TTTATTTTA
3193347 TTTATTTATAA
1 TTTATTT-T-A
*
3193358 ATT-TTTTA
1 TTTATTTTA
3193366 TTTATTTTA
1 TTTATTTTA
3193375 TTTATTTTA
1 TTTATTTTA
*
3193384 TTT-TATTA
1 TTTATTTTA
*
3193392 TTAATTTTA
1 TTTATTTTA
3193401 T
1 T
3193402 CTTGTTTATT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
8 9 0.20
9 30 0.65
10 4 0.09
11 3 0.07
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (9 bp):
TTTATTTTA
Found at i:3193352 original size:4 final size:4
Alignment explanation
Indices: 3193338--3193474 Score: 50
Period size: 4 Copynumber: 33.0 Consensus size: 4
3193328 AAATTATATT
**
3193338 TTTA TTTTA TTTA TTTA TAAA TTT- TTTA TTTA TTTTA TTTA TTTTA TTT-
1 TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA -TTTA TTTA
* * * * * *
3193387 TATTA TTAA TTTTA TCTTG TTTA TTT- GTTG TTTA TCT- TTAA TTGTA
1 T-TTA TTTA -TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA TT-TA
* * *
3193433 TTTT TTATA TTTA TTTAA TTT- TTTAA TTTA TATA ATTA TTTA
1 TTTA TT-TA TTTA TTT-A TTTA TTT-A TTTA TTTA TTTA TTTA
3193475 AAAAAAAAAT
Statistics
Matches: 97, Mismatches: 21, Indels: 29
0.66 0.14 0.20
Matches are distributed among these distances:
3 10 0.10
4 55 0.57
5 32 0.33
ACGTcount: A:0.26, C:0.01, G:0.03, T:0.70
Consensus pattern (4 bp):
TTTA
Found at i:3193409 original size:26 final size:25
Alignment explanation
Indices: 3193358--3193412 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
3193348 TTATTTATAA
* *
3193358 ATTTTTTATTTATTTTATTTATTTT
1 ATTTTTTATTAATTTTATTTAGTTT
3193383 ATTTTATTATTAATTTTATCTT-GTTT
1 ATTTT-TTATTAATTTTAT-TTAGTTT
3193409 ATTT
1 ATTT
3193413 GTTGTTTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 5 0.19
26 19 0.73
27 2 0.08
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.75
Consensus pattern (25 bp):
ATTTTTTATTAATTTTATTTAGTTT
Found at i:3193461 original size:17 final size:17
Alignment explanation
Indices: 3193432--3193475 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
3193422 CTTTAATTGT
*
3193432 ATTTTTTATATTTATTTA
1 ATTTTTTA-ATTTATATA
3193450 ATTTTTTAATTTATATA
1 ATTTTTTAATTTATATA
*
3193467 ATTATTTAA
1 ATTTTTTAA
3193476 AAAAAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
ATTTTTTAATTTATATA
Found at i:3195028 original size:3 final size:3
Alignment explanation
Indices: 3195020--3195052 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3195010 TAGAACCAAG
3195020 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3195053 GGGATAAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3199833 original size:20 final size:19
Alignment explanation
Indices: 3199805--3199848 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
3199795 AGTGAAAAAA
*
3199805 ATATAAAAATTAAAAATAT
1 ATATTAAAATTAAAAATAT
* *
3199824 GATATTAAAATTTATAATAT
1 -ATATTAAAATTAAAAATAT
3199844 ATATT
1 ATATT
3199849 GATATTTTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (19 bp):
ATATTAAAATTAAAAATAT
Found at i:3202296 original size:16 final size:16
Alignment explanation
Indices: 3202263--3202328 Score: 53
Period size: 16 Copynumber: 4.1 Consensus size: 16
3202253 TTTTATTTTT
*
3202263 AAAATATAAATATTTA
1 AAAATATAAATATATA
* *
3202279 AAAATATTATTATATA
1 AAAATATAAATATATA
* * *
3202295 AATATATATATAAATA
1 AAAATATAAATATATA
3202311 AATAAT-TAAATTATATA
1 AA-AATATAAA-TATATA
3202328 A
1 A
3202329 TATCAGGTCT
Statistics
Matches: 37, Mismatches: 11, Indels: 3
0.73 0.22 0.06
Matches are distributed among these distances:
16 29 0.78
17 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AAAATATAAATATATA
Found at i:3203403 original size:3 final size:3
Alignment explanation
Indices: 3203390--3203427 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
3203380 AAATTGAATC
3203390 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
3203428 TATTAATGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:3205199 original size:16 final size:16
Alignment explanation
Indices: 3205174--3205209 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3205164 TCAAATATTT
*
3205174 ATTTTCATTAATTAAA
1 ATTTTCATTAAATAAA
*
3205190 ATTTTTATTAAATAAA
1 ATTTTCATTAAATAAA
3205206 ATTT
1 ATTT
3205210 AGTTATAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTTCATTAAATAAA
Found at i:3205296 original size:30 final size:28
Alignment explanation
Indices: 3205262--3205363 Score: 87
Period size: 30 Copynumber: 3.5 Consensus size: 28
3205252 AGATAAAAAA
*
3205262 ATTTAAGAATTTAATTAAGTAAAAATAAAT
1 ATTTAA-AATTTAATTAA-TTAAAATAAAT
* * *
3205292 ATTTAAAGATTCAGTTTATTTAAAATAAAAT
1 ATTTAAA-ATTTA-ATTAATTAAAAT-AAAT
* * * *
3205323 ATTTAAGATTTAATTGATTATAATAAAA
1 ATTTAAAATTTAATTAATTAAAATAAAT
3205351 ATTTAAAATTTAA
1 ATTTAAAATTTAA
3205364 AATAATTATT
Statistics
Matches: 57, Mismatches: 12, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
28 15 0.26
29 9 0.16
30 20 0.35
31 13 0.23
ACGTcount: A:0.52, C:0.01, G:0.06, T:0.41
Consensus pattern (28 bp):
ATTTAAAATTTAATTAATTAAAATAAAT
Found at i:3205371 original size:29 final size:29
Alignment explanation
Indices: 3205315--3205372 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
3205305 GTTTATTTAA
* * *
3205315 AATAAAATATTTAAGATTTAATTGATTAT
1 AATAAAATATTTAAAATTTAAATAATTAT
3205344 AATAAAA-ATTTAAAATTTAAAATAATTAT
1 AATAAAATATTTAAAATTT-AAATAATTAT
3205373 TAAATTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 10 0.40
29 15 0.60
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (29 bp):
AATAAAATATTTAAAATTTAAATAATTAT
Found at i:3205405 original size:3 final size:3
Alignment explanation
Indices: 3205397--3205427 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
3205387 TGTTTTTGAT
3205397 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
3205428 TTTCTTTCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3217086 original size:13 final size:12
Alignment explanation
Indices: 3217064--3217102 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
3217054 GTGAAATTTT
*
3217064 TTTAAAAAAATAA
1 TTTAATAAAA-AA
*
3217077 TTTAATAAAAAC
1 TTTAATAAAAAA
3217089 TTTAATAAAAAA
1 TTTAATAAAAAA
3217101 TT
1 TT
3217103 AAAATCAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 14 0.61
13 9 0.39
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (12 bp):
TTTAATAAAAAA
Found at i:3217341 original size:13 final size:13
Alignment explanation
Indices: 3217323--3217348 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3217313 TAATTTATCG
3217323 ATTTTAATTTTTA
1 ATTTTAATTTTTA
3217336 ATTTTAATTTTTA
1 ATTTTAATTTTTA
3217349 CTTAATTATT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
ATTTTAATTTTTA
Found at i:3217873 original size:81 final size:81
Alignment explanation
Indices: 3217738--3217888 Score: 266
Period size: 81 Copynumber: 1.9 Consensus size: 81
3217728 AGCTTTCATG
*
3217738 GTCCAGCCAGTGCTGAAATTTTGTATAGTCACTTGGACATGTTAGACATTAATGGTTGGTCCCTT
1 GTCCAGCCAGTGCTGAAATTTTGTATAGTAACTTGGACATGTTAGACATTAATGGTTGGTCCCTT
3217803 ACGAGGGTCAGAAAAA
66 ACGAGGGTCAGAAAAA
* **
3217819 GTCCAGCCAGTGCTGAAATTTTGTATAGTAACTTGGACATTTTAGGTATTAATGGTTGGTCCCTT
1 GTCCAGCCAGTGCTGAAATTTTGTATAGTAACTTGGACATGTTAGACATTAATGGTTGGTCCCTT
3217884 ACGAG
66 ACGAG
3217889 CCCTTCCAAT
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 66 1.00
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (81 bp):
GTCCAGCCAGTGCTGAAATTTTGTATAGTAACTTGGACATGTTAGACATTAATGGTTGGTCCCTT
ACGAGGGTCAGAAAAA
Found at i:3218636 original size:2 final size:2
Alignment explanation
Indices: 3218629--3218654 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3218619 AAGCTTACAA
3218629 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
3218655 TACAAAGGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3220518 original size:98 final size:98
Alignment explanation
Indices: 3220409--3220596 Score: 358
Period size: 98 Copynumber: 1.9 Consensus size: 98
3220399 AGATATAATA
*
3220409 TGTAAAAGAATGAAATAAAAATTAACGTATCTAATTTTATTATTTACTTTTAATGTATTAGTTTT
1 TGTAAAAGAATGAAATAAAAATTAACATATCTAATTTTATTATTTACTTTTAATGTATTAGTTTT
3220474 ATCATTTTCTTTTAATAAATAAATAAATAAATT
66 ATCATTTTCTTTTAATAAATAAATAAATAAATT
*
3220507 TGTAAAAGAATGAAATAAAAATTAACATATCTAATTTTATTATTTACTTTTAATGTATTGGTTTT
1 TGTAAAAGAATGAAATAAAAATTAACATATCTAATTTTATTATTTACTTTTAATGTATTAGTTTT
3220572 ATCATTTTCTTTTAATAAATAAATA
66 ATCATTTTCTTTTAATAAATAAATA
3220597 TATTTGATTT
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
98 88 1.00
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.46
Consensus pattern (98 bp):
TGTAAAAGAATGAAATAAAAATTAACATATCTAATTTTATTATTTACTTTTAATGTATTAGTTTT
ATCATTTTCTTTTAATAAATAAATAAATAAATT
Found at i:3239875 original size:2 final size:2
Alignment explanation
Indices: 3239870--3239896 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3239860 ATATATATAT
3239870 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
3239897 TACATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3249580 original size:19 final size:19
Alignment explanation
Indices: 3249537--3249582 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
3249527 TTCATTAAAT
*
3249537 AACCTTTTGCTTATTCAAG
1 AACCTTTTGCTTATTCAAA
*
3249556 ACCCTTTTGCTTATTCAAA
1 AACCTTTTGCTTATTCAAA
3249575 AACCTTTT
1 AACCTTTT
3249583 TCTTGGTAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.26, C:0.24, G:0.07, T:0.43
Consensus pattern (19 bp):
AACCTTTTGCTTATTCAAA
Found at i:3253751 original size:22 final size:22
Alignment explanation
Indices: 3253726--3253769 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3253716 TTTTCTTGAA
3253726 TAATCAAGCAA-ATTTTCCATTC
1 TAATC-AGCAAGATTTTCCATTC
*
3253748 TAATCATCAAGATTTTCCATTC
1 TAATCAGCAAGATTTTCCATTC
3253770 CTCTAGGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.39
Consensus pattern (22 bp):
TAATCAGCAAGATTTTCCATTC
Found at i:3267416 original size:78 final size:77
Alignment explanation
Indices: 3267268--3267417 Score: 178
Period size: 78 Copynumber: 1.9 Consensus size: 77
3267258 ACATCATGCA
* * * * *
3267268 TGTTCCTGTTGCATTTTGCTGTACAATCTGCTTACCAGATTTTGGTTTCTTGTATTATTTGACAG
1 TGTTCCTGTTGCATTTTGCTGCACAATCAGCTTACCAGATTTCGGTTTCTAGTATTATATGACAG
*
3267333 TATTCTTACGCG
66 CATTCTTACGCG
** *
3267345 TGTTCCTGTTGCATTTTGCTGCATTATCAGCTTTACCAG-TGTTCGGTTTC-AGCTATTCTATGA
