Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold114
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: 3219552
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Warning! 36736 characters in sequence are not A, C, G, or T
File 10 of 13
Found at i:2372124 original size:1 final size:1
Alignment explanation
Indices: 2372118--2372144 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
2372108 CATTCTTCTG
2372118 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
2372145 CAGGTTTTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:2373620 original size:21 final size:21
Alignment explanation
Indices: 2373596--2373641 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
2373586 CCCCCTTGGT
*
2373596 TTTGCACAGGGCCTTAATGGA
1 TTTGCACACGGCCTTAATGGA
*
2373617 TTTGCACACGGCCTTCATGGA
1 TTTGCACACGGCCTTAATGGA
2373638 TTTG
1 TTTG
2373642 ATGCACACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.22, G:0.26, T:0.33
Consensus pattern (21 bp):
TTTGCACACGGCCTTAATGGA
Found at i:2385637 original size:22 final size:22
Alignment explanation
Indices: 2385584--2385638 Score: 83
Period size: 23 Copynumber: 2.5 Consensus size: 22
2385574 ATTAAAAGTT
* *
2385584 TTAAAATTTATTTGGTTGTAAA
1 TTAAAATTTATTTGGATATAAA
2385606 TTAAAAATTTATTTGGATATAAA
1 TT-AAAATTTATTTGGATATAAA
2385629 TTAAAATTTA
1 TTAAAATTTA
2385639 AGATTTATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 10 0.33
23 20 0.67
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (22 bp):
TTAAAATTTATTTGGATATAAA
Found at i:2386207 original size:19 final size:18
Alignment explanation
Indices: 2386183--2386250 Score: 57
Period size: 19 Copynumber: 3.4 Consensus size: 18
2386173 AAAGAGTTTA
2386183 TTTAAATATTAATAAAAAT
1 TTTAAAT-TTAATAAAAAT
2386202 TTTAAATTGATAA-AAAAAT
1 TTTAAATT--TAATAAAAAT
*
2386221 TTTAATTTTTATATTAAAAAT
1 TTTAA-ATTTA-A-TAAAAAT
2386242 ATTTAAATT
1 -TTTAAATT
2386251 CGATATATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
18 3 0.08
19 19 0.47
20 5 0.12
21 8 0.20
22 5 0.12
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (18 bp):
TTTAAATTTAATAAAAAT
Found at i:2386256 original size:22 final size:20
Alignment explanation
Indices: 2386195--2386256 Score: 63
Period size: 19 Copynumber: 3.0 Consensus size: 20
2386185 TAAATATTAA
2386195 TAAAAATTTTAAATTGATA-
1 TAAAAATTTTAAATTGATAT
* * *
2386214 AAAAAATTTTAATTTTTATAT
1 TAAAAATTTTAA-ATTGATAT
2386235 TAAAAATATTTAAATTCGATAT
1 TAAAAAT-TTTAAATT-GATAT
2386257 ATATTTTTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
19 11 0.33
20 5 0.15
21 8 0.24
22 9 0.27
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (20 bp):
TAAAAATTTTAAATTGATAT
Found at i:2386355 original size:25 final size:26
Alignment explanation
Indices: 2386327--2386376 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
2386317 TTTATTAACA
*
2386327 TTTAAAATAATATA-AATATAAATTT
1 TTTAAAAGAATATATAATATAAATTT
*
2386352 TTTAAAAGATTATATAATATAAATT
1 TTTAAAAGAATATATAATATAAATT
2386377 ATAATTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (26 bp):
TTTAAAAGAATATATAATATAAATTT
Found at i:2386397 original size:32 final size:32
Alignment explanation
Indices: 2386304--2386397 Score: 95
Period size: 32 Copynumber: 2.9 Consensus size: 32
2386294 TATTTCTCAT
* * *
2386304 TATAAGTTAATAA-TTTATTAACATTTAAAATAA
1 TATAAATT-ATAATTTTATTAAAATTT-ATATAA
*
2386337 TATAAA-TATAAATTTT-TTAAAAGATTATATAA
1 TATAAATTAT-AATTTTATTAAAA-TTTATATAA
2386369 TATAAATTATAATTTTATTAAAATTTATA
1 TATAAATTATAATTTTATTAAAATTTATA
2386398 AGATGATAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
31 2 0.04
32 30 0.59
33 19 0.37
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (32 bp):
TATAAATTATAATTTTATTAAAATTTATATAA
Found at i:2386407 original size:33 final size:31
Alignment explanation
Indices: 2386313--2386408 Score: 81
Period size: 33 Copynumber: 3.0 Consensus size: 31
2386303 TTATAAGTTA
*
2386313 ATAA-TTTATTAACATTTA-AAATAATATAAAT
1 ATAATTTTATTAAAATTTATAAAT-ATA-AAAT
* *
2386344 ATAAATTTT-TTAAAAGATTATATAATATAAATT
1 AT-AATTTTATTAAAA-TTTATA-AATATAAAAT
2386377 ATAATTTTATTAAAATTTATAAGATGATAAAA
1 ATAATTTTATTAAAATTTATAA-AT-ATAAAA
2386409 AGCTTTAATT
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
31 3 0.06
32 20 0.38
33 22 0.42
34 4 0.08
35 3 0.06
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (31 bp):
ATAATTTTATTAAAATTTATAAATATAAAAT
Found at i:2387416 original size:2 final size:2
Alignment explanation
Indices: 2387409--2387458 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
2387399 TCGAGAATCT
2387409 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
2387451 TA TA TA TA
1 TA TA TA TA
2387459 CACTAACTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2387763 original size:22 final size:23
Alignment explanation
Indices: 2387735--2387788 Score: 92
Period size: 22 Copynumber: 2.4 Consensus size: 23
2387725 AAATTTGATA
2387735 TATTTTATATTTATGTTGTAT-T
1 TATTTTATATTTATGTTGTATCT
*
2387757 TATTTTATTTTTATGTTGTATCT
1 TATTTTATATTTATGTTGTATCT
2387780 TATTTTATA
1 TATTTTATA
2387789 CTATATTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 20 0.69
23 9 0.31
ACGTcount: A:0.22, C:0.02, G:0.07, T:0.69
Consensus pattern (23 bp):
TATTTTATATTTATGTTGTATCT
Found at i:2388339 original size:16 final size:17
Alignment explanation
Indices: 2388320--2388356 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
2388310 ATGTTTAAAA
2388320 AATTTT-ATAT-TTAAT
1 AATTTTGATATATTAAT
2388335 GAATTTTGATATATTAAT
1 -AATTTTGATATATTAAT
2388353 AATT
1 AATT
2388357 ATTTCATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.32
17 8 0.42
18 5 0.26
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (17 bp):
AATTTTGATATATTAAT
Found at i:2390268 original size:2 final size:2
Alignment explanation
Indices: 2390261--2390298 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2390251 TAATACTGCG
2390261 TA TA TA TA TA 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 TA TA TA TA TA
2390299 GCTATTTTTT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2391116 original size:12 final size:12
Alignment explanation
Indices: 2391083--2391121 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
2391073 AGATTCAGAT
2391083 TTCCTTTTC-TC
1 TTCCTTTTCTTC
2391094 TTCCTTCTTCTTC
1 TTCCTT-TTCTTC
*
2391107 TTTCTTTTCTTC
1 TTCCTTTTCTTC
2391119 TTC
1 TTC
2391122 TCCTAACCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 6 0.25
12 11 0.46
13 7 0.29
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (12 bp):
TTCCTTTTCTTC
Found at i:2395490 original size:16 final size:16
Alignment explanation
Indices: 2395443--2395491 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
2395433 TACACTAATC
2395443 AATGATCATAATTAAA
1 AATGATCATAATTAAA
*
2395459 AATG-T-ACCAA--AAA
1 AATGATCA-TAATTAAA
2395472 AATGATCATAATTAAA
1 AATGATCATAATTAAA
2395488 AATG
1 AATG
2395492 TACCAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
13 7 0.27
14 4 0.15
15 4 0.15
16 11 0.42
ACGTcount: A:0.57, C:0.08, G:0.08, T:0.27
Consensus pattern (16 bp):
AATGATCATAATTAAA
Found at i:2395521 original size:29 final size:29
Alignment explanation
Indices: 2395443--2395512 Score: 140
Period size: 29 Copynumber: 2.4 Consensus size: 29
2395433 TACACTAATC
2395443 AATGATCATAATTAAAAATGTACCAAAAA
1 AATGATCATAATTAAAAATGTACCAAAAA
2395472 AATGATCATAATTAAAAATGTACCAAAAA
1 AATGATCATAATTAAAAATGTACCAAAAA
2395501 AATGATCATAAT
1 AATGATCATAAT
2395513 AATGAATGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.57, C:0.10, G:0.07, T:0.26
Consensus pattern (29 bp):
AATGATCATAATTAAAAATGTACCAAAAA
Found at i:2400770 original size:2 final size:2
