Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001981.1 Hibiscus syriacus cultivar Beakdansim tig00004035_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1059896
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 5
Found at i:419021 original size:66 final size:63
Alignment explanation
Indices: 418856--419056 Score: 226
Period size: 64 Copynumber: 3.1 Consensus size: 63
418846 TATATATTTT
* * *
418856 TTATATACTTAAATATTTTATATTATATACTTATATACTTTATTCTTTATAATTATACTTTATA
1 TTATATACTTATATACTTTATATTAT-TACTTATATACTTTATTCTTAATAATTATACTTTATA
* * *
418920 TT-TAATACTTATATACTTTATATTATTATTATATATACTTTATAT-TTAATACTTATGTATTTT
1 TTAT-ATACTTATATACTTTATATTATTACT-TATATACTTTAT-TCTTAATAATTA--TACTTT
418983 ATA
61 ATA
* * * *
418986 TTATATAGTTATATACTTTATATTATGTGCTTATATACTTTAGTCTTTATAATTATACTTTATA
1 TTATATACTTATATACTTTATATTAT-TACTTATATACTTTATTCTTAATAATTATACTTTATA
*
419050 ATATATA
1 TTATATA
419057 TATACATACA
Statistics
Matches: 115, Mismatches: 14, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
63 4 0.03
64 56 0.49
65 2 0.02
66 50 0.43
67 3 0.03
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.56
Consensus pattern (63 bp):
TTATATACTTATATACTTTATATTATTACTTATATACTTTATTCTTAATAATTATACTTTATA
Found at i:419161 original size:21 final size:21
Alignment explanation
Indices: 419128--419177 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
419118 TATATATGTA
419128 TATATACTTTA--TATATA--
1 TATATACTTTATGTATATACT
*
419145 TATATAGTTTATGTATATACT
1 TATATACTTTATGTATATACT
419166 TATATACTTTAT
1 TATATACTTTAT
419178 ATTTAAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 10 0.37
19 6 0.22
21 11 0.41
ACGTcount: A:0.36, C:0.06, G:0.04, T:0.54
Consensus pattern (21 bp):
TATATACTTTATGTATATACT
Found at i:419227 original size:11 final size:11
Alignment explanation
Indices: 419195--419294 Score: 52
Period size: 11 Copynumber: 9.7 Consensus size: 11
419185 CTATATAAAC
419195 TATATAATTTA
1 TATATAATTTA
* *
419206 TACAT-A-GTA
1 TATATAATTTA
419215 TATATAATTTA
1 TATATAATTTA
* **
419226 TA-ATTATACA
1 TATATAATTTA
*
419236 TA-AT-ATATA
1 TATATAATTTA
** *
419245 TATATAAGATG
1 TATATAATTTA
419256 TATAT-ATTTA
1 TATATAATTTA
* *
419266 AATATAATTCA
1 TATATAATTTA
419277 TATATAATTTA
1 TATATAATTTA
419288 TAT-TAAT
1 TATATAAT
419295 AAACTATATA
Statistics
Matches: 67, Mismatches: 17, Indels: 11
0.71 0.18 0.12
Matches are distributed among these distances:
9 12 0.18
10 23 0.34
11 32 0.48
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (11 bp):
TATATAATTTA
Found at i:419259 original size:26 final size:26
Alignment explanation
Indices: 419186--419250 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 26
419176 ATATTTAAAC
*
419186 TATATA-AACTATATAATTTATACATAG
1 TATATATAA-TATATAA-TTATACATAA
*
419213 TATATATAATTTATAATTATACATAA
1 TATATATAATATATAATTATACATAA
419239 TATATAT-ATATA
1 TATATATAATATA
419251 AGATGTATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 4 0.12
26 16 0.47
27 12 0.35
28 2 0.06
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.45
Consensus pattern (26 bp):
TATATATAATATATAATTATACATAA
Found at i:419262 original size:2 final size:2
Alignment explanation
Indices: 419118--419250 Score: 53
Period size: 2 Copynumber: 66.0 Consensus size: 2
419108 TTTATATGAT
* * * *
419118 TA TA TA TG TA TA TA TA CTT TA TA TA TA TA TA TA GTT TA TG TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA
* * * * *
419162 TA CT- TA TA TA CTT TA TA TT TA AA CTA TA TA AA CTA TA TA -A TT
1 TA -TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA
* * *
419204 TA TA CA TA GTA TA TA TA -A TT TA TA -A T- TA TA CA TA -A TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
419243 TA TA TA TA
1 TA TA TA TA
419251 AGATGTATAT
Statistics
Matches: 94, Mismatches: 24, Indels: 26
0.65 0.17 0.18
Matches are distributed among these distances:
1 6 0.06
2 80 0.85
3 8 0.09
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:419396 original size:2 final size:2
Alignment explanation
Indices: 419389--419679 Score: 155
Period size: 2 Copynumber: 147.0 Consensus size: 2
419379 GTGTATAGTT
* * *
419389 TA TA TA TA GTA TA TA -A TA -A TA TA AA TA TA AA CTA TA TA GTT
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA
* * *
419430 TA TA TA TA TA GTT TA TA TA TA TA TA TA TA TA CTT TA TA AA TA T-
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* * *
419473 TA TA TA -A TT TA TA TA -A TA -A TT TA TA T- TA -A TA AA CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * *
419511 TA GTT TA TA AA TA -A TA TA TA TA -A TT TA TA TA TA GTA TA TA -A
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
* * * *
419552 TA -A TG TA AA TA TA AA CTA TA TA GTT TA TA TA TA TA -A 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
* * * **
419594 TA CTT TA TA TA TA AA CTA TA -A TT TA TA TA TA -A TA TA TA TA GG
1 TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
419636 TGA TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
419678 TA
1 TA
419680 ATTGTTTCAA
Statistics
Matches: 216, Mismatches: 44, Indels: 58
0.68 0.14 0.18
Matches are distributed among these distances:
1 16 0.07
2 185 0.86
3 15 0.07
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (2 bp):
TA
Found at i:419434 original size:41 final size:40
Alignment explanation
Indices: 419382--419543 Score: 130
Period size: 41 Copynumber: 3.9 Consensus size: 40
419372 ATAATATGTG
419382 TATAGTTTATATATAGTATATAATAATATAAATATAAACTA
1 TATAGTTTATATATA-TATATAATAATATAAATATAAACTA
* * * *
419423 TATAGTTTATATATATAGT-TTATATATATATATATATACTT
1 TATAGTTTATATATATA-TATAATA-ATATAAATATAAACTA
* * * *
419464 TATAAATATTATATAATTTATATAATAATTTATATTAATAAACTA
1 TAT-AGT-TTATAT-ATATATATAATAATATA-AAT-ATAAACTA
* * *
419509 TATAGTTTATAAATA-ATATATATAATTTATATATA
1 TATAGTTTATATATATATATA-ATAATATAAATATA
419544 GTATATAATA
Statistics
Matches: 95, Mismatches: 17, Indels: 19
0.73 0.13 0.15
Matches are distributed among these distances:
40 9 0.09
41 38 0.40
42 12 0.13
43 16 0.17
44 11 0.12
45 9 0.09
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.48
Consensus pattern (40 bp):
TATAGTTTATATATATATATAATAATATAAATATAAACTA
Found at i:419467 original size:9 final size:9
Alignment explanation
Indices: 419434--419541 Score: 55
Period size: 9 Copynumber: 11.7 Consensus size: 9
419424 ATAGTTTATA
*
419434 TATATAGTT
1 TATATAATT
419443 TATATATATAT
1 TATATA-AT-T
*
419454 ATATATACTT
1 -TATATAATT
419464 TATA-AATAT
1 TATATAAT-T
419473 TATATAATT
1 TATATAATT
419482 TATATAATAAT
1 TATATAAT--T
419493 T-TAT-A-T
1 TATATAATT
**
419499 TA-ATAAAC
1 TATATAATT
*
419507 TATATAGTT
1 TATATAATT
*
419516 TATAAATAATA
1 TAT--ATAATT
419527 TATATAATT
1 TATATAATT
419536 TATATA
1 TATATA
419542 TAGTATATAA
Statistics
Matches: 76, Mismatches: 10, Indels: 26
0.68 0.09 0.23
Matches are distributed among these distances:
6 4 0.05
7 1 0.01
8 4 0.05
9 42 0.55
10 8 0.11
11 11 0.14
12 6 0.08
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (9 bp):
TATATAATT
Found at i:419467 original size:13 final size:13
Alignment explanation
Indices: 419421--419452 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
419411 AAATATAAAC
419421 TATATAGTTTATA
1 TATATAGTTTATA
419434 TATATAGTTTATA
1 TATATAGTTTATA
419447 TATATA
1 TATATA
419453 TATATATACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (13 bp):
TATATAGTTTATA
Found at i:419550 original size:63 final size:63
Alignment explanation
Indices: 419443--419674 Score: 198
Period size: 63 Copynumber: 3.7 Consensus size: 63
419433 ATATATAGTT
* * * * * *
419443 TATATA-TATATATATATACTTTATA-AATATTATATA-ATTTATATAATAATTTATATTAATAA
1 TATATAGTTTATATATATAATATATATAAT-TTATATATA-GTATATAATAATGTA-AAT-ATAA
419505 AC
62 AC
419507 TATATAGTTTATA-A-ATAATATATATAATTTATATATAGTATATAATAATGTAAATATAAAC
1 TATATAGTTTATATATATAATATATATAATTTATATATAGTATATAATAATGTAAATATAAAC
* * *
419568 TATATAGTTTATATATATAATATATATACTTTATATATA--A-ACT-ATAATTTATATATAATA-
1 TATATAGTTTATATATATAATATATATAATTTATATATAGTATA-TAATAATGTAAATATAA-AC
* * * *
419628 TATATAGGTGATATATATGTATATATATATATATATATATA-TATATA
1 TATATAGTTTATATATAT-AATATATATA-ATTTATATATAGTATATA
419675 TTATAATTGT
Statistics
Matches: 142, Mismatches: 14, Indels: 24
0.79 0.08 0.13
Matches are distributed among these distances:
60 30 0.21
61 31 0.22
62 12 0.08
63 52 0.37
64 12 0.08
65 5 0.04
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (63 bp):
TATATAGTTTATATATATAATATATATAATTTATATATAGTATATAATAATGTAAATATAAAC
Found at i:419613 original size:11 final size:10
Alignment explanation
Indices: 419516--419674 Score: 58
Period size: 11 Copynumber: 15.4 Consensus size: 10
419506 CTATATAGTT
419516 TATAAATAATA
1 TATAAAT-ATA
*
419527 TATATAATTTA
1 TATA-AATATA
*
419538 TATATAGTATA
1 TATA-AATATA
* *
419549 TAATAATGTAAA
1 T-ATAA-ATATA
419561 TATAAACTATA
1 TATAAA-TATA
**
419572 TAGTTTATATA
1 TA-TAAATATA
419583 TAT-AATATA
1 TATAAATATA
**
419592 TATACTTTATA
1 TATA-AATATA
419603 TATAAACTATA
1 TATAAA-TATA
*
419614 -AT--TTATA
1 TATAAATATA
419621 TAT-AATATA
1 TATAAATATA
**
419630 TATAGGTGATA
1 TATAAAT-ATA
**
419641 TATATGTATA
1 TATAAATATA
*
419651 TATATATATA
1 TATAAATATA
*
419661 TATATATATA
1 TATAAATATA
419671 TATA
1 TATA
419675 TTATAATTGT
Statistics
Matches: 117, Mismatches: 19, Indels: 25
0.73 0.12 0.16
Matches are distributed among these distances:
7 4 0.03
8 2 0.02
9 15 0.13
10 30 0.26
11 53 0.45
12 13 0.11
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.45
Consensus pattern (10 bp):
TATAAATATA
Found at i:435170 original size:19 final size:19
Alignment explanation
Indices: 435112--435170 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
435102 AAGAGAAATC
435112 TTTTTACTA-TTTTA-AATT
1 TTTTTA-TATTTTTATAATT
* * *
435130 ATTTTTA-ATTTATCTAAAT
1 -TTTTTATATTTTTATAATT
