Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 363 of 438
Found at i:113364629 original size:26 final size:26
Alignment explanation
Indices: 113364600--113364654 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
113364590 TGATACAAAT
113364600 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
113364626 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
113364652 TGA
1 TGA
113364655 CGGGAATTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.31, C:0.07, G:0.27, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:113366323 original size:27 final size:26
Alignment explanation
Indices: 113366266--113366371 Score: 115
Period size: 27 Copynumber: 3.9 Consensus size: 26
113366256 AGGAAGCGTC
* * *
113366266 CTGGTGGCTATGCTACAAATTATCTGAT
1 CTGGTGGCTCTGCCAC-AA-TATCTGTT
113366294 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACA-ATATCTGTT
113366321 CTGGTGGCTCTGCCACAATATCTGTAT
1 CTGGTGGCTCTGCCACAATATCTGT-T
* *
113366348 CTGGTGACT-TCGTCACAATATCTG
1 CTGGTGGCTCT-GCCACAATATCTG
113366372 GCAGCCTCGC
Statistics
Matches: 70, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
26 9 0.13
27 46 0.66
28 15 0.21
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.35
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACAATATCTGTT
Found at i:113368739 original size:10 final size:10
Alignment explanation
Indices: 113368724--113368758 Score: 52
Period size: 10 Copynumber: 3.3 Consensus size: 10
113368714 AAAACCCTAT
113368724 TTTTTCTTTC
1 TTTTTCTTTC
113368734 TTTTTCTTTCCC
1 TTTTTCTTT--C
113368746 TTTTTCTTTC
1 TTTTTCTTTC
113368756 TTT
1 TTT
113368759 CTTTCCCTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 13 0.57
12 10 0.43
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTTTCTTTC
Found at i:113368749 original size:22 final size:20
Alignment explanation
Indices: 113368724--113368771 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 20
113368714 AAAACCCTAT
113368724 TTTTTCTTTCTTTTTCTTTCCC
1 TTTTTCTTTC--TTTCTTTCCC
113368746 TTTTTCTTTCTTTCTTTCCC
1 TTTTTCTTTCTTTCTTTCCC
113368766 TGTTTT
1 T-TTTT
113368772 GTACGTGCCC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.44
21 4 0.16
22 10 0.40
ACGTcount: A:0.00, C:0.25, G:0.02, T:0.73
Consensus pattern (20 bp):
TTTTTCTTTCTTTCTTTCCC
Found at i:113369287 original size:21 final size:21
Alignment explanation
Indices: 113369237--113369310 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
113369227 CACTCACAAT
* *
113369237 CGGAGCACCCACAACCCCTGC
1 CGGAGCAACCACAACCCCCGC
*
113369258 CGGAGCAACCACAACCCCCGT
1 CGGAGCAACCACAACCCCCGC
* * **
113369279 TGGATCAACCACAACCCCCAT
1 CGGAGCAACCACAACCCCCGC
113369300 CGGAGCAACCA
1 CGGAGCAACCA
113369311 ATAAGGAATC
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.30, C:0.46, G:0.18, T:0.07
Consensus pattern (21 bp):
CGGAGCAACCACAACCCCCGC
Found at i:113370256 original size:26 final size:24
Alignment explanation
Indices: 113370217--113370275 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 24
113370207 TTATTTCATT
* *
113370217 AAATAAA-AAATTTAAAAATATAA
1 AAATAAATATATTTAAAAACATAA
113370240 TAAATCAAATATATTTAAAAACATAA
1 -AAAT-AAATATATTTAAAAACATAA
113370266 AAATAAATAT
1 AAATAAATAT
113370276 TAAAACAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 10 0.32
25 7 0.23
26 14 0.45
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (24 bp):
AAATAAATATATTTAAAAACATAA
Found at i:113370287 original size:22 final size:22
Alignment explanation
Indices: 113370246--113370304 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
113370236 ATAATAAATC
* *
113370246 AAATATAT-TTAAAA-ACATAA
1 AAATAAATATTAAAACAAATAA
113370266 AAATAAATATTAAAACAAATAA
1 AAATAAATATTAAAACAAATAA
*
113370288 AAAT-AATACTAAAACAA
1 AAATAAATATTAAAACAA
113370305 TTCTTAAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.21
21 18 0.53
22 9 0.26
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (22 bp):
AAATAAATATTAAAACAAATAA
Found at i:113370381 original size:15 final size:16
Alignment explanation
Indices: 113370351--113370383 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
113370341 AAATAGTTAT
113370351 ATTAAAAATTTAAAATA
1 ATTAAAAA-TTAAAATA
113370368 ATTAAAAA-TAAAATA
1 ATTAAAAATTAAAATA
113370383 A
1 A
113370384 ATATATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
17 8 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
ATTAAAAATTAAAATA
Found at i:113374236 original size:4 final size:4
Alignment explanation
Indices: 113374229--113374256 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
113374219 TATATATGTT
113374229 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
113374257 GATTGATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:113374468 original size:24 final size:22
Alignment explanation
Indices: 113374441--113374486 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
113374431 TTTGGTTTTC
113374441 TTTTTT-ATTTATATTGTTTGAATT
1 TTTTTTAATTT-TATT-TTT-AATT
113374465 TTTTTTAATTTTATTTTTAATT
1 TTTTTTAATTTTATTTTTAATT
113374487 AATTTTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 4 0.19
23 3 0.14
24 10 0.48
25 4 0.19
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (22 bp):
TTTTTTAATTTTATTTTTAATT
Found at i:113374492 original size:24 final size:26
Alignment explanation
Indices: 113374441--113374499 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 26
113374431 TTTGGTTTTC
113374441 TTTTTT-ATTTATATTGTTTGAA-TT
1 TTTTTTAATTTATATTGTTTGAATTT
113374465 TTTTTTAATTT-TATT-TTT-AATTAAT
1 TTTTTTAATTTATATTGTTTGAATT--T
113374490 TTTTTTAATT
1 TTTTTTAATT
113374500 AATAAACAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
22 2 0.06
23 4 0.13
24 10 0.32
25 15 0.48
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (26 bp):
TTTTTTAATTTATATTGTTTGAATTT
Found at i:113374494 original size:13 final size:13
Alignment explanation
Indices: 113374464--113374502 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
113374454 TTGTTTGAAT
113374464 TTTTTTTAATT--
1 TTTTTTTAATTAA
113374475 TTATTTTTAATTAA
1 TT-TTTTTAATTAA
113374489 TTTTTTTAATTAA
1 TTTTTTTAATTAA
113374502 T
1 T
113374503 AAACAAGGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.08
12 9 0.36
13 12 0.48
14 2 0.08
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTTTAATTAA
Found at i:113382387 original size:16 final size:16
Alignment explanation
Indices: 113382363--113382396 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
113382353 AATTAAGTAA
*
113382363 AATATATAAATTTTAT
1 AATAAATAAATTTTAT
113382379 AATAAATAAATTTTAT
1 AATAAATAAATTTTAT
113382395 AA
1 AA
113382397 AAAAATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AATAAATAAATTTTAT
Found at i:113387816 original size:20 final size:19
Alignment explanation
Indices: 113387793--113387842 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
113387783 TGTTAAAAAA
113387793 TATATTTTTTAAAATTAATT
1 TATATTTTTTAAAA-TAATT
* *
113387813 TATA-TTTTTGAAATACTT
1 TATATTTTTTAAAATAATT
*
113387831 TTTATTTTTTAA
1 TATATTTTTTAA
113387843 TTTATGTCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 7 0.28
19 14 0.56
20 4 0.16
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (19 bp):
TATATTTTTTAAAATAATT
Found at i:113391401 original size:4 final size:4
Alignment explanation
Indices: 113391394--113391475 Score: 51
Period size: 4 Copynumber: 20.5 Consensus size: 4
113391384 CTTTTGTTTG
* * * * * *
113391394 TTTA TTTA TTTA TTCA TCTA TTTA TTTG TTTA TATA TATA TATA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * *
113391442 -TTA -TTC TTTA GTTTTA TTTA TTCA TTCA TTTA TT
1 TTTA TTTA TTTA --TTTA TTTA TTTA TTTA TTTA TT
113391476 AGTAAATATT
Statistics
Matches: 63, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
3 5 0.08
4 54 0.86
6 4 0.06
ACGTcount: A:0.26, C:0.06, G:0.02, T:0.66
Consensus pattern (4 bp):
TTTA
Found at i:113391651 original size:3 final size:3
Alignment explanation
Indices: 113391643--113391668 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
113391633 CATTTTATTT
113391643 ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC AT
113391669 TATTATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:113391673 original size:3 final size:3
Alignment explanation
Indices: 113391667--113391724 Score: 64
Period size: 3 Copynumber: 19.7 Consensus size: 3
113391657 CATCATCATC
* * * *
113391667 ATT ATT ATT ATT ATT ATT ATT ACT ATT ATC ATT ATT A-T ACT ATT ACT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
113391714 ATT AGT ATT AT
1 ATT ATT ATT AT
113391725 ATTTATATTC
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
2 2 0.04
3 43 0.96
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:113392437 original size:27 final size:28
Alignment explanation
Indices: 113392407--113392465 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
113392397 GTATTATTTT
113392407 AATTT-ATTTAACATATTA-TTTATTTAA
1 AATTTGATTT-ACATATTACTTTATTTAA
* * *
113392434 AATTTGCTTTATATATTACTTTATTTCA
1 AATTTGATTTACATATTACTTTATTTAA
113392462 AATT
1 AATT
113392466 GTTTATATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 12 0.44
28 15 0.56
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.56
Consensus pattern (28 bp):
AATTTGATTTACATATTACTTTATTTAA
Found at i:113392472 original size:24 final size:26
Alignment explanation
Indices: 113392419--113392482 Score: 76
Period size: 28 Copynumber: 2.4 Consensus size: 26
113392409 TTTATTTAAC
113392419 ATATTATTTATTTAAAATTTGCTTTAT
1 ATATTATTTATTTAAAATTTGC-TTAT
* *
113392446 ATATTACTTTATTTCAAA-TTGTTTAT
1 ATATTA-TTTATTTAAAATTTGCTTAT
*
113392472 ATTTTATTTAT
1 ATATTATTTAT
113392483 GTTGAATCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 5 0.15