Alignment explanation
Indices: 2400765--2400793 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2400755 ATATATATAC
2400765 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2400794 ACTAAAAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2404890 original size:11 final size:11
Alignment explanation
Indices: 2404874--2404904 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
2404864 GTAACTTCAA
*
2404874 TGTCTTTGCCT
1 TGTCTTTGCCG
2404885 TGTCTTTGCCG
1 TGTCTTTGCCG
2404896 TGTCTTTGC
1 TGTCTTTGC
2404905 GGAAGATGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.26, G:0.23, T:0.52
Consensus pattern (11 bp):
TGTCTTTGCCG
Found at i:2407315 original size:2 final size:2
Alignment explanation
Indices: 2407310--2407347 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2407300 AGGTCTTTTT
2407310 TA TA TA TA TA 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 TA TA TA TA TA
2407348 AATAAAGAAG
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2408236 original size:2 final size:2
Alignment explanation
Indices: 2408231--2408281 Score: 79
Period size: 2 Copynumber: 26.5 Consensus size: 2
2408221 ACACACACAC
*
2408231 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2408273 A- AT -T AT AT A
1 AT AT AT AT AT A
2408282 GTTGATATAA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.04
2 43 0.96
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2408685 original size:2 final size:2
Alignment explanation
Indices: 2408674--2408716 Score: 70
Period size: 2 Copynumber: 21.5 Consensus size: 2
2408664 TTCTCTCACC
2408674 AT AT ACT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2408716 A
1 A
2408717 CAAAACTCTT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.03
2 36 0.92
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2426512 original size:2 final size:2
Alignment explanation
Indices: 2426507--2426539 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2426497 ATTGTGTGTG
2426507 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 T
2426540 GTAAATTTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2433540 original size:16 final size:16
Alignment explanation
Indices: 2433519--2433565 Score: 69
Period size: 16 Copynumber: 2.9 Consensus size: 16
2433509 TTCAATTAAT
*
2433519 AAAATAATTTAAATTA
1 AAAATAATTTAAATAA
2433535 AAAATAATTT-AATAA
1 AAAATAATTTAAATAA
2433550 AAAATAAATTTAAATA
1 AAAAT-AATTTAAATA
2433566 TTATCTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 9 0.32
16 15 0.54
17 4 0.14
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AAAATAATTTAAATAA
Found at i:2433819 original size:4 final size:4
Alignment explanation
Indices: 2433810--2433869 Score: 66
Period size: 4 Copynumber: 15.0 Consensus size: 4
2433800 TGATATCTGC
* * * * *
2433810 ATAT ATAT ATAT ATGT ATAT ATGT ATGT ATGT ATAT ATGT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
*
2433858 ATGT ATAT ATAT
1 ATAT ATAT ATAT
2433870 GTATGCATGA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 48 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (4 bp):
ATAT
Found at i:2433821 original size:8 final size:8
Alignment explanation
Indices: 2433810--2433873 Score: 78
Period size: 8 Copynumber: 8.2 Consensus size: 8
2433800 TGATATCTGC
*
2433810 ATATATAT
1 ATATATGT
2433818 ATATATGT
1 ATATATGT
2433826 ATATATGT
1 ATATATGT
*
2433834 ATGTATGT
1 ATATATGT
2433842 ATATATGT
1 ATATATGT
2433850 ATATA--T
1 ATATATGT
* *
2433856 ATATGTAT
1 ATATATGT
2433864 ATATATGT
1 ATATATGT
2433872 AT
1 AT
2433874 GCATGAAATG
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
6 5 0.10
8 43 0.90
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (8 bp):
ATATATGT
Found at i:2433828 original size:12 final size:12
Alignment explanation
Indices: 2433813--2433869 Score: 96
Period size: 12 Copynumber: 4.8 Consensus size: 12
2433803 TATCTGCATA
2433813 TATATATATATG
1 TATATATATATG
*
2433825 TATATATGTATG
1 TATATATATATG
*
2433837 TATGTATATATG
1 TATATATATATG
2433849 TATATATATATG
1 TATATATATATG
2433861 TATATATAT
1 TATATATAT
2433870 GTATGCATGA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 41 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.51
Consensus pattern (12 bp):
TATATATATATG
Found at i:2434323 original size:24 final size:24
Alignment explanation
Indices: 2434289--2434337 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
2434279 ATTTTTTATA
2434289 TAAAAAAATTATAATT-TAAAAAT
1 TAAAAAAATTATAATTATAAAAAT
*
2434312 TAAAAAATATTATAATTATCAAAAT
1 TAAAAAA-ATTATAATTATAAAAAT
2434337 T
1 T
2434338 TAAATATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.30
24 9 0.39
25 7 0.30
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (24 bp):
TAAAAAAATTATAATTATAAAAAT
Found at i:2435113 original size:19 final size:20
Alignment explanation
Indices: 2435069--2435113 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
2435059 ATTTTTTTAT
2435069 ATTAT-TATCATATTTAAAA
1 ATTATATATCATATTTAAAA
*
2435088 ATT-TATATTATATTT-AAA
1 ATTATATATCATATTTAAAA
2435106 ATTATATA
1 ATTATATA
2435114 AATTTATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTATATATCATATTTAAAA
Found at i:2442221 original size:2 final size:2
Alignment explanation
Indices: 2442214--2442252 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
2442204 ATAGTTATGC
*
2442214 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2442253 GATCTTATGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2448945 original size:12 final size:14
Alignment explanation
Indices: 2448832--2448938 Score: 50
Period size: 14 Copynumber: 7.6 Consensus size: 14
2448822 TTAAGATATT
2448832 TTATATTTATATAA
1 TTATATTTATATAA
2448846 --AT-TTTA-ATAAA
1 TTATATTTATAT-AA
*
2448857 TTAATATTTCATATTA
1 TT-ATATTT-ATATAA
*
2448873 -TATAATTTTTA-AA
1 TTAT-ATTTATATAA
**
2448886 TATATATTTATATCG
1 T-TATATTTATATAA
2448901 TGT-TATGTTATAATAA
1 T-TATAT-TTAT-ATAA
2448917 -TATATTTATATAA
1 TTATATTTATATAA
2448930 TTATATTTA
1 TTATATTTA
2448939 AAATTATTAG
Statistics
Matches: 69, Mismatches: 9, Indels: 30
0.64 0.08 0.28
Matches are distributed among these distances:
10 2 0.03
11 6 0.09
12 2 0.03
13 5 0.07
14 28 0.41
15 20 0.29
16 4 0.06
17 2 0.03
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (14 bp):
TTATATTTATATAA
Found at i:2450440 original size:14 final size:14
Alignment explanation
Indices: 2450423--2450476 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
2450413 TTAATTTTAA
*
2450423 ATTTTAAATTTATT
1 ATTTTAAATTAATT
*
2450437 ATTTTAGATTAAATT
1 ATTTTAAATT-AATT
*
2450452 A-TTTAAATTAATA
1 ATTTTAAATTAATT
*
2450465 ATTTTTAATTAA
1 ATTTTAAATTAA
2450477 AATAATATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
13 4 0.12
14 25 0.76
15 4 0.12
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (14 bp):
ATTTTAAATTAATT
Found at i:2450482 original size:19 final size:20
Alignment explanation
Indices: 2450454--2450499 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
2450444 ATTAAATTAT
*
2450454 TTAAATTAATA-ATTTTTAA
1 TTAAAATAATATATTTTTAA
*
2450473 TTAAAATAATATATTTTTAT
1 TTAAAATAATATATTTTTAA
2450493 TTAAAAT
1 TTAAAAT
2450500 TAATTATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 10 0.42
20 14 0.58
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TTAAAATAATATATTTTTAA
Found at i:2450523 original size:22 final size:21
Alignment explanation
Indices: 2450494--2450534 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
2450484 TATTTTTATT
2450494 TAAAATTAATTAT-AAAATATA
1 TAAAATTAA-TATCAAAATATA
2450515 TAAATATTAATATCAAAATA
1 TAAA-ATTAATATCAAAATA