1 TGTTCCTGTTGCATTTTGCTGCACAATCAGC-TTACCAGAT-TTCGGTTTCTAG-TATTATATGA
3267408 CAGCATTCTT
63 CAGCATTCTT
3267418 CTGCTTGGTA
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
77 29 0.48
78 32 0.52
ACGTcount: A:0.17, C:0.20, G:0.18, T:0.45
Consensus pattern (77 bp):
TGTTCCTGTTGCATTTTGCTGCACAATCAGCTTACCAGATTTCGGTTTCTAGTATTATATGACAG
CATTCTTACGCG
Found at i:3270479 original size:16 final size:18
Alignment explanation
Indices: 3270458--3270494 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
3270448 TTGGTTTAAT
3270458 AAAATAT-G-GACCTTGG
1 AAAATATAGAGACCTTGG
3270474 AAAATATAGGAGACCTTGG
1 AAAATATA-GAGACCTTGG
3270493 AA
1 AA
3270495 TAAAGATCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.39
18 1 0.06
19 10 0.56
ACGTcount: A:0.43, C:0.11, G:0.24, T:0.22
Consensus pattern (18 bp):
AAAATATAGAGACCTTGG
Found at i:3274867 original size:12 final size:12
Alignment explanation
Indices: 3274792--3274867 Score: 59
Period size: 12 Copynumber: 6.1 Consensus size: 12
3274782 TATATAAAAA
*
3274792 AATTTTATTTTTT
1 AATTTTA-TATTT
3274805 AATTATT-TATTT
1 AATT-TTATATTT
3274817 AATTTTATA-TT
1 AATTTTATATTT
*
3274828 CATTTATATATTT
1 AATTT-TATATTT
3274841 -ATTTATATATTTTT
1 AATTT-TATA--TTT
3274855 AATTTTATATTT
1 AATTTTATATTT
3274867 A
1 A
3274868 TATTAAAAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 15
0.76 0.03 0.21
Matches are distributed among these distances:
11 8 0.15
12 27 0.50
13 6 0.11
14 9 0.17
15 4 0.07
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (12 bp):
AATTTTATATTT
Found at i:3274888 original size:23 final size:23
Alignment explanation
Indices: 3274854--3274897 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
3274844 TATATATTTT
*
3274854 TAATTTTATATTTATATTAAAAA
1 TAATTTTATATTAATATTAAAAA
*
3274877 TAATATTT-TATTAATTTTAAA
1 TAAT-TTTATATTAATATTAAA
3274898 TCGAATACGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 15 0.83
24 3 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TAATTTTATATTAATATTAAAAA
Found at i:3275110 original size:18 final size:18
Alignment explanation
Indices: 3275075--3275109 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3275065 CATAAAAGTA
3275075 AATTTTATTTATTTTTTT
1 AATTTTATTTATTTTTTT
*
3275093 AATTTTCTTT-TTTTTTT
1 AATTTTATTTATTTTTTT
3275110 TTCAGGTAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (18 bp):
AATTTTATTTATTTTTTT
Found at i:3275297 original size:8 final size:8
Alignment explanation
Indices: 3275286--3275325 Score: 62
Period size: 8 Copynumber: 5.0 Consensus size: 8
3275276 TTCTTTTTTT
*
3275286 TTTTTTAA
1 TTTTTAAA
3275294 TTTTTAAA
1 TTTTTAAA
3275302 TTTTTAAA
1 TTTTTAAA
3275310 TTTTTAAA
1 TTTTTAAA
*
3275318 ATTTTAAA
1 TTTTTAAA
3275326 ATTTAATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TTTTTAAA
Found at i:3275327 original size:17 final size:16
Alignment explanation
Indices: 3275292--3275329 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
3275282 TTTTTTTTTT
*
3275292 AATTTTTAAATTTTTA
1 AATTTTTAAATTTTAA
3275308 AATTTTTAAAATTTTAA
1 AATTTTT-AAATTTTAA
3275325 AATTT
1 AATTT
3275330 AATTTTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
AATTTTTAAATTTTAA
Found at i:3275331 original size:7 final size:8
Alignment explanation
Indices: 3275295--3275329 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
3275285 TTTTTTTAAT
*
3275295 TTTTAAAT
1 TTTTAAAA
*
3275303 TTTTAAAT
1 TTTTAAAA
3275311 TTTTAAAA
1 TTTTAAAA
3275319 TTTTAAAA
1 TTTTAAAA
3275327 TTT
1 TTT
3275330 AATTTTTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
TTTTAAAA
Found at i:3277040 original size:38 final size:38
Alignment explanation
Indices: 3276989--3277064 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
3276979 AAAACATTGC
*
3276989 TCTCCAGTTCACCTAGTACAGGTCGAACTGGACAATGG
1 TCTCCAGTTCACCTAGTACAGGTCAAACTGGACAATGG
3277027 TCTCCAGTTCACCTAGTACAGGTCAAACTGGACAATGG
1 TCTCCAGTTCACCTAGTACAGGTCAAACTGGACAATGG
3277065 AGTATTCTCG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (38 bp):
TCTCCAGTTCACCTAGTACAGGTCAAACTGGACAATGG
Found at i:3282216 original size:14 final size:14
Alignment explanation
Indices: 3282199--3282233 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
3282189 CACGTTATGC
*
3282199 GTTTTATAGCACAA
1 GTTTTATAACACAA
*
3282213 GTTTTATAACATAA
1 GTTTTATAACACAA
3282227 GTTTTAT
1 GTTTTAT
3282234 TGCTAAACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (14 bp):
GTTTTATAACACAA
Found at i:3283729 original size:22 final size:22
Alignment explanation
Indices: 3283667--3283733 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 22
3283657 TTTTGTGTCC
3283667 TAAAATTAT-TTTATTAATA-TT
1 TAAAATTATATTTA-TAATATTT
* * *
3283688 TAAATTTAAAATTT-TTATATTT
1 TAAAATT-ATATTTATAATATTT
3283710 TAAAATTATATTTATAATATTT
1 TAAAATTATATTTATAATATTT
3283732 TA
1 TA
3283734 CTTTTTAACA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
21 15 0.42
22 18 0.50
23 3 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TAAAATTATATTTATAATATTT
Found at i:3283732 original size:29 final size:28
Alignment explanation
Indices: 3283691--3283746 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
3283681 TAATATTTAA
3283691 ATTTAAAATTTTTA-TATTTTAAAATTAT
1 ATTTAAAATTTTTACT-TTTTAAAATTAT
* *
3283719 ATTTATAATATTTTACTTTTTAACATTA
1 ATTTAAAAT-TTTTACTTTTTAAAATTA
3283747 AAAATTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 8 0.33
29 15 0.62
30 1 0.04
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (28 bp):
ATTTAAAATTTTTACTTTTTAAAATTAT
Found at i:3285106 original size:2 final size:2
Alignment explanation
Indices: 3285099--3285136 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3285089 TAGGTTATTA
3285099 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3285137 GAGTTTGCAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3294827 original size:56 final size:56
Alignment explanation
Indices: 3294761--3294875 Score: 221
Period size: 56 Copynumber: 2.1 Consensus size: 56
3294751 AAACTTCCTG
*
3294761 AAAGAAACCATCAAAATGTTAATGGTTGCACTAAACTTTTTACCATATTAAACAAT
1 AAAGAAACCATCAAAAAGTTAATGGTTGCACTAAACTTTTTACCATATTAAACAAT
3294817 AAAGAAACCATCAAAAAGTTAATGGTTGCACTAAACTTTTTACCATATTAAACAAT
1 AAAGAAACCATCAAAAAGTTAATGGTTGCACTAAACTTTTTACCATATTAAACAAT
3294873 AAA
1 AAA
3294876 ACCTAGATGA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.47, C:0.16, G:0.09, T:0.29
Consensus pattern (56 bp):
AAAGAAACCATCAAAAAGTTAATGGTTGCACTAAACTTTTTACCATATTAAACAAT
Found at i:3296501 original size:12 final size:12
Alignment explanation
Indices: 3296484--3296511 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
3296474 GTTCACTCTC
3296484 TCCTCGATACTT
1 TCCTCGATACTT
3296496 TCCTCGATACTT
1 TCCTCGATACTT
3296508 TCCT
1 TCCT
3296512 TCTTTAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.14, C:0.36, G:0.07, T:0.43
Consensus pattern (12 bp):
TCCTCGATACTT
Found at i:3298056 original size:2 final size:2
Alignment explanation
Indices: 3298043--3298079 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
3298033 TACTGTTAAA
* *
3298043 AT AT AT AC AT AT AT AT AT TT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3298080 ACTTTTTAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3302242 original size:20 final size:20
Alignment explanation
Indices: 3302180--3302242 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
3302170 AAATTTTTAA
* *
3302180 AAGTAAAATTTAGATAAAAT
1 AAGTAAATTTTAGATAATAT
* * *
3302200 AATTTAAATTTT-TATAATTT
1 AA-GTAAATTTTAGATAATAT
*
3302220 AAGTAAATTTTAGATAATCT
1 AAGTAAATTTTAGATAATAT
3302240 AAG
1 AAG
3302243 ACCATGCGCC
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
19 8 0.24
20 18 0.55
21 7 0.21
ACGTcount: A:0.49, C:0.02, G:0.08, T:0.41
Consensus pattern (20 bp):
AAGTAAATTTTAGATAATAT
Found at i:3307020 original size:12 final size:12
Alignment explanation
Indices: 3307003--3307029 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3306993 GAAGAATCTG
3307003 TTATTGCAGTGA
1 TTATTGCAGTGA
3307015 TTATTGCAGTGA
1 TTATTGCAGTGA
3307027 TTA
1 TTA
3307030 AAATCTTGTC
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:0.26, C:0.07, G:0.22, T:0.44
Consensus pattern (12 bp):
TTATTGCAGTGA
Found at i:3310781 original size:18 final size:18
Alignment explanation
Indices: 3310758--3310794 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3310748 ATGATACTGG
*
3310758 TGAAGCTCATACCTTTCT
1 TGAAGCGCATACCTTTCT
*
3310776 TGAAGCGCATATCTTTCT
1 TGAAGCGCATACCTTTCT
3310794 T
1 T
3310795 CTTTATATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.41
Consensus pattern (18 bp):
TGAAGCGCATACCTTTCT
Found at i:3314810 original size:21 final size:21
Alignment explanation
Indices: 3314776--3314819 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
3314766 ATAATTTTTT
*
3314776 AAATTTATAATTATTTTTTAAA
1 AAATTTATAATTA-TTATTAAA
*
3314798 AAATTTAT-TTTATTATTAAA
1 AAATTTATAATTATTATTAAA
3314818 AA
1 AA
3314820 TAAAATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 9 0.45
21 3 0.15
22 8 0.40
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
AAATTTATAATTATTATTAAA
Found at i:3315258 original size:31 final size:29
Alignment explanation
Indices: 3315223--3315292 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
3315213 AATTTTATTT
3315223 TATAAATTATTAACAAAATATAAAAAATAA
1 TATAAATTATTAACAAAATAT-AAAAATAA
** *
3315253 -ATATAATT-TTATTATAATATAAAAATAA
1 TATA-AATTATTAACAAAATATAAAAATAA
3315281 TATAAATATATT
1 TATAAAT-TATT
3315293 CAAAGGTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
28 11 0.33
29 16 0.48
30 6 0.18
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (29 bp):
TATAAATTATTAACAAAATATAAAAATAA
Found at i:3315292 original size:27 final size:29
Alignment explanation
Indices: 3315239--3315292 Score: 76
Period size: 27 Copynumber: 1.9 Consensus size: 29
3315229 TTATTAACAA
* *
3315239 AATATAAAAAATAAATATAATTTTATTAT
1 AATATAAAAAATAAATATAAATATATTAT
3315268 AATAT-AAAAAT-AATATAAATATATT
1 AATATAAAAAATAAATATAAATATATT
3315293 CAAAGGTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 12 0.52
28 6 0.26
29 5 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (29 bp):