435149 TTTTTATATTTTTATAATT
1 TTTTTATATTTTTATAATT
435168 TTT
1 TTT
435171 AATAATTATG
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
17 1 0.03
18 9 0.29
19 21 0.68
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTTATATTTTTATAATT
Found at i:435802 original size:21 final size:20
Alignment explanation
Indices: 435773--435857 Score: 116
Period size: 21 Copynumber: 4.2 Consensus size: 20
435763 TATATATATC
*
435773 TAATAGCACTATAGATAAAA
1 TAATAGCACTATAAATAAAA
435793 TAATAAGCACTATAAATAAAA
1 TAAT-AGCACTATAAATAAAA
**
435814 TAATAAGCACTATAAATATTA
1 TAAT-AGCACTATAAATAAAA
*
435835 TAATAGCACTAAAAATAAAA
1 TAATAGCACTATAAATAAAA
435855 TAA
1 TAA
435858 AATGAAGTGG
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
20 20 0.34
21 38 0.66
ACGTcount: A:0.59, C:0.09, G:0.06, T:0.26
Consensus pattern (20 bp):
TAATAGCACTATAAATAAAA
Found at i:435843 original size:41 final size:41
Alignment explanation
Indices: 435773--435857 Score: 118
Period size: 41 Copynumber: 2.1 Consensus size: 41
435763 TATATATATC
* *
435773 TAATAGCACTATAGATAAAATAATAAGCACTATAAATAAAA
1 TAATAGCACTATAAATAAAATAATAAGCACTAAAAATAAAA
**
435814 TAATAAGCACTATAAATATTATAAT-AGCACTAAAAATAAAA
1 TAAT-AGCACTATAAATAAAATAATAAGCACTAAAAATAAAA
435855 TAA
1 TAA
435858 AATGAAGTGG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
41 22 0.56
42 17 0.44
ACGTcount: A:0.59, C:0.09, G:0.06, T:0.26
Consensus pattern (41 bp):
TAATAGCACTATAAATAAAATAATAAGCACTAAAAATAAAA
Found at i:436385 original size:29 final size:29
Alignment explanation
Indices: 436352--436468 Score: 126
Period size: 29 Copynumber: 4.0 Consensus size: 29
436342 TTTCGGTTAT
436352 GGTGTTATTTTCGTAATTATTTTTAAAAG
1 GGTGTTATTTTCGTAATTATTTTTAAAAG
* * *
436381 TGTGTTATTTTTGTATTTATTTTTAAAAAAG
1 GGTGTTATTTTCGTAATTATTTTT--AAAAG
* *
436412 GGTGTTATTTTCGTAATTAATTTTAAAAC
1 GGTGTTATTTTCGTAATTATTTTTAAAAG
* * * * *
436441 GATGATATTTTGGCAATTATTGTTAAAA
1 GGTGTTATTTTCGTAATTATTTTTAAAA
436469 CAGTGATAAT
Statistics
Matches: 72, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
29 47 0.65
31 25 0.35
ACGTcount: A:0.31, C:0.03, G:0.15, T:0.50
Consensus pattern (29 bp):
GGTGTTATTTTCGTAATTATTTTTAAAAG
Found at i:436417 original size:31 final size:31
Alignment explanation
Indices: 436352--436439 Score: 126
Period size: 31 Copynumber: 2.9 Consensus size: 31
436342 TTTCGGTTAT
436352 GGTGTTATTTTCGTAATTATTTTT--AAAAG
1 GGTGTTATTTTCGTAATTATTTTTAAAAAAG
* * *
436381 TGTGTTATTTTTGTATTTATTTTTAAAAAAG
1 GGTGTTATTTTCGTAATTATTTTTAAAAAAG
*
436412 GGTGTTATTTTCGTAATTAATTTTAAAA
1 GGTGTTATTTTCGTAATTATTTTTAAAA
436440 CGATGATATT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 21 0.42
31 29 0.58
ACGTcount: A:0.30, C:0.02, G:0.15, T:0.53
Consensus pattern (31 bp):
GGTGTTATTTTCGTAATTATTTTTAAAAAAG
Found at i:436461 original size:60 final size:60
Alignment explanation
Indices: 436352--436468 Score: 155
Period size: 60 Copynumber: 1.9 Consensus size: 60
436342 TTTCGGTTAT
* * * * * * *
436352 GGTGTTATTTTCGTAATTATTTTTAAAAGTGTGTTATTTTTGTATTTATTTTTAAAAAAG
1 GGTGTTATTTTCGTAATTAATTTTAAAAGTATGATATTTTGGCAATTATTGTTAAAAAAG
436412 GGTGTTATTTTCGTAATTAATTTTAAAACG-ATGATATTTTGGCAATTATTGTTAAAA
1 GGTGTTATTTTCGTAATTAATTTTAAAA-GTATGATATTTTGGCAATTATTGTTAAAA
436469 CAGTGATAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
60 48 0.98
61 1 0.02
ACGTcount: A:0.31, C:0.03, G:0.15, T:0.50
Consensus pattern (60 bp):
GGTGTTATTTTCGTAATTAATTTTAAAAGTATGATATTTTGGCAATTATTGTTAAAAAAG
Found at i:436469 original size:29 final size:29
Alignment explanation
Indices: 436357--436487 Score: 95
Period size: 29 Copynumber: 4.4 Consensus size: 29
436347 GTTATGGTGT
* * ** *
436357 TATTTTCGTAATTATTTTTAAAAGTGTGT
1 TATTTTGGTAATTAATTTTAAAACAGTGA
* * * * *
436386 TATTTTTGTATTTATTTTTAAAAAAGGGTGT
1 TATTTTGGTAATTAATTTTAAAACA--GTGA
*
436417 TATTTTCGTAATTAATTTTAAAAC-GATGA
1 TATTTTGGTAATTAATTTTAAAACAG-TGA
*
436446 TATTTTGGCAATT-ATTGTTAAAACAGTGA
1 TATTTTGGTAATTAATT-TTAAAACAGTGA
*
436475 TAATTTGGTAATT
1 TATTTTGGTAATT
436488 GTTTAAAAAT
Statistics
Matches: 84, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
28 4 0.05
29 55 0.65
30 1 0.01
31 24 0.29
ACGTcount: A:0.32, C:0.04, G:0.15, T:0.50
Consensus pattern (29 bp):
TATTTTGGTAATTAATTTTAAAACAGTGA
Found at i:443141 original size:21 final size:20
Alignment explanation
Indices: 443113--443177 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 20
443103 TATATATATC
443113 TAAT-AGCACTATAAATAAAA
1 TAATAAGCACTA-AAATAAAA
443133 TAATAAGCACTACAAATAAAA
1 TAATAAGCACTA-AAATAAAA
443154 TAATAAGCACTAAGAATAAAA
1 TAATAAGCACTAA-AATAAAA
443175 TAA
1 TAA
443178 AATGAAGTGG
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
20 5 0.12
21 37 0.88
ACGTcount: A:0.62, C:0.11, G:0.06, T:0.22
Consensus pattern (20 bp):
TAATAAGCACTAAAATAAAA
Found at i:443762 original size:60 final size:59
Alignment explanation
Indices: 443693--443867 Score: 194
Period size: 60 Copynumber: 3.0 Consensus size: 59
443683 TTTCGGTTAT
* * *
443693 GGTGTTATTTTCGTAATTATTTTTAAAA-GTGTGTTATTTTCGTATTTATTTTTAAAAAA
1 GGTGTTATTTTCGTAATTATTTTTAAAACG-GTGATATTTTCGTAATTATTGTTAAAAAA
* * *
443752 GGGTGTTATTTTCGTAATTAATTTTAAAACGGTGATATTTTGGTAATTATTGTTAAAACA
1 -GGTGTTATTTTCGTAATTATTTTTAAAACGGTGATATTTTCGTAATTATTGTTAAAAAA
* * * * * *
443812 -GTGATATTTTGGTAATTATTGTTAAAACGATGCA-ATTTTGGTAAATATTGTTAAAA
1 GGTGTTATTTTCGTAATTATTTTTAAAACGGTG-ATATTTTCGTAATTATTGTTAAAA
443868 CAGTGATAAT
Statistics
Matches: 101, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
58 48 0.48
59 1 0.01
60 51 0.50
61 1 0.01
ACGTcount: A:0.32, C:0.04, G:0.17, T:0.47
Consensus pattern (59 bp):
GGTGTTATTTTCGTAATTATTTTTAAAACGGTGATATTTTCGTAATTATTGTTAAAAAA
Found at i:443839 original size:29 final size:29
Alignment explanation
Indices: 443698--443886 Score: 186
Period size: 29 Copynumber: 6.4 Consensus size: 29
443688 GTTATGGTGT
* * ** *
443698 TATTTTCGTAATTATTTTTAAAAGTGTGT
1 TATTTTGGTAATTATTGTTAAAACAGTGA
* * * * *
443727 TATTTTCGTATTTATTTTTAAAAAAGGGTGT
1 TATTTTGGTAATTATTGTTAAAACA--GTGA
* *
443758 TATTTTCGTAATTAATT-TTAAAACGGTGA
1 TATTTTGGTAATT-ATTGTTAAAACAGTGA
443787 TATTTTGGTAATTATTGTTAAAACAGTGA
1 TATTTTGGTAATTATTGTTAAAACAGTGA
443816 TATTTTGGTAATTATTGTTAAAAC-GATGCA
1 TATTTTGGTAATTATTGTTAAAACAG-TG-A
*
443846 -ATTTTGGTAAATATTGTTAAAACAGTGA
1 TATTTTGGTAATTATTGTTAAAACAGTGA
*
443874 TAATTTGGTAATT
1 TATTTTGGTAATT
443887 GTTTAAAAAA
Statistics
Matches: 140, Mismatches: 12, Indels: 16
0.83 0.07 0.10
Matches are distributed among these distances:
28 5 0.04
29 108 0.77
30 2 0.01
31 22 0.16
32 3 0.02
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (29 bp):
TATTTTGGTAATTATTGTTAAAACAGTGA
Found at i:454727 original size:40 final size:40
Alignment explanation
Indices: 454678--454764 Score: 165
Period size: 40 Copynumber: 2.2 Consensus size: 40
454668 TTTAACACTC
*
454678 CAAAATATGGTTACTTTTACTCTAAAATGAAACGTTGGGT
1 CAAAGTATGGTTACTTTTACTCTAAAATGAAACGTTGGGT
454718 CAAAGTATGGTTACTTTTACTCTAAAATGAAACGTTGGGT
1 CAAAGTATGGTTACTTTTACTCTAAAATGAAACGTTGGGT
454758 CAAAGTA
1 CAAAGTA
454765 GGGTCACTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (40 bp):
CAAAGTATGGTTACTTTTACTCTAAAATGAAACGTTGGGT
Found at i:456535 original size:35 final size:35
Alignment explanation
Indices: 456496--456570 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
456486 AAAATACTTT
*
456496 AATTTAGGGTTTATAATATAATTAAAGTATTTTGG
1 AATTTAGGGTTTAGAATATAATTAAAGTATTTTGG
* * *
456531 AATTTAGGGTTTAGAATGTAATTGAAGTGTTTTGG
1 AATTTAGGGTTTAGAATATAATTAAAGTATTTTGG
456566 AATTT
1 AATTT
456571 TGAATATGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.45
Consensus pattern (35 bp):
AATTTAGGGTTTAGAATATAATTAAAGTATTTTGG
Found at i:459110 original size:3 final size:3
Alignment explanation
Indices: 459102--459130 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
459092 ACTATCCTAT
459102 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
459131 TTTTGCTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:460472 original size:2 final size:2
Alignment explanation
Indices: 460465--460518 Score: 63
Period size: 2 Copynumber: 26.5 Consensus size: 2
460455 ATCCTATCCC
* * * *
460465 AT AT AT AT AT AT AT AT AT AA AC AA AT CT CAT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT
460508 AT AT AT AT AT A
1 AT AT AT AT AT A
460519 AACAAATCTC
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
2 44 0.98
3 1 0.02
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:462731 original size:30 final size:30
Alignment explanation
Indices: 462695--462762 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
462685 GATATTTAGT
*
462695 GGGCGGGTGGATGTGGGGTGGGCGGATGCA
1 GGGCGGGTGGATGTGGGGCGGGCGGATGCA
* *
462725 GGGCGGGCGGATGTGGGGCGGGTGGATGCA
1 GGGCGGGTGGATGTGGGGCGGGCGGATGCA
462755 GGGCGGGT
1 GGGCGGGT
462763 AAGGTCTCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.09, C:0.12, G:0.65, T:0.15
Consensus pattern (30 bp):
GGGCGGGTGGATGTGGGGCGGGCGGATGCA
Found at i:462762 original size:15 final size:15
Alignment explanation
Indices: 462695--462762 Score: 73
Period size: 15 Copynumber: 4.5 Consensus size: 15
462685 GATATTTAGT
**
462695 GGGCGGGTGGATGTG
1 GGGCGGGTGGATGCA
* *
462710 GGGTGGGCGGATGCA
1 GGGCGGGTGGATGCA
* **
462725 GGGCGGGCGGATGTG
1 GGGCGGGTGGATGCA
462740 GGGCGGGTGGATGCA
1 GGGCGGGTGGATGCA
462755 GGGCGGGT
1 GGGCGGGT
462763 AAGGTCTCAA
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 43 1.00
ACGTcount: A:0.09, C:0.12, G:0.65, T:0.15
Consensus pattern (15 bp):
GGGCGGGTGGATGCA
Found at i:464743 original size:21 final size:22
Alignment explanation
Indices: 464719--464759 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
464709 ATTTGGGAGT
* *
464719 TTTTAT-TCTCTTTGTGCTTTA
1 TTTTATATCTATTTGGGCTTTA