2450535 ATTTTTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
TAAAATTAATATCAAAATATA
Found at i:2451222 original size:3 final size:3
Alignment explanation
Indices: 2451214--2451243 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2451204 ACTCTTTTAC
2451214 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2451244 AATATTAACG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2465840 original size:15 final size:15
Alignment explanation
Indices: 2465805--2465840 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
2465795 GAAGAAAGTA
*
2465805 TTTTAATTTTTTTAT
1 TTTTAATTTTTATAT
*
2465820 TATTAATTTTTATAT
1 TTTTAATTTTTATAT
2465835 TTTTAA
1 TTTTAA
2465841 AATTATAGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTAATTTTTATAT
Found at i:2467052 original size:23 final size:24
Alignment explanation
Indices: 2467025--2467072 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
2467015 ACTTTAACCT
*
2467025 AATAAAT-AAATATAATTTTAAAA
1 AATAAATAAAATATAATATTAAAA
*
2467048 AATAATTAAAATATAATATTAAAA
1 AATAAATAAAATATAATATTAAAA
2467072 A
1 A
2467073 TATTATGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (24 bp):
AATAAATAAAATATAATATTAAAA
Found at i:2467120 original size:18 final size:18
Alignment explanation
Indices: 2467097--2467168 Score: 58
Period size: 17 Copynumber: 3.9 Consensus size: 18
2467087 AAAAATTTAA
2467097 ATTAATATAATATAAATT
1 ATTAATATAATATAAATT
*
2467115 ATTAATAT-ATTTAAATT
1 ATTAATATAATATAAATT
* *
2467132 -TTTATAAAATATATAATAT
1 ATTAATATAATATA-AAT-T
*
2467151 TTTAAATATAATTATAAA
1 ATT-AATATAA-TATAAA
2467169 AAACAAATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
16 5 0.12
17 12 0.29
18 11 0.26
19 1 0.02
20 2 0.05
21 7 0.17
22 4 0.10
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTAATATAATATAAATT
Found at i:2467747 original size:2 final size:2
Alignment explanation
Indices: 2467740--2467774 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2467730 ACCTAAAGAC
2467740 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2467775 CATAAGTGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2469141 original size:18 final size:19
Alignment explanation
Indices: 2469118--2469154 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2469108 AATTTAAAAT
2469118 TAAAATATA-TTAAATAAA
1 TAAAATATATTTAAATAAA
*
2469136 TAAAATTTATTTAAATAAA
1 TAAAATATATTTAAATAAA
2469155 ATAATGTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAAATATATTTAAATAAA
Found at i:2469326 original size:17 final size:19
Alignment explanation
Indices: 2469288--2469329 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
2469278 AAATTCACAC
2469288 ATTATAATTTATGTAATTT
1 ATTATAATTTATGTAATTT
*
2469307 ATTATAATTT-T-TATTTT
1 ATTATAATTTATGTAATTT
2469324 ATTATA
1 ATTATA
2469330 TTATAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 11 0.50
18 1 0.05
19 10 0.45
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
ATTATAATTTATGTAATTT
Found at i:2469796 original size:2 final size:2
Alignment explanation
Indices: 2469789--2469826 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2469779 TAAATGTCAA
2469789 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2469827 GCAGTGTCTC
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):
TC
Found at i:2471482 original size:42 final size:41
Alignment explanation
Indices: 2471417--2471514 Score: 117
Period size: 42 Copynumber: 2.4 Consensus size: 41
2471407 TTGTGTTTGT
*
2471417 ATTATATATATATATAAAATATATTTTTTTATTATATTTAA
1 ATTATATATATATATAAAATATATTTTATTATTATATTTAA
* * * * *
2471458 ATTATTATATATATATATATTATATTTTATTATTTTATTCAT
1 ATTA-TATATATATATAAAATATATTTTATTATTATATTTAA
*
2471500 GTTATATATAT-TATA
1 ATTATATATATATATA
2471515 GGACAGAGAT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
40 4 0.08
41 11 0.22
42 34 0.69
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (41 bp):
ATTATATATATATATAAAATATATTTTATTATTATATTTAA
Found at i:2473524 original size:20 final size:21
Alignment explanation
Indices: 2473475--2473522 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
2473465 GATTTGATTT
*
2473475 TATAATTTATGTATATAATAA
1 TATATTTTATGTATATAATAA
*
2473496 TATATTTTAT-TATATTATAA
1 TATATTTTATGTATATAATAA
2473516 T-TATTTT
1 TATATTTT
2473523 TAAAATATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 6 0.24
20 10 0.40
21 9 0.36
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
TATATTTTATGTATATAATAA
Found at i:2473556 original size:20 final size:19
Alignment explanation
Indices: 2473492--2473558 Score: 66
Period size: 20 Copynumber: 3.5 Consensus size: 19
2473482 TATGTATATA
*
2473492 ATAATATATTTTATTATATT
1 ATAATATATTTTA-TAAATT
*
2473512 ATAAT-TATTTT-TAAAAT
1 ATAATATATTTTATAAATT
**
2473529 ATTTTATATTTATATAAATT
1 ATAATATATTT-TATAAATT
2473549 ATAATATATT
1 ATAATATATT
2473559 CACATTTTAT
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
17 7 0.19
18 5 0.14
19 7 0.19
20 18 0.49
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATAATATATTTTATAAATT
Found at i:2473576 original size:57 final size:59
Alignment explanation
Indices: 2473471--2473581 Score: 138
Period size: 57 Copynumber: 1.9 Consensus size: 59
2473461 TAGCGATTTG
* * **
2473471 ATTTTATAATTTATGTATATAATAATATATTTTATTATATTATAATTAT-TTTTAAAAT
1 ATTTTATAATTTATATAAATAATAATATATTACATTATATTATAATTATATTTTAAAAT
* *
2473529 ATTTTAT-ATTTATATAAATTATAATATATTCACATTTTATTAT-ATTATATTTT
1 ATTTTATAATTTATATAAATAATAATATATT-ACATTATATTATAATTATATTTT
2473582 TATATCATAT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
57 25 0.56
58 20 0.44
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.58
Consensus pattern (59 bp):
ATTTTATAATTTATATAAATAATAATATATTACATTATATTATAATTATATTTTAAAAT
Found at i:2474088 original size:13 final size:13
Alignment explanation
Indices: 2474070--2474133 Score: 57
Period size: 11 Copynumber: 5.3 Consensus size: 13
2474060 AATAAAATAT
2474070 TTATATATTTATA
1 TTATATATTTATA
*
2474083 TTATATAATTAT-
1 TTATATATTTATA
* *
2474095 TT-TATTTTTAAA
1 TTATATATTTATA
*
2474107 TTATAT-TTTATG
1 TTATATATTTATA
2474119 TTA-A-ATTTATA
1 TTATATATTTATA
2474130 TTAT
1 TTAT
2474134 CTTTTTTAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 9
0.71 0.12 0.16
Matches are distributed among these distances:
11 15 0.38
12 11 0.28
13 14 0.35
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (13 bp):
TTATATATTTATA
Found at i:2474113 original size:18 final size:18
Alignment explanation
Indices: 2474092--2474153 Score: 72
Period size: 18 Copynumber: 3.4 Consensus size: 18
2474082 ATTATATAAT
2474092 TATTTTATTTTTAAATTA
1 TATTTTATTTTTAAATTA
*
2474110 TATTTTA-TGTTAAATTTA
1 TATTTTATTTTTAAA-TTA
* * *
2474128 TATTATCTTTTTTAATTA
1 TATTTTATTTTTAAATTA
2474146 TATTTTAT
1 TATTTTAT
2474154 GTGGAATTGT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
17 6 0.17
18 24 0.69
19 5 0.14
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (18 bp):
TATTTTATTTTTAAATTA
Found at i:2474117 original size:36 final size:36
Alignment explanation
Indices: 2474070--2474153 Score: 91
Period size: 36 Copynumber: 2.3 Consensus size: 36
2474060 AATAAAATAT
2474070 TTATATATTTATATTATATAATTAT-TT-TATTTTTAAA
1 TTATAT-TTTATATTA-A-AATTATATTATATTTTTAAA
* * * *
2474107 TTATATTTTATGTTAAATTTATATTATCTTTTTTAA
1 TTATATTTTATATTAAAATTATATTATATTTTTAAA
2474143 TTATATTTTAT
1 TTATATTTTAT
2474154 GTGGAATTGT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
34 5 0.12
35 3 0.07
36 27 0.66
37 6 0.15
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (36 bp):
TTATATTTTATATTAAAATTATATTATATTTTTAAA
Found at i:2478586 original size:3 final size:3
Alignment explanation