AATATAAAAAATAAATATAAATATATTAT
Found at i:3316477 original size:2 final size:2
Alignment explanation
Indices: 3316470--3316497 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3316460 CAGTAATTCT
3316470 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3316498 AATTTATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3320096 original size:10 final size:10
Alignment explanation
Indices: 3320083--3320125 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
3320073 TCTAATCAAA
3320083 TTATATATTT
1 TTATATATTT
3320093 TTAT-TAATTT
1 TTATAT-ATTT
3320103 TTATATATTT
1 TTATATATTT
3320113 TTA-A-ATTT
1 TTATATATTT
3320121 TTATA
1 TTATA
3320126 AAAAATAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
8 7 0.23
9 3 0.10
10 19 0.63
11 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TTATATATTT
Found at i:3320119 original size:18 final size:19
Alignment explanation
Indices: 3320083--3320125 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 19
3320073 TCTAATCAAA
3320083 TTATATATTTTTATTAATTT
1 TTATATATTTTTA-TAATTT
3320103 TTATATATTTTTA-AATTT
1 TTATATATTTTTATAATTT
3320121 TTATA
1 TTATA
3320126 AAAAATAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 10 0.43
20 13 0.57
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTATATATTTTTATAATTT
Found at i:3341769 original size:34 final size:35
Alignment explanation
Indices: 3341711--3341780 Score: 97
Period size: 34 Copynumber: 2.0 Consensus size: 35
3341701 ATTGGCTTTT
* * *
3341711 AATGTGTCTATGTTTTGCTTATCCATGAACTTAAA
1 AATGTGTCTATGTTTTACTGATCCATGAACCTAAA
*
3341746 AATGTGT-TGTGTTTTACTGATCCATGAACCTAAA
1 AATGTGTCTATGTTTTACTGATCCATGAACCTAAA
3341780 A
1 A
3341781 TCTTTAGTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 24 0.77
35 7 0.23
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (35 bp):
AATGTGTCTATGTTTTACTGATCCATGAACCTAAA
Found at i:3342848 original size:19 final size:19
Alignment explanation
Indices: 3342824--3342868 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
3342814 TAATAAAATA
*
3342824 TTAAATGTGATA-CATGAAT
1 TTAAATGTAATATC-TGAAT
3342843 TTAAATGTAATATCTGAAT
1 TTAAATGTAATATCTGAAT
3342862 TATAAAT
1 T-TAAAT
3342869 ATATTAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.44, C:0.04, G:0.11, T:0.40
Consensus pattern (19 bp):
TTAAATGTAATATCTGAAT
Found at i:3342939 original size:33 final size:31
Alignment explanation
Indices: 3342871--3342939 Score: 77
Period size: 33 Copynumber: 2.2 Consensus size: 31
3342861 TTATAAATAT
* * *
3342871 ATTAATTAATATTATATTTAAAATATTATTT
1 ATTAATTAATATCATATTTAAAATATAATTC
3342902 ATTAATTATATATCATAATTTAAAAT-TAATTAC
1 ATTAATTA-ATATCAT-ATTTAAAATATAATT-C
3342935 ATTAA
1 ATTAA
3342940 AAATGAGTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 8 0.25
32 10 0.31
33 14 0.44
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (31 bp):
ATTAATTAATATCATATTTAAAATATAATTC
Found at i:3350027 original size:30 final size:30
Alignment explanation
Indices: 3349968--3350027 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
3349958 CAATGTTATT
* *
3349968 ATTATACTTTTAGTTTTGAAGTAAATTAAAC
1 ATTATACTTTAAATTTT-AAGTAAATTAAAC
3349999 ATTATACTTTAAATTTT-AGTACAATTAAA
1 ATTATACTTTAAATTTTAAGTA-AATTAAA
3350028 AAATATTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 4 0.15
30 7 0.27
31 15 0.58
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.45
Consensus pattern (30 bp):
ATTATACTTTAAATTTTAAGTAAATTAAAC
Found at i:3354153 original size:14 final size:14
Alignment explanation
Indices: 3354113--3354153 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
3354103 GAAAGAACAT
3354113 ATCAATTATAA-TA
1 ATCAATTATAATTA
*
3354126 ATTATATTATAATTA
1 ATCA-ATTATAATTA
3354141 ATCAATTATAATT
1 ATCAATTATAATT
3354154 TATAACTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 3 0.12
14 16 0.67
15 5 0.21
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (14 bp):
ATCAATTATAATTA
Found at i:3355522 original size:174 final size:174
Alignment explanation
Indices: 3355232--3355582 Score: 684
Period size: 174 Copynumber: 2.0 Consensus size: 174
3355222 ACTCAAACTC
*
3355232 TTATAACTTCACTTAACTTTTAATATGAGGTTATGAGATTTAAAGCAAATCCCAATAGAAACAAG
1 TTATAACTTCACTTAACTTTTAATATGAGATTATGAGATTTAAAGCAAATCCCAATAGAAACAAG
3355297 GGTAATTTTATACCTAATCACTTATAAACTCCACTATCAAATGGATACAATTACACATTCATATG
66 GGTAATTTTATACCTAATCACTTATAAACTCCACTATCAAATGGATACAATTACACATTCATATG
3355362 TCTGGTCGCTGAGTTTTGTGTAAAAAGATAGATATAAAGTGATT
131 TCTGGTCGCTGAGTTTTGTGTAAAAAGATAGATATAAAGTGATT
3355406 TTATAACTTCACTTAACTTTTAATATGAGATTATGAGATTTAAAGCAAATCCCAATAGAAACAAG
1 TTATAACTTCACTTAACTTTTAATATGAGATTATGAGATTTAAAGCAAATCCCAATAGAAACAAG
*
3355471 GGTAATTTTCTACCTAATCACTTATAAACTCCACTATCAAATGGATACAATTACACATTCATATG
66 GGTAATTTTATACCTAATCACTTATAAACTCCACTATCAAATGGATACAATTACACATTCATATG
3355536 TCTGGTCGCTGAGTTTTGTGTAAAAAGATAGATATAAAGTGATT
131 TCTGGTCGCTGAGTTTTGTGTAAAAAGATAGATATAAAGTGATT
3355580 TTA
1 TTA
3355583 ATTGTAAATC
Statistics
Matches: 175, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
174 175 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (174 bp):
TTATAACTTCACTTAACTTTTAATATGAGATTATGAGATTTAAAGCAAATCCCAATAGAAACAAG
GGTAATTTTATACCTAATCACTTATAAACTCCACTATCAAATGGATACAATTACACATTCATATG
TCTGGTCGCTGAGTTTTGTGTAAAAAGATAGATATAAAGTGATT
Found at i:3361462 original size:2 final size:2
Alignment explanation
Indices: 3361455--3361479 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3361445 CAGACTGCAA
3361455 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
3361480 TTGGTTCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3371587 original size:314 final size:314
Alignment explanation
Indices: 3371016--3371644 Score: 1181
Period size: 314 Copynumber: 2.0 Consensus size: 314
3371006 GCTAAAAGGA
*
3371016 TACTACTTGCCACTTAAATATTCCCACTTGAGTACTCCTGCAAGTGTGCATATATGATAGATCTC
1 TACTACTTGCCACTTAAATATTCCCACTTGAGTACTCCTGCAAGTATGCATATATGATAGATCTC
*
3371081 ATCTGATGAGGTATTGGATTCCTGAATCCTGACCAAGTCCAATGACAAAGCTCAAATTGCATCAT
66 ATCTGATGAGGGATTGGATTCCTGAATCCTGACCAAGTCCAATGACAAAGCTCAAATTGCATCAT
3371146 AAAACGTTGATTTTGCTCAATTTGCTAGTGCCAATTCTTTGTTTGGGAAATTTCGAGCAAGTTGA
131 AAAACGTTGATTTTGCTCAATTTGCTAGTGCCAATTCTTTGTTTGGGAAATTTCGAGCAAGTTGA
3371211 TTTTTTCTCTTTTAAGGTACTTTCCCATTACGTTAAATTTCATTGACTTGCGGAGAAGTCTAAGG
196 TTTTTTCTCTTTTAAGGTACTTTCCCATTACGTTAAATTTCATTGACTTGCGGAGAAGTCTAAGG
* *
3371276 AAATGAAAA-TGAAAAAAAAAATTAAACGTCTAGTATTTAGCCACGAACAGGTGT
261 AAATGAAAACAG-AAAAAAAAATTAAACGTCTAGTATTTAGCCACGAACACGTGT
3371330 TACTACTTGCCACTTAAATATTCCCACTTGAGTACTCCTGCAAGTATGCATATATGATAGATCTC
1 TACTACTTGCCACTTAAATATTCCCACTTGAGTACTCCTGCAAGTATGCATATATGATAGATCTC
*
3371395 ATCTGATGAGGGATTGGATTCCTGAATCCTGACCAAGTCCAATGACAAAGCTCAATTTGCATCAT
66 ATCTGATGAGGGATTGGATTCCTGAATCCTGACCAAGTCCAATGACAAAGCTCAAATTGCATCAT
3371460 AAAACGTTGATTTTGCTCAATTTGCTAGTGCCAATTCTTTGTTTGGGAAATTTCGAGCAAGTTGA
131 AAAACGTTGATTTTGCTCAATTTGCTAGTGCCAATTCTTTGTTTGGGAAATTTCGAGCAAGTTGA
3371525 TTTTTTCTCTTTTAAGGTACTTTCCCATTACGTTAAATTTCATTGACTTGCGGA-ACAGTCTAAG
196 TTTTTTCTCTTTTAAGGTACTTTCCCATTACGTTAAATTTCATTGACTTGCGGAGA-AGTCTAAG
3371589 GAAATGAAAACAGAAAAAAAAATTAAACGTCTAGTATTTAGCCACGAACACGTGT
260 GAAATGAAAACAGAAAAAAAAATTAAACGTCTAGTATTTAGCCACGAACACGTGT
3371644 T
1 T
3371645 TGGAGTGTTG
Statistics
Matches: 308, Mismatches: 5, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
313 1 0.00
314 306 0.99
315 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Consensus pattern (314 bp):
TACTACTTGCCACTTAAATATTCCCACTTGAGTACTCCTGCAAGTATGCATATATGATAGATCTC
ATCTGATGAGGGATTGGATTCCTGAATCCTGACCAAGTCCAATGACAAAGCTCAAATTGCATCAT
AAAACGTTGATTTTGCTCAATTTGCTAGTGCCAATTCTTTGTTTGGGAAATTTCGAGCAAGTTGA
TTTTTTCTCTTTTAAGGTACTTTCCCATTACGTTAAATTTCATTGACTTGCGGAGAAGTCTAAGG
AAATGAAAACAGAAAAAAAAATTAAACGTCTAGTATTTAGCCACGAACACGTGT
Found at i:3373031 original size:34 final size:33
Alignment explanation
Indices: 3372993--3373126 Score: 96
Period size: 34 Copynumber: 4.0 Consensus size: 33
3372983 TATCAATAAA
3372993 TTAAAATATTTTATTAATAAATAAATATTAATTT
1 TTAAAATATTTTATTAATAAATAAATATT-ATTT
***
3373027 TTAAAATAAAATATATATATAAATTAAA-A-T-TTT
1 TTAAAATATTTTAT-TA-ATAAA-TAAATATTATTT
* *
3373060 TTAAAATA-TTTATTCATTAATAAATAATTATTAT
1 TTAAAATATTTTATTAATAAATAAAT-ATTATT-T
* ** * *
3373094 TTGATTTATTTTATTAATAAATTATTATTATTT
1 TTAAAATATTTTATTAATAAATAAATATTATTT
3373127 AATTTATTAA
Statistics
Matches: 77, Mismatches: 14, Indels: 19
0.70 0.13 0.17
Matches are distributed among these distances:
29 4 0.05
30 4 0.05
31 2 0.03
32 4 0.05
33 14 0.18
34 23 0.30
35 16 0.21
36 6 0.08
37 4 0.05
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (33 bp):
TTAAAATATTTTATTAATAAATAAATATTATTT
Found at i:3373113 original size:31 final size:31
Alignment explanation
Indices: 3373067--3373134 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
3373057 TTTTTAAAAT
*
3373067 ATTTA-TTCATTAATAAATAATTATTATTTG
1 ATTTATTTCATTAATAAATAATTATTATTTA
* *
3373097 ATTTATTTTATTAATAAATTATTATTATTTA
1 ATTTATTTCATTAATAAATAATTATTATTTA
3373128 ATTTATT
1 ATTTATT
3373135 AATAATATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 5 0.15
31 29 0.85
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (31 bp):
ATTTATTTCATTAATAAATAATTATTATTTA
Found at i:3373133 original size:26 final size:28
Alignment explanation
Indices: 3373085--3373139 Score: 87
Period size: 26 Copynumber: 2.0 Consensus size: 28
3373075 ATTAATAAAT
*
3373085 AATTATTATTTGATTTATTTTATTAATA
1 AATTATTATTTGATTTAATTTATTAATA
3373113 AATTATTA-TT-ATTTAATTTATTAATA
1 AATTATTATTTGATTTAATTTATTAATA
3373139 A
1 A
3373140 TATATAAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 16 0.62
27 2 0.08
28 8 0.31
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (28 bp):
AATTATTATTTGATTTAATTTATTAATA
Found at i:3378380 original size:23 final size:23
Alignment explanation
Indices: 3378348--3378419 Score: 74
Period size: 23 Copynumber: 3.1 Consensus size: 23
3378338 AGACTAGTTG
* *
3378348 AAAATCTGAGATTTGCATCTT-AA
1 AAAATATGAGATTTGAAT-TTCAA
3378371 AAAATATGAGATTTGAATTTCAA
1 AAAATATGAGATTTGAATTTCAA
* * * *
3378394 AAAATCTAAAATTTGAATCTCAA
1 AAAATATGAGATTTGAATTTCAA
3378417 AAA
1 AAA
3378420 GCTCTATAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