464740 TTTTATATCTATTTGGGCTT
1 TTTTATATCTATTTGGGCTT
464760 GTACTAAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.63
Consensus pattern (22 bp):
TTTTATATCTATTTGGGCTTTA
Found at i:467872 original size:3 final size:3
Alignment explanation
Indices: 467866--467963 Score: 79
Period size: 3 Copynumber: 30.7 Consensus size: 3
467856 GAAGAGGAGG
* * * * *
467866 AGA AGA AGA AGA AGA AGA AGA AGTA GGA AGG AGG AGG AGG AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AG-A AGA AGA AGA AGA AGA AGA AGA
* *
467912 AGA AGA AGAA AGTA GGA AGGA AGA AGA AGA AGA AGA GAGA AGGA AAA
1 AGA AGA AG-A AG-A AGA A-GA AGA AGA AGA AGA AGA -AGA A-GA AGA
467959 AGA AG
1 AGA AG
467964 TTGCCACATC
Statistics
Matches: 81, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
3 65 0.80
4 16 0.20
ACGTcount: A:0.58, C:0.00, G:0.40, T:0.02
Consensus pattern (3 bp):
AGA
Found at i:468363 original size:21 final size:21
Alignment explanation
Indices: 468338--468381 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
468328 TTTGATTGAA
468338 TTCAATAATTAAATTAATATT
1 TTCAATAATTAAATTAATATT
*
468359 TTCAATAATTATATTAATATT
1 TTCAATAATTAAATTAATATT
468380 TT
1 TT
468382 AATTAAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (21 bp):
TTCAATAATTAAATTAATATT
Found at i:474352 original size:55 final size:55
Alignment explanation
Indices: 474293--474602 Score: 525
Period size: 55 Copynumber: 5.6 Consensus size: 55
474283 TTCCCATAGG
474293 GAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACA
1 GAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACA
*
474348 GAAATTAATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATAC-
1 GAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACA
*
474402 GAAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACATATAAAGTGCCCATAC-
1 G-AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACA
474457 GAAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACA
1 G-AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACA
* * *
474513 GAAATTCATCCACTTAGTATGAATTTCTGAAGGTTACACATAAAGTGCCTATACA
1 GAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACA
* *
474568 AAAATTCATCAACTTAGTATGAATTTCTTAAGTTT
1 GAAATTCATCCACTTAGTATGAATTTCTTAAGTTT
474603 TTGCACACTT
Statistics
Matches: 242, Mismatches: 11, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
54 1 0.00
55 240 0.99
56 1 0.00
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (55 bp):
GAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACA
Found at i:481293 original size:55 final size:55
Alignment explanation
Indices: 481221--481637 Score: 581
Period size: 55 Copynumber: 7.6 Consensus size: 55
481211 ACCAATATGA
* * * **
481221 AAATTTATACACTTAGTATGAATTTCCT-AGTTTTACACATAAAGTGCCCATACAA
1 AAATTCATCCACTTAGTATGAATTTCTTAAG-TTTACACATAAAGTGCCCATACGG
* * *
481276 AAATTCATCCAGTTAGTATGAATTTCTTAAGTTTACATATAAAG-GCCCCATACGA
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTG-CCCATACGG
* * *
481331 AAATTCATCTACTTAGTATGAATTTCTTAAGTTTACACATAAATTGCTCATACGG
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACGG
*
481386 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCTCATACGG
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACGG
*
481441 AAATTCATCCACTTAGTATGAA-TT-TTAAGTTTACGCATAAAGTGCCCATACGG
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACGG
* * * * * *
481494 AAATTCATCCACTTTGTATGAATTTCTTATGTTTACACAAAAATTGCCCGTACGA
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACGG
* * *
481549 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTTCCCGTATGG
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACGG
*
481604 AAATTCATCCACATAGTATGAATTTCTTAAGTTT
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTT
481638 TTGCACACTT
Statistics
Matches: 326, Mismatches: 31, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
53 48 0.15
54 5 0.02
55 270 0.83
56 3 0.01
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (55 bp):
AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACGG
Found at i:481636 original size:218 final size:219
Alignment explanation
Indices: 481221--481637 Score: 617
Period size: 218 Copynumber: 1.9 Consensus size: 219
481211 ACCAATATGA
*
481221 AAATTTATACACTTAGTATGAATTTCCTAGTTTTACACATAAAGTGCCCATACAAAAATTCATCC
1 AAATTCATACACTTAGTATGAATTT-CTAGTTTTACACATAAAGTGCCCATACAAAAATTCATCC
* * * *
481286 AGTTAGTATGAATTTCTTAAGTTTACATATAAAGGCCCCATACGAAAATTCATCTACTTAGTATG
65 ACTTAGTATGAATTTCTTAAGTTTACACAAAAAGGCCCCATACGAAAATTCATCCACTTAGTATG
* *
481351 AATTTCTTAAGTTTACACATAAATTGCTCATACGGAAATTCATCCACTTAGTATGAATTTCTTAA
130 AATTTCTTAAGTTTACACATAAATTGCCCATACGGAAATTCATCCACATAGTATGAATTTCTTAA
481416 GTTTACACATAAAGTGCTCATACGG
195 GTTTACACATAAAGTGCTCATACGG
* * **
481441 AAATTCATCCACTTAGTATGAATTT-TAAG-TTTACGCATAAAGTGCCCATACGGAAATTCATCC
1 AAATTCATACACTTAGTATGAATTTCT-AGTTTTACACATAAAGTGCCCATACAAAAATTCATCC
* * * *
481504 ACTTTGTATGAATTTCTTATGTTTACACAAAAATTG-CCCGTACGAAAATTCATCCACTTAGTAT
65 ACTTAGTATGAATTTCTTAAGTTTACACAAAAA-GGCCCCATACGAAAATTCATCCACTTAGTAT
* *
481568 GAATTTCTTAAGTTTACACATAAAGTT-CCCGTATGGAAATTCATCCACATAGTATGAATTTCTT
129 GAATTTCTTAAGTTTACACATAAA-TTGCCCATACGGAAATTCATCCACATAGTATGAATTTCTT
481632 AAGTTT
193 AAGTTT
481638 TTGCACACTT
Statistics
Matches: 177, Mismatches: 17, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
218 149 0.84
219 5 0.03
220 23 0.13
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (219 bp):
AAATTCATACACTTAGTATGAATTTCTAGTTTTACACATAAAGTGCCCATACAAAAATTCATCCA
CTTAGTATGAATTTCTTAAGTTTACACAAAAAGGCCCCATACGAAAATTCATCCACTTAGTATGA
ATTTCTTAAGTTTACACATAAATTGCCCATACGGAAATTCATCCACATAGTATGAATTTCTTAAG
TTTACACATAAAGTGCTCATACGG
Found at i:485925 original size:60 final size:59
Alignment explanation
Indices: 485826--485939 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 59
485816 GGATTGCCAT
* * *
485826 ACTCAACAATGTAGTGACCTATAATCATGTTACCATTTTGTAAATTTTAATAGTTGGAGA
1 ACTCAACAATGTAGTGACCTATAATCAGGATA-CATTTTGTAAATTTCAATAGTTGGAGA
* * *
485886 ACTCAACAATGTAGTGACCTATAATTGGAGGATA-TTTTTGTAACTTTCAATAGT
1 ACTCAACAATGTAGTGACCTATAA-T-CAGGATACATTTTGTAAATTTCAATAGT
485940 CATATGACTA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
60 41 0.89
61 1 0.02
62 4 0.09
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (59 bp):
ACTCAACAATGTAGTGACCTATAATCAGGATACATTTTGTAAATTTCAATAGTTGGAGA
Found at i:510474 original size:159 final size:158
Alignment explanation
Indices: 510229--510582 Score: 496
Period size: 159 Copynumber: 2.2 Consensus size: 158
510219 AGTACATGAA
* * * * *
510229 CATGTGGTTCAAATTTTGT-GAAAATGGACTTGAAATAAATGATGAATTGAATATATAAGGAAAT
1 CATGTGGTTCAAATTTGGTAAAAAATGGACTTGAAATAAATGATGAATTGAAGAAATAAGAAAAT
* *
510293 AATGAAAAACTGAGGGATTAAATTGAAAAATAGAAAATTTGGTAT-AAAAAATAAGAATTGAAAG
66 AATGAAAAACTAAGGGACTAAATTGAAAAATAGAAAATTTGGTATCAAAAAAT-AGAATTGAAAG
*
510357 TACATATGTACTCTACGATGGTTTAGGAG
130 TACATATGTACTCTACGATGGTTTAGGAC
510386 CATGTGGTTCAAATTTGGTAAAAAAATGGACTTGAAATAAATGATGAATTGAAGAAATAAGAAAA
1 CATGTGGTTCAAATTTGGT-AAAAAATGGACTTGAAATAAATGATGAATTGAAGAAATAAGAAAA
* * * * * * * *
510451 TTATGAAAAATTAATGGACTAAATTGAAAAATAGAGAATTTGTTATCAAAAAGTGGAATTTAAAG
65 TAATGAAAAACTAAGGGACTAAATTGAAAAATAGAAAATTTGGTATCAAAAAATAGAATTGAAAG
*
510516 TACATATGTATTCTACGATGGTTTAGGAC
130 TACATATGTACTCTACGATGGTTTAGGAC
* * *
510545 CATGTGGTTCAAATTTGGCAAAAATTGGACTTAAAATA
1 CATGTGGTTCAAATTTGGTAAAAAATGGACTTGAAATA
510583 GAGGAGAAAC
Statistics
Matches: 174, Mismatches: 20, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
157 18 0.10
158 17 0.10
159 133 0.76
160 6 0.03
ACGTcount: A:0.45, C:0.06, G:0.19, T:0.30
Consensus pattern (158 bp):
CATGTGGTTCAAATTTGGTAAAAAATGGACTTGAAATAAATGATGAATTGAAGAAATAAGAAAAT
AATGAAAAACTAAGGGACTAAATTGAAAAATAGAAAATTTGGTATCAAAAAATAGAATTGAAAGT
ACATATGTACTCTACGATGGTTTAGGAC
Found at i:512124 original size:90 final size:90
Alignment explanation
Indices: 511966--512414 Score: 621
Period size: 90 Copynumber: 5.0 Consensus size: 90
511956 AGAGAAGATA
* * * * * *
511966 AACCTTGCATCAATATTTCCAGCGGGGAGTTCATAATGAGAAGAACTCATCCGACAAAGGAGAAG
1 AACCTTGCATCAACATTT-CAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAG
* * *
512031 AAGTTCTTAGTGAGAATAACTTGTTC
65 AAGTTCATAATGAGAAGAACTTGTTC
* * * ** *
512057 AACATTGCATCAACATTTCAGTGGAGAGTTAATAATGAGAAGGACTCATCCAAAAAGGGACAAGA
1 AACCTTGCATCAACATTTCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGA
* *
512122 AGTTCAAAATAAGAAGAACTTGTTC
66 AGTTCATAATGAGAAGAACTTGTTC
* *
512147 AACCTTGCATCAACATTTAAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAGGA
1 AACCTTGCATCAACATTTCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGA
* *
512212 AGTTAAAAATGAGAAGAACTTGTTC
66 AGTTCATAATGAGAAGAACTTGTTC
* *
512237 AACCTTGCATGAACATTTCAGTGGGGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGA
1 AACCTTGCATCAACATTTCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGA
* *
512302 AGTTCATAATAAGAATAACTTGTTC
66 AGTTCATAATGAGAAGAACTTGTTC
* *
512327 AACCTTTG-ATCAACGTTTCCAGTGGAGAGTTCATAATGAGAAGAACCCATCCAACGAGGGAGAA
1 AACC-TTGCATCAACATTT-CAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAA
512391 GAAGTTCATAATGAGAAGAACTTG
64 GAAGTTCATAATGAGAAGAACTTG
512415 ATTGACCTTA
Statistics
Matches: 317, Mismatches: 39, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
90 233 0.74
91 84 0.26
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (90 bp):
AACCTTGCATCAACATTTCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGA
AGTTCATAATGAGAAGAACTTGTTC
Found at i:512709 original size:17 final size:19
Alignment explanation
Indices: 512666--512718 Score: 67
Period size: 17 Copynumber: 2.9 Consensus size: 19
512656 AACTAAACCC
512666 AAAC-AACCCAGACCCAACA
1 AAACAAACCCAGACCC-ACA
512685 AAACAAACCCAGACCCA-A
1 AAACAAACCCAGACCCACA
*
512703 ATA-AAACCCAGACCCA