Indices: 2478578--2478612 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2478568 CAAATTTACT
2478578 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2478613 CTAACAGAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2481282 original size:10 final size:10
Alignment explanation
Indices: 2481269--2481357 Score: 58
Period size: 10 Copynumber: 8.7 Consensus size: 10
2481259 TATTATAATA
2481269 TTAATATTTT
1 TTAATATTTT
**
2481279 TTAATATGAT
1 TTAATATTTT
2481289 TTAATCA-TTT
1 TTAAT-ATTTT
* *
2481299 TTAATATAATA
1 TTAATAT-TTT
2481310 TTAATA-TTT
1 TTAATATTTT
**
2481319 TTAATATAAT
1 TTAATATTTT
2481329 TTAATCA-TTT
1 TTAAT-ATTTT
2481339 TTAATATAATTT
1 TTAATAT--TTT
2481351 TTAATAT
1 TTAATAT
2481358 GAAATATATT
Statistics
Matches: 59, Mismatches: 12, Indels: 14
0.69 0.14 0.16
Matches are distributed among these distances:
9 9 0.15
10 31 0.53
11 9 0.15
12 10 0.17
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.57
Consensus pattern (10 bp):
TTAATATTTT
Found at i:2481331 original size:40 final size:40
Alignment explanation
Indices: 2481262--2481453 Score: 165
Period size: 40 Copynumber: 4.7 Consensus size: 40
2481252 TTTTATATAT
* *
2481262 TATAATATTAATATTTTTTAATATGATTTAATCATTTTTAA
1 TATAATTTTAATA-TTTTTAATATAATTTAATCATTTTTAA
*
2481303 TATAATATTAATATTTTTAATATAATTTAATCATTTTTAA
1 TATAATTTTAATATTTTTAATATAATTTAATCATTTTTAA
** * ** *
2481343 TATAATTTTTAATA--TGAAATATATTTTTGGTAATTTTTAA
1 TATAA-TTTTAATATTTTTAATATA-ATTTAATCATTTTTAA
* * * *
2481383 AATAATTTTAATAATTTTTTATATAATTATGAT-ATTTTTTA
1 TATAATTTTAAT-ATTTTTAATATAATT-TAATCATTTTTAA
* *
2481424 TGTAATTTTGATAATTTATTAATATAATTT
1 TATAATTTTAAT-ATTT-TTAATATAATTT
2481454 TAATTAATAA
Statistics
Matches: 125, Mismatches: 19, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
39 14 0.11
40 48 0.38
41 44 0.35
42 19 0.15
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (40 bp):
TATAATTTTAATATTTTTAATATAATTTAATCATTTTTAA
Found at i:2481391 original size:21 final size:21
Alignment explanation
Indices: 2481262--2481454 Score: 146
Period size: 20 Copynumber: 9.4 Consensus size: 21
2481252 TTTTATATAT
* * *
2481262 TATAATATTAATATTTTTTAA
1 TATAATTTTGATAATTTTTAA
* * *
2481283 TATGA-TTTAATCATTTTTAA
1 TATAATTTTGATAATTTTTAA
* *
2481303 TATAATATTAAT-ATTTTTAA
1 TATAATTTTGATAATTTTTAA
* *
2481323 TATAA-TTTAATCATTTTTAA
1 TATAATTTTGATAATTTTTAA
* **
2481343 TATAATTTT--TAATATGAAA
1 TATAATTTTGATAATTTTTAA
* *
2481362 TATATTTTTGGTAATTTTTAA
1 TATAATTTTGATAATTTTTAA
* * *
2481383 AATAATTTTAATAATTTTTTA
1 TATAATTTTGATAATTTTTAA
* *
2481404 TATAATTATGAT-ATTTTTTA
1 TATAATTTTGATAATTTTTAA
*
2481424 TGTAATTTTGATAATTTATTAA
1 TATAATTTTGATAATTT-TTAA
2481446 TATAATTTT
1 TATAATTTT
2481455 AATTAATAAA
Statistics
Matches: 138, Mismatches: 27, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
19 19 0.14
20 60 0.43
21 48 0.35
22 11 0.08
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (21 bp):
TATAATTTTGATAATTTTTAA
Found at i:2481419 original size:20 final size:21
Alignment explanation
Indices: 2481373--2481452 Score: 81
Period size: 21 Copynumber: 3.8 Consensus size: 21
2481363 ATATTTTTGG
* * * *
2481373 TAATTTTTAAAATAATTTTAA
1 TAATTTTTTATATAATTATGA
2481394 TAATTTTTTATATAATTATGA
1 TAATTTTTTATATAATTATGA
* *
2481415 T-ATTTTTTATGTAATTTTGA
1 TAATTTTTTATATAATTATGA
*
2481435 TAATTTATTAATATAATT
1 TAATTT-TTTATATAATT
2481453 TTAATTAATA
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
20 18 0.37
21 22 0.45
22 9 0.18
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (21 bp):
TAATTTTTTATATAATTATGA
Found at i:2486838 original size:20 final size:20
Alignment explanation
Indices: 2486802--2486854 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
2486792 AAATATGAAA
*
2486802 AAATATATTAA-AATTTATAT
1 AAATATA-TAATAATTTAAAT
*
2486822 AAATATATAATATTTTAAAT
1 AAATATATAATAATTTAAAT
2486842 ATAATA-ATAATAA
1 A-AATATATAATAA
2486855 AAAATAATGT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 3 0.11
20 21 0.75
21 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
AAATATATAATAATTTAAAT
Found at i:2489305 original size:23 final size:22
Alignment explanation
Indices: 2489279--2489323 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
2489269 TAAATTTTTT
2489279 AAAAGATT-TATTTTATATATTTA
1 AAAAG-TTATATTTT-TATATTTA
2489302 AAAAGTTATATTTTTATATTTA
1 AAAAGTTATATTTTTATATTTA
2489324 TATTTAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.53
Consensus pattern (22 bp):
AAAAGTTATATTTTTATATTTA
Found at i:2489625 original size:2 final size:2
Alignment explanation
Indices: 2489587--2489611 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2489577 TTGATGATTT
2489587 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 T
2489612 GTGTGTGTAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2496862 original size:2 final size:2
Alignment explanation
Indices: 2496855--2496887 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2496845 GTGCATTTAA
2496855 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2496888 AGGTCAGAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2503912 original size:11 final size:12
Alignment explanation
Indices: 2503886--2503914 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2503876 TAATTATTTA
2503886 TTTAAATTTCTT
1 TTTAAATTTCTT
2503898 TTTAAATTT-TT
1 TTTAAATTTCTT
2503909 TTTAAA
1 TTTAAA
2503915 AATTAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 8 0.47
12 9 0.53
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (12 bp):
TTTAAATTTCTT
Found at i:2504148 original size:18 final size:17
Alignment explanation
Indices: 2504118--2504151 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
2504108 AAACAAAAAA
2504118 TATGTATTATATATATG
1 TATGTATTATATATATG
2504135 TATGTATGTATATATAT
1 TATGTAT-TATATATAT
2504152 ATATATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (17 bp):
TATGTATTATATATATG
Found at i:2512794 original size:6 final size:6
Alignment explanation
Indices: 2512780--2512825 Score: 74
Period size: 6 Copynumber: 7.7 Consensus size: 6
2512770 GTTGGAATCC
* *
2512780 ATGGAA ATGGCA ATGGCA ATGGCA ATGGCA ATGGCA ATGGAA ATGG
1 ATGGCA ATGGCA ATGGCA ATGGCA ATGGCA ATGGCA ATGGCA ATGG
2512826 GCATGTGAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.37, C:0.11, G:0.35, T:0.17
Consensus pattern (6 bp):
ATGGCA
Found at i:2512806 original size:18 final size:18
Alignment explanation
Indices: 2512780--2512825 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
2512770 GTTGGAATCC
2512780 ATGGAAATGGCAATGGCA
1 ATGGAAATGGCAATGGCA
*
2512798 ATGGCAATGGCAATGGCA
1 ATGGAAATGGCAATGGCA
2512816 ATGGAAATGG
1 ATGGAAATGG
2512826 GCATGTGAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.37, C:0.11, G:0.35, T:0.17
Consensus pattern (18 bp):
ATGGAAATGGCAATGGCA
Found at i:2513204 original size:2 final size:2
Alignment explanation
Indices: 2513197--2513229 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2513187 TAATTGCGAT
2513197 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2513230 TTTTCAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2516245 original size:2 final size:2
Alignment explanation
Indices: 2516238--2516264 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2516228 TCAATTTGTT
2516238 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
2516265 GAGTTTTACC
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:2517366 original size:16 final size:15
Alignment explanation
Indices: 2517335--2517367 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
2517325 TGGAGAGAGA
2517335 TTTTAGATAGAATTT
1 TTTTAGATAGAATTT
2517350 TTTTGAGATA-AATTT