26 9 0.27
27 9 0.27
28 10 0.30
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.61
Consensus pattern (26 bp):
ATATTATTTATTTAAAATTTGCTTAT
Found at i:113395432 original size:46 final size:46
Alignment explanation
Indices: 113395388--113395700 Score: 439
Period size: 46 Copynumber: 6.8 Consensus size: 46
113395378 CTCTGATATA
* *
113395388 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG
1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATG
* * * * *
113395434 AAACGTGTAAGACCATGGTTGAAAGATGCCATAGCAACCTGATATG
1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATG
*
113395480 AAATGTGTAAGACCATAGTTGAAAGATACCATGGCAACGTGACATG
1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATG
113395526 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATG
1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATG
**
113395572 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACGGGG
1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGAC-ATG
** *
113395619 AAATGAATAAGACCATGGTTGAATGATACCATGGCAACGTGACA-G
1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATG
* * * * *
113395664 AAAATGAGTAAAACCATAGTTGAAAGACACTATGGCA
1 -AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
113395701 TCATGTCGAA
Statistics
Matches: 243, Mismatches: 22, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
45 1 0.00
46 201 0.83
47 41 0.17
ACGTcount: A:0.39, C:0.15, G:0.25, T:0.21
Consensus pattern (46 bp):
AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATG
Found at i:113397634 original size:30 final size:31
Alignment explanation
Indices: 113397590--113397648 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
113397580 CAATTCATAT
* *
113397590 ATATCTCATGTCACATAGCATGTTTCATTCC
1 ATATCTCATATCACATAGCATGTATCATTCC
*
113397621 ATAT-TCATATCACATATCATGTATCATT
1 ATATCTCATATCACATAGCATGTATCATT
113397649 TATATCACAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.41
Consensus pattern (31 bp):
ATATCTCATATCACATAGCATGTATCATTCC
Found at i:113401883 original size:35 final size:35
Alignment explanation
Indices: 113401837--113401907 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
113401827 ACAATAAGCT
113401837 TTTCCGGTTACTTGTGCATTAGATCAGAATGGATC
1 TTTCCGGTTACTTGTGCATTAGATCAGAATGGATC
113401872 TTTCCGGTTACTTGTGCATTAGATCAGAATGGATC
1 TTTCCGGTTACTTGTGCATTAGATCAGAATGGATC
113401907 T
1 T
113401908 CTCATGGTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.38
Consensus pattern (35 bp):
TTTCCGGTTACTTGTGCATTAGATCAGAATGGATC
Found at i:113406796 original size:16 final size:17
Alignment explanation
Indices: 113406775--113406808 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
113406765 TCCATGTTGC
113406775 AAAATAAAAG-AGAAAA
1 AAAATAAAAGAAGAAAA
*
113406791 AAAATAAAGGAAGAAAA
1 AAAATAAAAGAAGAAAA
113406808 A
1 A
113406809 GAAGAGGAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (17 bp):
AAAATAAAAGAAGAAAA
Found at i:113409341 original size:29 final size:30
Alignment explanation
Indices: 113409307--113409383 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 30
113409297 TTTTTTTCCT
*
113409307 AATTTGATACCTAAATTT-TTTTTGGGCCC
1 AATTTGATACCTAAATTTCTTTTTAGGCCC
* * * **
113409336 ACTTTGGTACCTAAGTTTCTTTTTAGGTTC
1 AATTTGATACCTAAATTTCTTTTTAGGCCC
*
113409366 AATTTGACACCTAAATTT
1 AATTTGATACCTAAATTT
113409384 ATTAAATGTT
Statistics
Matches: 37, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
29 15 0.41
30 22 0.59
ACGTcount: A:0.25, C:0.17, G:0.13, T:0.45
Consensus pattern (30 bp):
AATTTGATACCTAAATTTCTTTTTAGGCCC
Found at i:113425267 original size:42 final size:42
Alignment explanation
Indices: 113425188--113425268 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
113425178 CATGCAGGGG
*
113425188 ACACACGGCCAGACAACACGCCCATGAGGCTAGCCGTGTATC
1 ACACACGGCCAGACAACACGCCCATGAGGCTACCCGTGTATC
* * *
113425230 ACACACGGCCTAGAC-ACACGCCCGTGTGTCTACCCGTGT
1 ACACACGGCC-AGACAACACGCCCATGAGGCTACCCGTGT
113425269 GGATAATATA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 30 0.88
43 4 0.12
ACGTcount: A:0.25, C:0.37, G:0.23, T:0.15
Consensus pattern (42 bp):
ACACACGGCCAGACAACACGCCCATGAGGCTACCCGTGTATC
Found at i:113426257 original size:138 final size:143
Alignment explanation
Indices: 113426003--113426260 Score: 350
Period size: 138 Copynumber: 1.8 Consensus size: 143
113425993 ATGCCGATGC
113426003 CATGTCCCAGACATGGTCTTACACTGACTATCGAAATCGAGGCCGACGCCATGTCCCAGACATGG
1 CATGTCCCAGACATGGTCTTACACTGACTATCGAAATCGAGGCCGACGCCATGTCCCAGACATGG
** ** *
113426068 TTTTACACTAGCTCTCGCATATCTGTGCCAATGCCATATCCCGGACATGGTCTTATACTGACACA
66 TCATACACTAGCTCTC-CATATCCATGCCAATGCCATATCCCAGACATGGTCTTATACTGACACA
113426133 TCTCGTAGCCGGTG
130 TCTCGTAGCCGGTG
* ** *
113426147 CATGTCCCAGACAT-GTCTTACACTGGCT-TAC-ATCTCGAGGCCGATG-CATGTCCCAGACAT-
1 CATGTCCCAGACATGGTCTTACACTGACTAT-CGAAATCGAGGCCGACGCCATGTCCCAGACATG
*
113426207 GTCATACACTAGCTCT-CA-ACTCCATGCCAATGCCATGTCCCAGACATGGTCTTA
65 GTCATACACTAGCTCTCCATA-TCCATGCCAATGCCATATCCCAGACATGGTCTTA
113426261 CATTAGCTCT
Statistics
Matches: 102, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
137 1 0.01
138 32 0.31
140 14 0.14
141 14 0.14
142 13 0.13
143 14 0.14
144 14 0.14
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (143 bp):
CATGTCCCAGACATGGTCTTACACTGACTATCGAAATCGAGGCCGACGCCATGTCCCAGACATGG
TCATACACTAGCTCTCCATATCCATGCCAATGCCATATCCCAGACATGGTCTTATACTGACACAT
CTCGTAGCCGGTG
Found at i:113429110 original size:45 final size:45
Alignment explanation
Indices: 113428948--113429121 Score: 201
Period size: 45 Copynumber: 3.8 Consensus size: 45
113428938 GGTTGAGCAT
* *
113428948 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
113428993 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCAT
1 -CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--C-G
113429041 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
113429086 CCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
113429122 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 12, Indels: 17
0.79 0.09 0.12
Matches are distributed among these distances:
43 5 0.05
45 37 0.34
46 29 0.27
47 28 0.26
48 3 0.03
50 6 0.06
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (45 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:113445912 original size:46 final size:46
Alignment explanation
Indices: 113445859--113445987 Score: 197
Period size: 46 Copynumber: 2.8 Consensus size: 46
113445849 TGGTTGAGCA
*
113445859 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACG
113445905 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACG
* * * *
113445951 -CCTGAGCTCATTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCTGAGTTCACTTATGG
113445988 GCGGGTTACA
Statistics
Matches: 77, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
45 2 0.03
46 75 0.97
ACGTcount: A:0.20, C:0.19, G:0.29, T:0.32
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACG
Found at i:113454596 original size:43 final size:43
Alignment explanation
Indices: 113454549--113454665 Score: 128
Period size: 43 Copynumber: 2.7 Consensus size: 43
113454539 CAGGCAAGCC
* *
113454549 GAAGCAATTATACTGACACACGAGGTGCATTACCGAACGAACT
1 GAAGCAATTATACTGACACACGAGGTGCATCACCGAACAAACT
** ** * *
113454592 GAAGCAATTATACTGGTACAC-ATGGTGCATCATTGAATAAATT
1 GAAGCAATTATACTGACACACGA-GGTGCATCACCGAACAAACT
* *
113454635 GAAGCAATTATACTAACACACGAGATGCATC
1 GAAGCAATTATACTGACACACGAGGTGCATC
113454666 GTTAGACGAA
Statistics
Matches: 60, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
42 1 0.02
43 58 0.97
44 1 0.02
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (43 bp):
GAAGCAATTATACTGACACACGAGGTGCATCACCGAACAAACT
Found at i:113461258 original size:15 final size:16
Alignment explanation
Indices: 113461228--113461261 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
113461218 ATGGGTAAGG
113461228 CACACGGTCGTAAGCAA
1 CACACGGTCG-AAGCAA
113461245 CACACGGTCG-AGCAA
1 CACACGGTCGAAGCAA
113461260 CA
1 CA
113461262 TGGGTGTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
17 10 0.59
ACGTcount: A:0.35, C:0.32, G:0.24, T:0.09
Consensus pattern (16 bp):
CACACGGTCGAAGCAA
Found at i:113467850 original size:58 final size:57
Alignment explanation
Indices: 113467713--113467849 Score: 138
Period size: 58 Copynumber: 2.4 Consensus size: 57
113467703 TAATGAAAAA
* *
113467713 TTTC-AGCTTAACGAGCTTTTTTACCCTAACTTTTGCTTATGTCATCCAACTAAAGGT
1 TTTCTAGCTTAACGAGCTTTTTTACCCTAACTTTTGATTAAGTCATCCAAC-AAAGGT
* * * * **
113467770 TTTCTA-CTTAACAAGGGTTTTTTTCTCTAACTTTTGATTAAGTTGTCCAA-AGAAGGAT
1 TTTCTAGCTTAACGA-GCTTTTTTACCCTAACTTTTGATTAAGTCATCCAACA-AAGG-T
113467828 TTT-TAGCTTAACGAGCTTTTTT
1 TTTCTAGCTTAACGAGCTTTTTT
113467850 TGTGTAGTTT
Statistics
Matches: 65, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
56 1 0.02
57 24 0.37
58 40 0.62
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.44
Consensus pattern (57 bp):
TTTCTAGCTTAACGAGCTTTTTTACCCTAACTTTTGATTAAGTCATCCAACAAAGGT
Found at i:113468112 original size:9 final size:9
Alignment explanation
Indices: 113468098--113468123 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
113468088 GAAAAAGGGT
113468098 TGAAAATGG
1 TGAAAATGG
113468107 TGAAAATGG
1 TGAAAATGG
113468116 TGAAAATG
1 TGAAAATG
113468124 ACCTAAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (9 bp):
TGAAAATGG
Found at i:113470352 original size:40 final size:39
Alignment explanation
Indices: 113470308--113470528 Score: 271
Period size: 39 Copynumber: 5.6 Consensus size: 39
113470298 GTTCAAAACA
* * ** * *
113470308 CCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAATG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
** *
113470348 CCTTCGGGACTTAATCCGGATATCACAACTCGCACAATTG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