1 AAACAAACCCAGACCCA
512719 TACCCAAACC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 13 0.41
18 3 0.09
19 5 0.16
20 11 0.34
ACGTcount: A:0.53, C:0.40, G:0.06, T:0.02
Consensus pattern (19 bp):
AAACAAACCCAGACCCACA
Found at i:512797 original size:17 final size:16
Alignment explanation
Indices: 512764--512797 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
512754 CTGCTATAAA
*
512764 ACCCTAACCTAATGAT
1 ACCCTAACCTAAAGAT
512780 ACCCTAACCCTAAAGAT
1 ACCCTAA-CCTAAAGAT
512797 A
1 A
512798 TCATTCATGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.41, C:0.32, G:0.06, T:0.21
Consensus pattern (16 bp):
ACCCTAACCTAAAGAT
Found at i:522273 original size:15 final size:15
Alignment explanation
Indices: 522253--522295 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
522243 ATACTAACGT
522253 TCTTCTTCTTCTCCA
1 TCTTCTTCTTCTCCA
*
522268 TCTTCTTCTT-TGCA
1 TCTTCTTCTTCTCCA
*
522282 TCGTCCTTCTTCTC
1 TC-TTCTTCTTCTC
522296 TTCATCTTCC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 5 0.22
15 17 0.74
16 1 0.04
ACGTcount: A:0.05, C:0.37, G:0.05, T:0.53
Consensus pattern (15 bp):
TCTTCTTCTTCTCCA
Found at i:524849 original size:91 final size:91
Alignment explanation
Indices: 524606--524969 Score: 485
Period size: 90 Copynumber: 4.1 Consensus size: 91
524596 AGAAAAGATA
* * * * * *
524606 AACCTTGCATCAACGTTTCCAGCGGGGAGTTTATAATGAGAAGAACTCAT-C--TGA-TGAGAAT
1 AACCTTGCATCAACATTTCCAGCGAGGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAG
* *
524667 AAGTTCATAATGAGAAGAATTTTTTC
66 AAGTTCATAATGAGAAGAACTTGTTC
* * *
524693 AA-CTGTGCATCAACATTTCAATG-GA-GAGTTCATAATGAGAATAACTCATCCAACTAGGGAGA
1 AACCT-TGCATCAACATTTCCA-GCGAGGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGA
524755 AGAAGTTCATAATGAGAAGAACTTGTTC
64 AGAAGTTCATAATGAGAAGAACTTGTTC
* * *
524783 AACCTTGCACCAACATTTCCAGCGAGGAGTTCATAATGAGAAGAGCTCATCCGACGAGGGAGAAG
1 AACCTTGCATCAACATTTCCAGCGAGGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAG
524848 AAGTTCATAATGAGAAGAACTTGTTC
66 AAGTTCATAATGAGAAGAACTTGTTC
*
524874 AACCTTGCATCAACATTT-CAGTG-GAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAA
1 AACCTTGCATCAACATTTCCAGCGAG-GAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAA
*
524937 GAAGTTCATAATGAGAAGAACCTGTTC
65 GAAGTTCATAATGAGAAGAACTTGTTC
*
524964 GACCTT
1 AACCTT
524970 AGCTCATTTT
Statistics
Matches: 244, Mismatches: 23, Indels: 17
0.86 0.08 0.06
Matches are distributed among these distances:
86 24 0.10
87 18 0.07
88 1 0.00
89 3 0.01
90 118 0.48
91 80 0.33
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.25
Consensus pattern (91 bp):
AACCTTGCATCAACATTTCCAGCGAGGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAG
AAGTTCATAATGAGAAGAACTTGTTC
Found at i:524906 original size:181 final size:177
Alignment explanation
Indices: 524606--524969 Score: 541
Period size: 181 Copynumber: 2.0 Consensus size: 177
524596 AGAAAAGATA
* * * * * * *
524606 AACCTTGCATCAACGTTTCCAGCGGGGAGTTTATAATGAGAAGAACTCATCTGATGAGAATAAGT
1 AACCTTGCACCAACATTTCCAGCGAGGAGTTCATAATGAGAAGAACTCATCCGAGGAGAAGAAGT
* * *
524671 TCATAATGAGAAGAATTTTTTCAACTGTGCATCAACATTTCAATGGAGAGTTCATAATGAGAATA
66 TCATAATGAGAAGAACTTGTTCAACTGTGCATCAACATTTCAATGGAGAGTTCATAATGAGAAGA
* *
524736 ACTCATCCAACTAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTC
131 ACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACCTGTTC
*
524783 AACCTTGCACCAACATTTCCAGCGAGGAGTTCATAATGAGAAGAGCTCATCCGACGAGGGAGAAG
1 AACCTTGCACCAACATTTCCAGCGAGGAGTTCATAATGAGAAGAACTCAT-C--CGA-GGAGAAG
*
524848 AAGTTCATAATGAGAAGAACTTGTTCAACCT-TGCATCAACATTTCAGTGGAGAGTTCATAATGA
62 AAGTTCATAATGAGAAGAACTTGTTCAA-CTGTGCATCAACATTTCAATGGAGAGTTCATAATGA
524912 GAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACCTGTTC
126 GAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACCTGTTC
*
524964 GACCTT
1 AACCTT
524970 AGCTCATTTT
Statistics
Matches: 167, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
177 45 0.27
178 1 0.01
180 2 0.01
181 117 0.70
182 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.25
Consensus pattern (177 bp):
AACCTTGCACCAACATTTCCAGCGAGGAGTTCATAATGAGAAGAACTCATCCGAGGAGAAGAAGT
TCATAATGAGAAGAACTTGTTCAACTGTGCATCAACATTTCAATGGAGAGTTCATAATGAGAAGA
ACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACCTGTTC
Found at i:528570 original size:20 final size:21
Alignment explanation
Indices: 528544--528598 Score: 85
Period size: 20 Copynumber: 2.7 Consensus size: 21
528534 ATTATAAGCC
528544 ATCAGTATCGATACTCATGGG
1 ATCAGTATCGATACTCATGGG
*
528565 -TCAGTATCGATACTGATGGG
1 ATCAGTATCGATACTCATGGG
*
528585 ATCAATATCGATAC
1 ATCAGTATCGATAC
528599 CACTACCCTG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 19 0.61
21 12 0.39
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (21 bp):
ATCAGTATCGATACTCATGGG
Found at i:531829 original size:27 final size:28
Alignment explanation
Indices: 531799--531857 Score: 111
Period size: 27 Copynumber: 2.1 Consensus size: 28
531789 CATCATCTTA
531799 TGTGCTAAACTGTAAAAGAATCAACT-C
1 TGTGCTAAACTGTAAAAGAATCAACTCC
531826 TGTGCTAAACTGTAAAAGAATCAACTCC
1 TGTGCTAAACTGTAAAAGAATCAACTCC
531854 TGTG
1 TGTG
531858 AGTTTCAGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 26 0.84
28 5 0.16
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (28 bp):
TGTGCTAAACTGTAAAAGAATCAACTCC
Found at i:534277 original size:75 final size:75
Alignment explanation
Indices: 534185--534333 Score: 262
Period size: 75 Copynumber: 2.0 Consensus size: 75
534175 GACTAAGTTA
* *
534185 TGAAATAGAGAGCCGATCTACATAAAATTCTCTATCATTTGGTATAAGAAATTCATGTAAAGCAT
1 TGAAATAGAGAGCCGATCTACATAAAATTCTCTATCATTAGGTATAAGAAATTCATCTAAAGCAT
534250 GCTTGGATGG
66 GCTTGGATGG
* *
534260 TGAAATAGAGAGTCGATCTACATCAAATTCTCTATCATTAGGTATAAGAAATTCATCTAAAGCAT
1 TGAAATAGAGAGCCGATCTACATAAAATTCTCTATCATTAGGTATAAGAAATTCATCTAAAGCAT
534325 GCTTGGATG
66 GCTTGGATG
534334 TTGAGATTTG
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 70 1.00
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (75 bp):
TGAAATAGAGAGCCGATCTACATAAAATTCTCTATCATTAGGTATAAGAAATTCATCTAAAGCAT
GCTTGGATGG
Found at i:546031 original size:14 final size:14
Alignment explanation
Indices: 546002--546047 Score: 65
Period size: 14 Copynumber: 3.1 Consensus size: 14
545992 CGTTCGTGAA
546002 CGTTCGATTATATGTT
1 CGTTC-ATT-TATGTT
*
546018 TGTTCATTTATGTT
1 CGTTCATTTATGTT
546032 CGTTCATTTATGTT
1 CGTTCATTTATGTT
546046 CG
1 CG
546048 AACAGAGGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 21 0.75
15 3 0.11
16 4 0.14
ACGTcount: A:0.15, C:0.13, G:0.17, T:0.54
Consensus pattern (14 bp):
CGTTCATTTATGTT
Found at i:546326 original size:10 final size:10
Alignment explanation
Indices: 546302--546357 Score: 51
Period size: 10 Copynumber: 5.4 Consensus size: 10
546292 TTGATTTTTG
*
546302 TGTTTGTGT-
1 TGTTTGTTTA
546311 TGTTTGTTTA
1 TGTTTGTTTA
546321 TGTTTGTTTA
1 TGTTTGTTTA
*
546331 TGTTCATTTATTA
1 TGTT--TGT-TTA
*
546344 TGTTCGTTTA
1 TGTTTGTTTA
546354 TGTT
1 TGTT
546358 CGTTCGTTTG
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
9 8 0.21
10 21 0.54
11 1 0.03
12 2 0.05
13 7 0.18
ACGTcount: A:0.11, C:0.04, G:0.20, T:0.66
Consensus pattern (10 bp):
TGTTTGTTTA
Found at i:546358 original size:10 final size:10
Alignment explanation
Indices: 546311--546398 Score: 59
Period size: 10 Copynumber: 8.1 Consensus size: 10
546301 GTGTTTGTGT
*
546311 TGTTTGTTTA
1 TGTTCGTTTA
*
546321 TGTTTGTTTA
1 TGTTCGTTTA
*
546331 TGTTCATTTATTA
1 TGTTC--GT-TTA
546344 TGTTCGTTTA
1 TGTTCGTTTA
*
546354 TGTTCGTTCGTTTG
1 ---T-GTTCGTTTA
546368 TGTTCGTTTA
1 TGTTCGTTTA
* *
546378 CGTTCGTTTC
1 TGTTCGTTTA
546388 TGTTCGTTTA
1 TGTTCGTTTA
546398 T
1 T
546399 CATTTAAATG
Statistics
Matches: 62, Mismatches: 9, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
10 42 0.68
11 2 0.03
12 1 0.02
13 9 0.15
14 8 0.13
ACGTcount: A:0.09, C:0.10, G:0.19, T:0.61
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:546364 original size:14 final size:14
Alignment explanation
Indices: 546345--546375 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
546335 CATTTATTAT
546345 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
*
546359 GTTCGTTTGTGTTC
1 GTTCGTTTATGTTC
546373 GTT
1 GTT
546376 TACGTTCGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.03, C:0.13, G:0.26, T:0.58
Consensus pattern (14 bp):
GTTCGTTTATGTTC
Found at i:546383 original size:20 final size:20
Alignment explanation
Indices: 546358--546397 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
546348 CGTTTATGTT
*
546358 CGTTCGTTTGTGTTCGTTTA
1 CGTTCGTTTCTGTTCGTTTA
546378 CGTTCGTTTCTGTTCGTTTA
1 CGTTCGTTTCTGTTCGTTTA
546398 TCATTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.05, C:0.17, G:0.23, T:0.55
Consensus pattern (20 bp):
CGTTCGTTTCTGTTCGTTTA
Found at i:551824 original size:19 final size:19
Alignment explanation
Indices: 551803--551839 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
551793 CTTTCCGTTT
*
551803 TTTTTTGTAT-TTATTATA
1 TTTTTAGTATCTTATTATA
551821 TTTTTAGTATCTTATTATA
1 TTTTTAGTATCTTATTATA
551840 CTCTTTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.24, C:0.03, G:0.05, T:0.68
Consensus pattern (19 bp):
TTTTTAGTATCTTATTATA
Found at i:551883 original size:16 final size:16
Alignment explanation
Indices: 551862--551893 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
551852 AATATACTGT
*
551862 TTATTTATTATTATTA
1 TTATTTATTATCATTA
551878 TTATTTATTATCATTA
1 TTATTTATTATCATTA
551894 ATGTGTATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (16 bp):
TTATTTATTATCATTA
Found at i:562527 original size:75 final size:76
Alignment explanation
Indices: 562414--562557 Score: 204
Period size: 75 Copynumber: 1.9 Consensus size: 76
562404 AGTACTTCGC
* * *