22 2 0.05
23 40 0.95
ACGTcount: A:0.49, C:0.10, G:0.10, T:0.32
Consensus pattern (23 bp):
AAAATATGAGATTTGAATTTCAA
Found at i:3378425 original size:24 final size:24
Alignment explanation
Indices: 3378381--3378430 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
3378371 AAAATATGAG
*
3378381 ATTTGAATTTCAAAAAATCTA-AA
1 ATTTGAATCTCAAAAAATCTATAA
*
3378404 ATTTGAATCTCAAAAAGCTCTATAA
1 ATTTGAATCTCAAAAA-ATCTATAA
3378429 AT
1 AT
3378431 AGAGCTCATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 15 0.65
24 4 0.17
25 4 0.17
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.34
Consensus pattern (24 bp):
ATTTGAATCTCAAAAAATCTATAA
Found at i:3381690 original size:9 final size:8
Alignment explanation
Indices: 3381676--3381701 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
3381666 AATAAAGAAG
3381676 AAAAAAAT
1 AAAAAAAT
3381684 AAAAAAAT
1 AAAAAAAT
3381692 AAAAAAAT
1 AAAAAAAT
3381700 AA
1 AA
3381702 TAATAATACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAAAAT
Found at i:3381987 original size:44 final size:43
Alignment explanation
Indices: 3381832--3382148 Score: 208
Period size: 44 Copynumber: 7.1 Consensus size: 43
3381822 CTTTTAAAAA
* ** *
3381832 AAAAATTTAAAAGGCTCTTCTAAATAGAGATTTAATGACATTTTT
1 AAAAATTTAAAAGGCTCTTCTAAGTAGAGGCTCAATGAC--TTTT
* * *
3381877 AAAAATTTAAAAAGATCATCTAAGTAGAGGCTCAATGACTTTT
1 AAAAATTTAAAAGGCTCTTCTAAGTAGAGGCTCAATGACTTTT
* * *** *
3381920 GAAAATATAAAGATATTTCTT-TAAGCAGAGGCTCAATGACTTTT
1 AAAAATTTAAA-A-GGCTCTTCTAAGTAGAGGCTCAATGACTTTT
* ** * **
3381964 AAAAATTTAAAGAGGCTCTTTTAAAAAGAGGCTTAACAACTTTT
1 AAAAATTTAAA-AGGCTCTTCTAAGTAGAGGCTCAATGACTTTT
* * *
3382008 AAAAATTTAAAGAGGCTCTTTTAAGTAGAGGCTCGATAACTTTT
1 AAAAATTTAAA-AGGCTCTTCTAAGTAGAGGCTCAATGACTTTT
* * * * **
3382052 AAAAATTGAAAACGGTTCCTCTAAGCAGAGGCTCAACAAC-TTT
1 AAAAATTTAAAA-GGCTCTTCTAAGTAGAGGCTCAATGACTTTT
* *
3382095 AAAATTTTCATCTTGAAAAAAGCTCCTCTAAGTAGAGGCTCAATGAC-TTT
1 AAAA-----AT-TT--AAAAGGCTCTTCTAAGTAGAGGCTCAATGACTTTT
3382145 AAAA
1 AAAA
3382149 TCTCATATTG
Statistics
Matches: 219, Mismatches: 41, Indels: 19
0.78 0.15 0.07
Matches are distributed among these distances:
43 25 0.11
44 122 0.56
45 36 0.16
48 2 0.01
49 1 0.00
50 29 0.13
51 4 0.02
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.32
Consensus pattern (43 bp):
AAAAATTTAAAAGGCTCTTCTAAGTAGAGGCTCAATGACTTTT
Found at i:3382077 original size:132 final size:132
Alignment explanation
Indices: 3381832--3382087 Score: 295
Period size: 132 Copynumber: 1.9 Consensus size: 132
3381822 CTTTTAAAAA
* * * *
3381832 AAAAATTTAAAAGGCTCTTCTAAATAGAGATTTAATGACATTTTTAAAAATTTAAAAAGATCATC
1 AAAAATTTAAAAGGCTCTTCTAAAAAGAGACTTAATCACACTTTTAAAAATTTAAAAAGATCATC
* * * * *
3381897 TAAGTAGAGGCTCAATGACTTTTGAAAATATAAAGATATTTCTTTAAGCAGAGGCTCAATGACTT
66 TAAGTAGAGGCTCAATAACTTTTAAAAATATAAAGAGATTCCTCTAAGCAGAGGCTCAATGACTT
3381962 TT
131 TT
* * * * *
3381964 AAAAATTTAAAGAGGCTCTTTTAAAAAGAGGCTTAA-CA-ACTTTTAAAAATTTAAAGAGGCTCT
1 AAAAATTTAAA-AGGCTCTTCTAAAAAGAGACTTAATCACACTTTTAAAAATTTAAA-AAGATCA
* * *
3382027 TTTAAGTAGAGGCTCGATAACTTTTAAAAAT-TGAAA-ACGGTTCCTCTAAGCAGAGGCTCAA
64 TCTAAGTAGAGGCTCAATAACTTTTAAAAATAT-AAAGA-GATTCCTCTAAGCAGAGGCTCAA
3382088 CAACTTTAAA
Statistics
Matches: 103, Mismatches: 17, Indels: 8
0.80 0.13 0.06
Matches are distributed among these distances:
131 18 0.17
132 65 0.63
133 20 0.19
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (132 bp):
AAAAATTTAAAAGGCTCTTCTAAAAAGAGACTTAATCACACTTTTAAAAATTTAAAAAGATCATC
TAAGTAGAGGCTCAATAACTTTTAAAAATATAAAGAGATTCCTCTAAGCAGAGGCTCAATGACTT
TT
Found at i:3382183 original size:48 final size:48
Alignment explanation
Indices: 3382068--3382678 Score: 592
Period size: 49 Copynumber: 12.7 Consensus size: 48
3382058 TGAAAACGGT
* *
3382068 TCCTCTAAGCAGAGGCTCAACAACTTTAAAATTTTCATCTTGAAAAAAGC
1 TCCTCTAAGTAGAGGCTCAACAACTTTAAAA-TCTCATCTTG-AAAAAGC
** * *
3382118 TCCTCTAAGTAGAGGCTCAATGACTTTAAAATCTCATATTGGAAAAGC
1 TCCTCTAAGTAGAGGCTCAACAACTTTAAAATCTCATCTTGAAAAAGC
* * * * * *
3382166 TCCTCTAAGCAGAGGCTCAACGACTTTAAAGCTATTATATT-AGAAAAGC
1 TCCTCTAAGTAGAGGCTCAACAACTTTAAA-ATCTCATCTTGA-AAAAGC
* * *
3382215 TCCTCTAAGTAGAGGTTCAACGACTTTAAAAATCTCATCTTGGAAAAGC
1 TCCTCTAAGTAGAGGCTCAACAACTTT-AAAATCTCATCTTGAAAAAGC
* *
3382264 TCCTCTAAGCAGAGGCTCTACAACTTTAAAAATCTCATCTTGAAAAAGC
1 TCCTCTAAGTAGAGGCTCAACAACTTT-AAAATCTCATCTTGAAAAAGC
* * ** * *
3382313 TCTTCTAAGCAGAGGCTCAATGACTTTAAAAGTCT-A-ATTGGAAAAGC
1 TCCTCTAAGTAGAGGCTCAACAACTTTAAAA-TCTCATCTTGAAAAAGC
* * *
3382360 TCTTCTAAGTAGAGGTTCAACGACTTTAAAAT-TCAT-TTGAAAAAAGC
1 TCCTCTAAGTAGAGGCTCAACAACTTTAAAATCTCATCTTG-AAAAAGC
* * *
3382407 TCTTCTAAGTAGAGGCTCTACAACTTTAAAAATCTCATCTTGAAAAAGT
1 TCCTCTAAGTAGAGGCTCAACAACTTT-AAAATCTCATCTTGAAAAAGC
* * * * * *
3382456 TTCTCTAAGCAGAGGCTTAACAATTTTAAAATTATCATCTTG-AAAATC
1 TCCTCTAAGTAGAGGCTCAACAACTTTAAAA-TCTCATCTTGAAAAAGC
* * * *
3382504 TCTTCTAAATAGAGGCTCAACAACTTTAAAATTTC-TTTTGAAAAAGC
1 TCCTCTAAGTAGAGGCTCAACAACTTTAAAATCTCATCTTGAAAAAGC
* * *
3382551 TCCTCTAAGTAGAGGCTCAACAACTTTAAAAATCT-ATATTAAAAAATC
1 TCCTCTAAGTAGAGGCTCAACAACTTT-AAAATCTCATCTTGAAAAAGC
** * * * *
3382599 TATTCTAAGCAGAGGCTTAACAATTTTAAAAATC-CATCTTAAAAAAGC
1 TCCTCTAAGTAGAGGCTCAACAACTTT-AAAATCTCATCTTGAAAAAGC
* * *
3382647 TCTTCTAAGTAGAGGTTCAATAACTTTAAAAT
1 TCCTCTAAGTAGAGGCTCAACAACTTTAAAAT
3382679 TTTCATATGT
Statistics
Matches: 470, Mismatches: 75, Indels: 35
0.81 0.13 0.06
Matches are distributed among these distances:
45 1 0.00
46 9 0.02
47 105 0.22
48 153 0.33
49 168 0.36
50 34 0.07
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.30
Consensus pattern (48 bp):
TCCTCTAAGTAGAGGCTCAACAACTTTAAAATCTCATCTTGAAAAAGC
Found at i:3382446 original size:143 final size:144
Alignment explanation
Indices: 3382071--3382679 Score: 696
Period size: 143 Copynumber: 4.2 Consensus size: 144
3382061 AAACGGTTCC
* *
3382071 TCTAAGCAGAGGCTCAACAACTTTAAAATTTTCATCTTGAAAAAAGCTCCTCTAAGTAGAGGCTC
1 TCTAAGTAGAGGTTCAACAACTTTAAAA--TTCATCTTG-AAAAAGCTCCTCTAAGTAGAGGCTC
** * * *
3382136 AATGACTTT-AAAATCTCATATTGGAAAAGCTCCTCTAAGCAGAGGCTCAACGACTTT-AAAGCT
63 AACAACTTTAAAAATCTCATATTGAAAAAGCTCTTCTAAGCAGAGGCTCAACAACTTTAAAAG-T
* *
3382199 ATTATATTAGAAAAGCTCC
127 -CTATATTAGAAAAGCTCT
* * * *
3382218 TCTAAGTAGAGGTTCAACGACTTTAAAAATCTCATCTTGGAAAAGCTCCTCTAAGCAGAGGCTCT
1 TCTAAGTAGAGGTTCAACAACTTT-AAAAT-TCATCTTGAAAAAGCTCCTCTAAGTAGAGGCTCA
* **
3382283 ACAACTTTAAAAATCTCATCTTGAAAAAGCTCTTCTAAGCAGAGGCTCAATGACTTTAAAAGTCT
64 ACAACTTTAAAAATCTCATATTGAAAAAGCTCTTCTAAGCAGAGGCTCAACAACTTTAAAAGTCT
*
3382348 A-ATTGGAAAAGCTCT
129 ATATTAGAAAAGCTCT
* * *
3382363 TCTAAGTAGAGGTTCAACGACTTTAAAATTCAT-TTGAAAAAAGCTCTTCTAAGTAGAGGCTCTA
1 TCTAAGTAGAGGTTCAACAACTTTAAAATTCATCTTG-AAAAAGCTCCTCTAAGTAGAGGCTCAA
* * * *
3382427 CAACTTTAAAAATCTCATCTTGAAAAAG-TTTCTCTAAGCAGAGGCTTAACAATTTTAAAA-T-T
65 CAACTTTAAAAATCTCATATTGAAAAAGCTCT-TCTAAGCAGAGGCTCAACAACTTTAAAAGTCT
* *
3382489 ATCATCTTGAAAATCTCT
129 AT-AT-TAGAAAAGCTCT
* * *
3382507 TCTAAATAGAGGCTCAACAACTTTAAAATTTC-TTTTGAAAAAGCTCCTCTAAGTAGAGGCTCAA
1 TCTAAGTAGAGGTTCAACAACTTTAAAA-TTCATCTTGAAAAAGCTCCTCTAAGTAGAGGCTCAA
* * * * * * *
3382571 CAACTTTAAAAATCT-ATATTAAAAAATCTATTCTAAGCAGAGGCTTAACAATTTTAAAAATCCA
65 CAACTTTAAAAATCTCATATTGAAAAAGCTCTTCTAAGCAGAGGCTCAACAACTTTAAAAGTCTA
* *
3382635 TCTTAAAAAAGCTCT
130 TATTAGAAAAGCTCT
*
3382650 TCTAAGTAGAGGTTCAATAACTTTAAAATT
1 TCTAAGTAGAGGTTCAACAACTTTAAAATT
3382680 TTCATATGTT
Statistics
Matches: 406, Mismatches: 42, Indels: 33
0.84 0.09 0.07
Matches are distributed among these distances:
141 2 0.00
142 8 0.02
143 153 0.38
144 85 0.21
145 44 0.11
146 32 0.08
147 74 0.18
148 8 0.02
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.30
Consensus pattern (144 bp):
TCTAAGTAGAGGTTCAACAACTTTAAAATTCATCTTGAAAAAGCTCCTCTAAGTAGAGGCTCAAC
AACTTTAAAAATCTCATATTGAAAAAGCTCTTCTAAGCAGAGGCTCAACAACTTTAAAAGTCTAT
ATTAGAAAAGCTCT
Found at i:3383536 original size:22 final size:22
Alignment explanation
Indices: 3383501--3383543 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3383491 ATATGTCATT
*
3383501 CTTTTTTTGCTTTTTCTTTTTG
1 CTTTTTTTGCTTTTTATTTTTG
3383523 CTTTTCTTTG-TTTTTATTTTT
1 CTTTT-TTTGCTTTTTATTTTT
3383544 TTGTTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.02, C:0.12, G:0.07, T:0.79
Consensus pattern (22 bp):
CTTTTTTTGCTTTTTATTTTTG
Found at i:3387439 original size:25 final size:26
Alignment explanation
Indices: 3387409--3387461 Score: 99
Period size: 25 Copynumber: 2.1 Consensus size: 26
3387399 AAAAAATCTG
3387409 GATAAATATATCCT-CCAAACGAAAA
1 GATAAATATATCCTCCCAAACGAAAA
3387434 GATAAATATATCCTCCCAAACGAAAA
1 GATAAATATATCCTCCCAAACGAAAA
3387460 GA
1 GA
3387462 ATCATAGAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 14 0.52
26 13 0.48
ACGTcount: A:0.51, C:0.21, G:0.09, T:0.19
Consensus pattern (26 bp):
GATAAATATATCCTCCCAAACGAAAA
Found at i:3389652 original size:3 final size:3
Alignment explanation
Indices: 3389634--3389686 Score: 65
Period size: 3 Copynumber: 18.3 Consensus size: 3
3389624 TATAGTATAG
* * *
3389634 TAT TAG TAT CAT TAT TAT TAC TAT TA- TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3389681 T-T TAT T
1 TAT TAT T
3389687 TTCATTTTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
2 4 0.10
3 38 0.90
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:3389669 original size:20 final size:20
Alignment explanation
Indices: 3389634--3389686 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
3389624 TATAGTATAG
*
3389634 TATTAGTATCATTATTATTAC
1 TATTA-TATTATTATTATTAC
*
3389655 TATTATATTATTATTATTAT
1 TATTATATTATTATTATTAC
*
3389675 TATTATTTTATT
1 TATTATATTATT
3389687 TTCATTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 24 0.83
21 5 0.17
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (20 bp):
TATTATATTATTATTATTAC
Found at i:3390134 original size:10 final size:10
Alignment explanation
Indices: 3390119--3390167 Score: 71
Period size: 10 Copynumber: 4.8 Consensus size: 10
3390109 GACTAAGAGG
3390119 TTTTTTGGAT
1 TTTTTTGGAT
*
3390129 TTTTTTAGAT
1 TTTTTTGGAT
*
3390139 TTGTTTTGAAT
1 TT-TTTTGGAT
3390150 TTTTTTGGAT
1 TTTTTTGGAT
3390160 TTTTTTGG
1 TTTTTTGG
3390168 GTTTGGTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