1 TTTT-AGATAGAATTT
2517365 TTT
1 TTT
2517368 AGTAACGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (15 bp):
TTTTAGATAGAATTT
Found at i:2517754 original size:37 final size:37
Alignment explanation
Indices: 2517710--2517785 Score: 125
Period size: 37 Copynumber: 2.1 Consensus size: 37
2517700 AAAATTATGA
*
2517710 AATTATTTGATAATCGATAATATTTTTTTAAAAAAAT
1 AATTATTTAATAATCGATAATATTTTTTTAAAAAAAT
* *
2517747 AATTATTTAATTATCGATAATATTTTTTTTAAAAAAT
1 AATTATTTAATAATCGATAATATTTTTTTAAAAAAAT
2517784 AA
1 AA
2517786 GTCGACAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (37 bp):
AATTATTTAATAATCGATAATATTTTTTTAAAAAAAT
Found at i:2517796 original size:37 final size:37
Alignment explanation
Indices: 2517722--2517796 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
2517712 TTATTTGATA
* ***
2517722 ATCGATAATATTTTTTTAAAAAAATAATTATTTAATT
1 ATCGATAATATTTTTTTAAAAAAATAAGTAGACAATT
* *
2517759 ATCGATAATATTTTTTTTAAAAAATAAGTCGACAATT
1 ATCGATAATATTTTTTTAAAAAAATAAGTAGACAATT
2517796 A
1 A
2517797 AAATAATAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.44
Consensus pattern (37 bp):
ATCGATAATATTTTTTTAAAAAAATAAGTAGACAATT
Found at i:2524990 original size:2 final size:2
Alignment explanation
Indices: 2524983--2525011 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2524973 AGCGATTCAA
2524983 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2525012 AGTAAAAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2525496 original size:15 final size:16
Alignment explanation
Indices: 2525471--2525508 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
2525461 TAATAAATGC
*
2525471 TTATTATTTTAATATA
1 TTATAATTTTAATATA
*
2525487 TT-TAATTTTATTATA
1 TTATAATTTTAATATA
2525502 TTATAAT
1 TTATAAT
2525509 AATTAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTATAATTTTAATATA
Found at i:2526282 original size:26 final size:25
Alignment explanation
Indices: 2526253--2526314 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 25
2526243 TTATTTGATT
2526253 TATAAAA-ATTTTAATTATTAA-ATATA
1 TATAAAATATTTT--TTATTAACATA-A
2526279 TATAATAATATTTTTTATTAACATAA
1 TATAA-AATATTTTTTATTAACATAA
2526305 TAT-AAATATT
1 TATAAAATATT
2526315 CGATAAATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
24 6 0.18
25 1 0.03
26 16 0.48
27 5 0.15
28 5 0.15
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (25 bp):
TATAAAATATTTTTTATTAACATAA
Found at i:2527443 original size:26 final size:24
Alignment explanation
Indices: 2527389--2527444 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 24
2527379 CATTTATTAT
*
2527389 TTATTATTTTTAATATATTAAATA
1 TTATTATTTTTAATAAATTAAATA
2527413 TTATTATTTTTATATAGAATT-AATA
1 TTATTATTTTTA-ATA-AATTAAATA
2527438 TATATTA
1 T-TATTA
2527445 AAAATTATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 12 0.43
25 8 0.29
26 8 0.29
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (24 bp):
TTATTATTTTTAATAAATTAAATA
Found at i:2528118 original size:17 final size:18
Alignment explanation
Indices: 2528089--2528134 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
2528079 TTATGGAAAA
*
2528089 TATATATTATAA-TTTAT
1 TATATAATATAATTTTAT
2528106 T-TATTAATATAATTTTAT
1 TATA-TAATATAATTTTAT
2528124 TATATAATATA
1 TATATAATATA
2528135 TATTAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 2 0.08
17 8 0.32
18 13 0.52
19 2 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TATATAATATAATTTTAT
Found at i:2528429 original size:22 final size:23
Alignment explanation
Indices: 2528399--2528445 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
2528389 TTATTTAAAT
2528399 TTAATTATAAAAATATATTAATA
1 TTAATTATAAAAATATATTAATA
* *
2528422 TTAA-TATAAAAATATTTTTATA
1 TTAATTATAAAAATATATTAATA
2528444 TT
1 TT
2528446 TTAATATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TTAATTATAAAAATATATTAATA
Found at i:2534629 original size:33 final size:32
Alignment explanation
Indices: 2534592--2534668 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 32
2534582 TTAATTTGAT
2534592 TATAAATATAATTTGACATATA-TAATTATATAA
1 TATAAATATAA-TTGACATATATTAA-TATATAA
* *
2534625 TATAAAAATAATTGATATATATTTAATATATAA
1 TATAAATATAATTGACATATA-TTAATATATAA
*
2534658 TAAAAATATAA
1 TATAAATATAA
2534669 AATTATATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
32 9 0.24
33 26 0.68
34 3 0.08
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (32 bp):
TATAAATATAATTGACATATATTAATATATAA
Found at i:2534675 original size:54 final size:54
Alignment explanation
Indices: 2534609--2534732 Score: 187
Period size: 54 Copynumber: 2.3 Consensus size: 54
2534599 ATAATTTGAC
* * *
2534609 ATATATAATTATATAATATAAAAAT-AATTGATATATATTTAATATATAATAAAA
1 ATATAAAATTATATAATA-AAAAATAAAATAATATATATTTAATATATAATAAAA
**
2534663 ATATAAAATTATATTTTAAAAAATAAAATAATATATATTTAATATATAATAAAA
1 ATATAAAATTATATAATAAAAAATAAAATAATATATATTTAATATATAATAAAA
2534717 ATATAAAATTATATAA
1 ATATAAAATTATATAA
2534733 AATTATATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
53 6 0.10
54 56 0.90
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.40
Consensus pattern (54 bp):
ATATAAAATTATATAATAAAAAATAAAATAATATATATTTAATATATAATAAAA
Found at i:2534676 original size:32 final size:32
Alignment explanation
Indices: 2534640--2534731 Score: 114
Period size: 32 Copynumber: 3.2 Consensus size: 32
2534630 AAATAATTGA
2534640 TATATATTTAATATATAATAAAAATATAAAAT
1 TATATATTTAATATATAATAAAAATATAAAAT
2534672 TATAT-TTTAA-A-A-AAT--AAA-AT--AA-
1 TATATATTTAATATATAATAAAAATATAAAAT
2534694 TATATATTTAATATATAATAAAAATATAAAAT
1 TATATATTTAATATATAATAAAAATATAAAAT
2534726 TATATA
1 TATATA
2534732 AAATTATATT
Statistics
Matches: 50, Mismatches: 0, Indels: 20
0.71 0.00 0.29
Matches are distributed among these distances:
22 5 0.10
23 7 0.14
24 1 0.02
25 3 0.06
26 6 0.12
28 6 0.12
29 3 0.06
30 1 0.02
31 7 0.14
32 11 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (32 bp):
TATATATTTAATATATAATAAAAATATAAAAT
Found at i:2534683 original size:20 final size:20
Alignment explanation
Indices: 2534660--2534769 Score: 80
Period size: 20 Copynumber: 5.2 Consensus size: 20
2534650 ATATATAATA
2534660 AAAATATAAAATTATATTTT
1 AAAATATAAAATTATATTTT
*
2534680 AAAAAATAAAATAATATATATTT
1 AAAATATAAAAT--TATAT-TTT
* * * *
2534703 AATATATAATAA--AAATATA
1 AAAATATAA-AATTATATTTT
2534722 AAATTATATAAAATTATATTTT
1 AAA--ATATAAAATTATATTTT
* *
2534744 AAAAAATAAAATAATACTTTT
1 AAAATATAAAATTATA-TTTT
2534765 AAAAT
1 AAAAT
2534770 GGTGAAATAA
Statistics
Matches: 68, Mismatches: 13, Indels: 17
0.69 0.13 0.17
Matches are distributed among these distances:
19 3 0.04
20 27 0.40
21 14 0.21
22 12 0.18
23 10 0.15
24 2 0.03
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAATATAAAATTATATTTT
Found at i:2534684 original size:22 final size:24
Alignment explanation
Indices: 2534659--2534702 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
2534649 AATATATAAT
*
2534659 AAAAATATAA-AAT-TATATTTTA
1 AAAAATAAAATAATATATATTTTA
2534681 AAAAATAAAATAATATATATTT
1 AAAAATAAAATAATATATATTT
2534703 AATATATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 3 0.16
24 7 0.37
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
AAAAATAAAATAATATATATTTTA
Found at i:2534969 original size:16 final size:15
Alignment explanation
Indices: 2534948--2534977 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2534938 AATAAAATAA
2534948 AATAATATAATTTATT
1 AATAATAT-ATTTATT
2534964 AATAATATATTTAT
1 AATAATATATTTAT
2534978 ATATTTTTAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AATAATATATTTATT
Found at i:2537243 original size:14 final size:15
Alignment explanation