562414 TTAGGATGAAAACCCAAGAGGGCATCCTAAGTTG-AAAAAAAAGAAAAAGGAAAAG-GAAAAAAA
1 TTAGGATGAAAACCCAAGAGGGCACCCTAAATTGAAAAAAAAAG-AAAAGAAAAAGAGAAAAAAA
562477 CAAAAAAATCGT
65 CAAAAAAATCGT
* *
562489 TTAGGGTGAAAACCCGAA-AGGGCGCCCTAAATTGAAAAAAAAAGAAAAGAAAAAGAGAAAAAAA
1 TTAGGATGAAAACCC-AAGAGGGCACCCTAAATTGAAAAAAAAAGAAAAGAAAAAGAGAAAAAAA
562553 CAAAA
65 CAAAA
562558 GAAAAAGAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
75 37 0.61
76 24 0.39
ACGTcount: A:0.58, C:0.11, G:0.20, T:0.10
Consensus pattern (76 bp):
TTAGGATGAAAACCCAAGAGGGCACCCTAAATTGAAAAAAAAAGAAAAGAAAAAGAGAAAAAAAC
AAAAAAATCGT
Found at i:562536 original size:5 final size:5
Alignment explanation
Indices: 562522--562573 Score: 52
Period size: 5 Copynumber: 10.0 Consensus size: 5
562512 GCCCTAAATT
* *
562522 GAAAA AAAAA GAAAA GAAAAA GAGAAA -AAAA CAAAA GAAAAA GAAAA
1 GAAAA GAAAA GAAAA G-AAAA GA-AAA GAAAA GAAAA G-AAAA GAAAA
562569 GAAAA
1 GAAAA
562574 TAAGGTAGGT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
4 3 0.08
5 24 0.60
6 13 0.32
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:562547 original size:13 final size:13
Alignment explanation
Indices: 562525--562568 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
562515 CTAAATTGAA
562525 AAAAAAAGAAAAG
1 AAAAAAAGAAAAG
*
562538 AAAAAGAGAAAA-
1 AAAAAAAGAAAAG
562550 AAACAAAAGAAAAAG
1 AAA-AAAAG-AAAAG
562565 AAAA
1 AAAA
562569 GAAAATAAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 3 0.12
13 15 0.58
14 5 0.19
15 3 0.12
ACGTcount: A:0.84, C:0.02, G:0.14, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAAAAG
Found at i:562549 original size:21 final size:20
Alignment explanation
Indices: 562524--562573 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 20
562514 CCTAAATTGA
*
562524 AAAAAAAAGAAAAGAAAAAG
1 AAAAAAAACAAAAGAAAAAG
562544 AGAAAAAAACAAAAGAAAAAG
1 A-AAAAAAACAAAAGAAAAAG
562565 AAAAGAAAA
1 AAAA-AAAA
562574 TAAGGTAGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.84, C:0.02, G:0.14, T:0.00
Consensus pattern (20 bp):
AAAAAAAACAAAAGAAAAAG
Found at i:563816 original size:99 final size:99
Alignment explanation
Indices: 563643--564010 Score: 362
Period size: 99 Copynumber: 3.6 Consensus size: 99
563633 CAACCCGCAG
* * * *
563643 TTTCAACTTCACGACGAAGGGA-ATCGTGCACACAAGACATCACAAGCTCAACTTCACAGCGAAG
1 TTTCAACTTCACAACGAA-GGATAT--TGGACTCAAGACAACACAAGCTCAACTTCACAGCGAAG
* * *
563707 AGGAGGCTGACTATCAACTTTCCAATTTCAGAGCCAA
63 AGGAGACTGACTATCAAATTCCCAATTTCAGAGCCAA
* * * *
563744 TTTCAACTTCACAACGAATGATATTGGACTCAAGACAGCACAAGCTCAACTTCACAGTGAAGGGG
1 TTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACAGCGAAGAGG
* *
563809 CGACTGACTGTCAAATTCCCAATTTCAGAGCCAA
66 AGACTGACTATCAAATTCCCAATTTCAGAGCCAA
* * * *
563843 TTTCAACTTCAGAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAG-GG
1 TTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACAGCGAAGAGG
* * * * *
563907 ACGGCTGGTGGTCAATAAATAATTTCCCAGTTTCAGAGCCAA
66 A-GAC---T-GACTAT-CA-AA-TTCCCAATTTCAGAGCCAA
* ** * * * *
563949 TTTCAACTTTACAGTGAAGGATATTTGACTCGAGACAACACAAGTTCAACTTCACAACGAAG
1 TTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACAGCGAAG
564011 GAATGACTAG
Statistics
Matches: 227, Mismatches: 31, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
98 2 0.01
99 122 0.54
100 2 0.01
101 19 0.08
102 1 0.00
103 3 0.01
104 1 0.00
105 2 0.01
106 75 0.33
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (99 bp):
TTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACAGCGAAGAGG
AGACTGACTATCAAATTCCCAATTTCAGAGCCAA
Found at i:563979 original size:106 final size:104
Alignment explanation
Indices: 563732--564067 Score: 387
Period size: 106 Copynumber: 3.2 Consensus size: 104
563722 AACTTTCCAA
* * * *
563732 TTTCAGAGCCAATTTCAACTTCACAACGAATGATATTGGACTCAAGACAGCACAAGCTCAACTTC
1 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTC
** * * *
563797 ACAGTGAAGGGGCGACTGACTGTC-----AAA-TTCCCAA
66 ACAACGAAGGGACGACTG-GTGTCAATAAAAATTTCCCAG
*
563831 TTTCAGAGCCAATTTCAACTTCAGAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTC
1 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTC
*
563896 ACAACGAAGGGACGGCTGGTGGTCAATAAATAATTTCCCAG
66 ACAACGAAGGGACGACTGGT-GTCAATAAA-AATTTCCCAG
* * * *
563937 TTTCAGAGCCAATTTCAACTTTACAGTGAAGGATATTTGACTCGAGACAACACAAGTTCAACTTC
1 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTC
* * *
564002 ACAACGAAGGAATGACTAGTTGTCAATAAACAATTTCCCAG
66 ACAACGAAGGGACGACT-GGTGTCAATAAA-AATTTCCCAG
* * * *
564043 TTCCATAGACAATTCCAACTTCACA
1 TTTCAGAGCCAATTTCAACTTCACA
564068 AACGGATTGA
Statistics
Matches: 202, Mismatches: 26, Indels: 11
0.85 0.11 0.05
Matches are distributed among these distances:
98 1 0.00
99 77 0.38
104 1 0.00
105 2 0.01
106 119 0.59
107 2 0.01
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.24
Consensus pattern (104 bp):
TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTC
ACAACGAAGGGACGACTGGTGTCAATAAAAATTTCCCAG
Found at i:565671 original size:19 final size:20
Alignment explanation
Indices: 565647--565685 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
565637 ATCCTTTCCG
*
565647 TTTTTTTGTAT-TTATTATA
1 TTTTTTAGTATCTTATTATA
565666 TTTTTTAGTATCTTATTATA
1 TTTTTTAGTATCTTATTATA
565686 CTCTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (20 bp):
TTTTTTAGTATCTTATTATA
Found at i:565720 original size:3 final size:3
Alignment explanation
Indices: 565712--565745 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
565702 TACTGTTTAT
*
565712 TTA TTA TTA TTA TTA TTA TTA TTTA TTA TCA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
565746 ACATGTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:565825 original size:2 final size:2
Alignment explanation
Indices: 565818--565842 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
565808 AGTTATGTTT
565818 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
565843 TTTAGTGTTT
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:571268 original size:25 final size:25
Alignment explanation
Indices: 571240--571289 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
571230 GTTCTGCCAC
*
571240 TGTAGCCGACAATGATTGGAAATTA
1 TGTAGCCAACAATGATTGGAAATTA
571265 TGTAGCCAACAATGATTGGAAATTA
1 TGTAGCCAACAATGATTGGAAATTA
571290 GAGATTTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (25 bp):
TGTAGCCAACAATGATTGGAAATTA
Found at i:580726 original size:15 final size:16
Alignment explanation
Indices: 580702--580734 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
580692 TTTCCTTTTT
580702 TTGAACTAATAAG-AG
1 TTGAACTAATAAGTAG
*
580717 TTGAAGTAATAAGTAG
1 TTGAACTAATAAGTAG
580733 TT
1 TT
580735 TGATTTCGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.42, C:0.03, G:0.21, T:0.33
Consensus pattern (16 bp):
TTGAACTAATAAGTAG
Found at i:585276 original size:3 final size:3
Alignment explanation
Indices: 585268--585322 Score: 85
Period size: 3 Copynumber: 18.7 Consensus size: 3
585258 TTTGCAATAT
* *
585268 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TCA TTA TTA TTA TTT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
585315 TTA TTA TT
1 TTA TTA TT
585323 TATTTAAATA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
2 1 0.02
3 46 0.98
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:585662 original size:31 final size:30
Alignment explanation
Indices: 585616--585675 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
585606 ATATTTTTAA
585616 ATAAATAAATATTTTATTT-ATAAATATAT
1 ATAAATAAATATTTTATTTCATAAATATAT
*
585645 ATAAATTAATATATTTTATTTCATAATTATA
1 ATAAA-TAA-ATATTTTATTTCATAAATATA
585676 ATTTTGAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 5 0.19
30 3 0.11
31 11 0.41
32 8 0.30
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (30 bp):
ATAAATAAATATTTTATTTCATAAATATAT
Found at i:586161 original size:2 final size:2
Alignment explanation
Indices: 586154--586198 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
586144 TTTCAAAAAT
*
586154 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA -A TA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
586194 TA TA T
1 TA TA T
586199 TATTTTATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:586207 original size:20 final size:21
Alignment explanation
Indices: 586184--586225 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
586174 TATATATATA
586184 TATTAAT-ATTTATATTATTT
1 TATTAATGATTTATATTATTT
* *
586204 TATTAATGTTTTATTTTATTT
1 TATTAATGATTTATATTATTT
586225 T
1 T
586226 TCAAGTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (21 bp):
TATTAATGATTTATATTATTT
Found at i:595256 original size:21 final size:21
Alignment explanation
Indices: 595230--595269 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
595220 CCCCCTTTGA
*
595230 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
595251 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
595270 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:597927 original size:73 final size:74
Alignment explanation
Indices: 597732--597937 Score: 227
Period size: 73 Copynumber: 2.8 Consensus size: 74
597722 CAAAGCCAAA
* * * * ***
597732 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCTAGGAGGAACCGATTCCCCCCTGAATGGTT
1 AATTCCAGAATGCTCGGAGGGAACCGA-TCCCCCCAAGGAGGAACCGATTCCCCCCTGAAACATT
*
597797 TGGCTCTGAG
65 TGGCTCCGAG
* * *
597807 ATTTCCAGAATGCTCGGAAGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCT-AAACATT
1 AATTCCAGAATGCTCGGAGGGAACCGATCCCCCCA-AGGAGGAACCGATTCCCCCCTGAAACATT
**
597871 T-TTTCCGAG
65 TGGCTCCGAG
* * *
597880 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCAAGGGGGTACCGATTCCCCCCTG
1 AATTCCAGAATGCTCGGAGGGAACCGAT-CCCCCCAAGGAGGAACCGATTCCCCCCTG
597938 TTCAACGGTC
Statistics
Matches: 109, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