10 26 0.76
11 8 0.24
ACGTcount: A:0.12, C:0.00, G:0.18, T:0.69
Consensus pattern (10 bp):
TTTTTTGGAT
Found at i:3390146 original size:21 final size:20
Alignment explanation
Indices: 3390119--3390167 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
3390109 GACTAAGAGG
3390119 TTTTTTGGATTTTTTTAGAT
1 TTTTTTGGATTTTTTTAGAT
* *
3390139 TTGTTTTGAATTTTTTTGGAT
1 TT-TTTTGGATTTTTTTAGAT
3390160 TTTTTTGG
1 TTTTTTGG
3390168 GTTTGGTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 7 0.28
21 18 0.72
ACGTcount: A:0.12, C:0.00, G:0.18, T:0.69
Consensus pattern (20 bp):
TTTTTTGGATTTTTTTAGAT
Found at i:3401886 original size:119 final size:119
Alignment explanation
Indices: 3401754--3402078 Score: 325
Period size: 118 Copynumber: 2.7 Consensus size: 119
3401744 GACTCAATCA
* * * * * *
3401754 TAGTCACTGTATTTTGACTTATGGTTTCGTCCCAATCACTTGATCTTAGCTCAATATAGATCATT
1 TAGTCATTTTATTTTGACTTATGGTTTCATCCCGATCACTTGATCTTAGCTTAATCTAGATCATT
* * * * *
3401819 TCTTATAATTGATAGTTTTATC-CTGATCATTTATTCTTGACCTTAAC-TAGGTCC
66 TCTTATAATTCATAGTTTCATCTC-GATCATCTATTCTTAACCTCAACTTA-GTCC
* * ** * * *
3401873 TAGTCGTTTTATTTTGACTCATGGTTTCATCTTGGTCACTTGGTCTT-GCTTAATCCAGATCATT
1 TAGTCATTTTATTTTGACTTATGGTTTCATCCCGATCACTTGATCTTAGCTTAATCTAGATCATT
* * * * * * *
3401937 TCTGATGATTCTTAGTTTCATCTCGATCATCTATTTTTAACCTCGACTTATTCT
66 TCTTATAATTCATAGTTTCATCTCGATCATCTATTCTTAACCTCAACTTAGTCC
* *
3401991 TAGTCATTTTATTTTGAC-TAGTGATTTCATCCCGATCACTTAATCTTAGCTTAATCTAGATCAT
1 TAGTCATTTTATTTTGACTTA-TGGTTTCATCCCGATCACTTGATCTTAGCTTAATCTAGATCAT
* * *
3402055 TTCTTATGATTTATGGTTTCATCT
65 TTCTTATAATTCATAGTTTCATCT
3402079 TAGTCATCTA
Statistics
Matches: 164, Mismatches: 38, Indels: 8
0.78 0.18 0.04
Matches are distributed among these distances:
117 1 0.01
118 88 0.54
119 75 0.46
ACGTcount: A:0.22, C:0.19, G:0.13, T:0.46
Consensus pattern (119 bp):
TAGTCATTTTATTTTGACTTATGGTTTCATCCCGATCACTTGATCTTAGCTTAATCTAGATCATT
TCTTATAATTCATAGTTTCATCTCGATCATCTATTCTTAACCTCAACTTAGTCC
Found at i:3402120 original size:119 final size:116
Alignment explanation
Indices: 3401694--3402136 Score: 381
Period size: 119 Copynumber: 3.7 Consensus size: 116
3401684 CTCAATGCAA
* * * * * * *
3401694 ATCATTTTTTATGATTCAT-GATTTCGTTCTGATCATTTATTTTTTACCTCGACTCAATCATAGT
1 ATCATTTCTTATGATTTATAG-TTTC-ATCTGATCATCTATTTTTGACCTTGACT-AATCTTAGT
** * * * * *
3401758 CACTGTATTTTGACTTATGGTTTCGTCCCAATCACTTGATCTTAGCTCAATATAG
63 CGTTTTATTTTGAC-TATGGTTTCATCCCGATCACTTGATCTTAGCTTAATCTAG
* * * * * * * *
3401813 ATCATTTCTTATAATTGATAGTTTTATCCTGATCATTTATTCTTGACCTTAACTAGGTCCTAGTC
1 ATCATTTCTTATGATTTATAGTTTCAT-CTGATCATCTATTTTTGACCTTGACTA-ATCTTAGTC
** * * *
3401878 GTTTTATTTTGACTCATGGTTTCATCTTGGTCACTTGGTCTT-GCTTAATCCAG
64 GTTTTATTTTGACT-ATGGTTTCATCCCGATCACTTGATCTTAGCTTAATCTAG
* * * *
3401931 ATCATTTCTGATGATTCT-TAGTTTCATCTCGATCATCTATTTTTAACCTCGACTTATTCTTAGT
1 ATCATTTCTTATGATT-TATAGTTTCATCT-GATCATCTATTTTTGACCTTGAC-TAATCTTAGT
* * *
3401995 CATTTTATTTTGACTAGTGATTTCATCCCGATCACTTAATCTTAGCTTAATCTAG
63 CGTTTTATTTTGACTA-TGGTTTCATCCCGATCACTTGATCTTAGCTTAATCTAG
* * *
3402050 ATCATTTCTTATGATTTATGGTTTCATCTTAGTCATCTATTTTTGATCTTGACTCAATCTT-GAT
1 ATCATTTCTTATGATTTATAGTTTCATCTGA-TCATCTATTTTTGACCTTGACT-AATCTTAG-T
*
3402114 CGTTTTATTTTCACTCATGGTTT
63 CGTTTTATTTTGACT-ATGGTTT
3402137 TAGCTCGATT
Statistics
Matches: 258, Mismatches: 52, Indels: 28
0.76 0.15 0.08
Matches are distributed among these distances:
117 3 0.01
118 95 0.37
119 158 0.61
120 2 0.01
ACGTcount: A:0.22, C:0.19, G:0.12, T:0.47
Consensus pattern (116 bp):
ATCATTTCTTATGATTTATAGTTTCATCTGATCATCTATTTTTGACCTTGACTAATCTTAGTCGT
TTTATTTTGACTATGGTTTCATCCCGATCACTTGATCTTAGCTTAATCTAG
Found at i:3402447 original size:26 final size:26
Alignment explanation
Indices: 3402418--3402474 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
3402408 CTAGTTTAGA
*
3402418 CCCATTTATG-TCTACGCCCATTCGGG
1 CCCATTTATGTTC-ACGCCCATTCGAG
*
3402444 CCCATTTATGTTCAGGCCCATTCGAG
1 CCCATTTATGTTCACGCCCATTCGAG
3402470 CCCAT
1 CCCAT
3402475 CTGTATCTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 26 0.93
27 2 0.07
ACGTcount: A:0.18, C:0.35, G:0.18, T:0.30
Consensus pattern (26 bp):
CCCATTTATGTTCACGCCCATTCGAG
Found at i:3402646 original size:3 final size:3
Alignment explanation
Indices: 3402628--3402721 Score: 101
Period size: 3 Copynumber: 33.3 Consensus size: 3
3402618 TATAGTATAG
* * * *
3402628 TAT TAG TAT CAT TAT TAT TAC TCT TAT TAT TAT TA- TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
3402675 TAT TAT TAT TAT TAC TAT TAT TAT TA- TAT T-T T-T TAT T-T TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3402718 TAT T
1 TAT T
3402722 TTCATTTTTT
Statistics
Matches: 76, Mismatches: 10, Indels: 10
0.79 0.10 0.10
Matches are distributed among these distances:
2 12 0.16
3 64 0.84
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:3402680 original size:38 final size:38
Alignment explanation
Indices: 3402615--3402716 Score: 115
Period size: 38 Copynumber: 2.8 Consensus size: 38
3402605 TTTTTACATA
* * * *
3402615 TATTA-TAGTATAGTATTAGTATCATTATTATTACT-C
1 TATTATTATTATATTATTATTATTATTATTATTACTAC
*
3402651 TTATTATTATTATATTATTATTATTATTATTATTATTAC
1 -TATTATTATTATATTATTATTATTATTATTATTACTAC
3402690 TATTATTATTATATT-TT-TTATT-TTATT
1 TATTATTATTATATTATTATTATTATTATT
3402717 TTATTTTCAT
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
35 5 0.09
36 5 0.09
37 7 0.12
38 40 0.69
39 1 0.02
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.62
Consensus pattern (38 bp):
TATTATTATTATATTATTATTATTATTATTATTACTAC
Found at i:3402728 original size:6 final size:5
Alignment explanation
Indices: 3402651--3402729 Score: 52
Period size: 6 Copynumber: 14.4 Consensus size: 5
3402641 ATTATTACTC
* * *
3402651 TTATT ATTATT ATATT ATTATT ATTATT ATTATT ATTACTA TTATT ATTATA
1 TTATT -TTATT TTATT -TTATT -TTATT -TTATT -TTA-TT TTATT -TTATT
3402703 TT-TT TTATT TTATT TTATT TTCATT TT
1 TTATT TTATT TTATT TTATT TT-ATT TT
3402730 TTCTTCTTTC
Statistics
Matches: 62, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
4 3 0.05
5 21 0.34
6 37 0.60
7 1 0.02
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (5 bp):
TTATT
Found at i:3408068 original size:15 final size:16
Alignment explanation
Indices: 3408050--3408079 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3408040 TTTTTTTAAA
3408050 TTTTGTTTT-ATTTTG
1 TTTTGTTTTCATTTTG
3408065 TTTTGTTTTCATTTT
1 TTTTGTTTTCATTTT
3408080 TTTGTTTGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.07, C:0.03, G:0.10, T:0.80
Consensus pattern (16 bp):
TTTTGTTTTCATTTTG
Found at i:3408544 original size:15 final size:14
Alignment explanation
Indices: 3408526--3408556 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
3408516 TTCCTTTGTG
3408526 TTTTGATTTTGATTT
1 TTTTGATTTTG-TTT
3408541 TTTTGATTTTGTTT
1 TTTTGATTTTGTTT
3408555 TT
1 TT
3408557 ATTCTTTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.10, C:0.00, G:0.13, T:0.77
Consensus pattern (14 bp):
TTTTGATTTTGTTT
Found at i:3408551 original size:21 final size:21
Alignment explanation
Indices: 3408520--3408572 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
3408510 GAAATTTTCC
* *
3408520 TTTGTGTTTTGATTTTGATTTT
1 TTTGTATTTTG-TTTTGATTCT
*
3408542 TTTG-ATTTTGTTTTTATTCT
1 TTTGTATTTTGTTTTGATTCT
3408562 TTTGTATTTTG
1 TTTGTATTTTG
3408573 GTTGCTTGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 12 0.44
21 11 0.41
22 4 0.15
ACGTcount: A:0.09, C:0.02, G:0.15, T:0.74
Consensus pattern (21 bp):
TTTGTATTTTGTTTTGATTCT
Found at i:3412693 original size:13 final size:14
Alignment explanation
Indices: 3412675--3412705 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
3412665 CAAGCAACCA
3412675 AAAACA-AAAAAAT
1 AAAACACAAAAAAT
3412688 AAAACACAAAAAAT
1 AAAACACAAAAAAT
3412702 AAAA
1 AAAA
3412706 AATAAAACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.84, C:0.10, G:0.00, T:0.06
Consensus pattern (14 bp):
AAAACACAAAAAAT
Found at i:3412699 original size:21 final size:21
Alignment explanation
Indices: 3412673--3412719 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 21
3412663 TTCAAGCAAC
3412673 CAAAAACA-AAAAAATAAAACA
1 CAAAAA-ATAAAAAATAAAACA
3412694 CAAAAAATAAAAAATAAAACA
1 CAAAAAATAAAAAATAAAACA
3412715 CAAAA
1 CAAAA
3412720 GAAAATTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 1 0.04
21 24 0.96
ACGTcount: A:0.81, C:0.13, G:0.00, T:0.06
Consensus pattern (21 bp):
CAAAAAATAAAAAATAAAACA
Found at i:3412712 original size:14 final size:14
Alignment explanation
Indices: 3412674--3412712 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
3412664 TCAAGCAACC
3412674 AAAAACAAAAAAATA
1 AAAAAC-AAAAAATA
*
3412689 AAACACAAAAAATA
1 AAAAACAAAAAATA
*
3412703 AAAAATAAAA
1 AAAAACAAAA
3412713 CACAAAAGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 16 0.76
15 5 0.24
ACGTcount: A:0.85, C:0.08, G:0.00, T:0.08
Consensus pattern (14 bp):
AAAAACAAAAAATA
Found at i:3420618 original size:48 final size:48
Alignment explanation
Indices: 3420550--3420967 Score: 555
Period size: 48 Copynumber: 8.7 Consensus size: 48
3420540 AAAATGAAAA
3420550 TTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAGAAT
1 TTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAGAAT
* * * *
3420598 TTTAAAGTTATAGAGCCTCTGTTGAGAGGAGCTTTTTCAA-AATGAAAA
1 TTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAG-AAT
* * * * *
3420646 TTTAAAGTTATGAAGCTTCTGTTGAGAGGAGCTTTTTC-AGATGAGATT
1 TTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGA-AAGAAT
3420694 TTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAGAAT
1 TTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAGAAT
3420742 TTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCTGAA-ATAA-AAT
1 TTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTC--AAGA-AAGAAT
*
3420791 TTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTCCGAA-ATAA-AAT
1 TTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTC-AAGA-AAGAAT
*
3420839 TTTAAAGTTGTGGAGCCTCTATTGAGAGGAGCTTTTTCAAG-AAGAAAT
1 TTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAG-AAT
*
3420887 TTTAAAGTTGTGGAACCTCTGTTGAGAGGAGCTTTTTTCAAG-AAGAAAT