Indices: 2537226--2537255 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2537216 AAATATTAAA
2537226 ATTAAA-ATTTTTTT
1 ATTAAATATTTTTTT
2537240 ATTAAATATTTTTTT
1 ATTAAATATTTTTTT
2537255 A
1 A
2537256 CGAATTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTAAATATTTTTTT
Found at i:2541810 original size:2 final size:2
Alignment explanation
Indices: 2541803--2541834 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2541793 ACTTTCCTGC
2541803 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2541835 TATTTTAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2546242 original size:6 final size:6
Alignment explanation
Indices: 2546231--2546256 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2546221 TCTGCTTTAT
2546231 GTGTCA GTGTCA GTGTCA GTGTCA GT
1 GTGTCA GTGTCA GTGTCA GTGTCA GT
2546257 TCTCAACTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.35, T:0.35
Consensus pattern (6 bp):
GTGTCA
Found at i:2548437 original size:9 final size:9
Alignment explanation
Indices: 2548423--2548470 Score: 60
Period size: 9 Copynumber: 5.0 Consensus size: 9
2548413 GTGGCTGAAG
2548423 CTCTTCCTC
1 CTCTTCCTC
2548432 CTCTTCATCCTC
1 CTC-T--TCCTC
2548444 CTCTTCCTC
1 CTCTTCCTC
*
2548453 TTCTTCCTC
1 CTCTTCCTC
2548462 CTCTTCCTC
1 CTCTTCCTC
2548471 ACCATCATCG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 24 0.71
10 1 0.03
11 1 0.03
12 8 0.24
ACGTcount: A:0.02, C:0.52, G:0.00, T:0.46
Consensus pattern (9 bp):
CTCTTCCTC
Found at i:2548453 original size:18 final size:18
Alignment explanation
Indices: 2548430--2548470 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
2548420 AAGCTCTTCC
2548430 TCCTCTTCATCCTCCTCT
1 TCCTCTTCATCCTCCTCT
*
2548448 TCCTCTTCTTCCTCCTCT
1 TCCTCTTCATCCTCCTCT
2548466 TCCTC
1 TCCTC
2548471 ACCATCATCG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.02, C:0.51, G:0.00, T:0.46
Consensus pattern (18 bp):
TCCTCTTCATCCTCCTCT
Found at i:2548511 original size:9 final size:9
Alignment explanation
Indices: 2548430--2548515 Score: 57
Period size: 9 Copynumber: 9.6 Consensus size: 9
2548420 AAGCTCTTCC
*
2548430 TCCTCTTCA
1 TCCTCCTCA
*
2548439 TCCTCCTCT
1 TCCTCCTCA
* *
2548448 TCCTCTTCT
1 TCCTCCTCA
*
2548457 TCCTCCTCT
1 TCCTCCTCA
2548466 TCCTCAC-CA
1 TCCTC-CTCA
* *
2548475 TCATCGTCA
1 TCCTCCTCA
* *
2548484 TCATCGTCA
1 TCCTCCTCA
* *
2548493 TCATCATCA
1 TCCTCCTCA
2548502 TCCTCCTCA
1 TCCTCCTCA
2548511 TCCTC
1 TCCTC
2548516 ATCTCCACTG
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
9 64 0.98
10 1 0.02
ACGTcount: A:0.13, C:0.47, G:0.02, T:0.38
Consensus pattern (9 bp):
TCCTCCTCA
Found at i:2558379 original size:2 final size:2
Alignment explanation
Indices: 2558372--2558420 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
2558362 CAGCAGGTTG
2558372 CT CT 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 CT CT
2558414 CT CT CT C
1 CT CT CT C
2558421 ACACACACAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:2558837 original size:31 final size:33
Alignment explanation
Indices: 2558781--2558841 Score: 99
Period size: 31 Copynumber: 1.9 Consensus size: 33
2558771 AAAAATACAA
2558781 ATATAATATAAATATATCAATATATCAAAATTT
1 ATATAATATAAATATATCAATATATCAAAATTT
*
2558814 ATATAA-ATAAAT-TATTAATATATCAAAA
1 ATATAATATAAATATATCAATATATCAAAA
2558842 AATTTTATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 15 0.56
32 6 0.22
33 6 0.22
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (33 bp):
ATATAATATAAATATATCAATATATCAAAATTT
Found at i:2563310 original size:17 final size:18
Alignment explanation
Indices: 2563290--2563328 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
2563280 TTTTAATTTT
2563290 TTTATAAA-ATTAAAATA
1 TTTATAAATATTAAAATA
*
2563307 TTTA-AAATATTAAAATT
1 TTTATAAATATTAAAATA
2563324 TTTAT
1 TTTAT
2563329 TTATAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTATAAATATTAAAATA
Found at i:2567825 original size:1 final size:1
Alignment explanation
Indices: 2567819--2567845 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
2567809 AGTAGAAGGG
2567819 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
2567846 GGAGGTTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2568098 original size:54 final size:53
Alignment explanation
Indices: 2567996--2568098 Score: 145
Period size: 54 Copynumber: 1.9 Consensus size: 53
2567986 ATATTTAAAT
* **
2567996 AAATTAAATTAAAATTAATCGATTTGATTAAATATATTATTTTTATTTTTTAC
1 AAATTAAATTAAAATTAATCAATTTGATTAAATATATTATTTGAATTTTTTAC
*
2568049 AAATTAAAATTAAAATTAATCAATTT-ATTAAATCTATTATTCTGAATTTT
1 AAATT-AAATTAAAATTAATCAATTTGATTAAATATATTATT-TGAATTTT
2568099 CACTCATATT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
53 19 0.43
54 25 0.57
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.49
Consensus pattern (53 bp):
AAATTAAATTAAAATTAATCAATTTGATTAAATATATTATTTGAATTTTTTAC
Found at i:2570906 original size:217 final size:217
Alignment explanation
Indices: 2570526--2570934 Score: 694
Period size: 217 Copynumber: 1.9 Consensus size: 217
2570516 ACAATCATGA
* **
2570526 AAATTTCTTGGTGCGGGGGAGAAAGAAAACAAAACATAAAAAAGGTGAAAGCCTCAATATGGGAA
1 AAATTTCTTGGTGCGAGGGAGAAAGAAAACAAAACATAAAAAAGGTGAAAGCCTCAATATAAGAA
* *
2570591 CAGAAATTCAGTGCAATTTTCCATGCATTACAAGCATTCTACAAGTTAAAGATATAATTTTGAAT
66 CAGAAATTCAGTGCAATTTTCCATGCATTACAAGCATTCTACAAGTTAAAGATATAACTTTCAAT
2570656 TTGATAACAAAATCAACTCATTCAACAATCAAAACCAAA-AAAGATGTATAGAGAATGCTTTTAT
131 TTGATAACAAAATCAACTCATTCAACAATCAAAA-CAAAGAAAGATGTATAGAGAATGCTTTTAT
2570720 AAATTTCTTGGTGTTAAAGATAT
195 AAATTTCTTGGTGTTAAAGATAT
* ***
2570743 AAATTTCTTGGTGTGAGGGAGAAAGAAAACAAATTTTAAAAAAGGTGAAAGCCTCAATATAAGAA
1 AAATTTCTTGGTGCGAGGGAGAAAGAAAACAAAACATAAAAAAGGTGAAAGCCTCAATATAAGAA
*
2570808 CAGAAATTCAGTGCAATTTTCCATGCATTACAAGCATTCTACAAGTTAAAGATGTAACTTTCAAT
66 CAGAAATTCAGTGCAATTTTCCATGCATTACAAGCATTCTACAAGTTAAAGATATAACTTTCAAT
* *
2570873 TTGATAACAAAATCAACTCATTCAACCATCAAAACAAAGGAAGATGTATAGAGAATGCTTTT
131 TTGATAACAAAATCAACTCATTCAACAATCAAAACAAAGAAAGATGTATAGAGAATGCTTTT
2570935 GCTTCTTAGA
Statistics
Matches: 179, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
216 4 0.02
217 175 0.98
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.27
Consensus pattern (217 bp):
AAATTTCTTGGTGCGAGGGAGAAAGAAAACAAAACATAAAAAAGGTGAAAGCCTCAATATAAGAA
CAGAAATTCAGTGCAATTTTCCATGCATTACAAGCATTCTACAAGTTAAAGATATAACTTTCAAT
TTGATAACAAAATCAACTCATTCAACAATCAAAACAAAGAAAGATGTATAGAGAATGCTTTTATA
AATTTCTTGGTGTTAAAGATAT
Found at i:2585119 original size:365 final size:365
Alignment explanation
Indices: 2584449--2585179 Score: 1462
Period size: 365 Copynumber: 2.0 Consensus size: 365
2584439 TCAACTGAAA
2584449 ATCTGATCAGTCAAAGTTAGCTAGTACACTAGCATAAAGGCTACATGTTGGGGCACAAAAATATG
1 ATCTGATCAGTCAAAGTTAGCTAGTACACTAGCATAAAGGCTACATGTTGGGGCACAAAAATATG
2584514 AAGATTGATCCTGGTAATTTCAAGAAATAAAACCAAAAAGGGAAAAGAACATGAAATGTAAAAAA
66 AAGATTGATCCTGGTAATTTCAAGAAATAAAACCAAAAAGGGAAAAGAACATGAAATGTAAAAAA
2584579 ATTAAAGAATTCAATGAAGATATATTTTCGGATAGAAGAAATATATTAATCATTCAGATTAGGAG
131 ATTAAAGAATTCAATGAAGATATATTTTCGGATAGAAGAAATATATTAATCATTCAGATTAGGAG
2584644 AAGTGTCCAACATTCCAATACTTTAGTGAAACTAAATCATATATAGTTTCAGAAGACAAGCAATA
196 AAGTGTCCAACATTCCAATACTTTAGTGAAACTAAATCATATATAGTTTCAGAAGACAAGCAATA
2584709 TGGTTCCTAAGAATTAACCATCCAAAACAATAACTTCCCAGAAAGAAAGAAAAGTGAGGGTAGGG
261 TGGTTCCTAAGAATTAACCATCCAAAACAATAACTTCCCAGAAAGAAAGAAAAGTGAGGGTAGGG
2584774 GGGAGATACCGAATATTCTGAAGAGAAGATGGCAGACTAT
326 GGGAGATACCGAATATTCTGAAGAGAAGATGGCAGACTAT
2584814 ATCTGATCAGTCAAAGTTAGCTAGTACACTAGCATAAAGGCTACATGTTGGGGCACAAAAATATG
1 ATCTGATCAGTCAAAGTTAGCTAGTACACTAGCATAAAGGCTACATGTTGGGGCACAAAAATATG