73 49 0.45
74 17 0.16
75 43 0.39
ACGTcount: A:0.24, C:0.31, G:0.23, T:0.21
Consensus pattern (74 bp):
AATTCCAGAATGCTCGGAGGGAACCGATCCCCCCAAGGAGGAACCGATTCCCCCCTGAAACATTT
GGCTCCGAG
Found at i:600062 original size:7 final size:7
Alignment explanation
Indices: 600050--600167 Score: 83
Period size: 7 Copynumber: 14.4 Consensus size: 7
600040 TCCAGTAAAG
600050 AAAGAAA
1 AAAGAAA
600057 AAAGAAA
1 AAAGAAA
600064 AATCCAGCAAA
1 AA---AG-AAA
600075 GAAAGAAA
1 -AAAGAAA
600083 AAAGAAAA
1 AAAG-AAA
600091 AAATGAAA
1 AAA-GAAA
600099 AAAGAAA
1 AAAGAAA
600106 AATGAGAAA
1 AA--AGAAA
600115 AAAGAAAAA
1 AAAG--AAA
600124 AAAGAAA
1 AAAGAAA
600131 AAAGATGAA
1 AAAGA--AA
600140 AAAGGAAA
1 AAA-GAAA
600148 AAGGAGAAA
1 AA--AGAAA
600157 AAAGGAAA
1 AAA-GAAA
600165 AAA
1 AAA
600168 TTGAACCAAG
Statistics
Matches: 94, Mismatches: 0, Indels: 33
0.74 0.00 0.26
Matches are distributed among these distances:
7 30 0.32
8 26 0.28
9 28 0.30
10 5 0.05
11 3 0.03
12 2 0.02
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (7 bp):
AAAGAAA
Found at i:600075 original size:26 final size:26
Alignment explanation
Indices: 600039--600091 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
600029 TCTTATACTC
*
600039 ATCCAGTAAAGAAAGAAAAAAGAAAA
1 ATCCAGCAAAGAAAGAAAAAAGAAAA
600065 ATCCAGCAAAGAAAGAAAAAAGAAAA
1 ATCCAGCAAAGAAAGAAAAAAGAAAA
600091 A
1 A
600092 AATGAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.70, C:0.09, G:0.15, T:0.06
Consensus pattern (26 bp):
ATCCAGCAAAGAAAGAAAAAAGAAAA
Found at i:600098 original size:9 final size:8
Alignment explanation
Indices: 600076--600167 Score: 66
Period size: 8 Copynumber: 11.2 Consensus size: 8
600066 TCCAGCAAAG
600076 AAAG-AAA
1 AAAGAAAA
600083 AAAGAAAA
1 AAAGAAAA
600091 AAATG-AAA
1 AAA-GAAAA
600099 AAAG-AAA
1 AAAGAAAA
*
600106 AATGAGAAA
1 AAAGA-AAA
600115 AAAGAAAA
1 AAAGAAAA
600123 AAA-AGAAA
1 AAAGA-AAA
600131 AAAGATGAAA
1 AAAGA--AAA
*
600141 AAGGAAAA
1 AAAGAAAA
*
600149 AGGAGAAAA
1 A-AAGAAAA
*
600158 AAGGAAAA
1 AAAGAAAA
600166 AA
1 AA
600168 TTGAACCAAG
Statistics
Matches: 70, Mismatches: 7, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
7 12 0.17
8 35 0.50
9 15 0.21
10 8 0.11
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.03
Consensus pattern (8 bp):
AAAGAAAA
Found at i:600100 original size:16 final size:16
Alignment explanation
Indices: 600079--600167 Score: 99
Period size: 17 Copynumber: 5.4 Consensus size: 16
600069 AGCAAAGAAA
*
600079 GAAAAAAGAAAAAAAT
1 GAAAAAAGAAAAAAAG
*
600095 GAAAAAAG-AAAAATG
1 GAAAAAAGAAAAAAAG
*
600110 AGAAAAAAGAAAAAAAA
1 -GAAAAAAGAAAAAAAG
*
600127 GAAAAAAGATGAAAAAG
1 GAAAAAAGA-AAAAAAG
*
600144 GAAAAAGGAGAAAAAAG
1 GAAAAAAGA-AAAAAAG
600161 GAAAAAA
1 GAAAAAA
600168 TTGAACCAAG
Statistics
Matches: 60, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
15 5 0.08
16 25 0.42
17 30 0.50
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (16 bp):
GAAAAAAGAAAAAAAG
Found at i:600126 original size:42 final size:42
Alignment explanation
Indices: 600080--600167 Score: 142
Period size: 42 Copynumber: 2.1 Consensus size: 42
600070 GCAAAGAAAG
*
600080 AAAAAAGAAAAAA-ATGAAAAAAGAAAAATGAGAAAAAAGAA
1 AAAAAAGAAAAAAGATGAAAAAAGAAAAAGGAGAAAAAAGAA
* *
600121 AAAAAAGAAAAAAGATGAAAAAGGAAAAAGGAGAAAAAAGGA
1 AAAAAAGAAAAAAGATGAAAAAAGAAAAAGGAGAAAAAAGAA
600163 AAAAA
1 AAAAA
600168 TTGAACCAAG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
41 13 0.30
42 30 0.70
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.03
Consensus pattern (42 bp):
AAAAAAGAAAAAAGATGAAAAAAGAAAAAGGAGAAAAAAGAA
Found at i:605129 original size:22 final size:22
Alignment explanation
Indices: 605103--605157 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
605093 TACATCTACA
605103 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
*
605125 CTCTTTAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
*
605147 CTTTTCAAAGA
1 CTCTTCAAAGA
605158 GGAAAGCTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (22 bp):
CTCTTCAAAGATGATAGATTCT
Found at i:606046 original size:76 final size:76
Alignment explanation
Indices: 605920--606330 Score: 768
Period size: 76 Copynumber: 5.4 Consensus size: 76
605910 TCATAGTTTC
*
605920 TCATCTGTAAGTCCTACAGTTCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
605985 AAGCCTTAGGG
66 AAGCCTTAGGG
605996 TCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
606061 AAGCCTTAGGG
66 AAGCCTTAGGG
*
606072 TCATCTGTAAGTCCTACAATGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
606137 AAGCCTTAGGG
66 AAGCCTTAGGG
606148 TCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
606213 AAGCCTTAGGG
66 AAGCCTTAGGG
* *
606224 TCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGACGTTTTCA
1 TCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
606289 AAGCCTTAGGG
66 AAGCCTTAGGG
* *
606300 TCATCTGTAAGCCCTTCAGTGCATGATGTTT
1 TCATCTGTAAGTCCTACAGTGCATGATGTTT
606331 TTAGGACCTC
Statistics
Matches: 328, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
76 328 1.00
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (76 bp):
TCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
AAGCCTTAGGG
Found at i:606502 original size:12 final size:11
Alignment explanation
Indices: 606485--606544 Score: 72
Period size: 11 Copynumber: 5.6 Consensus size: 11
606475 TTCATTTTTC
606485 ATTATTATTATT
1 ATTATTA-TATT
606497 ATTATTATA-T
1 ATTATTATATT
606507 A-TATTATATT
1 ATTATTATATT
606517 A-TATTATATT
1 ATTATTATATT
* *
606527 ATTATTAAATA
1 ATTATTATATT
606538 ATTATTA
1 ATTATTA
606545 CAAAGCCCAA
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
9 7 0.16
10 14 0.32
11 16 0.36
12 7 0.16
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
ATTATTATATT
Found at i:606516 original size:5 final size:5
Alignment explanation
Indices: 606487--606533 Score: 60
Period size: 5 Copynumber: 9.0 Consensus size: 5
606477 CATTTTTCAT
606487 TATTA TTATTA TTATTA TA-TA TATTA TATTA TATTA TATTA TTATTA
1 TATTA -TATTA -TATTA TATTA TATTA TATTA TATTA TATTA -TATTA
606534 AATAATTATT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
4 4 0.10
5 19 0.49
6 16 0.41
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TATTA
Found at i:606544 original size:3 final size:3
Alignment explanation
Indices: 606485--606533 Score: 61
Period size: 3 Copynumber: 17.3 Consensus size: 3
606475 TTCATTTTTC
606485 ATT ATT ATT ATT ATT ATT A-T ATAT ATT A-T ATT A-T ATT A-T ATT
1 ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT
606527 ATT ATT A
1 ATT ATT A
606534 AATAATTATT
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
2 8 0.20
3 30 0.73
4 3 0.07
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:607820 original size:3 final size:3
Alignment explanation
Indices: 607808--607854 Score: 62
Period size: 3 Copynumber: 16.0 Consensus size: 3
607798 TTATTTGCAA
*
607808 TAT TATT TAT TAT TAT TAT TAT TAT T-T CAT TAT TAT T-T TAT TAT
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
607852 TAT
1 TAT
607855 ATATATATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 3 0.08
3 33 0.85
4 3 0.08
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:607830 original size:19 final size:19
Alignment explanation
Indices: 607808--607852 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
607798 TTATTTGCAA
607808 TATTATTT-ATTATTATTAT
1 TATTATTTCATTATTATT-T
607827 TATTATTTCATTATTATTT
1 TATTATTTCATTATTATTT
607846 TATTATT
1 TATTATT
607853 ATATATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (19 bp):
TATTATTTCATTATTATTT
Found at i:607848 original size:28 final size:30
Alignment explanation
Indices: 607784--607854 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
607774 TTTTAATTCC
607784 TTTTATT-TTAATCATTATTTGCAATATTAT
1 TTTTATTATT-ATCATTATTTGCAATATTAT
* *
607814 TTATTATTATTATTATTATTT-CATTATTA-
1 TT-TTATTATTATCATTATTTGCAATATTAT
607843 TTTTATTATTAT
1 TTTTATTATTAT
607855 ATATATATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
28 10 0.27
29 2 0.05
30 9 0.24
31 14 0.38
32 2 0.05
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (30 bp):
TTTTATTATTATCATTATTTGCAATATTAT
Found at i:607859 original size:2 final size:2
Alignment explanation
Indices: 607852--607891 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
607842 ATTTTATTAT
607852 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
607892 ATAATATTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:608089 original size:119 final size:119
Alignment explanation
Indices: 607960--608177 Score: 269
Period size: 120 Copynumber: 1.8 Consensus size: 119
607950 TTTTAATATA
* * * * *
607960 TATTTATTTATTTTTCAATAT-TAAGAAAGGA-CAGTCTTAAAACAACTGGATGCCCATTTTCTG
1 TATTTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGCCC-TTTTATG
*
608023 ATATTTTTAAATAAATAAATATCCTATTTTATAAATTATCTATTATTTGTTTTAAT
65 ATATTTCTAAATAAATAAATATCCTA-TTTATAAATTATCTATTATTTGTTTTAAT
* * * ** * *
608079 TATTTGTTTATTTTTTAATATCGAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTCCTTTTATGA
1 TATTTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGCCCTTTTATGA
**
608144 TATTTCTAAATAAATAAATATTTTATTTATAAAT
66 TATTTCTAAATAAATAAATATCCTATTTATAAAT
608178 ATATATAAAT
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
119 28 0.34
120 37 0.45
121 17 0.21
ACGTcount: A:0.36, C:0.10, G:0.09, T:0.45
Consensus pattern (119 bp):
TATTTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGCCCTTTTATGA
TATTTCTAAATAAATAAATATCCTATTTATAAATTATCTATTATTTGTTTTAAT
Found at i:608187 original size:29 final size:32
Alignment explanation
Indices: 608153--608212 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 32
608143 ATATTTCTAA
608153 ATAAA-TAA-ATATTTTATTT-ATAAATATAT
1 ATAAATTAATATATTTTATTTCATAAATATAT
* *
608182 ATAAATTAATATATTTTTTTTCATAATTATA