1 TTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGC-TTTTTCAAGAAAG-AAT
* * *
3420936 TTTAAAGTTGTTGAGCCTCTGCTAAGAGGAGC
1 TTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGC
3420968 CCTTTTCTGT
Statistics
Matches: 334, Mismatches: 25, Indels: 21
0.88 0.07 0.06
Matches are distributed among these distances:
46 2 0.01
47 6 0.02
48 233 0.70
49 89 0.27
50 4 0.01
ACGTcount: A:0.30, C:0.11, G:0.25, T:0.34
Consensus pattern (48 bp):
TTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAGAAT
Found at i:3420894 original size:145 final size:145
Alignment explanation
Indices: 3420541--3420967 Score: 616
Period size: 145 Copynumber: 3.0 Consensus size: 145
3420531 NNNNNNNNNA
3420541 AAATGAAAA-TTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAGAATTTTAAAG
1 AAATGAAAATTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAGAATTTTAAAG
* * * * *
3420605 TTATAGAGCCTCTGTTGAGAGGAGCTTTTTC-AAAATGAAAA-TTTAAAGTTATGAAGCTTCTGT
66 TTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCTAAAAT-AAAATTTTAAAGTTGTGGAGCCTCTGT
*
3420668 TGAGAGGAGCTTTTTC
130 TGAGAGGAGCTTTTCC
* * *
3420684 AGATGAGATTTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAGAATTTTAAAG
1 AAATGAAAATTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAGAATTTTAAAG
*
3420749 TTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCTGAAATAAAATTTTAAAGTTGTGGAGCCTCTGTT
66 TTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCTAAAATAAAATTTTAAAGTTGTGGAGCCTCTGTT
3420814 GAGAGGAGCTTTTCC
131 GAGAGGAGCTTTTCC
*
3420829 GAAAT-AAAATTTTAAAGTTGTGGAGCCTCTATTGAGAGGAGCTTTTTCAAG-AAGAAATTTTAA
1 -AAATGAAAATTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAG-AATTTTAA
* * *
3420892 AGTTGTGGAACCTCTGTTGAGAGGAGCTTTTT-TCAAGAA-GAAATTTTAAAGTTGTTGAGCCTC
64 AGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCT-AA-AATAAAATTTTAAAGTTGTGGAGCCTC
* *
3420955 TGCTAAGAGGAGC
127 TGTTGAGAGGAGC
3420968 CCTTTTCTGT
Statistics
Matches: 257, Mismatches: 20, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
143 6 0.02
144 92 0.36
145 154 0.60
146 5 0.02
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.34
Consensus pattern (145 bp):
AAATGAAAATTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAGAATTTTAAAG
TTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCTAAAATAAAATTTTAAAGTTGTGGAGCCTCTGTT
GAGAGGAGCTTTTCC
Found at i:3421166 original size:6 final size:5
Alignment explanation
Indices: 3421134--3421184 Score: 52
Period size: 5 Copynumber: 10.0 Consensus size: 5
3421124 ACTAATATTT
*
3421134 AACAA AACAA AACAA AA-AA GTAAAAA AACAA AACAGA AA-AA AACAA
1 AACAA AACAA AACAA AACAA --AACAA AACAA AACA-A AACAA AACAA
3421180 AACAA
1 AACAA
3421185 GTAAACAAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
4 5 0.12
5 28 0.70
6 5 0.12
7 2 0.05
ACGTcount: A:0.80, C:0.14, G:0.04, T:0.02
Consensus pattern (5 bp):
AACAA
Found at i:3421166 original size:15 final size:16
Alignment explanation
Indices: 3421142--3421200 Score: 84
Period size: 16 Copynumber: 3.7 Consensus size: 16
3421132 TTAACAAAAC
3421142 AAAACAAAAAAGTAAA
1 AAAACAAAAAAGTAAA
*
3421158 AAAACAAAACAG-AAA
1 AAAACAAAAAAGTAAA
3421173 AAAACAAAACAAGTAAA
1 AAAACAAAA-AAGTAAA
*
3421190 CAAACAAAAAA
1 AAAACAAAAAA
3421201 AAAAGAAAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
15 12 0.32
16 15 0.39
17 11 0.29
ACGTcount: A:0.80, C:0.12, G:0.05, T:0.03
Consensus pattern (16 bp):
AAAACAAAAAAGTAAA
Found at i:3421181 original size:21 final size:20
Alignment explanation
Indices: 3421137--3421184 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
3421127 AATATTTAAC
3421137 AAAACAAAACAAAAAAGTAAA
1 AAAACAAAACAAAAAAG-AAA
*
3421158 AAAACAAAACAGAAAAA-AAC
1 AAAACAAAACA-AAAAAGAAA
3421178 AAAACAA
1 AAAACAA
3421185 GTAAACAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 9 0.36
21 11 0.44
22 5 0.20
ACGTcount: A:0.81, C:0.12, G:0.04, T:0.02
Consensus pattern (20 bp):
AAAACAAAACAAAAAAGAAA
Found at i:3421195 original size:32 final size:31
Alignment explanation
Indices: 3421134--3421203 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 31
3421124 ACTAATATTT
3421134 AACAAAACAAAACAAAAAAGTAAAAAAACAA
1 AACAAAACAAAACAAAAAAGTAAAAAAACAA
*
3421165 AACAGAAA-AAAACAAAACAAGTAAACAAACAA
1 AACA-AAACAAAACAAAA-AAGTAAAAAAACAA
*
3421197 AAAAAAA
1 AACAAAA
3421204 AGAAAGACGT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 16 0.46
32 19 0.54
ACGTcount: A:0.80, C:0.13, G:0.04, T:0.03
Consensus pattern (31 bp):
AACAAAACAAAACAAAAAAGTAAAAAAACAA
Found at i:3433323 original size:119 final size:118
Alignment explanation
Indices: 3433159--3433514 Score: 387
Period size: 119 Copynumber: 3.0 Consensus size: 118
3433149 TGATTTCGTT
* * *
3433159 CTGATCATTTATTTTTGACCTCGACTCAATCATAGTCACTGTATTTTGACTTATGGTTTCGTCCC
1 CTGATCATTTATTTTTGACCTCGACT-AATCCTAGTCACTTTATTTTGACTTATGGTTTCATCCC
* *
3433224 AATCACTTGATCTTAGCTCAATCTAGATCATTTCTTATAATTCATAGTTTTATC
65 GATCACTTGATCTTAGCTCAATCTAGATCATTTCTTATGATTCATAGTTTTATC
* ** * * * **
3433278 CTGATCATTTATTCTTGACCTTAACTAGGTCCTAGTCGCTTTATTTTGACTCATGGTTTCATCTT
1 CTGATCATTTATTTTTGACCTCGACTA-ATCCTAGTCACTTTATTTTGACTTATGGTTTCATCCC
* * * * * *
3433343 GGTCACTTGGTCTTA-CTTAATCCAGATCATTT-TTGATGATTCTTAGTTTCAT-
65 GATCACTTGATCTTAGCTCAATCTAGATCATTTCTT-ATGATTCATAGTTTTATC
* * * * *
3433395 CTCGATCATCTATTTTTAACCTCGACTTATTCCTAGTCATTTTATTTTGAC-TAGTGATTTCATC
1 CT-GATCATTTATTTTTGACCTCGAC-TAATCCTAGTCACTTTATTTTGACTTA-TGGTTTCATC
* * *
3433459 CCGATCACTTAATCTTAGCTCAATCTAGATCATTTCTTATGATTTATGGTTTTATC
63 CCGATCACTTGATCTTAGCTCAATCTAGATCATTTCTTATGATTCATAGTTTTATC
3433515 TTAGTCATCT
Statistics
Matches: 189, Mismatches: 40, Indels: 15
0.77 0.16 0.06
Matches are distributed among these distances:
117 5 0.03
118 88 0.47
119 94 0.50
120 2 0.01
ACGTcount: A:0.22, C:0.21, G:0.12, T:0.45
Consensus pattern (118 bp):
CTGATCATTTATTTTTGACCTCGACTAATCCTAGTCACTTTATTTTGACTTATGGTTTCATCCCG
ATCACTTGATCTTAGCTCAATCTAGATCATTTCTTATGATTCATAGTTTTATC
Found at i:3433439 original size:118 final size:119
Alignment explanation
Indices: 3433159--3433498 Score: 357
Period size: 118 Copynumber: 2.9 Consensus size: 119
3433149 TGATTTCGTT
* * * * *
3433159 CTGATCATTTATTTTTGACCTCGACTCAATCATAGTCACTGTATTTTGACTTATGGTTTCGTCCC
1 CTGATCATTTATTTTTGACCTCGACTTAATCCTAGTCACTTTATTTTGACTCATGGTTTCATCCC
* *
3433224 AATCACTTGATCTTAGCTCAATCTAGATCATTTCTTATAATTCATAGTTTTATC
66 AATCACTTGATCTTAGCTCAATCCAGATCATTTCTTATAATTCATAGTTTCATC
* ** * * *
3433278 CTGATCATTTATTCTTGACCTTAAC-TAGGTCCTAGTCGCTTTATTTTGACTCATGGTTTCATCT
1 CTGATCATTTATTTTTGACCTCGACTTA-ATCCTAGTCACTTTATTTTGACTCATGGTTTCATCC
*** * * * *
3433342 TGGTCACTTGGTCTTA-CTTAATCCAGATCATTT-TTGATGATTCTTAGTTTCAT-
65 CAATCACTTGATCTTAGCTCAATCCAGATCATTTCTT-ATAATTCATAGTTTCATC
* * * * *
3433395 CTCGATCATCTATTTTTAACCTCGACTTATTCCTAGTCATTTTATTTTGACT-AGTGATTTCATC
1 CT-GATCATTTATTTTTGACCTCGACTTAATCCTAGTCACTTTATTTTGACTCA-TGGTTTCATC
* * *
3433459 CCGATCACTTAATCTTAGCTCAATCTAGATCATTTCTTAT
64 CCAATCACTTGATCTTAGCTCAATCCAGATCATTTCTTAT
3433499 GATTTATGGT
Statistics
Matches: 178, Mismatches: 36, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
117 5 0.03
118 89 0.50
119 82 0.46
120 2 0.01
ACGTcount: A:0.23, C:0.21, G:0.11, T:0.45
Consensus pattern (119 bp):
CTGATCATTTATTTTTGACCTCGACTTAATCCTAGTCACTTTATTTTGACTCATGGTTTCATCCC
AATCACTTGATCTTAGCTCAATCCAGATCATTTCTTATAATTCATAGTTTCATC
Found at i:3433557 original size:119 final size:116
Alignment explanation
Indices: 3433131--3433573 Score: 367
Period size: 119 Copynumber: 3.7 Consensus size: 116
3433121 CTCAACGCAA
* * * * *
3433131 ATCATTTTTTATGATTTAT-GATTTCGT-TCTGATCATTTATTTTTGACCTCGACTCAATCATAG
1 ATCATTTCTTATGATTTATAG-TTT--TATCTGATCATCTATTTTTAACCTTGACT-AATCCTAG
** * * *
3433194 TCACTGTATTTTGACTTATGGTTTCGTCCCAATCACTTGATCTTAGCTCAATCTAG
62 TCGTTTTATTTTGAC-TATGGTTTCATCCCGATCACTTGATCTTAGCTCAATCTAG
* * * * * * *
3433250 ATCATTTCTTATAATTCATAGTTTTATCCTGATCATTTATTCTTGACCTTAACTAGGTCCTAGTC
1 ATCATTTCTTATGATTTATAGTTTTAT-CTGATCATCTATTTTTAACCTTGACTA-ATCCTAGTC
* ** * * * *
3433315 GCTTTATTTTGACTCATGGTTTCATCTTGGTCACTTGGTCTTA-CTTAATCCAG
64 GTTTTATTTTGACT-ATGGTTTCATCCCGATCACTTGATCTTAGCTCAATCTAG
* * *
3433368 ATCATTT-TTGATGATTCT-TAGTTTCATCTCGATCATCTATTTTTAACCTCGACTTATTCCTAG
1 ATCATTTCTT-ATGATT-TATAGTTTTATCT-GATCATCTATTTTTAACCTTGAC-TAATCCTAG
* * *
3433431 TCATTTTATTTTGACTAGTGATTTCATCCCGATCACTTAATCTTAGCTCAATCTAG
62 TCGTTTTATTTTGACTA-TGGTTTCATCCCGATCACTTGATCTTAGCTCAATCTAG
* * * * *
3433487 ATCATTTCTTATGATTTATGGTTTTATCTTAGTCATCTATTTTTTATCTTGACTCAAT-CTTGAT
1 ATCATTTCTTATGATTTATAGTTTTATCTGA-TCATCTATTTTTAACCTTGACT-AATCCTAG-T
*
3433551 CGTTTTATTTTTACTCATGGTTT
63 CGTTTTATTTTGACT-ATGGTTT
3433574 TAGCTCGATT
Statistics
Matches: 259, Mismatches: 48, Indels: 34
0.76 0.14 0.10
Matches are distributed among these distances:
117 6 0.02
118 96 0.37
119 153 0.59
120 4 0.02
ACGTcount: A:0.22, C:0.19, G:0.12, T:0.48
Consensus pattern (116 bp):
ATCATTTCTTATGATTTATAGTTTTATCTGATCATCTATTTTTAACCTTGACTAATCCTAGTCGT
TTTATTTTGACTATGGTTTCATCCCGATCACTTGATCTTAGCTCAATCTAG
Found at i:3433884 original size:26 final size:26
Alignment explanation
Indices: 3433855--3433911 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
3433845 CCAGTTTAGA
*
3433855 CCCATTTATG-TCTACGCCCATTCGGG
1 CCCATTTATGTTC-ACGCCCATTCGAG
*
3433881 CCCATTTATGTTCAGGCCCATTCGAG
1 CCCATTTATGTTCACGCCCATTCGAG
3433907 CCCAT
1 CCCAT
3433912 CTGTGTCTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 26 0.93
27 2 0.07
ACGTcount: A:0.18, C:0.35, G:0.18, T:0.30
Consensus pattern (26 bp):
CCCATTTATGTTCACGCCCATTCGAG
Found at i:3434077 original size:3 final size:3
Alignment explanation
Indices: 3434059--3434126 Score: 93
Period size: 3 Copynumber: 23.0 Consensus size: 3
3434049 TATAGTATAG
* * *
3434059 TAT TAG TAT CAT TAT TAT TAC TAT TAT TAT TAT TAT TAT TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
3434106 TAT TAT TAT TAT TAC TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT
3434127 ATTTTTTATT
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
2 2 0.04
3 54 0.96
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:3435011 original size:13 final size:13
Alignment explanation