* *
113470388 CCTTCGGGCTTAGCCCGGGTATCATAGCTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
* * *
113470427 CCTTCGGGCTTAGCCCGGATATCATAGCTTGTACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
* * *
113470466 CCTTCGGGCTTAGCCCGGGTATCATAGCTTGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
113470505 CCTTCGGGCTTAGCCCGGATATCA
1 CCTTCGGGCTTAGCCCGGATATCA
113470529 CTCGAACATT
Statistics
Matches: 161, Mismatches: 20, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
39 122 0.76
40 39 0.24
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (39 bp):
CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
Found at i:113470422 original size:39 final size:39
Alignment explanation
Indices: 113470338--113470528 Score: 283
Period size: 39 Copynumber: 4.9 Consensus size: 39
113470328 TATGGTAACC
* ** * *
113470338 CGCACAAATGCCTTCGGGACTTAATCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCATAGCT
*
113470378 CGCACAATTGCCTTCGGGCTTAGCCCGGGTATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
113470417 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
* * *
113470456 TGTACAATTGCCTTCGGGCTTAGCCCGGGTATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
*
113470495 TGCACAATTGCCTTCGGGCTTAGCCCGGATATCA
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCA
113470529 CTCGAACATT
Statistics
Matches: 139, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
39 122 0.88
40 17 0.12
ACGTcount: A:0.21, C:0.29, G:0.23, T:0.26
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
Found at i:113475332 original size:25 final size:25
Alignment explanation
Indices: 113475304--113475352 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
113475294 CTATTTTTGA
* *
113475304 TAGTATATCCTGAAACTGCTATAGG
1 TAGTATATACTGAAACTACTATAGG
*
113475329 TAGTATATACTGAGACTACTATAG
1 TAGTATATACTGAAACTACTATAG
113475353 ATAGATTGTA
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:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (25 bp):
TAGTATATACTGAAACTACTATAGG
Found at i:113483286 original size:12 final size:12
Alignment explanation
Indices: 113483269--113483339 Score: 50
Period size: 12 Copynumber: 6.4 Consensus size: 12
113483259 AATATATGTA
113483269 TATATAATAAAT
1 TATATAATAAAT
113483281 TATATAAT-AAT
1 TATATAATAAAT
113483292 GTAT-T--TAAAT
1 -TATATAATAAAT
113483302 TAT-TAA-ATAA-
1 TATATAATA-AAT
*
113483312 TATAT-TTAAAT
1 TATATAATAAAT
*
113483323 TAAATAATAAAT
1 TATATAATAAAT
113483335 TATAT
1 TATAT
113483340 TTATTTATGT
Statistics
Matches: 46, Mismatches: 4, Indels: 18
0.68 0.06 0.26
Matches are distributed among these distances:
9 5 0.11
10 9 0.20
11 12 0.26
12 20 0.43
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (12 bp):
TATATAATAAAT
Found at i:113483301 original size:21 final size:21
Alignment explanation
Indices: 113483276--113483342 Score: 82
Period size: 21 Copynumber: 3.1 Consensus size: 21
113483266 GTATATATAA
*
113483276 TAAATTATATAATAATGTATT
1 TAAATTATATAATAATATATT
113483297 TAAATTAT-TAAATAATATATT
1 TAAATTATAT-AATAATATATT
*
113483318 TAAATTAAATAATAAATTATATT
1 TAAATTATATAAT-AA-TATATT
113483341 TA
1 TA
113483343 TTTATGTTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
20 1 0.03
21 28 0.70
22 3 0.08
23 8 0.20
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (21 bp):
TAAATTATATAATAATATATT
Found at i:113483330 original size:54 final size:56
Alignment explanation
Indices: 113483272--113483394 Score: 143
Period size: 54 Copynumber: 2.3 Consensus size: 56
113483262 ATATGTATAT
113483272 ATAATAAATTATATAATAATGTAT-TTAAA-T-T-ATTAAATAATATATTTAAATTAA
1 ATAATAAATTATATAATAATGTATGTTAAATTGTAATT-AA-AATATATTTAAATTAA
* * *
113483326 ATAATAAATTATAT--TTATTTATGTTAAATTGTAATTAAAATATATTTATATTAA
1 ATAATAAATTATATAATAATGTATGTTAAATTGTAATTAAAATATATTTAAATTAA
*
113483380 AAAATAAATT-TATAA
1 ATAATAAATTATATAA
113483395 AATATTTATA
Statistics
Matches: 59, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
52 6 0.10
53 8 0.14
54 39 0.66
55 3 0.05
56 3 0.05
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (56 bp):
ATAATAAATTATATAATAATGTATGTTAAATTGTAATTAAAATATATTTAAATTAA
Found at i:113483352 original size:27 final size:28
Alignment explanation
Indices: 113483310--113483407 Score: 94
Period size: 27 Copynumber: 3.5 Consensus size: 28
113483300 ATTATTAAAT
*
113483310 AATATATTTAAATTAAATAATAAATT-A
1 AATATATTTATATTAAATAATAAATTAA
* * * **
113483337 TATTTATTTATGTTAAATTGT-AATTAA
1 AATATATTTATATTAAATAATAAATTAA
*
113483364 AATATATTTATATTAAAAAATAAATTTATA
1 AATATATTTATATTAAATAATAAA-TTA-A
113483394 AA-ATATTTATATTA
1 AATATATTTATATTA
113483408 TATTTGTAAT
Statistics
Matches: 55, Mismatches: 12, Indels: 6
0.75 0.16 0.08
Matches are distributed among these distances:
26 4 0.07
27 31 0.56
28 2 0.04
29 15 0.27
30 3 0.05
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (28 bp):
AATATATTTATATTAAATAATAAATTAA
Found at i:113485302 original size:25 final size:24
Alignment explanation
Indices: 113485258--113485304 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
113485248 TATTATATAT
113485258 AATAAAACAAATAAAGAAAGAATA
1 AATAAAACAAATAAAGAAAGAATA
*
113485282 AATAAATAGAAATAGAA-AAAGAA
1 AATAAA-ACAAATA-AAGAAAGAA
113485305 AGCCAAAGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 6 0.30
25 12 0.60
26 2 0.10
ACGTcount: A:0.74, C:0.02, G:0.11, T:0.13
Consensus pattern (24 bp):
AATAAAACAAATAAAGAAAGAATA
Found at i:113493369 original size:40 final size:40
Alignment explanation
Indices: 113493325--113493528 Score: 295
Period size: 40 Copynumber: 5.1 Consensus size: 40
113493315 CAGGATTTAA
* * *
113493325 CCGGATATAGCT-ACTCGCTCGAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
*
113493365 CCGGATATAGTAACTCGCACCAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
113493405 CCGGATATAGTAACTCGTACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
113493445 CCGGATATAGTAACTCGCACAAATGCCTTTGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
113493485 CCGGA-ACTAGTCACTAGCGCAAATGCCTTCGGGACTTAGC
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGC
113493525 CCGG
1 CCGG
113493529 TTATCATCCA
Statistics
Matches: 151, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
39 2 0.01
40 149 0.99
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:113494728 original size:6 final size:5
Alignment explanation
Indices: 113494697--113494741 Score: 54
Period size: 5 Copynumber: 8.6 Consensus size: 5
113494687 CATGAGAGCC
* *
113494697 TTTCT TTTTT TTTTT TTTCT TTTCT TTCTCT TTCTCT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TT-TCT TT-TCT TTTCT TTT
113494742 TTTCATCATC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
5 26 0.70
6 11 0.30
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTCT
Found at i:113501317 original size:39 final size:39
Alignment explanation
Indices: 113501257--113501471 Score: 281
Period size: 39 Copynumber: 5.5 Consensus size: 39
113501247 AAGCCAAGTA
* * * * *
113501257 CCTTCGGGATTTAACCGGATATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGATATAG-TAACTCGCACAAATG
* *
113501296 CCTTCGGGACATAGCCCGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGATATAGTAACTCGCACAAATG
113501335 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCC-GATATAGTAACTCGCACAAATG
113501375 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCC-GATATAGTAACTCGCACAAATG
* * * *
113501415 CCTTCGGGACTTAGCCC-AAACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGATA-TAGTAACTCGCACAAATG
113501454 CCTTCGGGACTTAGCCCG
1 CCTTCGGGACTTAGCCCG
113501472 GTTATCATCC
Statistics
Matches: 160, Mismatches: 12, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
38 3 0.02
39 79 0.49
40 78 0.49
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (39 bp):
CCTTCGGGACTTAGCCCGATATAGTAACTCGCACAAATG
Found at i:113501368 original size:40 final size:40
Alignment explanation
Indices: 113501257--113501472 Score: 289
Period size: 40 Copynumber: 5.5 Consensus size: 40
113501247 AAGCCAAGTA
* * * *
113501257 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
113501296 CCTTCGGGACATAGCCC-GATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
113501335 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
113501375 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * *
113501415 CCTTCGGGACTTAGCCC--AAACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
113501454 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
113501473 TTATCATCCA
Statistics
Matches: 160, Mismatches: 11, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
38 3 0.02
39 77 0.48
40 80 0.50
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:113501390 original size:79 final size:78
Alignment explanation
Indices: 113501257--113501471 Score: 283
Period size: 79 Copynumber: 2.7 Consensus size: 78
113501247 AAGCCAAGTA
* * * * *
113501257 CCTTCGGGATTTA-ACCGGATATAGCTACTCGCTCGAATGCCTTCGGGACATAGCCCGATATAGT
1 CCTTCGGGACTTAGCCCGGATATAG-TACTCGCACAAATGCCTTCGGGACTTAGCCCGATATAGT
*
113501321 AACTCGCACCAATG
65 AACTCGCACAAATG
113501335 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
1 CCTTCGGGACTTAGCCCGGATATAGT-ACTCGCACAAATGCCTTCGGGACTTAGCCC-GATATAG
113501400 TAACTCGCACAAATG
64 TAACTCGCACAAATG
* * *
113501415 CCTTCGGGACTTAGCCC--AAACTAGTCACTAGCGCAAATGCCTTCGGGACTTAGCCCG
1 CCTTCGGGACTTAGCCCGGATA-TAGT-ACTCGCACAAATGCCTTCGGGACTTAGCCCG
113501472 GTTATCATCC
Statistics
Matches: 123, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
78 16 0.13
79 69 0.56
80 38 0.31
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (78 bp):
CCTTCGGGACTTAGCCCGGATATAGTACTCGCACAAATGCCTTCGGGACTTAGCCCGATATAGTA
ACTCGCACAAATG
Found at i:113502662 original size:6 final size:6