1 ATAAATTAATATATTTTATTTCATAAATATA
608213 ATTTTGAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 5 0.19
30 3 0.12
31 10 0.38
32 8 0.31
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (32 bp):
ATAAATTAATATATTTTATTTCATAAATATAT
Found at i:609507 original size:23 final size:24
Alignment explanation
Indices: 609476--609521 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
609466 AATAGAATAT
* *
609476 AATATATATAACACCAAT-ATAAA
1 AATAAATATAACAACAATCATAAA
609499 AATAAATATAACAACAATCATAA
1 AATAAATATAACAACAATCATAA
609522 CGTTAACAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.63, C:0.13, G:0.00, T:0.24
Consensus pattern (24 bp):
AATAAATATAACAACAATCATAAA
Found at i:615644 original size:22 final size:22
Alignment explanation
Indices: 615610--615655 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
615600 TACGGAAGTA
*
615610 CTGTATCAAGGGAATCGGTTCC
1 CTGTAGCAAGGGAATCGGTTCC
*
615632 CTGTAGCAGGGGAATCGGTTCC
1 CTGTAGCAAGGGAATCGGTTCC
615654 CT
1 CT
615656 ATTTGTAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.20, C:0.24, G:0.30, T:0.26
Consensus pattern (22 bp):
CTGTAGCAAGGGAATCGGTTCC
Found at i:615726 original size:25 final size:25
Alignment explanation
Indices: 615698--615746 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
615688 GCTGTAGCAG
*
615698 GGTAATGTAGCACGTTACTGTTCAC
1 GGTAATGTAGAACGTTACTGTTCAC
* *
615723 GGTAATGTAGAAGGTTATTGTTCA
1 GGTAATGTAGAACGTTACTGTTCA
615747 TTACTGTTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.35
Consensus pattern (25 bp):
GGTAATGTAGAACGTTACTGTTCAC
Found at i:621554 original size:45 final size:47
Alignment explanation
Indices: 621503--621595 Score: 118
Period size: 45 Copynumber: 2.0 Consensus size: 47
621493 TTCTTAAGGA
* * * *
621503 ATTTCTATGTGGTCCTTAGGGACATA-T-TATGTGGCATTTCGGTGC
1 ATTTCTACGCGGTCCTTAGGGACAAATTCTATGTGGCACTTCGGTGC
* *
621548 ATTTCTACGCGTTCCTTCGGGACAAATTCTATGTGGCACTTCGGTGC
1 ATTTCTACGCGGTCCTTAGGGACAAATTCTATGTGGCACTTCGGTGC
621595 A
1 A
621596 AATTTATACA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
45 21 0.52
46 1 0.03
47 18 0.45
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.37
Consensus pattern (47 bp):
ATTTCTACGCGGTCCTTAGGGACAAATTCTATGTGGCACTTCGGTGC
Found at i:622278 original size:25 final size:25
Alignment explanation
Indices: 622209--622278 Score: 122
Period size: 25 Copynumber: 2.8 Consensus size: 25
622199 AGTAGAGTAA
* *
622209 TGTAGCAGGTTACTGTTCACGGTAC
1 TGTAGCAGGTTATTGTTCATGGTAC
622234 TGTAGCAGGTTATTGTTCATGGTAC
1 TGTAGCAGGTTATTGTTCATGGTAC
622259 TGTAGCAGGTTATTGTTCAT
1 TGTAGCAGGTTATTGTTCAT
622279 TACTGTTCAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.20, C:0.14, G:0.27, T:0.39
Consensus pattern (25 bp):
TGTAGCAGGTTATTGTTCATGGTAC
Found at i:622287 original size:10 final size:10
Alignment explanation
Indices: 622272--622298 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
622262 AGCAGGTTAT
622272 TGTTCATTAC
1 TGTTCATTAC
622282 TGTTCATTAC
1 TGTTCATTAC
622292 TGTTCAT
1 TGTTCAT
622299 ACGTATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.19, C:0.19, G:0.11, T:0.52
Consensus pattern (10 bp):
TGTTCATTAC
Found at i:631978 original size:59 final size:59
Alignment explanation
Indices: 631886--632006 Score: 224
Period size: 59 Copynumber: 2.1 Consensus size: 59
631876 AATAGATGGA
631886 TAAGTATCCTATCGAACCCTCCTAGTAGCAATGAAAAGGCAAACTCGATAATATGGCTC
1 TAAGTATCCTATCGAACCCTCCTAGTAGCAATGAAAAGGCAAACTCGATAATATGGCTC
* *
631945 TAAGTGTCCTATCGAACCCTCCTAGTCGCAATGAAAAGGCAAACTCGATAATATGGCTC
1 TAAGTATCCTATCGAACCCTCCTAGTAGCAATGAAAAGGCAAACTCGATAATATGGCTC
632004 TAA
1 TAA
632007 ACAACCCTCC
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (59 bp):
TAAGTATCCTATCGAACCCTCCTAGTAGCAATGAAAAGGCAAACTCGATAATATGGCTC
Found at i:634643 original size:15 final size:15
Alignment explanation
Indices: 634619--634652 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
634609 ATGCCAAAGG
*
634619 AAGGGCATCGATACT
1 AAGGGCATCGATAAT
*
634634 AAGGGTATCGATAAT
1 AAGGGCATCGATAAT
634649 AAGG
1 AAGG
634653 TATAAGTATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.12, G:0.29, T:0.21
Consensus pattern (15 bp):
AAGGGCATCGATAAT
Found at i:635124 original size:15 final size:15
Alignment explanation
Indices: 635104--635142 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
635094 AGAATATAAG
635104 TATATGTATATGTGT
1 TATATGTATATGTGT
635119 TATATGTATATGTGT
1 TATATGTATATGTGT
635134 TATATGTAT
1 TATATGTAT
635143 TGTTCTACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.28, C:0.00, G:0.18, T:0.54
Consensus pattern (15 bp):
TATATGTATATGTGT
Found at i:635486 original size:23 final size:23
Alignment explanation
Indices: 635428--635486 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 23
635418 CGAGAGTTCT
* *
635428 ACGCGGTCCTTCGGGACAATTCT
1 ACGCGGTCATTCGGGACAATTCA
** *
635451 ACATGGT-ACTTCGGGACATTTCA
1 ACGCGGTCA-TTCGGGACAATTCA
635474 ACGCGGTCATTCG
1 ACGCGGTCATTCG
635487 AGATAATACT
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.20, C:0.27, G:0.25, T:0.27
Consensus pattern (23 bp):
ACGCGGTCATTCGGGACAATTCA
Found at i:639573 original size:15 final size:15
Alignment explanation
Indices: 639549--639582 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
639539 ATACCAAAGG
639549 AAGGGCATCGATACT
1 AAGGGCATCGATACT
*
639564 AAGGGTATCGATACT
1 AAGGGCATCGATACT
639579 AAGG
1 AAGG
639583 TATAAGTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.35, C:0.15, G:0.29, T:0.21
Consensus pattern (15 bp):
AAGGGCATCGATACT
Found at i:640185 original size:23 final size:23
Alignment explanation
Indices: 640159--640260 Score: 75
Period size: 23 Copynumber: 4.4 Consensus size: 23
640149 GGTTCTACAC
640159 GGTCCTTCGGGACAATTCTATGT
1 GGTCCTTCGGGACAATTCTATGT
* * *
640182 GGTCCTTCGAGACATTTCTACGT
1 GGTCCTTCGGGACAATTCTATGT
*
640205 GGT--TATCAGGGACAATACTATGT
1 GGTCCT-TC-GGGACAATTCTATGT
* * * * *
640228 GATCATTTGAGACATTTCTATGT
1 GGTCCTTCGGGACAATTCTATGT
640251 GG-CACTTCGG
1 GGTC-CTTCGG
640261 TGAAATTTAT
Statistics
Matches: 58, Mismatches: 16, Indels: 10
0.69 0.19 0.12
Matches are distributed among these distances:
21 1 0.02
22 3 0.05
23 52 0.90
24 1 0.02
25 1 0.02
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.34
Consensus pattern (23 bp):
GGTCCTTCGGGACAATTCTATGT
Found at i:642878 original size:59 final size:59
Alignment explanation
Indices: 642742--642878 Score: 195
Period size: 59 Copynumber: 2.3 Consensus size: 59
642732 CAGTAGGCTG
* * *
642742 CATATTCGGGATTACACTAAAGTATAACTAGTGCATATGGTGGGCACGACCTTATGTGT
1 CATATTCGGGATTACACTAAAATATAACTAGTGCAGATGGTGGACACGACCTTATGTGT
* * *
642801 CATATTCGGGACTACACTAAAATATAACTAGTGTAGATGGTGGACACGACCTTATGTTT
1 CATATTCGGGATTACACTAAAATATAACTAGTGCAGATGGTGGACACGACCTTATGTGT
*
642860 CATACTCGGG-TTAGCACTA
1 CATATTCGGGATTA-CACTA
642879 CGGTGTATAT
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
58 2 0.03
59 67 0.97
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (59 bp):
CATATTCGGGATTACACTAAAATATAACTAGTGCAGATGGTGGACACGACCTTATGTGT
Found at i:646919 original size:19 final size:19
Alignment explanation
Indices: 646891--646927 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 19
646881 GTGCTACAAT
646891 AAAAAGAAACAACAAAGAAG
1 AAAAAGAAACAA-AAAGAAG
646911 AAAAA-AAACAAAAAGAA
1 AAAAAGAAACAAAAAGAA
646928 AATAAAAGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 6 0.35
20 5 0.29
ACGTcount: A:0.81, C:0.08, G:0.11, T:0.00
Consensus pattern (19 bp):
AAAAAGAAACAAAAAGAAG
Found at i:646928 original size:15 final size:17
Alignment explanation
Indices: 646901--646934 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
646891 AAAAAGAAAC
646901 AACAAAGAAGAAAA-AA
1 AACAAAGAAGAAAATAA
646917 AACAAA-AAGAAAATAA
1 AACAAAGAAGAAAATAA
646933 AA
1 AA
646935 GACTCCTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.82, C:0.06, G:0.09, T:0.03
Consensus pattern (17 bp):
AACAAAGAAGAAAATAA
Found at i:646934 original size:19 final size:20
Alignment explanation
Indices: 646891--646936 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
646881 GTGCTACAAT
*
646891 AAAAAGAAACAACAAAGAAG
1 AAAAAGAAACAACAAAGAAA
646911 AAAAA-AAACAA-AAAGAAA
1 AAAAAGAAACAACAAAGAAA
646929 ATAAAAGA
1 A-AAAAGA
646937 CTCCTATAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 7 0.30
19 10 0.43
20 6 0.26
ACGTcount: A:0.80, C:0.07, G:0.11, T:0.02
Consensus pattern (20 bp):
AAAAAGAAACAACAAAGAAA
Found at i:647021 original size:28 final size:26
Alignment explanation
Indices: 646965--647022 Score: 64
Period size: 28 Copynumber: 2.2 Consensus size: 26
646955 AGTGCCAAAG
*
646965 AAAGAAAAGAAAAAGAAGAAATATTC
1 AAAGAAAAGAAAAAGAAGAAATATGC
*
646991 AAAGAAAAAGAAAAGTGAAGAAAGT-TGC
1 AAAG-AAAAGAAAA-AGAAGAAA-TATGC
647019 AAAG
1 AAAG
647023 TACATTCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 4 0.15
27 9 0.33
28 13 0.48
29 1 0.04
ACGTcount: A:0.66, C:0.03, G:0.21, T:0.10
Consensus pattern (26 bp):
AAAGAAAAGAAAAAGAAGAAATATGC
Found at i:647172 original size:16 final size:16
Alignment explanation
Indices: 647138--647186 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
647128 GTAAGTTATC
* * *
647138 TTCACTTTCTTACTAT
1 TTCATTTTCTTATTCT
647154 TTCATTTTCTTATTCT
1 TTCATTTTCTTATTCT
647170 TTCATCTATTCTTATTC
1 TTCAT-T-TTCTTATTC
647187 CATTACCTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 18 0.64
17 1 0.04
18 9 0.32
ACGTcount: A:0.16, C:0.22, G:0.00, T:0.61
Consensus pattern (16 bp):
TTCATTTTCTTATTCT
Found at i:651271 original size:16 final size:16
Alignment explanation
Indices: 651237--651285 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
651227 GTAAGTTATC
* * *
651237 TTCACTTTCTTACTAT
1 TTCATTTTCTTATTCT
651253 TTCATTTTCTTATTCT
1 TTCATTTTCTTATTCT