Indices: 3434992--3435023 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
3434982 TCCATCGCAG
3434992 ATTTTTCCTTTTT
1 ATTTTTCCTTTTT
*
3435005 CTTTTTCCTTTTT
1 ATTTTTCCTTTTT
3435018 ATTTTT
1 ATTTTT
3435024 ATTTTATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (13 bp):
ATTTTTCCTTTTT
Found at i:3439747 original size:15 final size:14
Alignment explanation
Indices: 3439729--3439759 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
3439719 TTCCTTTGTG
3439729 TTTTGATTTTGATTT
1 TTTTGATTTTG-TTT
3439744 TTTTGATTTTGTTT
1 TTTTGATTTTGTTT
3439758 TT
1 TT
3439760 ATTCTTTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.10, C:0.00, G:0.13, T:0.77
Consensus pattern (14 bp):
TTTTGATTTTGTTT
Found at i:3439754 original size:21 final size:21
Alignment explanation
Indices: 3439723--3439775 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
3439713 GAAATTTTCC
* *
3439723 TTTGTGTTTTGATTTTGATTTT
1 TTTGTATTTTG-TTTTGATTCT
*
3439745 TTTG-ATTTTGTTTTTATTCT
1 TTTGTATTTTGTTTTGATTCT
3439765 TTTGTATTTTG
1 TTTGTATTTTG
3439776 GTTGCTTGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 12 0.44
21 11 0.41
22 4 0.15
ACGTcount: A:0.09, C:0.02, G:0.15, T:0.74
Consensus pattern (21 bp):
TTTGTATTTTGTTTTGATTCT
Found at i:3440556 original size:17 final size:17
Alignment explanation
Indices: 3440534--3440571 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
3440524 TTTTTTAGAA
3440534 ATTTTATTAATTTTTTT
1 ATTTTATTAATTTTTTT
**
3440551 ATTTTATTTCTTTTTTT
1 ATTTTATTAATTTTTTT
3440568 ATTT
1 ATTT
3440572 AAATTTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (17 bp):
ATTTTATTAATTTTTTT
Found at i:3443139 original size:14 final size:14
Alignment explanation
Indices: 3443120--3443152 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
3443110 TTTTTTTTTC
*
3443120 AAAAATTTAAATAA
1 AAAAATTCAAATAA
3443134 AAAAA-TCAAATAA
1 AAAAATTCAAATAA
3443147 AAAAAT
1 AAAAAT
3443153 CAATAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (14 bp):
AAAAATTCAAATAA
Found at i:3443148 original size:12 final size:13
Alignment explanation
Indices: 3443128--3443159 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
3443118 TCAAAAATTT
3443128 AAATAAAAAAATC
1 AAATAAAAAAATC
3443141 AAATAAAAAAATC
1 AAATAAAAAAATC
3443154 -AATAAA
1 AAATAAA
3443160 TTTTTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.78, C:0.06, G:0.00, T:0.16
Consensus pattern (13 bp):
AAATAAAAAAATC
Found at i:3443961 original size:14 final size:14
Alignment explanation
Indices: 3443924--3443954 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
3443914 CAAGCAACCA
3443924 AAAAC-AAAAAAAT
1 AAAACAAAAAAAAT
3443937 AAAACAAAAAAAAT
1 AAAACAAAAAAAAT
3443951 AAAA
1 AAAA
3443955 AATAAAACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.87, C:0.06, G:0.00, T:0.06
Consensus pattern (14 bp):
AAAACAAAAAAAAT
Found at i:3444413 original size:28 final size:28
Alignment explanation
Indices: 3444380--3444435 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
3444370 TACCTAAGCC
3444380 CAAAACATGTAAAAATAAAGGTTGTGTG
1 CAAAACATGTAAAAATAAAGGTTGTGTG
*
3444408 CAAAACATGTAAGAATAAAGGTTGTGTG
1 CAAAACATGTAAAAATAAAGGTTGTGTG
3444436 TAATAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.45, C:0.07, G:0.23, T:0.25
Consensus pattern (28 bp):
CAAAACATGTAAAAATAAAGGTTGTGTG
Found at i:3455213 original size:47 final size:47
Alignment explanation
Indices: 3455148--3455500 Score: 334
Period size: 47 Copynumber: 7.7 Consensus size: 47
3455138 TAGATAAGAT
* * ** * *
3455148 TTTTAAAGTCATTAAGCCTCAACTTAGAGGGGTTTTTTCAAGATGAA
1 TTTTAAAGTTATTGAGCCTCTGCTTAGAGGAGCTTTTTCAAGATGAA
3455195 TTTTAAAGTTATTGAGCCTCTGCTTAGAGGAGC-TTTTCAAGATGAA
1 TTTTAAAGTTATTGAGCCTCTGCTTAGAGGAGCTTTTTCAAGATGAA
* *
3455241 -TTTAAAGTTATTAAGCCTTTGCTTAGAGGAGCTTTTTCAAGATGAA
1 TTTTAAAGTTATTGAGCCTCTGCTTAGAGGAGCTTTTTCAAGATGAA
* *
3455287 TTTTAAAGTTGTTGAGCCTCTGCTTAGAGGAGCTTTTTCAAGATAAA
1 TTTTAAAGTTATTGAGCCTCTGCTTAGAGGAGCTTTTTCAAGATGAA
* ** * * * *
3455334 GTTTAAAGTTATTTTGCCTCTCCTTAAAAGAGCTTTTTCAAGATGGAT
1 TTTTAAAGTTATTGAGCCTCTGCTTAGAGGAGCTTTTTCAAGAT-GAA
* * ** *
3455382 TTTTAAAGTTGTTGAGCCTCTTCTTAGATAAGCCTTTT-----TGAA
1 TTTTAAAGTTATTGAGCCTCTGCTTAGAGGAGCTTTTTCAAGATGAA
* * * *
3455424 TTTTAAAGTTGTTGAGTCTCTGCTTAGAAGAGAATTTTT-AA-AT---
1 TTTTAAAGTTATTGAGCCTCTGCTTAGAGGAG-CTTTTTCAAGATGAA
* * *
3455467 TTTTAAAAGTTGTTGAGCCTCTGCATAGAAGAGC
1 TTTT-AAAGTTATTGAGCCTCTGCTTAGAGGAGC
3455501 CTCTTTAAAT
Statistics
Matches: 258, Mismatches: 40, Indels: 20
0.81 0.13 0.06
Matches are distributed among these distances:
42 30 0.12
43 9 0.03
44 26 0.10
45 30 0.12
46 27 0.10
47 106 0.41
48 30 0.12
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (47 bp):
TTTTAAAGTTATTGAGCCTCTGCTTAGAGGAGCTTTTTCAAGATGAA
Found at i:3455278 original size:92 final size:94
Alignment explanation
Indices: 3455149--3455409 Score: 364
Period size: 92 Copynumber: 2.8 Consensus size: 94
3455139 AGATAAGATT
* * * * *
3455149 TTTAAAGTCATTAAGCCTCAACTTAGAGGGGTTTTTTCAAGATGAATTTTAAAGTTATTGAGCCT
1 TTTAAAGTTATTAAGCCTCTACTTAGAGGAGCTTTTTCAAGATGAATTTTAAAGTTGTTGAGCCT
*
3455214 CTGCTTAGAGGAGC-TTTTCAAGATGAA-
66 CTGCTTAGAGGAGCTTTTTCAAGATAAAG
* *
3455241 TTTAAAGTTATTAAGCCTTTGCTTAGAGGAGCTTTTTCAAGATGAATTTTAAAGTTGTTGAGCCT
1 TTTAAAGTTATTAAGCCTCTACTTAGAGGAGCTTTTTCAAGATGAATTTTAAAGTTGTTGAGCCT
3455306 CTGCTTAGAGGAGCTTTTTCAAGATAAAG
66 CTGCTTAGAGGAGCTTTTTCAAGATAAAG
** * * * *
3455335 TTTAAAGTTATTTTGCCTCTCCTTAAAAGAGCTTTTTCAAGATGGATTTTTAAAGTTGTTGAGCC
1 TTTAAAGTTATTAAGCCTCTACTTAGAGGAGCTTTTTCAAGAT-GAATTTTAAAGTTGTTGAGCC
*
3455400 TCTTCTTAGA
65 TCTGCTTAGA
3455410 TAAGCCTTTT
Statistics
Matches: 150, Mismatches: 16, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
92 72 0.48
93 12 0.08
94 37 0.25
95 29 0.19
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (94 bp):
TTTAAAGTTATTAAGCCTCTACTTAGAGGAGCTTTTTCAAGATGAATTTTAAAGTTGTTGAGCCT
CTGCTTAGAGGAGCTTTTTCAAGATAAAG
Found at i:3455314 original size:139 final size:137
Alignment explanation
Indices: 3455170--3455451 Score: 338
Period size: 139 Copynumber: 2.0 Consensus size: 137
3455160 TAAGCCTCAA
* * * * * * *
3455170 CTTAGAGGGGTTTTTTCAAGATGAATTTTAAAGTTATTGAGCCTCTGCTTAGAGGAGC-TTTTCA
1 CTTAGAGGAGCTTTTTCAAGATAAAGTTTAAAGTTATTGAGCCTCTCCTTAAAAGAGCTTTTTCA
* *
3455234 AGAT-GA-ATTTAAAGTTATTAAGCCT-TTGCTTAGAGGAGCTTTTTCAAGATGAATTTTAAAGT
66 AGATGGATATTTAAAGTTATTAAGCCTCTT-CTTAGAGAAGCCTTTT-----TGAATTTTAAAGT
3455296 TGTTGAGCCTCTG
125 TGTTGAGCCTCTG
**
3455309 CTTAGAGGAGCTTTTTCAAGATAAAGTTTAAAGTTATTTTGCCTCTCCTTAAAAGAGCTTTTTCA
1 CTTAGAGGAGCTTTTTCAAGATAAAGTTTAAAGTTATTGAGCCTCTCCTTAAAAGAGCTTTTTCA
* * * *
3455374 AGATGGATTTTTAAAGTTGTTGAGCCTCTTCTTAGATAAGCCTTTTTGAATTTTAAAGTTGTTGA
66 AGATGGATATTTAAAGTTATTAAGCCTCTTCTTAGAGAAGCCTTTTTGAATTTTAAAGTTGTTGA
*
3455439 GTCTCTG
131 GCCTCTG
3455446 CTTAGA
1 CTTAGA
3455452 AGAGAATTTT
Statistics
Matches: 123, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
137 31 0.25
139 49 0.40
140 10 0.08
141 2 0.02
142 29 0.24
143 2 0.02
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.40
Consensus pattern (137 bp):
CTTAGAGGAGCTTTTTCAAGATAAAGTTTAAAGTTATTGAGCCTCTCCTTAAAAGAGCTTTTTCA
AGATGGATATTTAAAGTTATTAAGCCTCTTCTTAGAGAAGCCTTTTTGAATTTTAAAGTTGTTGA
GCCTCTG
Found at i:3455450 original size:42 final size:43
Alignment explanation
Indices: 3455193--3455649 Score: 259
Period size: 44 Copynumber: 10.2 Consensus size: 43
3455183 TTTCAAGATG
* * *
3455193 AATTTT-AAAGTTATTGAGCCTCTGCTTAGAGGAG-CTTTTCA
1 AATTTTAAAAGTTGTTGAGCCTCTGCTTAGAAGAGCCTTTTTA
* * * *
3455234 AGATGAATTT-AAAGTTATTAAGCCTTTGCTTAGAGGAG-CTTTTTCA
1 A-AT---TTTAAAAGTTGTTGAGCCTCTGCTTAGAAGAGCCTTTTT-A
* *
3455280 AGATGAATTTTAAAGTTGTTGAGCCTCTGCTTAGAGGAG-CTTTTTCA
1 A-AT---TTTAAAAGTTGTTGAGCCTCTGCTTAGAAGAGCCTTTTT-A
* ** * *
3455327 AGATAAAGTTT-AAAGTTATTTTGCCTCTCCTTAAAAGAG-CTTTTTCAA
1 A-AT----TTTAAAAGTTGTTGAGCCTCTGCTTAGAAGAGCCTTTTT--A
* * *
3455375 GATGGATTTTTAAAGTTGTTGAGCCTCTTCTTAGATA-AGCCTTTTTG
1 -A---ATTTTAAAAGTTGTTGAGCCTCTGCTTAGA-AGAGCCTTTTTA
* **
3455422 AATTTT-AAAGTTGTTGAGTCTCTGCTTAGAAGAGAATTTTTA
1 AATTTTAAAAGTTGTTGAGCCTCTGCTTAGAAGAGCCTTTTTA
* *
3455464 AATTTTTAAAAGTTGTTGAGCCTCTGCATAGAAGAGCCTCTTTA
1 AA-TTTTAAAAGTTGTTGAGCCTCTGCTTAGAAGAGCCTTTTTA
* * * * *
3455508 AATTTTCAAAAGTCGTTGAACCTCTGCTTAAAAGAACCTCTTTA
1 AATTTT-AAAAGTTGTTGAGCCTCTGCTTAGAAGAGCCTTTTTA
** * * * *
3455552 AATTTTCAAAAGTCATTGAGCCTCAGTTTAGAGGAGCCTCTTTA
1 AATTTT-AAAAGTTGTTGAGCCTCTGCTTAGAAGAGCCTTTTTA
* * * *
3455596 AATTTTCAAAAGTTGTTGAGCCTATACTCAGAGGAG-CTTTTTA
1 AATTTT-AAAAGTTGTTGAGCCTCTGCTTAGAAGAGCCTTTTTA
*
3455639 GATTTTCAAAA
1 AATTTT-AAAA
3455650 ATATCGTTGA
Statistics
Matches: 346, Mismatches: 52, Indels: 34
0.80 0.12 0.08
Matches are distributed among these distances:
41 2 0.01
42 33 0.10
43 29 0.08
44 131 0.38
45 34 0.10
46 12 0.03
47 68 0.20
48 26 0.08
49 8 0.02
51 3 0.01
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.39
Consensus pattern (43 bp):
AATTTTAAAAGTTGTTGAGCCTCTGCTTAGAAGAGCCTTTTTA
Found at i:3455489 original size:44 final size:44
Alignment explanation
Indices: 3455386--3455649 Score: 275
Period size: 44 Copynumber: 6.1 Consensus size: 44
3455376 ATGGATTTTT
* * *
3455386 AAAGTTGTTGAGCCTCTTCTTAGATA-AGCCTTTTTGAATTTT--
1 AAAGTTGTTGAGCCTCTGCTTAGA-AGAGCCTCTTTAAATTTTCA
* ** * *
3455428 AAAGTTGTTGAGTCTCTGCTTAGAAGAGAATTTTTAAATTTTTA
1 AAAGTTGTTGAGCCTCTGCTTAGAAGAGCCTCTTTAAATTTTCA
*
3455472 AAAGTTGTTGAGCCTCTGCATAGAAGAGCCTCTTTAAATTTTCA
1 AAAGTTGTTGAGCCTCTGCTTAGAAGAGCCTCTTTAAATTTTCA
* * * *
3455516 AAAGTCGTTGAACCTCTGCTTAAAAGAACCTCTTTAAATTTTCA
1 AAAGTTGTTGAGCCTCTGCTTAGAAGAGCCTCTTTAAATTTTCA
** * * *
3455560 AAAGTCATTGAGCCTCAGTTTAGAGGAGCCTCTTTAAATTTTCA
1 AAAGTTGTTGAGCCTCTGCTTAGAAGAGCCTCTTTAAATTTTCA
* * * * * *
3455604 AAAGTTGTTGAGCCTATACTCAGAGGAG-CTTTTTAGATTTTCA
1 AAAGTTGTTGAGCCTCTGCTTAGAAGAGCCTCTTTAAATTTTCA
3455647 AAA
1 AAA
3455650 ATATCGTTGA
Statistics
Matches: 187, Mismatches: 32, Indels: 5
0.83 0.14 0.02
Matches are distributed among these distances:
41 1 0.01
42 35 0.19
43 16 0.09
44 135 0.72
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (44 bp):
AAAGTTGTTGAGCCTCTGCTTAGAAGAGCCTCTTTAAATTTTCA
Found at i:3455831 original size:13 final size:13
Alignment explanation