2584879 AAGATTGATCCTGGTAATTTCAAGAAATAAAACCAAAAAGGGAAAAGAACATGAAATGTAAAAAA
66 AAGATTGATCCTGGTAATTTCAAGAAATAAAACCAAAAAGGGAAAAGAACATGAAATGTAAAAAA
2584944 ATTAAAGAATTCAATGAAGATATATTTTCGGATAGAAGAAATATATTAATCATTCAGATTAGGAG
131 ATTAAAGAATTCAATGAAGATATATTTTCGGATAGAAGAAATATATTAATCATTCAGATTAGGAG
2585009 AAGTGTCCAACATTCCAATACTTTAGTGAAACTAAATCATATATAGTTTCAGAAGACAAGCAATA
196 AAGTGTCCAACATTCCAATACTTTAGTGAAACTAAATCATATATAGTTTCAGAAGACAAGCAATA
2585074 TGGTTCCTAAGAATTAACCATCCAAAACAATAACTTCCCAGAAAGAAAGAAAAGTGAGGGTAGGG
261 TGGTTCCTAAGAATTAACCATCCAAAACAATAACTTCCCAGAAAGAAAGAAAAGTGAGGGTAGGG
2585139 GGGAGATACCGAATATTCTGAAGAGAAGATGGCAGACTAT
326 GGGAGATACCGAATATTCTGAAGAGAAGATGGCAGACTAT
2585179 A
1 A
2585180 AGTGAAGTGC
Statistics
Matches: 366, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
365 366 1.00
ACGTcount: A:0.44, C:0.13, G:0.19, T:0.24
Consensus pattern (365 bp):
ATCTGATCAGTCAAAGTTAGCTAGTACACTAGCATAAAGGCTACATGTTGGGGCACAAAAATATG
AAGATTGATCCTGGTAATTTCAAGAAATAAAACCAAAAAGGGAAAAGAACATGAAATGTAAAAAA
ATTAAAGAATTCAATGAAGATATATTTTCGGATAGAAGAAATATATTAATCATTCAGATTAGGAG
AAGTGTCCAACATTCCAATACTTTAGTGAAACTAAATCATATATAGTTTCAGAAGACAAGCAATA
TGGTTCCTAAGAATTAACCATCCAAAACAATAACTTCCCAGAAAGAAAGAAAAGTGAGGGTAGGG
GGGAGATACCGAATATTCTGAAGAGAAGATGGCAGACTAT
Found at i:2586934 original size:10 final size:9
Alignment explanation
Indices: 2586909--2586981 Score: 55
Period size: 8 Copynumber: 8.0 Consensus size: 9
2586899 ATATTTATAT
2586909 TATAT-AAA
1 TATATAAAA
2586917 TATA-AAAA
1 TATATAAAA
2586925 TATATTAAAA
1 TATA-TAAAA
*
2586935 TTTATATAAA
1 TATATA-AAA
2586945 TATATAAAA
1 TATATAAAA
*
2586954 T-TTTAAATA
1 TATATAAA-A
2586963 TAATTATAAAA
1 T-A-TATAAAA
2586974 TATA-AAAA
1 TATATAAAA
2586982 AATAATAATA
Statistics
Matches: 53, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
8 20 0.38
9 10 0.19
10 16 0.30
11 2 0.04
12 5 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (9 bp):
TATATAAAA
Found at i:2586945 original size:20 final size:19
Alignment explanation
Indices: 2586917--2586989 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 19
2586907 ATTATATAAA
2586917 TATAAAAATATATTAAAATT
1 TATAAAAATATA-TAAAATT
*
2586937 TATATAAATATATAAAATT
1 TATAAAAATATATAAAATT
* *
2586956 T-TAAATATAATTATAAAATA
1 TATAAAAAT-A-TATAAAATT
*
2586976 TAAAAAAATA-ATAA
1 TATAAAAATATATAA
2586990 TAAATATATA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
18 9 0.20
19 9 0.20
20 21 0.48
21 5 0.11
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
TATAAAAATATATAAAATT
Found at i:2586946 original size:28 final size:28
Alignment explanation
Indices: 2586904--2586981 Score: 99
Period size: 28 Copynumber: 2.8 Consensus size: 28
2586894 CTGAAATATT
2586904 TATATTATATAAATATAAAAATATATTAAA
1 TATATTATATAAATATAAAAAT-T-TTAAA
2586934 -AT-TTATATAAATATATAAAATTTTAAA
1 TATATTATATAAATATA-AAAATTTTAAA
2586961 TATAATTATA-AAATATAAAAA
1 TAT-ATTATATAAATATAAAAA
2586982 AATAATAATA
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
27 5 0.11
28 20 0.45
29 14 0.32
30 5 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (28 bp):
TATATTATATAAATATAAAAATTTTAAA
Found at i:2586950 original size:8 final size:8
Alignment explanation
Indices: 2586909--2587004 Score: 53
Period size: 8 Copynumber: 12.4 Consensus size: 8
2586899 ATATTTATAT
2586909 TATATAAA
1 TATATAAA
*
2586917 TATAAAAA
1 TATATAAA
2586925 TATATTAAAA
1 TATA-T-AAA
2586935 TTTATATAAA
1 --TATATAAA
2586945 TATATAAA
1 TATATAAA
* *
2586953 -ATTTTAA
1 TATATAAA
2586960 -ATAT-AA
1 TATATAAA
2586966 T-TATAAA
1 TATATAAA
2586973 -ATATAAA
1 TATATAAA
* *
2586980 AAAAT-AA
1 TATATAAA
2586987 TA-ATAAA
1 TATATAAA
*
2586994 TATATACA
1 TATATAAA
2587002 TAT
1 TAT
2587005 TATCAAATTT
Statistics
Matches: 70, Mismatches: 8, Indels: 20
0.71 0.08 0.20
Matches are distributed among these distances:
6 7 0.10
7 23 0.33
8 29 0.41
10 6 0.09
11 1 0.01
12 4 0.06
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (8 bp):
TATATAAA
Found at i:2591596 original size:18 final size:18
Alignment explanation
Indices: 2591569--2591611 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
2591559 CCAACTCCAC
*
2591569 TGAATTAATCACAAATGT
1 TGAATAAATCACAAATGT
2591587 TGAATAAATCACAAATGT
1 TGAATAAATCACAAATGT
*
2591605 TTAATAA
1 TGAATAA
2591612 GATAAATCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.33
Consensus pattern (18 bp):
TGAATAAATCACAAATGT
Found at i:2593009 original size:2 final size:2
Alignment explanation
Indices: 2593002--2593026 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2592992 CCATTTTCAT
2593002 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 T
2593027 TAACATTATC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2593730 original size:29 final size:28
Alignment explanation
Indices: 2593693--2593763 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 28
2593683 AAAACTATTT
*
2593693 TTTTAATAAAAATATAATAAATTAATTAAA
1 TTTT-ATAAAAAT-TAAAAAATTAATTAAA
* * *
2593723 TTTTATAAATATTAAAAAATTTATTTAA
1 TTTTATAAAAATTAAAAAATTAATTAAA
*
2593751 TTTTATTAAAATT
1 TTTTATAAAAATT
2593764 TATATTTTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 24 0.69
29 7 0.20
30 4 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
TTTTATAAAAATTAAAAAATTAATTAAA
Found at i:2594291 original size:34 final size:37
Alignment explanation
Indices: 2594251--2594332 Score: 109
Period size: 34 Copynumber: 2.3 Consensus size: 37
2594241 CTCATTAAAA
*
2594251 TTTTTAAAATAATAAT-AAAATAATTA-TTATA-ATT
1 TTTTTAAAATAATAATGAAAATAATTAGTTAAATATT
* *
2594285 TTTTTAAACT-TTAATGAAAATAATTAGTTAAATATT
1 TTTTTAAAATAATAATGAAAATAATTAGTTAAATATT
2594321 TTTTTAAAATAA
1 TTTTTAAAATAA
2594333 AAATTTAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
33 4 0.10
34 19 0.49
35 4 0.10
36 12 0.31
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (37 bp):
TTTTTAAAATAATAATGAAAATAATTAGTTAAATATT
Found at i:2594620 original size:22 final size:24
Alignment explanation
Indices: 2594577--2594639 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 24
2594567 TATTAAAAAA
2594577 TTAAATTAAAATTTATAT-AAATATTT
1 TTAAA-TAAAA-TTA-ATCAAATATTT
2594603 TT-AA-AAAATTAATCAAATATTT
1 TTAAATAAAATTAATCAAATATTT
2594625 TTAAATAAAATTAAT
1 TTAAATAAAATTAAT
2594640 TTTCAATCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
21 2 0.06
22 13 0.38
23 6 0.18
24 9 0.26
25 2 0.06
26 2 0.06
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
TTAAATAAAATTAATCAAATATTT
Found at i:2595793 original size:21 final size:21
Alignment explanation
Indices: 2595769--2595809 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2595759 AATAATTTTT
2595769 TATTTAAAT-TTAATTATAAAA
1 TATTTAAATATTAA-TATAAAA
2595790 TATTTAAATATTAATATAAA
1 TATTTAAATATTAATATAAA
2595810 TAATATCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TATTTAAATATTAATATAAAA
Found at i:2599986 original size:2 final size:2
Alignment explanation
Indices: 2599979--2600009 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2599969 AGCTGTTGAG
2599979 AT AT AT AT AT AT AT 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 A
2600010 GAAAACTTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2612311 original size:2 final size:2
Alignment explanation
Indices: 2612304--2612344 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2612294 TATGAACGAT
2612304 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2612345 AGAAGAAGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2613620 original size:25 final size:26
Alignment explanation
Indices: 2613575--2613660 Score: 70
Period size: 25 Copynumber: 3.4 Consensus size: 26
2613565 AATTTATATT
* * *