Alignment explanation
Indices: 113502644--113502692 Score: 75
Period size: 6 Copynumber: 8.5 Consensus size: 6
113502634 CATGAGAGCC
*
113502644 TTTCTT TTT-TT TTTCTT TTTCTT TTTCTT TTTCTT TCTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
113502690 TTT
1 TTT
113502693 TTTCATCATC
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
5 9 0.23
6 30 0.77
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTCTT
Found at i:113502668 original size:12 final size:12
Alignment explanation
Indices: 113502644--113502692 Score: 75
Period size: 11 Copynumber: 4.2 Consensus size: 12
113502634 CATGAGAGCC
113502644 TTTCTTTTT-TT
1 TTTCTTTTTCTT
113502655 TTTCTTTTTCTT
1 TTTCTTTTTCTT
113502667 TTTCTTTTTCTT
1 TTTCTTTTTCTT
*
113502679 TCTC-TTTTCTT
1 TTTCTTTTTCTT
113502690 TTT
1 TTT
113502693 TTTCATCATC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
11 18 0.51
12 17 0.49
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTCTTTTTCTT
Found at i:113503282 original size:16 final size:17
Alignment explanation
Indices: 113503261--113503304 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 17
113503251 TCCTCTTTCA
113503261 TTTATTTT-CTTTATTT
1 TTTATTTTACTTTATTT
*
113503277 TTTATTTTATTTTATTT
1 TTTATTTTACTTTATTT
113503294 TAATTATTTTA
1 T--TTATTTTA
113503305 TTTGAATTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 8 0.33
17 8 0.33
19 8 0.33
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTATTTTACTTTATTT
Found at i:113503286 original size:5 final size:5
Alignment explanation
Indices: 113503261--113503307 Score: 51
Period size: 5 Copynumber: 9.4 Consensus size: 5
113503251 TCCTCTTTCA
* * *
113503261 TTTAT TTTCT TTATTT TTTAT TTTAT TTTAT TTTA- ATTAT TTTAT TT
1 TTTAT TTTAT TT-TAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TT
113503308 GAATTCTTGA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
4 3 0.09
5 28 0.80
6 4 0.11
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:113503302 original size:14 final size:14
Alignment explanation
Indices: 113503283--113503312 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
113503273 ATTTTTTATT
*
113503283 TTATTTTATTTTAA
1 TTATTTTATTTGAA
113503297 TTATTTTATTTGAA
1 TTATTTTATTTGAA
113503311 TT
1 TT
113503313 CTTGAAATTT
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:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (14 bp):
TTATTTTATTTGAA
Found at i:113503302 original size:19 final size:17
Alignment explanation
Indices: 113503261--113503307 Score: 60
Period size: 19 Copynumber: 2.7 Consensus size: 17
113503251 TCCTCTTTCA
*
113503261 TTTATTTT-CTTTATTT
1 TTTATTTTATTTTATTT
113503277 TTTATTTTATTTTATTT
1 TTTATTTTATTTTATTT
113503294 TAATTATTTTATTT
1 T--TTATTTTATTT
113503308 GAATTCTTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 8 0.30
17 8 0.30
19 11 0.41
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTATTTTATTTTATTT
Found at i:113519322 original size:18 final size:18
Alignment explanation
Indices: 113519256--113519345 Score: 65
Period size: 20 Copynumber: 4.6 Consensus size: 18
113519246 GAGGGGTGTT
*
113519256 ACAGAGATGCCAAATAGGGC
1 ACAGAG-TG-CAAACAGGGC
* *
113519276 ACAAATGTGCATACAGGAGC
1 ACAGA-GTGCAAACAGG-GC
*
113519296 ACCGAAGTGCAAA-AGGGC
1 ACAG-AGTGCAAACAGGGC
113519314 ACCAGAGTGCATAACAGGGC
1 A-CAGAGTGCA-AACAGGGC
113519334 ACAGATGTGCAA
1 ACAGA-GTGCAA
113519346 TTAGGGATAC
Statistics
Matches: 56, Mismatches: 7, Indels: 15
0.72 0.09 0.19
Matches are distributed among these distances:
18 9 0.16
19 18 0.32
20 27 0.48
21 2 0.04
ACGTcount: A:0.39, C:0.21, G:0.29, T:0.11
Consensus pattern (18 bp):
ACAGAGTGCAAACAGGGC
Found at i:113523345 original size:46 final size:45
Alignment explanation
Indices: 113523170--113523347 Score: 166
Period size: 46 Copynumber: 3.9 Consensus size: 45
113523160 TGTAACCCGC
**
113523170 CCATAAGCGAACTTAGACTCAACTCAACGAGCTCGGGCAT-TTGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTC-GG-ATGTTGCAT
* * *
113523216 CCATAAGTGAACTCGGACTCAAGTCAACGAGCTCGGATGCCTAGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGA----T-GTTGCAT
* * *
113523266 -C-TCA-CGAACTCGGACTCAACTCATCGAGTTCGGATGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGATGTT-GCAT
* *
113523309 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATG
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGATG
113523348 CCCAAATATC
Statistics
Matches: 108, Mismatches: 14, Indels: 20
0.76 0.10 0.14
Matches are distributed among these distances:
42 3 0.03
43 4 0.04
44 2 0.02
45 4 0.04
46 60 0.56
47 26 0.24
48 3 0.03
49 1 0.01
50 5 0.05
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (45 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGATGTTGCAT
Found at i:113526585 original size:25 final size:25
Alignment explanation
Indices: 113526553--113526661 Score: 89
Period size: 25 Copynumber: 4.4 Consensus size: 25
113526543 CTCCCTCTCA
*
113526553 AGCCATATAACAGGAAGCTCATGTG
1 AGCCATATAACAGGAAGCTCATGCG
* * *
113526578 AGCCATATAACGGGAAGCTTATCCG
1 AGCCATATAACAGGAAGCTCATGCG
** **
113526603 AGCTGTATAAC-GAGAAGCTCATAAG
1 AGCCATATAACAG-GAAGCTCATGCG
* * *
113526628 AGCCATAT-TCAGGATGCTTATGCG
1 AGCCATATAACAGGAAGCTCATGCG
113526652 AGCCA-ATAAC
1 AGCCATATAAC
113526662 GAGTAGCTCC
Statistics
Matches: 64, Mismatches: 17, Indels: 7
0.73 0.19 0.08
Matches are distributed among these distances:
23 2 0.03
24 16 0.25
25 46 0.72
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (25 bp):
AGCCATATAACAGGAAGCTCATGCG
Found at i:113532633 original size:7 final size:7
Alignment explanation
Indices: 113532623--113532664 Score: 84
Period size: 7 Copynumber: 6.0 Consensus size: 7
113532613 CTCAATCCTC
113532623 AATCCCT
1 AATCCCT
113532630 AATCCCT
1 AATCCCT
113532637 AATCCCT
1 AATCCCT
113532644 AATCCCT
1 AATCCCT
113532651 AATCCCT
1 AATCCCT
113532658 AATCCCT
1 AATCCCT
113532665 CCATCACCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.29, C:0.43, G:0.00, T:0.29
Consensus pattern (7 bp):
AATCCCT
Found at i:113532893 original size:6 final size:6
Alignment explanation
Indices: 113532882--113532911 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
113532872 CATTGGTAGT
113532882 GAGGGA GAGGGA GAGGGA GAGGGA GAGGGA
1 GAGGGA GAGGGA GAGGGA GAGGGA GAGGGA
113532912 CATGGGATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (6 bp):
GAGGGA
Found at i:113534126 original size:3 final size:3
Alignment explanation
Indices: 113534118--113534173 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
113534108 CCTCTTTCAC
*
113534118 TAA TAA TAA TTA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
113534166 TAA TAA TA
1 TAA TAA TA
113534174 GAGTTGGTTA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:113535897 original size:25 final size:25
Alignment explanation
Indices: 113535863--113535912 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
113535853 CTTAATATAA
113535863 TACATGTATATATATTGCATTCTTT
1 TACATGTATATATATTGCATTCTTT
113535888 TACATGTATATATATTGCATTCTTT
1 TACATGTATATATATTGCATTCTTT
113535913 CTCAATCGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.12, G:0.08, T:0.52
Consensus pattern (25 bp):
TACATGTATATATATTGCATTCTTT
Found at i:113544338 original size:39 final size:40
Alignment explanation
Indices: 113544224--113544409 Score: 191
Period size: 40 Copynumber: 4.7 Consensus size: 40
113544214 ACGACTCACT
**
113544224 CAAATGCCTTCGGGACAAAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* * *
113544264 CGAATGCCTTCGGGACTTAACCCGGGTTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
113544304 CAAATGCCTTCGGG-CTTAGCCCGGATTTATTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * * *
113544343 CGAATACCTTC-GGATTCTTAGTCCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGGA--CTTAGCCCGGATTTAGTAAC-TCGCA
*
113544385 CAAA-GTCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
113544410 CATCATTCAA
Statistics
Matches: 121, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
38 2 0.02
39 31 0.26
40 56 0.46
41 22 0.18
42 10 0.08
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:113548972 original size:50 final size:52
Alignment explanation
Indices: 113548918--113549044 Score: 160
Period size: 50 Copynumber: 2.6 Consensus size: 52
113548908 GAAGAAAGGG
*
113548918 AGAAGAGAAGAGA-AGA-AAGA-AAGAAAAAATCAGTAGAAAAAGAAGATTAC
1 AGAAGAGAAGAGAGAGAGAAGAGAAG-AAAAATCAGTAAAAAAAGAAGATTAC
* *
113548968 AG-A-AGAAGAGAGGGAGAAGAGAAGAAAATTCAGTAAAAAAAGAAGATTAC
1 AGAAGAGAAGAGAGAGAGAAGAGAAGAAAAATCAGTAAAAAAAGAAGATTAC
*
113549018 AG-A-AGAAGAGAGGGAGAAGAGAAGAAA
1 AGAAGAGAAGAGAGAGAGAAGAGAAGAAA
113549045 TAAAATGTAT
Statistics
Matches: 71, Mismatches: 3, Indels: 6
0.89 0.04 0.08
Matches are distributed among these distances:
48 8 0.11
49 3 0.04
50 57 0.80
51 3 0.04
ACGTcount: A:0.61, C:0.03, G:0.29, T:0.07
Consensus pattern (52 bp):
AGAAGAGAAGAGAGAGAGAAGAGAAGAAAAATCAGTAAAAAAAGAAGATTAC
Found at i:113555758 original size:150 final size:150
Alignment explanation
Indices: 113555564--113556165 Score: 878
Period size: 150 Copynumber: 4.1 Consensus size: 150
113555554 ATTATTTTCG
113555564 TTTTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTATATTAATTT
1 TTTTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTG-TTTTTATATTAATTT
* * * *
113555629 AGTAAATAATCCTGATTTTGGCCCTTTGTTTGTATTTTTTAAATTTTTGGATTTTA-TTTTTAAA
65 AGTAAATAACCCTAATTTTGGCCCTTTGTTTGTATTTTTAAAATTTTTGAATTTTATTTTTTAAA
**
113555693 ATATACTATTTCCGTATTTTA
130 ATATACTATTTTTGTATTTTA
*
113555714 TTTTTTATCTTATTTTAGTACATAATGTTTCAAATGTATTATTTTA--------ATATT--TTT-
1 TTTTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTATATTAATTTA
* *
113555768 -CACATAACCCTAATTTTGGCCCTTTGTTTGTATTTTTAAAATTTTTGAATTTTATTTTTTAAAA