651269 TTCATCTATTCTTATTC
1 TTCAT-T-TTCTTATTC
651286 CATTACCTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 18 0.64
17 1 0.04
18 9 0.32
ACGTcount: A:0.16, C:0.22, G:0.00, T:0.61
Consensus pattern (16 bp):
TTCATTTTCTTATTCT
Found at i:660346 original size:18 final size:18
Alignment explanation
Indices: 660320--660356 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
660310 GTTTTTGGGG
*
660320 AATTAGAATCTGTGAAGA
1 AATTAGAATCTGTCAAGA
*
660338 AATTGGAATCTGTCAAGA
1 AATTAGAATCTGTCAAGA
660356 A
1 A
660357 TTGAAATCCA
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:0.43, C:0.08, G:0.22, T:0.27
Consensus pattern (18 bp):
AATTAGAATCTGTCAAGA
Found at i:660364 original size:17 final size:18
Alignment explanation
Indices: 660326--660364 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
660316 GGGGAATTAG
* *
660326 AATCTGTGAAGAAATTGG
1 AATCTGTCAAGAAATTGA
660344 AATCTGTCAAG-AATTGA
1 AATCTGTCAAGAAATTGA
660361 AATC
1 AATC
660365 CAATTTCATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.41, C:0.10, G:0.21, T:0.28
Consensus pattern (18 bp):
AATCTGTCAAGAAATTGA
Found at i:670991 original size:31 final size:32
Alignment explanation
Indices: 670956--671021 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
670946 GATATTCGGG
670956 TCGAGTCGAGTCGG-GTTTTTAAGTATGATAT
1 TCGAGTCGAGTCGGAGTTTTTAAGTATGATAT
* * * *
670987 TCGAGTTGGGTCGGATTTTTTAAGTGTGATAT
1 TCGAGTCGAGTCGGAGTTTTTAAGTATGATAT
671019 TCG
1 TCG
671022 GGTCTGGTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 12 0.40
32 18 0.60
ACGTcount: A:0.20, C:0.09, G:0.30, T:0.41
Consensus pattern (32 bp):
TCGAGTCGAGTCGGAGTTTTTAAGTATGATAT
Found at i:671610 original size:17 final size:18
Alignment explanation
Indices: 671585--671630 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
671575 ATATGAATTG
*
671585 GATTCCAATTCC-TGACA
1 GATTCCAATTCCTTCACA
*
671602 GATTTCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
671620 GATTCCAATTC
1 GATTCCAATTC
671631 TCTCAGAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.35
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:673917 original size:35 final size:35
Alignment explanation
Indices: 673871--673944 Score: 148
Period size: 35 Copynumber: 2.1 Consensus size: 35
673861 TTACAAGCAC
673871 ATTAACTAATACTTTTGTTGACTTTTGCAGATTCA
1 ATTAACTAATACTTTTGTTGACTTTTGCAGATTCA
673906 ATTAACTAATACTTTTGTTGACTTTTGCAGATTCA
1 ATTAACTAATACTTTTGTTGACTTTTGCAGATTCA
673941 ATTA
1 ATTA
673945 CTTTGGGACC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.46
Consensus pattern (35 bp):
ATTAACTAATACTTTTGTTGACTTTTGCAGATTCA
Found at i:676001 original size:37 final size:37
Alignment explanation
Indices: 675954--676042 Score: 133
Period size: 37 Copynumber: 2.4 Consensus size: 37
675944 TTTTGTTCAG
*
675954 GTCGGATCGGGTTTTTTAAGTGTGATATTCGGGTCGA
1 GTCGGATCGGGTTTTTTAAGTGTGATATTCAGGTCGA
* *
675991 GTCGGGTCGGGTTTTTTAAGTGTGATATTCAGGTCGG
1 GTCGGATCGGGTTTTTTAAGTGTGATATTCAGGTCGA
*
676028 GTCGGCTTCGGGTTT
1 GTCGG-ATCGGGTTT
676043 AGGGTGAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
37 39 0.83
38 8 0.17
ACGTcount: A:0.12, C:0.12, G:0.37, T:0.38
Consensus pattern (37 bp):
GTCGGATCGGGTTTTTTAAGTGTGATATTCAGGTCGA
Found at i:676636 original size:17 final size:17
Alignment explanation
Indices: 676611--676675 Score: 85
Period size: 17 Copynumber: 3.8 Consensus size: 17
676601 TATGGAATTG
*
676611 GATTTCAATTCCTGACA
1 GATTCCAATTCCTGACA
676628 GATTCCAATTCCTGACA
1 GATTCCAATTCCTGACA
* *
676645 GATTTCAATTCCTTCACA
1 GATTCCAATTCC-TGACA
*
676663 GATTCTAATTCCT
1 GATTCCAATTCCT
676676 TCAGAAATAT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
17 28 0.67
18 14 0.33
ACGTcount: A:0.28, C:0.26, G:0.09, T:0.37
Consensus pattern (17 bp):
GATTCCAATTCCTGACA
Found at i:676676 original size:18 final size:18
Alignment explanation
Indices: 676625--676678 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
676615 TCAATTCCTG
* *
676625 ACAGATTCCAATTCC-TG
1 ACAGATTCTAATTCCTTC
676642 ACAGATT-TCAATTCCTTC
1 ACAGATTCT-AATTCCTTC
676660 ACAGATTCTAATTCCTTC
1 ACAGATTCTAATTCCTTC
676678 A
1 A
676679 GAAATATTCC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
17 13 0.41
18 18 0.56
19 1 0.03
ACGTcount: A:0.30, C:0.28, G:0.07, T:0.35
Consensus pattern (18 bp):
ACAGATTCTAATTCCTTC
Found at i:679192 original size:36 final size:36
Alignment explanation
Indices: 679145--679393 Score: 390
Period size: 36 Copynumber: 6.9 Consensus size: 36
679135 GATATGTTCC
* *
679145 TGCTTCACTACTCTTTTGTGAATGCTGGATTTGTAT
1 TGCTTCACTACTCTTTTGTGAAGGCTGGATTTGCAT
*
679181 TGCTTCACTACTCTTTTGTGAAGGCTGGATTTGTAT
1 TGCTTCACTACTCTTTTGTGAAGGCTGGATTTGCAT
679217 TGCTTCACTACTCTTTTGTGAAGGCTGGATTTGCAT
1 TGCTTCACTACTCTTTTGTGAAGGCTGGATTTGCAT
* *
679253 CGCTTCACTACTCTTTTGTGAATGCTGGATTTGCAT
1 TGCTTCACTACTCTTTTGTGAAGGCTGGATTTGCAT
679289 TGCTTCACTACTCTTTTGTGAAGGCTGGATTTGCAT
1 TGCTTCACTACTCTTTTGTGAAGGCTGGATTTGCAT
* * *
679325 TGCTTCACTACTCTTTTTTGAAGGCTAGATTTGGAT
1 TGCTTCACTACTCTTTTGTGAAGGCTGGATTTGCAT
* * * *
679361 CGCTTCATTACTCTTTTGTGAATGATGGATTTG
1 TGCTTCACTACTCTTTTGTGAAGGCTGGATTTG
679394 AGGCTGATTT
Statistics
Matches: 198, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 198 1.00
ACGTcount: A:0.17, C:0.18, G:0.21, T:0.44
Consensus pattern (36 bp):
TGCTTCACTACTCTTTTGTGAAGGCTGGATTTGCAT
Found at i:679335 original size:108 final size:108
Alignment explanation
Indices: 679146--679393 Score: 433
Period size: 108 Copynumber: 2.3 Consensus size: 108
679136 ATATGTTCCT
*
679146 GCTTCACTACTCTTTTGTGAATGCTGGATTTGTATTGCTTCACTACTCTTTTGTGAAGGCTGGAT
1 GCTTCACTACTCTTTTGTGAATGCTGGATTTGCATTGCTTCACTACTCTTTTGTGAAGGCTGGAT
* *
679211 TTGTATTGCTTCACTACTCTTTTGTGAAGGCTGGATTTGCATC
66 TTGCATTGCTTCACTACTCTTTTGTGAAGGCTAGATTTGCATC
679254 GCTTCACTACTCTTTTGTGAATGCTGGATTTGCATTGCTTCACTACTCTTTTGTGAAGGCTGGAT
1 GCTTCACTACTCTTTTGTGAATGCTGGATTTGCATTGCTTCACTACTCTTTTGTGAAGGCTGGAT
* *
679319 TTGCATTGCTTCACTACTCTTTTTTGAAGGCTAGATTTGGATC
66 TTGCATTGCTTCACTACTCTTTTGTGAAGGCTAGATTTGCATC
* *
679362 GCTTCATTACTCTTTTGTGAATGATGGATTTG
1 GCTTCACTACTCTTTTGTGAATGCTGGATTTG
679394 AGGCTGATTT
Statistics
Matches: 133, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
108 133 1.00
ACGTcount: A:0.17, C:0.18, G:0.21, T:0.44
Consensus pattern (108 bp):
GCTTCACTACTCTTTTGTGAATGCTGGATTTGCATTGCTTCACTACTCTTTTGTGAAGGCTGGAT
TTGCATTGCTTCACTACTCTTTTGTGAAGGCTAGATTTGCATC
Found at i:688788 original size:36 final size:36
Alignment explanation
Indices: 688745--688821 Score: 129
Period size: 36 Copynumber: 2.1 Consensus size: 36
688735 AGGAACGAAA
688745 TGTTTCGACTAATGTAGCAGGAATCATA-TGCATTCT
1 TGTTTCGACTAATGTAGCA-GAATCATACTGCATTCT
688781 TGTTTCGACTAATGTAGCAGAATCATATCTGCATTCT
1 TGTTTCGACTAATGTAGCAGAATCATA-CTGCATTCT
688818 TGTT
1 TGTT
688822 CAATCTTTCA
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
35 8 0.21
36 19 0.49
37 12 0.31
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.39
Consensus pattern (36 bp):
TGTTTCGACTAATGTAGCAGAATCATACTGCATTCT
Found at i:703862 original size:12 final size:12
Alignment explanation
Indices: 703847--703874 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
703837 TTCAATTAGG
703847 ATTTAAAATATT
1 ATTTAAAATATT
703859 ATTTAAAATATT
1 ATTTAAAATATT
703871 ATTT
1 ATTT
703875 TATTTTATCT
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
ATTTAAAATATT
Found at i:704449 original size:18 final size:18
Alignment explanation
Indices: 704426--704486 Score: 95
Period size: 18 Copynumber: 3.4 Consensus size: 18
704416 CTTTATATTA
704426 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTTTCT
704444 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTTTCT
* * *
704462 GTTATTTAATTCTTATCT
1 TTTATTTAATTATTTTCT
704480 TTTATTT
1 TTTATTT
704487 TAAAAGAAGT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.21, C:0.07, G:0.02, T:0.70
Consensus pattern (18 bp):
TTTATTTAATTATTTTCT
Found at i:707236 original size:9 final size:9
Alignment explanation
Indices: 707222--707253 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
707212 TGAAACATTC
*
707222 TCATCCTTG
1 TCATCCTCG
707231 TCATCCTCG
1 TCATCCTCG
707240 TCATCCTCG
1 TCATCCTCG
707249 TCATC
1 TCATC
707254 ATCTCTCCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.12, C:0.41, G:0.09, T:0.38
Consensus pattern (9 bp):
TCATCCTCG
Found at i:707369 original size:15 final size:15
Alignment explanation
Indices: 707333--707377 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
707323 TTCAGTCTAT
*
707333 TCTTCATCAGCATCA
1 TCTTCATCATCATCA
707348 T-TGTCATCATCATCA
1 TCT-TCATCATCATCA
*
707363 TCTTCATCCTCATCA
1 TCTTCATCATCATCA
707378 GCAATCCCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 1 0.04
15 24 0.92
16 1 0.04
ACGTcount: A:0.24, C:0.33, G:0.04, T:0.38
Consensus pattern (15 bp):
TCTTCATCATCATCA
Found at i:709185 original size:24 final size:24
Alignment explanation
Indices: 709153--709208 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
709143 CTATTCTTTC
709153 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
709177 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
709201 GCTTCAAT
1 GCTTCAAT
709209 CGAACTTCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (24 bp):
GCTTCAATTGAGCTCAAATTTTAG
Found at i:709467 original size:30 final size:30
Alignment explanation
Indices: 709431--709496 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
709421 AGTGAACCGG
* * *
709431 CGGTTCAAATCGGTTTTGCCGATTTTCAGC
1 CGGTTCAAACCGATTTTCCCGATTTTCAGC
**
709461 CGGTTCACCCCGATTTTCCCGATTTTCAGC
1 CGGTTCAAACCGATTTTCCCGATTTTCAGC
709491 CGGTTC
1 CGGTTC
709497 TTCCAGTTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.14, C:0.30, G:0.21, T:0.35
Consensus pattern (30 bp):
CGGTTCAAACCGATTTTCCCGATTTTCAGC
Done.