2613575 AAATTAATATTTATTTGAAA-TACTA
1 AAATTAAAATTTATGTCAAATTACTA
*
2613600 AAATTAAAATTTATGTCAAATTATTA
1 AAATTAAAATTTATGTCAAATTACTA
* * * *
2613626 AAA-T-ATATTAATGTATAAATTAATA
1 AAATTAAAATTTATGT-CAAATTACTA
2613651 AAATTAAAAT
1 AAATTAAAAT
2613661 GAGCAAAATA
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
24 8 0.17
25 29 0.60
26 8 0.17
27 3 0.06
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.41
Consensus pattern (26 bp):
AAATTAAAATTTATGTCAAATTACTA
Found at i:2613707 original size:13 final size:14
Alignment explanation
Indices: 2613686--2613715 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2613676 ATAGAATTGG
*
2613686 TATTTTTAAAATAA
1 TATTTTAAAAATAA
2613700 TATTTTAAAAATAA
1 TATTTTAAAAATAA
2613714 TA
1 TA
2613716 ATAATAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TATTTTAAAAATAA
Found at i:2613910 original size:21 final size:21
Alignment explanation
Indices: 2613886--2613940 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
2613876 TTAAATATTC
2613886 TTAATATTATTATTATTTTAA
1 TTAATATTATTATTATTTTAA
* *
2613907 TTAAT-TTTTTATATTTTTTAA
1 TTAATATTATTAT-TATTTTAA
*
2613928 TTAA-ATTAATATT
1 TTAATATTATTATT
2613941 TGATTAATTC
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
20 7 0.25
21 21 0.75
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TTAATATTATTATTATTTTAA
Found at i:2614021 original size:19 final size:20
Alignment explanation
Indices: 2613999--2614044 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
2613989 GATAATAATT
2613999 TAAAAAATTAATA-AAA-TAA
1 TAAAAAA-TAATACAAATTAA
2614018 TAAACAAATAATACAAATTAA
1 TAAA-AAATAATACAAATTAA
2614039 -AAAAAA
1 TAAAAAA
2614045 AAGATAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
19 12 0.50
20 9 0.38
21 3 0.12
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (20 bp):
TAAAAAATAATACAAATTAA
Found at i:2614409 original size:3 final size:3
Alignment explanation
Indices: 2614396--2614430 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
2614386 ATTCTATGTC
2614396 ATT ATT AATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT A
2614431 GATATAAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:2616193 original size:10 final size:11
Alignment explanation
Indices: 2616180--2616216 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
2616170 TATAATACGA
2616180 TATAAAAA-AT
1 TATAAAAATAT
2616190 TATAAAAATAT
1 TATAAAAATAT
*
2616201 AATAAAAATA-
1 TATAAAAATAT
2616211 TATAAA
1 TATAAA
2616217 CGAATTAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 13 0.54
11 11 0.46
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
TATAAAAATAT
Found at i:2616205 original size:11 final size:10
Alignment explanation
Indices: 2616179--2616216 Score: 53
Period size: 11 Copynumber: 3.9 Consensus size: 10
2616169 ATATAATACG
2616179 ATATA-AAAA
1 ATATATAAAA
2616188 AT-TATAAAA
1 ATATATAAAA
2616197 ATATAATAAAA
1 ATAT-ATAAAA
2616208 ATATATAAA
1 ATATATAAA
2616217 CGAATTAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
8 2 0.08
9 8 0.31
10 6 0.23
11 10 0.38
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
ATATATAAAA
Found at i:2619413 original size:20 final size:21
Alignment explanation
Indices: 2619384--2619425 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
2619374 AATCAATTTA
2619384 ATTAAATTTTAAAT-TTTTTT
1 ATTAAATTTTAAATATTTTTT
* *
2619404 ATTAATTTTTTAATATTTTTT
1 ATTAAATTTTAAATATTTTTT
2619425 A
1 A
2619426 AAATATCTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
ATTAAATTTTAAATATTTTTT
Found at i:2621149 original size:13 final size:14
Alignment explanation
Indices: 2621125--2621154 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2621115 ATTATAAAAT
2621125 ATATTAAAAAATTA
1 ATATTAAAAAATTA
*
2621139 ATATTAAAAATTTA
1 ATATTAAAAAATTA
2621153 AT
1 AT
2621155 CAATCGAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
ATATTAAAAAATTA
Found at i:2621866 original size:42 final size:43
Alignment explanation
Indices: 2621782--2621866 Score: 100
Period size: 42 Copynumber: 2.0 Consensus size: 43
2621772 TTTAAGATCA
*
2621782 CATGATCAAATCACCACAAATTAACTACAAAAACATATCAAAC
1 CATGATCAAATCACCACAAATTAACTACAAAAACATACCAAAC
* ** ** *
2621825 CATGATCAAATTACC-GTAATTAACTTTAAAAACATGCCAAAC
1 CATGATCAAATCACCACAAATTAACTACAAAAACATACCAAAC
2621867 ATTATCTTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
42 21 0.60
43 14 0.40
ACGTcount: A:0.49, C:0.24, G:0.05, T:0.22
Consensus pattern (43 bp):
CATGATCAAATCACCACAAATTAACTACAAAAACATACCAAAC
Found at i:2623495 original size:2 final size:2
Alignment explanation
Indices: 2623488--2623512 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2623478 ACTAAATGCC
2623488 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2623513 AAATTATGTC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2644062 original size:11 final size:12
Alignment explanation
Indices: 2644041--2644069 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
2644031 AAGATGCTAG
2644041 CTTTTTCCTTTT
1 CTTTTTCCTTTT
2644053 CTTTTT-CTTTT
1 CTTTTTCCTTTT
2644064 CTTTTT
1 CTTTTT
2644070 ATTTCATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (12 bp):
CTTTTTCCTTTT
Found at i:2644453 original size:30 final size:32
Alignment explanation
Indices: 2644400--2644460 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
2644390 ATAAATTAAA
*
2644400 TTAAAAAAATGAAACTAATAATT-AATATATT
1 TTAAAAAAATGAAACAAATAATTAAATATATT
2644431 TTAAAAAAAT-AAA-AAATAAATTAAATATAT
1 TTAAAAAAATGAAACAAAT-AATTAAATATAT
2644461 ATATAATTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
29 3 0.11
30 7 0.26
31 17 0.63
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (32 bp):
TTAAAAAAATGAAACAAATAATTAAATATATT
Found at i:2645988 original size:19 final size:17
Alignment explanation
Indices: 2645964--2646020 Score: 61
Period size: 13 Copynumber: 3.5 Consensus size: 17
2645954 CAATACGTTG
2645964 TTAAAAAATTATTTAATAT
1 TTAAAAAA-TATTTAA-AT
2645983 TTAAAAAAT-TTTAAA-
1 TTAAAAAATATTTAAAT
2645998 -T-AAAAATA-TTAAAT
1 TTAAAAAATATTTAAAT
2646012 TTAAAAAAT
1 TTAAAAAAT
2646021 TTATTTTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.32
14 1 0.03
15 1 0.03
16 7 0.21
17 5 0.15
18 1 0.03
19 8 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TTAAAAAATATTTAAAT
Found at i:2645999 original size:18 final size:19
Alignment explanation
Indices: 2645964--2645999 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2645954 CAATACGTTG
*
2645964 TTAAAAAATTATTTAATAT
1 TTAAAAAATTATTAAATAT
2645983 TTAAAAAATT-TTAAATA
1 TTAAAAAATTATTAAATA
2646000 AAAATATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TTAAAAAATTATTAAATAT
Found at i:2646254 original size:18 final size:17
Alignment explanation
Indices: 2646231--2646268 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
2646221 ATTCAATACA
*
2646231 AAATTTTATTTATATTTT
1 AAATTTAATTTA-ATTTT
2646249 AAATTTAATTTAATTTT
1 AAATTTAATTTAATTTT
2646266 AAA
1 AAA
2646269 AATTATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
AAATTTAATTTAATTTT
Found at i:2646425 original size:2 final size:2
Alignment explanation
Indices: 2646420--2646445 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2646410 CAAAAAAATA
2646420 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
2646446 TGGTTTTGAT
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:2646850 original size:2 final size:2
Alignment explanation
Indices: 2646845--2646869 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2646835 ATTTTCATCA
2646845 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2646870 AAGAAAAGAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.