66 GTAAATAACCCTAATTTTGGCCCTTTGTTTGTATTTTTAAAATTTTTGAATTTTATTTTTTAAAA
*
113555832 -ATATTATTTTTGTATTTTA
131 TATACTATTTTTGTATTTTA
** *
113555851 TTTTTT-TATTATTTTAGTGGATAATATTTCAAATGTATTATTTTAGTGTTTTTTTATATTAATT
1 TTTTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTG--TTTTTATATTAATT
* *
113555915 TAGTAAATAACCCTGATTTTGGCCCTTTGTTTGTATTTTTAAAA-TTTTCAGATTTTATTTTTTA
64 TAGTAAATAACCCTAATTTTGGCCCTTTGTTTGTATTTTTAAAATTTTTGA-ATTTTATTTTTTA
113555979 AAATATACTATTTTTGTATTTTA
128 AAATATACTATTTTTGTATTTTA
113556002 TTTTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTATATTAATTTA
1 TTTTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTATATTAATTTA
* *
113556067 GTAAATAACTCTAATTTTGTCCCTTTGTTTGTATTTTTAAAATTTTTGAATTTTATTTTTTAAAA
66 GTAAATAACCCTAATTTTGGCCCTTTGTTTGTATTTTTAAAATTTTTGAATTTTATTTTTTAAAA
**
113556132 TATACTATTTTAATATTTTA
131 TATACTATTTTTGTATTTTA
113556152 -TTTTTATATTATTT
1 TTTTTTATATTATTT
113556166 AAAAAAAAAC
Statistics
Matches: 405, Mismatches: 28, Indels: 39
0.86 0.06 0.08
Matches are distributed among these distances:
136 35 0.09
137 70 0.17
138 9 0.02
139 3 0.01
141 5 0.01
146 5 0.01
148 3 0.01
149 19 0.05
150 188 0.46
151 29 0.07
152 39 0.10
ACGTcount: A:0.28, C:0.06, G:0.08, T:0.58
Consensus pattern (150 bp):
TTTTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTATATTAATTTA
GTAAATAACCCTAATTTTGGCCCTTTGTTTGTATTTTTAAAATTTTTGAATTTTATTTTTTAAAA
TATACTATTTTTGTATTTTA
Found at i:113555849 original size:23 final size:24
Alignment explanation
Indices: 113555794--113555849 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
113555784 TGGCCCTTTG
* *
113555794 TTTGTATTTTTAAAATTTTTGAAT
1 TTTGTATTTTTAAAAATATTGAAT
* *
113555818 TTTAT-TTTTTAAAAATATT-ATT
1 TTTGTATTTTTAAAAATATTGAAT
113555840 TTTGTATTTT
1 TTTGTATTTT
113555850 ATTTTTTTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
22 6 0.23
23 16 0.62
24 4 0.15
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (24 bp):
TTTGTATTTTTAAAAATATTGAAT
Found at i:113556040 original size:288 final size:289
Alignment explanation
Indices: 113555519--113556165 Score: 916
Period size: 288 Copynumber: 2.2 Consensus size: 289
113555509 TATTTTTAAA
* * * * *
113555519 ATTTTTAAAATTTTCGGATCTTATTTTTTAAATATATTATTTTCG-----T-TTTTTATATTATT
1 ATTTTTAAAATTTTTGAATTTTATTTTTTAAAAATATTATTTTAGTATTTTATTTTTATATTATT
* *
113555578 TTAGTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTATATTAATTTAGTAAATAATCCTG
66 TTAGTACATAATATTTCAAATGTATTATTTTAGTGTTTTTTATATTAATTTAGTAAATAACCCTG
* **
113555643 ATTTTGGCCCTTTGTTTGTATTTTTTAAATTTTTGGATTTTATTTTTAAAATATACTATTTCCGT
131 ATTTTGGCCCTTTGTTTGTATTTTTAAAATTTTCAGATTTTATTTTTAAAATATACTATTTCCGT
*
113555708 ATTTTATTTTTTATCTTATTTTAGTACATAATGTTTCAAATGTATTATTTTA-ATATT-TTT-CA
196 ATTTTATTTTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTTATATATTATTTACA
*
113555770 CATAACCCTAATTTTGGCCCTTTGTTTGT
261 AATAACCCTAATTTTGGCCCTTTGTTTGT
* *
113555799 ATTTTTAAAATTTTTGAATTTTATTTTTTAAAAATATTATTTTTGTATTTTATTTTTTTATTATT
1 ATTTTTAAAATTTTTGAATTTTATTTTTTAAAAATATTATTTTAGTATTTTATTTTTATATTATT
**
113555864 TTAGTGGATAATATTTCAAATGTATTATTTTAGTGTTTTTTTATATTAATTTAGTAAATAACCCT
66 TTAGTACATAATATTTCAAATGTATTATTTTAGTG-TTTTTTATATTAATTTAGTAAATAACCCT
**
113555929 GATTTTGGCCCTTTGTTTGTATTTTTAAAATTTTCAGATTTTATTTTTTAAAATATACTATTTTT
130 GATTTTGGCCCTTTGTTTGTATTTTTAAAATTTTCAGATTTTA-TTTTTAAAATATACTATTTCC
113555994 GTATTTTATTTTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTATA
194 GTATTTTATTTTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTTA-------TATA
* * *
113556059 TTAATTTAGTAAATAACTCTAATTTTGTCCCTTTGTTTGT
252 TT-ATTTA-CAAATAACCCTAATTTTGGCCCTTTGTTTGT
* *
113556099 ATTTTTAAAATTTTTGAATTTTATTTTTTAAAATATACTATTTTAATATTTTATTTTTATATTAT
1 ATTTTTAAAATTTTTGAATTTTATTTTTTAAAA-ATATTATTTTAGTATTTTATTTTTATATTAT
113556164 TT
65 TT
113556166 AAAAAAAAAC
Statistics
Matches: 322, Mismatches: 24, Indels: 21
0.88 0.07 0.06
Matches are distributed among these distances:
280 40 0.12
285 1 0.00
286 44 0.14
287 68 0.21
288 72 0.22
296 5 0.02
298 3 0.01
300 60 0.19
301 29 0.09
ACGTcount: A:0.28, C:0.06, G:0.08, T:0.58
Consensus pattern (289 bp):
ATTTTTAAAATTTTTGAATTTTATTTTTTAAAAATATTATTTTAGTATTTTATTTTTATATTATT
TTAGTACATAATATTTCAAATGTATTATTTTAGTGTTTTTTATATTAATTTAGTAAATAACCCTG
ATTTTGGCCCTTTGTTTGTATTTTTAAAATTTTCAGATTTTATTTTTAAAATATACTATTTCCGT
ATTTTATTTTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTTATATATTATTTACA
AATAACCCTAATTTTGGCCCTTTGTTTGT
Found at i:113556232 original size:17 final size:17
Alignment explanation
Indices: 113556206--113556238 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
113556196 CAAAATTTTT
113556206 TTTTCATATTTTATTTC
1 TTTTCATATTTTATTTC
*
113556223 TTTTCTTATTTTATTT
1 TTTTCATATTTTATTT
113556239 TTTCATTAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTCATATTTTATTTC
Found at i:113556271 original size:16 final size:16
Alignment explanation
Indices: 113556203--113556281 Score: 52
Period size: 16 Copynumber: 4.9 Consensus size: 16
113556193 TCCCAAAATT
*
113556203 TTTTTTTCATATTTTA
1 TTTTTTTAATATTTTA
**
113556219 TTTCTTTTCTTATTTTA
1 TTT-TTTTAATATTTTA
* * ***
113556236 TTTTTTCATTAAGATA
1 TTTTTTTAATATTTTA
113556252 -TTTTTTAATATTTTA
1 TTTTTTTAATATTTTA
* *
113556267 TTTTTATACTATTTT
1 TTTTTTTAATATTTT
113556282 TGTAAAATAG
Statistics
Matches: 48, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
15 10 0.21
16 23 0.48
17 15 0.31
ACGTcount: A:0.22, C:0.06, G:0.01, T:0.71
Consensus pattern (16 bp):
TTTTTTTAATATTTTA
Found at i:113556665 original size:10 final size:10
Alignment explanation
Indices: 113556646--113556679 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
113556636 AAAAAATTAC
113556646 CCTT-TTTTT
1 CCTTCTTTTT
113556655 CCTTCTTTTT
1 CCTTCTTTTT
*
113556665 CTTTCTTTTT
1 CCTTCTTTTT
113556675 CCTTC
1 CCTTC
113556680 CCTTCCTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (10 bp):
CCTTCTTTTT
Found at i:113556765 original size:3 final size:3
Alignment explanation
Indices: 113556742--113556816 Score: 70
Period size: 3 Copynumber: 26.0 Consensus size: 3
113556732 CCTGCTTTTC
* *
113556742 CTT CTT CTC CTT CTT -TCT CTT CTT CTT CTT C-T CTT -TT TTT CTT
1 CTT CTT CTT CTT CTT CT-T CTT CTT CTT CTT CTT CTT CTT CTT CTT
*
113556785 CTT C-T CTT CTTT CTT -TT CTT CTT CTC CTT CTT
1 CTT CTT CTT C-TT CTT CTT CTT CTT CTT CTT CTT
113556817 TTTTCCCAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
2 9 0.15
3 47 0.78
4 4 0.07
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:113556773 original size:24 final size:22
Alignment explanation
Indices: 113556742--113556815 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 22
113556732 CCTGCTTTTC
113556742 CTTCTTCTCCTTCTTTCTCTTCTT
1 CTTCTTCT-CTTCTTT-TCTTCTT
*
113556766 CTTCTTCTCTTTTTTTCTTCTT
1 CTTCTTCTCTTCTTTTCTTCTT
113556788 C-TCTTCT-TTCTTTTCTTCTT
1 CTTCTTCTCTTCTTTTCTTCTT
*
113556808 CTCCTTCT
1 CTTCTTCT
113556816 TTTTTCCCAA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
20 13 0.28
21 11 0.24
22 8 0.17
23 6 0.13
24 8 0.17
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (22 bp):
CTTCTTCTCTTCTTTTCTTCTT
Found at i:113556798 original size:39 final size:41
Alignment explanation
Indices: 113556737--113556822 Score: 131
Period size: 40 Copynumber: 2.1 Consensus size: 41
113556727 TGCCGCCTGC
*
113556737 TTTTCCTTCTTCTCCTTCTTTCTCTTCTTCTTCTTC-TCTT
1 TTTTCCTTCTTCTCCTTCTTTCTCTTCTTCTTCTCCTTCTT
* *
113556777 TTTTTCTTCTTCT-CTTCTTTCTTTTCTTCTTCTCCTTCTT
1 TTTTCCTTCTTCTCCTTCTTTCTCTTCTTCTTCTCCTTCTT
113556817 TTTTCC
1 TTTTCC
113556823 CAAAATGAGG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
39 20 0.49
40 21 0.51
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (41 bp):
TTTTCCTTCTTCTCCTTCTTTCTCTTCTTCTTCTCCTTCTT
Found at i:113556816 original size:9 final size:8
Alignment explanation
Indices: 113556742--113556809 Score: 63
Period size: 8 Copynumber: 8.6 Consensus size: 8
113556732 CCTGCTTTTC
113556742 CTTCTTCT
1 CTTCTTCT
113556750 CCTTCTT-T
1 -CTTCTTCT
113556758 C-TCTTCTT
1 CTTCTTC-T
113556766 CTTCTTCT
1 CTTCTTCT
* *
113556774 CTTTTTTT
1 CTTCTTCT
113556782 CTTCTTCT
1 CTTCTTCT
113556790 CTTCTT-T
1 CTTCTTCT
113556797 CTT-TTCTT
1 CTTCTTC-T
113556805 CTTCT
1 CTTCT
113556810 CCTTCTTTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
6 6 0.12
7 5 0.10
8 26 0.53
9 12 0.24
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (8 bp):
CTTCTTCT
Found at i:113557324 original size:24 final size:23
Alignment explanation
Indices: 113557290--113557334 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
113557280 TGACATGGTT
* *
113557290 TTTTTTTAATATTAATTTTTAATA
1 TTTTTTAAATAAT-ATTTTTAATA
113557314 TTTTTTAAATAATATTTTTAA
1 TTTTTTAAATAATATTTTTAA
113557335 AATATAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
TTTTTTAAATAATATTTTTAATA
Found at i:113557344 original size:16 final size:14
Alignment explanation
Indices: 113557309--113557338 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
113557299 TATTAATTTT
*
113557309 TAATATTTTTTAAA
1 TAATATTTTTAAAA
113557323 TAATATTTTTAAAA
1 TAATATTTTTAAAA
113557337 TA
1 TA
113557339 TAATATCAGT
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TAATATTTTTAAAA
Found at i:113567152 original size:31 final size:32
Alignment explanation
Indices: 113567111--113567176 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 32
113567101 TTTAAATTAA
*
113567111 TTAATTAGATA-AATATTATTTTATTAATATT
1 TTAATGAGATATAATATTATTTTATTAATATT
* *
113567142 TTAATGAGATATTTATTATTATTTTATTATTATT
1 TTAATGAGATA--TAATATTATTTTATTAATATT
113567176 T
1 T
113567177 ATTTAGTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
31 10 0.34
34 19 0.66
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (32 bp):