Indices: 3455802--3455830 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
3455792 CCATTTTGTA
3455802 TTTTATTATTATT
1 TTTTATTATTATT
3455815 TTTTATT-TTATT
1 TTTTATTATTATT
3455827 TTTT
1 TTTT
3455831 TCCTTCTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTATTATTATT
Found at i:3456835 original size:8 final size:9
Alignment explanation
Indices: 3456809--3456834 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
3456799 AGGTAAAAAA
3456809 AATTTTTTT
1 AATTTTTTT
3456818 AATTTTTTT
1 AATTTTTTT
3456827 AATTTTTT
1 AATTTTTT
3456835 ATATATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (9 bp):
AATTTTTTT
Found at i:3457362 original size:22 final size:23
Alignment explanation
Indices: 3457321--3457369 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
3457311 ATATTTATAG
3457321 AAAATTTTCAATATAATAAA-AA
1 AAAATTTTCAATATAATAAATAA
3457343 AAAATTTTCAA-A-AATTTAAATAA
1 AAAATTTTCAATATAA--TAAATAA
3457366 AAAA
1 AAAA
3457370 AAGAAATCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 2 0.08
21 1 0.04
22 15 0.62
23 6 0.25
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (23 bp):
AAAATTTTCAATATAATAAATAA
Found at i:3457838 original size:17 final size:17
Alignment explanation
Indices: 3457801--3457838 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
3457791 TCAAAAATTT
*
3457801 AAATAAAAAAATAAATC
1 AAATAAAAAAATAAATA
*
3457818 AAATAAAAAAATCAATA
1 AAATAAAAAAATAAATA
3457835 AAAT
1 AAAT
3457839 TTTTAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.18
Consensus pattern (17 bp):
AAATAAAAAAATAAATA
Found at i:3457943 original size:442 final size:437
Alignment explanation
Indices: 3457263--3458147 Score: 1441
Period size: 442 Copynumber: 2.0 Consensus size: 437
3457253 GATGCTTTAC
*
3457263 GAAATTCCTAGATGATAAGATTTCTTTAAATATTACCAGTGTATTGAAATATTTATAGAAAATTT
1 GAAATTCCTAGATGATAAGATTTCTTTAAATATTACCAGTGTATTGAAATATTTATAGAAAAATT
3457328 TCAATATAATAAAAAAAAATTTTCAAAAATTTAAATAAAAAAAAGAAATCAAATAAAAAATCAAT
66 TCAATATAATAAAAAAAAATTTTCAAAAATTTAAATAAAAAAAAGAAATCAAATAAAAAATCAAT
* * **
3457393 AAAATTTCTAAAAAATATATATAATAAATGCATCAATATATCAGCATTTTGCATTGCACGTATAA
131 AAAATTTCTAAAAAAAAAATATAATAAATGCATCAATATATCAGCATTTTGCATTGCACACATAA
* * * *
3457458 TAAAGTTTTTTCGAAAAGTAAATTTGAACCTCCGAAGATGAGATTTTAGGGTATTTCGAGAAACG
196 TAAAGTTTTTTCGAAAAGTAAATTTGAACCTCCGAAAATGAGATTTGAAGGTATTCCGAGAAACG
* *
3457523 ATGCCTAAGAAATTTCTAGGTGAGAAGAAATTCTTCTAATATTATCAACGTACTAAGACATTTTA
261 ATACCTAAGAAATTTCTAGGTGAGAAGAAATTCTTATAATATTATCAACGTACTAAGACATTTTA
* *
3457588 AGAATTATTTCAATAAAATGGTTCTAATTTATTTTTCTCAAATAAAATTTAAACAATAAATATGG
326 AAAATTATTTCAAAAAAATGGTTCTAATTTATTTTTCTCAAATAAAATTTAAACAATAAATATGG
*
3457653 AACAATAAT-AAAAAAATCAAAATTTCAATAAATAAAGGAAATCAAG
391 AACAATAATAAAAAAAATCAAAATTTCAATAAATAAAAGAAATCAAG
*
3457699 GAAATTCCTATATGATAAGATTTCTTTAAATATTACCAGTGTATTGAAATATTTATAGAAAAATT
1 GAAATTCCTAGATGATAAGATTTCTTTAAATATTACCAGTGTATTGAAATATTTATAGAAAAATT
***** *
3457764 TCAATATAATAAAATTTTCTTTTTTCTTCAAAAATTTAAAT-AAAAAAATAAATCAAATAAAAAA
66 TCAATATAATAAAA----AAAAATT-TTCAAAAATTTAAATAAAAAAAAGAAATCAAAT-AAAAA
* *
3457828 ATCAATAAAATTTTTAAAAAAAAGAATATAATACATGCATCAATATATCAGCATTTTGCATTGCA
125 ATCAATAAAATTTCTAAAAAAAA-AATATAATAAATGCATCAATATATCAGCATTTTGCATTGCA
* *
3457893 CACATACTAAAGTTTTTTCGAAAAGTAAATTTGAACCTTCGAAAATGAGATTTGAAGGTATTCCG
189 CACATAATAAAGTTTTTTCGAAAAGTAAATTTGAACCTCCGAAAATGAGATTTGAAGGTATTCCG
* * *
3457958 AGAAACGATACCTAAGAAATTTTTAGGTGAGAAGAAGTTCTTATAATATTATCAACGTACTAGGA
254 AGAAACGATACCTAAGAAATTTCTAGGTGAGAAGAAATTCTTATAATATTATCAACGTACTAAGA
3458023 CATTTTAAAAATTATTTCAAAAAAATGGTTCTAATTTATTTTTCTCAAATAAAATTTAAACAATA
319 CATTTTAAAAATTATTTCAAAAAAATGGTTCTAATTTATTTTTCTCAAATAAAATTTAAACAATA
3458088 AATATGGAACAATAATAAAAAAAATCAAAATTTCAATAAATAAAAGAAATCAAG
384 AATATGGAACAATAATAAAAAAAATCAAAATTTCAATAAATAAAAGAAATCAAG
3458142 GAAATT
1 GAAATT
3458148 ATTTTTCAAA
Statistics
Matches: 413, Mismatches: 28, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
436 77 0.19
440 18 0.04
441 41 0.10
442 235 0.57
443 42 0.10
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.33
Consensus pattern (437 bp):
GAAATTCCTAGATGATAAGATTTCTTTAAATATTACCAGTGTATTGAAATATTTATAGAAAAATT
TCAATATAATAAAAAAAAATTTTCAAAAATTTAAATAAAAAAAAGAAATCAAATAAAAAATCAAT
AAAATTTCTAAAAAAAAAATATAATAAATGCATCAATATATCAGCATTTTGCATTGCACACATAA
TAAAGTTTTTTCGAAAAGTAAATTTGAACCTCCGAAAATGAGATTTGAAGGTATTCCGAGAAACG
ATACCTAAGAAATTTCTAGGTGAGAAGAAATTCTTATAATATTATCAACGTACTAAGACATTTTA
AAAATTATTTCAAAAAAATGGTTCTAATTTATTTTTCTCAAATAAAATTTAAACAATAAATATGG
AACAATAATAAAAAAAATCAAAATTTCAATAAATAAAAGAAATCAAG
Found at i:3464710 original size:14 final size:14
Alignment explanation
Indices: 3464682--3464715 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
3464672 GAAATTTGTG
*
3464682 AAAATT-TTTATTA
1 AAAATTATTTACTA
3464695 AAAATTATTTACTA
1 AAAATTATTTACTA
3464709 AAAATTA
1 AAAATTA
3464716 AAGTAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (14 bp):
AAAATTATTTACTA
Found at i:3465612 original size:18 final size:19
Alignment explanation
Indices: 3465589--3465624 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3465579 TTTAATCCTT
3465589 AAAAATTT-TATTTAATAA
1 AAAAATTTATATTTAATAA
3465607 AAAAATTTATATTTAATA
1 AAAAATTTATATTTAATA
3465625 CAATATCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AAAAATTTATATTTAATAA
Found at i:3470012 original size:3 final size:3
Alignment explanation
Indices: 3470006--3470048 Score: 70
Period size: 3 Copynumber: 14.3 Consensus size: 3
3469996 TAGATTTTTT
3470006 TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA T
3470049 CAATATGTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.05
3 33 0.87
4 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3470133 original size:15 final size:14
Alignment explanation
Indices: 3470113--3470153 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
3470103 ATTATTATTA
3470113 TTTTTTTTTCTTTCT
1 TTTTTTTTTCTTT-T
3470128 TTTTTTTTTCTTTT
1 TTTTTTTTTCTTTT
*
3470142 TGTTTTTGTTCT
1 T-TTTTTTTTCT
3470154 AATTCCCACA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 2 0.08
15 22 0.92
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.85
Consensus pattern (14 bp):
TTTTTTTTTCTTTT
Found at i:3471041 original size:21 final size:20
Alignment explanation
Indices: 3471004--3471044 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3470994 TTATTTGTTG
*
3471004 ATTTTTATTCTAATTTATTT
1 ATTTTTATCCTAATTTATTT
*
3471024 ATTTTTATCCATATTTTATTT
1 ATTTTTATCC-TAATTTATTT
3471045 TTTGATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.68
Consensus pattern (20 bp):
ATTTTTATCCTAATTTATTT
Found at i:3471660 original size:20 final size:21
Alignment explanation
Indices: 3471635--3471677 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3471625 AAATTAGTTA
3471635 TTTTAA-AGATTAATAAAATT
1 TTTTAATAGATTAATAAAATT
* *
3471655 TTTTAATAGTTTGATAAAATT
1 TTTTAATAGATTAATAAAATT
3471676 TT
1 TT
3471678 ATTTTAAGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (21 bp):
TTTTAATAGATTAATAAAATT
Found at i:3471889 original size:104 final size:104
Alignment explanation
Indices: 3471775--3471993 Score: 366
Period size: 104 Copynumber: 2.1 Consensus size: 104
3471765 CAATAGTTTA
* *
3471775 GAAAGATTTAACTTTAAGATTTAAATCCTAAAATAATTTGGTAGAATTAGGAATTTTATTTTATA
1 GAAA-ATTTAACTTTAAGATTTAAATCCAAAAATAATTTGGTAAAATTAGGAATTTTATTTTATA
* *
3471840 AAAATCACTAAATCTACTAATTGTTTTGTAAGATTTAATT
65 AAAATCACTAAATCTACTAATAGTTTGGTAAGATTTAATT
3471880 GAAAATTTAACTTTAAGATTTAAATCCAAAAATAATTTGGTAAAATTAGGAATTTTATTTTATAA
1 GAAAATTTAACTTTAAGATTTAAATCCAAAAATAATTTGGTAAAATTAGGAATTTTATTTTATAA
* *
3471945 AAATCACTAAATCTTCTAATAGTTTGGTAATATTTAATT
66 AAATCACTAAATCTACTAATAGTTTGGTAAGATTTAATT
*
3471984 GAAATTTTAA
1 GAAAATTTAA
3471994 ATTTTCTAAT
Statistics
Matches: 107, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
104 103 0.96
105 4 0.04
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (104 bp):
GAAAATTTAACTTTAAGATTTAAATCCAAAAATAATTTGGTAAAATTAGGAATTTTATTTTATAA
AAATCACTAAATCTACTAATAGTTTGGTAAGATTTAATT
Found at i:3471971 original size:52 final size:52
Alignment explanation
Indices: 3471806--3471974 Score: 130
Period size: 52 Copynumber: 3.2 Consensus size: 52
3471796 TAAATCCTAA
*
3471806 AATAATTTGGTAGAATTAGGAATTTTATTTTATAAAAATCACTAAATCTACT
1 AATAATTTGGTAAAATTAGGAATTTTATTTTATAAAAATCACTAAATCTACT
** * * * * ** * * * **
3471858 AATTGTTTTGTAAGATTTAATTGAAAATTTAACTT-T-AAGAT--TTAAATCCAAA
1 AATAATTTGGTAA-AATT-A--GGAATTTTATTTTATAAAAATCACTAAATCTACT
*
3471910 AATAATTTGGTAAAATTAGGAATTTTATTTTATAAAAATCACTAAATCTTCT
1 AATAATTTGGTAAAATTAGGAATTTTATTTTATAAAAATCACTAAATCTACT
*
3471962 AATAGTTTGGTAA
1 AATAATTTGGTAA
3471975 TATTTAATTG
Statistics
Matches: 80, Mismatches: 29, Indels: 16
0.64 0.23 0.13
Matches are distributed among these distances:
48 9 0.11
49 1 0.01
50 5 0.06
51 3 0.04
52 44 0.55
53 3 0.04
54 5 0.06
55 1 0.01
56 9 0.11
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.41
Consensus pattern (52 bp):
AATAATTTGGTAAAATTAGGAATTTTATTTTATAAAAATCACTAAATCTACT
Found at i:3473517 original size:25 final size:26
Alignment explanation
Indices: 3473461--3473517 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 26
3473451 AGTTTATTTT
* * *
3473461 AATATTTAAATTTTATTAAAGTTAAT
1 AATATTAAAATTTTATTAAAGTAAAA
*
3473487 TA-ATTAAAATTTTATTAAA-TAAAA
1 AATATTAAAATTTTATTAAAGTAAAA
3473511 AATATTA
1 AATATTA
3473518 TTAATTAATA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
24 4 0.16
25 20 0.80
26 1 0.04
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (26 bp):
AATATTAAAATTTTATTAAAGTAAAA
Found at i:3475012 original size:29 final size:30
Alignment explanation
Indices: 3474954--3475022 Score: 90
Period size: 29 Copynumber: 2.3 Consensus size: 30
3474944 GTTTTAAAAG
3474954 TTAGGGTTTTAAGATTTTGGAGTTTTGGATT
1 TTAGGGTTTT-AGATTTTGGAGTTTTGGATT
3474985 TTAGGGTTTT-GA-TTT-GAGTTTTAAGGATT
1 TTAGGGTTTTAGATTTTGGAGTTTT--GGATT
3475014 TTAGGGTTT
1 TTAGGGTTT
3475023 GGTCTTAGGG
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
27 7 0.19
28 3 0.08
29 16 0.44
31 10 0.28
ACGTcount: A:0.19, C:0.00, G:0.29, T:0.52
Consensus pattern (30 bp):
TTAGGGTTTTAGATTTTGGAGTTTTGGATT
Done.