TTAATGAGATATAATATTATTTTATTAATATT
Found at i:113569366 original size:46 final size:46
Alignment explanation
Indices: 113569314--113569587 Score: 372
Period size: 46 Copynumber: 6.0 Consensus size: 46
113569304 GCTCTCTGAA
*
113569314 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * *
113569360 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
**
113569406 ATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * *
113569452 A-GAAAGTGAGTAAGACCATGGTTGAAAGATACCATGGAAACGTGAC
1 ATGAAA-TGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
**
113569498 ATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * * * *
113569544 A-AAAAGTGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 ATGAAA-TGAGTAAGACCATGGTTGAAAGATACCATGGCAACATG
113569588 TCGAAGATAA
Statistics
Matches: 201, Mismatches: 24, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
45 7 0.03
46 190 0.95
47 4 0.02
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.20
Consensus pattern (46 bp):
ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
Found at i:113569471 original size:92 final size:92
Alignment explanation
Indices: 113569325--113569582 Score: 446
Period size: 92 Copynumber: 2.8 Consensus size: 92
113569315 TGAAATGTGT
*
113569325 AAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAA-TGTGTAAGACCATGGTTGAAAGA
1 AAGACCATGGTTGAAAGATACCATGGCAACATGATA-GAAAGTGAGTAAGACCATGGTTGAAAGA
113569389 TACCATGGCAACGTGACATGAAATGAAC
65 TACCATGGCAACGTGACATGAAATGAAC
113569417 AAGACCATGGTTGAAAGATACCATGGCAACATGATAGAAAGTGAGTAAGACCATGGTTGAAAGAT
1 AAGACCATGGTTGAAAGATACCATGGCAACATGATAGAAAGTGAGTAAGACCATGGTTGAAAGAT
*
113569482 ACCATGGAAACGTGACATGAAATGAAC
66 ACCATGGCAACGTGACATGAAATGAAC
* * *
113569509 AAGACCATGGTTGAAAGATACCATGGCAACATGATAAAAAGTGAGTAAGACCATAGTTGAAAGAC
1 AAGACCATGGTTGAAAGATACCATGGCAACATGATAGAAAGTGAGTAAGACCATGGTTGAAAGAT
*
113569574 ACTATGGCA
66 ACCATGGCA
113569583 TCATGTCGAA
Statistics
Matches: 158, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
91 4 0.03
92 154 0.97
ACGTcount: A:0.42, C:0.15, G:0.24, T:0.19
Consensus pattern (92 bp):
AAGACCATGGTTGAAAGATACCATGGCAACATGATAGAAAGTGAGTAAGACCATGGTTGAAAGAT
ACCATGGCAACGTGACATGAAATGAAC
Found at i:113569728 original size:26 final size:26
Alignment explanation
Indices: 113569671--113569765 Score: 70
Period size: 26 Copynumber: 3.6 Consensus size: 26
113569661 TCAAATGATG
* *
113569671 AATGGTTTTATGAATTGGTTATACAA
1 AATGGTTGTATGAAATGGTTATACAA
113569697 AATGGTTGTATGAAAT-GTT-TACAA
1 AATGGTTGTATGAAATGGTTATACAA
** * *
113569721 GAATTGGTCATATGGAAAT-ATATGTACAA
1 -AA-TGGTTGTAT-GAAATGGT-TATACAA
*
113569750 AATAGTTGTATGAAAT
1 AATGGTTGTATGAAAT
113569766 AATTAAGAAG
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
24 5 0.09
25 5 0.09
26 26 0.46
27 12 0.21
28 3 0.05
29 5 0.09
ACGTcount: A:0.39, C:0.04, G:0.20, T:0.37
Consensus pattern (26 bp):
AATGGTTGTATGAAATGGTTATACAA
Found at i:113572635 original size:12 final size:12
Alignment explanation
Indices: 113572613--113572641 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
113572603 AATTGATCAC
113572613 ATATA-TTAAAA
1 ATATATTTAAAA
113572624 ATATATTTAAAA
1 ATATATTTAAAA
113572636 ATATAT
1 ATATAT
113572642 ATTTTATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATATTTAAAA
Found at i:113574646 original size:43 final size:43
Alignment explanation
Indices: 113574585--113574671 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
113574575 CAGATTGCAC
113574585 AGAAATTTTACAAATGGACTATTTGCGTCTTAAAAACTACCGT
1 AGAAATTTTACAAATGGACTATTTGCGTCTTAAAAACTACCGT
113574628 AGAAATTTTACAAATGGACTATTTGCGTCTTAAAAACTACCGT
1 AGAAATTTTACAAATGGACTATTTGCGTCTTAAAAACTACCGT
113574671 A
1 A
113574672 CATCTTTCCT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (43 bp):
AGAAATTTTACAAATGGACTATTTGCGTCTTAAAAACTACCGT
Found at i:113577848 original size:2 final size:2
Alignment explanation
Indices: 113577841--113577872 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
113577831 AATTTTACCT
113577841 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
113577873 ATTTAATTAA
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):
TA
Found at i:113578512 original size:23 final size:23
Alignment explanation
Indices: 113578486--113578536 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
113578476 CACACATATA
113578486 TCACTTTGTATCATATTACTTAT
1 TCACTTTGTATCATATTACTTAT
113578509 TCACTTTGTATCATATTACTTAT
1 TCACTTTGTATCATATTACTTAT
113578532 TCACT
1 TCACT
113578537 ACATTTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.25, C:0.20, G:0.04, T:0.51
Consensus pattern (23 bp):
TCACTTTGTATCATATTACTTAT
Found at i:113578569 original size:17 final size:17
Alignment explanation
Indices: 113578542--113578574 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
113578532 TCACTACATT
113578542 TTTATTTCACATATTCAC
1 TTTATTTCACA-ATTCAC
113578560 TTTA-TTCACAATTCA
1 TTTATTTCACAATTCA
113578575 TAAAAATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 6 0.40
18 4 0.27
ACGTcount: A:0.30, C:0.21, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTATTTCACAATTCAC
Found at i:113579779 original size:10 final size:10
Alignment explanation
Indices: 113579752--113579789 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
113579742 TTAAATTCTA
113579752 AAAGATAAAT
1 AAAGATAAAT
113579762 ACAA-ATAAAT
1 A-AAGATAAAT
*
113579772 AAAGATAATT
1 AAAGATAAAT
113579782 AAAGATAA
1 AAAGATAA
113579790 CAACTAAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.68, C:0.03, G:0.08, T:0.21
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:113580613 original size:11 final size:10
Alignment explanation
Indices: 113580577--113580637 Score: 53
Period size: 9 Copynumber: 6.6 Consensus size: 10
113580567 AAATAAATTC
113580577 TTTTAAT-AT
1 TTTTAATAAT
113580586 TTTT-AT-A-
1 TTTTAATAAT
113580593 TTTT-ATAAT
1 TTTTAATAAT
113580602 TTTTAAATAAT
1 TTTT-AATAAT
*
113580613 TATTAAT-AT
1 TTTTAATAAT
*
113580622 TTTTTATAAT
1 TTTTAATAAT
113580632 TTTTAA
1 TTTTAA
113580638 ATTTTATATA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
7 6 0.14
8 4 0.09
9 15 0.35
10 10 0.23
11 8 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
TTTTAATAAT
Found at i:113580647 original size:18 final size:19
Alignment explanation
Indices: 113580577--113580652 Score: 79
Period size: 18 Copynumber: 4.2 Consensus size: 19
113580567 AAATAAATTC
113580577 TTTTAATATTTT-TAT-AT
1 TTTTAATATTTTATATAAT
*
113580594 TTTATAAT-TTTTAAATAAT
1 TTT-TAATATTTTATATAAT
* *
113580613 TATTAATATTTTTTATAAT
1 TTTTAATATTTTATATAAT
*
113580632 TTTTAA-ATTTTATATAGT
1 TTTTAATATTTTATATAAT
113580650 TTT
1 TTT
113580653 GAACTCATCT
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
17 7 0.15
18 23 0.48
19 18 0.38
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64
Consensus pattern (19 bp):
TTTTAATATTTTATATAAT
Found at i:113582398 original size:18 final size:18
Alignment explanation
Indices: 113582377--113582411 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
113582367 AGCAGATTAG
113582377 CCCTTCTCAGCAACCAAA
1 CCCTTCTCAGCAACCAAA
113582395 CCCTTCTCAGCAACCAA
1 CCCTTCTCAGCAACCAA
113582412 CTTTCAACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.46, G:0.06, T:0.17
Consensus pattern (18 bp):
CCCTTCTCAGCAACCAAA
Found at i:113584115 original size:20 final size:20
Alignment explanation
Indices: 113584075--113584115 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
113584065 GGAATTATGT
*
113584075 TATGGACTGAAAGTATAAGG
1 TATGGACTGAAAGCATAAGG
*
113584095 TATGGACTGAAAGCATGAGG
1 TATGGACTGAAAGCATAAGG
113584115 T
1 T
113584116 TCCTAGTGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.37, C:0.07, G:0.32, T:0.24
Consensus pattern (20 bp):
TATGGACTGAAAGCATAAGG
Found at i:113584737 original size:8 final size:8
Alignment explanation
Indices: 113584724--113584752 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
113584714 TTATGTTTAA
113584724 TATATTAT
1 TATATTAT
113584732 TATATTAT
1 TATATTAT
113584740 TATATTAT
1 TATATTAT
113584748 TATAT
1 TATAT
113584753 AATAAAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATATTAT
Found at i:113584753 original size:10 final size:9
Alignment explanation
Indices: 113584723--113584820 Score: 76
Period size: 10 Copynumber: 10.7 Consensus size: 9
113584713 TTTATGTTTA
113584723 ATATATTAT
1 ATATATTAT
113584732 -TATATTAT
1 ATATATTAT
113584740 -TATATTATT
1 ATATATTA-T
* *
113584749 ATATAATAA
1 ATATATTAT
* *
113584758 AGATATTTT
1 ATATATTAT
* *
113584767 ATGTTTTA-
1 ATATATTAT
113584775 ATTATATTAT
1 A-TATATTAT
113584785 ATTATATTAT
1 A-TATATTAT
113584795 ATTATATTAT
1 A-TATATTAT
113584805 ATTATATTAT
1 A-TATATTAT
113584815 ATATAT
1 ATATAT
113584821 AAACTAAAGA
Statistics
Matches: 73, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
8 16 0.22
9 20 0.27
10 37 0.51
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (9 bp):
ATATATTAT
Found at i:113584785 original size:5 final size:5
Alignment explanation
Indices: 113584775--113584820 Score: 85
Period size: 5 Copynumber: 9.4 Consensus size: 5
113584765 TTATGTTTTA
113584775 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT A-TAT AT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
113584821 AAACTAAAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 4 0.10
5 36 0.90
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTAT
Found at i:113586446 original size:23 final size:23
Alignment explanation
Indices: 113586416--113586501 Score: 90
Period size: 21 Copynumber: 3.9 Consensus size: 23
113586406 GCTTTATCGA
*
113586416 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTTATGTGTCGTATT
**
113586439 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACCTTATGTGTCGTATT
* *
113586460 GCAGGCACCTTGTGTGTCGT-TT
1 TCAGGCACCTTATGTGTCGTATT
*
113586482 T-AGGCACTTTATGTGTCGTA
1 TCAGGCACCTTATGTGTCGTA
113586502 CTCTAATCAG
Statistics
Matches: 52, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
21 34 0.65
23 18 0.35
ACGTcount: A:0.15, C:0.21, G:0.27, T:0.37
Consensus pattern (23 bp):
TCAGGCACCTTATGTGTCGTATT
Found at i:113591318 original size:8 final size:8
Alignment explanation
Indices: 113591305--113591409 Score: 59
Period size: 8 Copynumber: 13.6 Consensus size: 8
113591295 TTATGTTTAA
113591305 TATATTAT
1 TATATTAT
113591313 TATATTAT
1 TATATTAT
113591321 TATATTAT
1 TATATTAT
*
113591329 TATATAATAAA
1 TATAT--T-AT
*
113591340 GATATT-T
1 TATATTAT
*
113591347 TATGTT-T
1 TATATTAT
113591354 TA-ATTA-
1 TATATTAT
113591360 TAT-TATAT
1 TATAT-TAT
113591368 TATATTA-
1 TATATTAT
113591375 TAT-TATAT
1 TATAT-TAT
113591383 TATATTA-
1 TATATTAT
113591390 TAT-TATAT
1 TATAT-TAT
113591398 TATATTA-
1 TATATTAT
113591405 TATAT
1 TATAT
113591410 AAACTAAAGA
Statistics
Matches: 77, Mismatches: 6, Indels: 29
0.69 0.05 0.26
Matches are distributed among these distances:
6 7 0.09
7 24 0.31
8 36 0.47
9 4 0.05
10 1 0.01
11 5 0.06
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (8 bp):
TATATTAT
Found at i:113591366 original size:5 final size:5
Alignment explanation
Indices: 113591356--113591407 Score: 104
Period size: 5 Copynumber: 10.4 Consensus size: 5
113591346 TTATGTTTTA
113591356 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
113591406 AT
1 AT
113591408 ATAAACTAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 47 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTAT
Found at i:113593033 original size:23 final size:23
Alignment explanation
Indices: 113593003--113593088 Score: 90
Period size: 21 Copynumber: 3.9 Consensus size: 23
113592993 GCTTTATCGA
* *
113593003 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTCATGTGTCGTATT
*
113593026 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACCTCATGTGTCGTATT
*
113593047 TCAGGCACCTCGTGTGTCGT-TT
1 TCAGGCACCTCATGTGTCGTATT
* *
113593069 T-AGGCACTTTATGTGTCGTA
1 TCAGGCACCTCATGTGTCGTA
113593089 CTCTGATCAG
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
21 35 0.65
22 1 0.02
23 18 0.33
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (23 bp):
TCAGGCACCTCATGTGTCGTATT
Found at i:113594733 original size:23 final size:23
Alignment explanation
Indices: 113594706--113594779 Score: 112
Period size: 23 Copynumber: 3.2 Consensus size: 23
113594696 TGGTAGGAGC
*
113594706 TTATTGGCACTTTGGTGCGATTG
1 TTATTGGCACTTTAGTGCGATTG
*
113594729 TTATTGACACTTTAGTGCGATTG
1 TTATTGGCACTTTAGTGCGATTG
* *
113594752 TTATTGGCACTTCAATGCGATTG
1 TTATTGGCACTTTAGTGCGATTG
113594775 TTATT
1 TTATT
113594780 ATGGAGTGTT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.19, C:0.14, G:0.23, T:0.45
Consensus pattern (23 bp):
TTATTGGCACTTTAGTGCGATTG
Found at i:113594888 original size:27 final size:27
Alignment explanation
Indices: 113594853--113594907 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
113594843 GTCTGAAGTT
*
113594853 TAAATTTGTGTATTTGTATTGAGTTAA
1 TAAACTTGTGTATTTGTATTGAGTTAA
113594880 TAAACTTGTGTATTTGTATTGAGTTAA
1 TAAACTTGTGTATTTGTATTGAGTTAA
113594907 T
1 T
113594908 GTCTAGTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.29, C:0.02, G:0.18, T:0.51
Consensus pattern (27 bp):
TAAACTTGTGTATTTGTATTGAGTTAA
Found at i:113596956 original size:14 final size:14
Alignment explanation
Indices: 113596933--113596964 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
113596923 GTTCCATGAT
113596933 AATG-GGTTAGGTA
1 AATGTGGTTAGGTA
113596946 AATGTGGTTAGGTA
1 AATGTGGTTAGGTA
113596960 AATGT
1 AATGT
113596965 TTCATGATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.31, C:0.00, G:0.34, T:0.34
Consensus pattern (14 bp):
AATGTGGTTAGGTA
Found at i:113602656 original size:26 final size:26
Alignment explanation
Indices: 113602599--113602682 Score: 152
Period size: 26 Copynumber: 3.3 Consensus size: 26
113602589 TGATACAAAT
*
113602599 TGATAATAGGTTAGGTAAATG-TTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
113602624 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
113602650 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
113602676 TGATAAT
1 TGATAAT
113602683 AATTTCATGT
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
25 20 0.35
26 37 0.65
ACGTcount: A:0.33, C:0.04, G:0.25, T:0.38
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:113604191 original size:26 final size:26
Alignment explanation
Indices: 113604162--113604214 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
113604152 TTTACAGTTT
113604162 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCCTAGG-GATAAATTGACCGAAA
* *
113604188 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCGAAA
113604214 T
1 T
113604215 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCGAAA
Found at i:113607583 original size:27 final size:27
Alignment explanation
Indices: 113607387--113607637 Score: 241
Period size: 27 Copynumber: 9.3 Consensus size: 27
113607377 TTCTGCCTTC
* * * * *
113607387 GGCACTCCTTCTTCCACCCCTGCCTTT
1 GGCACTCCGTCTTCGACACCGGCGTTT
* * * *
113607414 GGCACTCCTTCTTCCACCCCGGCCTTT
1 GGCACTCCGTCTTCGACACCGGCGTTT
* * * * *
113607441 GGAACTCCTTCTTCAACTCCGGCTTTT
1 GGCACTCCGTCTTCGACACCGGCGTTT
** * * * *
113607468 GGGGCTACTTCTTCCACACCGGCATTT
1 GGCACTCCGTCTTCGACACCGGCGTTT
113607495 GGCACTCCGTCTTCGACACCGGCGTTT
1 GGCACTCCGTCTTCGACACCGGCGTTT
*
113607522 GGCACTCCATCTTCGACACCGGCGTTT
1 GGCACTCCGTCTTCGACACCGGCGTTT
*
113607549 GGCACTCCGTCTTCGACACCTGCGTTT
1 GGCACTCCGTCTTCGACACCGGCGTTT
** *
113607576 GGGGCTCCGTCTTCGACACCGGCATTT
1 GGCACTCCGTCTTCGACACCGGCGTTT
* * *
113607603 GGAACTCCGTCCTCGACACCGGCTTTT
1 GGCACTCCGTCTTCGACACCGGCGTTT
*
113607630 GGAACTCC
1 GGCACTCC
113607638 CTCAACGCCG
Statistics
Matches: 196, Mismatches: 28, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 196 1.00
ACGTcount: A:0.12, C:0.38, G:0.21, T:0.29
Consensus pattern (27 bp):
GGCACTCCGTCTTCGACACCGGCGTTT
Found at i:113607637 original size:81 final size:81
Alignment explanation
Indices: 113607390--113607637 Score: 280
Period size: 81 Copynumber: 3.1 Consensus size: 81
113607380 TGCCTTCGGC
* * * * * * *
113607390 ACTCCTTCTTCCACCCCTGCCTTTGGCACTCCTTCTTCCACCCCGGCCTTTGGAACTCCTTCTTC
1 ACTCCTTCTTCCACACCTGCATTTGGCACTCCGTCTTCGACACCGGCATTTGGAACTCCATCTTC
* * *
113607455 AACTCCGGCTTTTGGG
66 GACACCGGCTTTTGGA
* * * * *
113607471 GCTACTTCTTCCACACCGGCATTTGGCACTCCGTCTTCGACACCGGCGTTTGGCACTCCATCTTC
1 ACTCCTTCTTCCACACCTGCATTTGGCACTCCGTCTTCGACACCGGCATTTGGAACTCCATCTTC
* *
113607536 GACACCGGCGTTTGGC
66 GACACCGGCTTTTGGA
* * * ** * *
113607552 ACTCCGTCTTCGACACCTGCGTTTGGGGCTCCGTCTTCGACACCGGCATTTGGAACTCCGTCCTC
1 ACTCCTTCTTCCACACCTGCATTTGGCACTCCGTCTTCGACACCGGCATTTGGAACTCCATCTTC
113607617 GACACCGGCTTTTGGA
66 GACACCGGCTTTTGGA
113607633 ACTCC
1 ACTCC
113607638 CTCAACGCCG
Statistics
Matches: 138, Mismatches: 29, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
81 138 1.00
ACGTcount: A:0.12, C:0.38, G:0.20, T:0.29
Consensus pattern (81 bp):
ACTCCTTCTTCCACACCTGCATTTGGCACTCCGTCTTCGACACCGGCATTTGGAACTCCATCTTC
GACACCGGCTTTTGGA
Found at i:113614952 original size:146 final size:148
Alignment explanation
Indices: 113614651--113614954 Score: 497
Period size: 146 Copynumber: 2.1 Consensus size: 148
113614641 GTAAAAGTTT
113614651 TGATTTTTTTTAAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAATATATTTTTTAGTCATTTT
1 TGATTTTTTTTAAAAAAGAG-AAGTTTAGATTTTTAAAAATAAAAATATATTTTTTAGTCATTTT
* *
113614716 AAAGGAAAAGTTTAAATTTTTAAAACAAAACTTTGATCTTTTTCAACTATTTCGAAATAAAGTTT
65 AAAGGAAAAGTTTAAAATTTTAAAACAAAACTTTGATCTTTTTCAACTATTTCGAAATAAAATTT
*
113614781 TGATTTTTAAGAAAAATAA
130 TAATTTTTAAGAAAAATAA
*
113614800 TAATTTTTTTTAGAAAAAGAG-AGTTTAGATTTTTAAAAAT-AAAA-ATATTTTTTAGTCATTTT
1 TGATTTTTTTTA-AAAAAGAGAAGTTTAGATTTTTAAAAATAAAAATATATTTTTTAGTCATTTT
**
113614862 AAAGGAAAAGTTTAAAATTTTAAAACAAAGTTTTGATCTTTTTCAACTATTTCGAAATAAAATTT
65 AAAGGAAAAGTTTAAAATTTTAAAACAAAACTTTGATCTTTTTCAACTATTTCGAAATAAAATTT
* *
113614927 TAATTTTTAAGAAAAGTAG
130 TAATTTTTAAGAAAAATAA
113614946 TGATTTTTT
1 TGATTTTTT
113614955 AAAAAGAAAA
Statistics
Matches: 145, Mismatches: 9, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
146 103 0.71
147 4 0.03
148 19 0.13
149 11 0.08
150 8 0.06
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.43
Consensus pattern (148 bp):
TGATTTTTTTTAAAAAAGAGAAGTTTAGATTTTTAAAAATAAAAATATATTTTTTAGTCATTTTA
AAGGAAAAGTTTAAAATTTTAAAACAAAACTTTGATCTTTTTCAACTATTTCGAAATAAAATTTT
AATTTTTAAGAAAAATAA
Found at i:113614984 original size:146 final size:146
Alignment explanation
Indices: 113614655--113614988 Score: 462
Period size: 146 Copynumber: 2.3 Consensus size: 146
113614645 AAGTTTTGAT
* *
113614655 TTTTTTTAAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAATATATTTTTTAGTCATTTTAAAG
1 TTTTTTT-AAAAAGAGAAAGTTTAGA-TTTTAAAAAAAAAAAAATATTTTTTAGTCATTTTAAAG
* * *
113614720 GAAAAGTTTAAATTTTTAAAACAAAACTTTGATCTTTTTCAACTATTTCGAAATAAAGTTTTGAT
64 GAAAAGTTTAAAATTTTAAAACAAAACTTTGATCTTTTTCAACTATTTCGAAATAAAATTTTAAT
113614785 TTTTAAGAAAAATAATAA
129 TTTTAAGAAAAATAATAA
* * *
113614803 TTTTTTTTAGAAAA-AGAGAGTTTAGATTTT-TAAAAATAAAAATATTTTTTAGTCATTTTAAAG
1 -TTTTTTTA-AAAAGAGAAAGTTTAGATTTTAAAAAAAAAAAAATATTTTTTAGTCATTTTAAAG
**
113614866 GAAAAGTTTAAAATTTTAAAACAAAGTTTTGATCTTTTTCAACTATTTCGAAATAAAATTTTAAT
64 GAAAAGTTTAAAATTTTAAAACAAAACTTTGATCTTTTTCAACTATTTCGAAATAAAATTTTAAT
* * *
113614931 TTTTAAGAAAAGTAGTGA
129 TTTTAAGAAAAATAATAA
* *
113614949 -TTTTTTAAAAAGA-AAACTTT-GATTTTACAAAAAAAAAAAT
1 TTTTTTTAAAAAGAGAAAGTTTAGATTTTAAAAAAAAAAAAAT
113614989 CCGACCACCG
Statistics
Matches: 165, Mismatches: 17, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
142 6 0.04
143 20 0.12
144 8 0.05
146 104 0.63
147 4 0.02
148 12 0.07
149 11 0.07
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.41
Consensus pattern (146 bp):
TTTTTTTAAAAAGAGAAAGTTTAGATTTTAAAAAAAAAAAAATATTTTTTAGTCATTTTAAAGGA
AAAGTTTAAAATTTTAAAACAAAACTTTGATCTTTTTCAACTATTTCGAAATAAAATTTTAATTT
TTAAGAAAAATAATAA
Found at i:113618328 original size:24 final size:24
Alignment explanation
Indices: 113618291--113618339 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
113618281 ATTTTTTTTT
*
113618291 TAAATTTTATAATTTTAAAAAATA
1 TAAATTTTAGAATTTTAAAAAATA
* * *
113618315 TAAATTTTGGAATTTTTATAAATA
1 TAAATTTTAGAATTTTAAAAAATA
113618339 T
1 T
113618340 TTTGAATTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (24 bp):
TAAATTTTAGAATTTTAAAAAATA
Found at i:113618343 original size:20 final size:21
Alignment explanation
Indices: 113618318--113618363 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
113618308 AAAAATATAA
113618318 ATTTTGGAATTTTT-ATAAA-T
1 ATTTTGGAATTTTTGA-AAATT
113618338 ATTTT-GAATTTTTGAAAATT
1 ATTTTGGAATTTTTGAAAATT
113618358 ATTTTG
1 ATTTTG
113618364 ATTTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.57
Consensus pattern (21 bp):
ATTTTGGAATTTTTGAAAATT
Found at i:113618364 original size:20 final size:19
Alignment explanation
Indices: 113618313--113618369 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
113618303 TTTTAAAAAA
*
113618313 TATAAAT-TTTGGAATTTT
1 TATAAATATTTTGAATTTT
113618331 TATAAATATTTTGAATTTT
1 TATAAATATTTTGAATTTT
113618350 TGA-AAATTATTTTG-ATTTT
1 T-ATAAA-TATTTTGAATTTT
113618369 T
1 T
113618370 TTTTTTTTGT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
18 7 0.20
19 20 0.57
20 8 0.23
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:113620122 original size:28 final size:27
Alignment explanation
Indices: 113620072--113620124 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
113620062 CTATTCAGAA
* *
113620072 ATCAATGTTAACTGGGCCTTAGCCCAT
1 ATCAATATTAACTGGGCCATAGCCCAT
113620099 ATCAATATTAATCTGGGCCATAGCCC
1 ATCAATATTAA-CTGGGCCATAGCCC
113620125 CTTACAGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 10 0.43
28 13 0.57
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.28
Consensus pattern (27 bp):
ATCAATATTAACTGGGCCATAGCCCAT
Found at i:113620204 original size:60 final size:59
Alignment explanation
Indices: 113620086--113620220 Score: 157
Period size: 60 Copynumber: 2.2 Consensus size: 59
113620076 ATGTTAACTG
* *
113620086 GGCCTTAGCCCATATCAATATTAATCTGGGCCATAGCCCCTTACAGTATCAGAGTATATTA
1 GGCC-TAGCCCATATCAATATTAATCTAGGCCATAGCCCATTACAG-ATCAGAGTATATTA
* * *
113620147 GGCCTAGCCCATATCAGTATTAATCTAGGCCGTAGCCCTATTACA-AGTC-GAGATATATTG
1 GGCCTAGCCCATATCAATATTAATCTAGGCCATAGCCC-ATTACAGA-TCAGAG-TATATTA
*
113620207 GGCCTTGCCCATAT
1 GGCCTAGCCCATAT
113620221 TAACACAGTT
Statistics
Matches: 65, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
59 4 0.06
60 52 0.80
61 9 0.14
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (59 bp):
GGCCTAGCCCATATCAATATTAATCTAGGCCATAGCCCATTACAGATCAGAGTATATTA
Found at i:113620883 original size:8 final size:8
Alignment explanation
Indices: 113620868--113620899 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
113620858 TCACAAATGC
113620868 CGGCTTTT
1 CGGCTTTT
*
113620876 CAGCTTTT
1 CGGCTTTT
113620884 CGGCTTTT
1 CGGCTTTT
113620892 CGGCTTTT
1 CGGCTTTT
113620900 GCCGATCTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.03, C:0.25, G:0.22, T:0.50
Consensus pattern (8 bp):
CGGCTTTT
Found at i:113622929 original size:13 final size:13
Alignment explanation
Indices: 113622911--113622953 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
113622901 TAAATTTTTC
113622911 CTAAATATTATCA
1 CTAAATATTATCA
113622924 CTAAATA--ATC-
1 CTAAATATTATCA
*
113622934 CAAAATATTATCA
1 CTAAATATTATCA
113622947 CTAAATA
1 CTAAATA
113622954 ATTCAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 6 0.24
11 3 0.12
12 3 0.12
13 13 0.52
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:113622941 original size:23 final size:23
Alignment explanation
Indices: 113622913--113622962 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
113622903 AATTTTTCCT
113622913 AAATATTATCACTAAATAATCCA
1 AAATATTATCACTAAATAATCCA
*
113622936 AAATATTATCACTAAATAATTCA
1 AAATATTATCACTAAATAATCCA
113622959 AAAT
1 AAAT
113622963 TTAAAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (23 bp):
AAATATTATCACTAAATAATCCA
Found at i:113625302 original size:27 final size:27
Alignment explanation
Indices: 113625264--113625325 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
113625254 TGCAAAAGTC
113625264 TATAGGAAAAATTAGCTTATTTACCTT
1 TATAGGAAAAATTAGCTTATTTACCTT
113625291 TATAGGAAAAATTAGCTTATTTACCTT
1 TATAGGAAAAATTAGCTTATTTACCTT
113625318 TATGAGGA
1 TAT-AGGA
113625326 TATCTTCTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 30 0.88
28 4 0.12
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.39
Consensus pattern (27 bp):
TATAGGAAAAATTAGCTTATTTACCTT
Found at i:113625779 original size:27 final size:27
Alignment explanation
Indices: 113625741--113625797 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
113625731 TTCTAGGGTT
* * *
113625741 TGGGGGAGGTACCGCTAATGATTTATG
1 TGGGAGAGGTACCACAAATGATTTATG
113625768 TGGGAGAGGTACCACAAATGATTTATG
1 TGGGAGAGGTACCACAAATGATTTATG
113625795 TGG
1 TGG
113625798 TGCGTGCTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.26, C:0.11, G:0.35, T:0.28
Consensus pattern (27 bp):
TGGGAGAGGTACCACAAATGATTTATG
Found at i:113627844 original size:48 final size:48
Alignment explanation
Indices: 113627769--113627995 Score: 240
Period size: 48 Copynumber: 4.7 Consensus size: 48
113627759 TAATATGTGT
* *
113627769 GCCAGTGTAAGACCACGTCTGGGACATGGCATCGGCCACGATATGAGA
1 GCCAATGTAAGACCATGTCTGGGACATGGCATCGGCCACGATATGAGA
** * * * * * * * *
113627817 TTCAATGTAAGAACAAGTTTGGAACATGGCATCGGCGATGTTGTGAGA
1 GCCAATGTAAGACCATGTCTGGGACATGGCATCGGCCACGATATGAGA
* *
113627865 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGACCAC-ATTATGAGA
1 GCCAATGTAAGACCATGTCTGGGACATGGCATCGGCCACGA-TATGAGA
* * * * *
113627913 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGACATGTGA
1 GCCAATGTAAGACCATGTCTGGGACATGGCATCGGCCACGATATGAGA
* * *
113627961 GCCAATGTAAAACCATGTTTGGAACATGGCATCGG
1 GCCAATGTAAGACCATGTCTGGGACATGGCATCGG
113627996 TAACTCACTC
Statistics
Matches: 144, Mismatches: 33, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
48 143 0.99
49 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (48 bp):
GCCAATGTAAGACCATGTCTGGGACATGGCATCGGCCACGATATGAGA
Found at i:113630366 original size:5 final size:5
Alignment explanation
Indices: 113630356--113630382 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
113630346 TATGAAGTGT
113630356 AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AA
113630383 ATATATTCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:113631273 original size:23 final size:23
Alignment explanation
Indices: 113631247--113631314 Score: 111
Period size: 23 Copynumber: 3.0 Consensus size: 23
113631237 GCTAAATTTT
*
113631247 TCTTAAATATTATCACTAATTAA
1 TCTTAAATATTATCACTAAATAA
113631270 TCTTAAATATTATCACTAAATAA
1 TCTTAAATATTATCACTAAATAA
113631293 T-TCTAAATATTATCACTAAATA
1 TCT-TAAATATTATCACTAAATA
113631315 TTTCAAAATT
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
22 1 0.02
23 42 0.98
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (23 bp):
TCTTAAATATTATCACTAAATAA
Found at i:113631289 original size:13 final size:13
Alignment explanation
Indices: 113631250--113631316 Score: 65
Period size: 13 Copynumber: 5.6 Consensus size: 13
113631240 AAATTTTTCT
113631250 TAAATATTATCAC
1 TAAATATTATCAC
* *
113631263 T-AAT-TAATC-T
1 TAAATATTATCAC
113631273 TAAATATTATCAC
1 TAAATATTATCAC
*
113631286 TAAATA--AT-TC
1 TAAATATTATCAC
113631296 TAAATATTATCAC
1 TAAATATTATCAC
113631309 TAAATATT
1 TAAATATT
113631317 TCAAAATTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
10 8 0.19
11 9 0.21
12 9 0.21
13 16 0.38
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (13 bp):
TAAATATTATCAC
Found at i:113642031 original size:40 final size:39
Alignment explanation
Indices: 113641904--113642033 Score: 163
Period size: 40 Copynumber: 3.3 Consensus size: 39
113641894 ATGCTGGAAA
* *
113641904 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGCGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-AGTGG
* * *
113641944 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTCG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGC-AGTGG
*
113641984 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGCACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCA-GTGG
113642024 TTATATCCGG
1 TTATATCCGG
113642034 TTGTATTCCG
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
39 4 0.05
40 73 0.95
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.23
Consensus pattern (39 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCAGTGG
Found at i:113650103 original size:40 final size:39
Alignment explanation
Indices: 113649976--113650105 Score: 163
Period size: 40 Copynumber: 3.3 Consensus size: 39
113649966 ATGCTGGAAA
* *
113649976 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGCGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-AGTGG
* * *
113650016 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTCG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGC-AGTGG
*
113650056 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGCACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCA-GTGG
113650096 TTATATCCGG
1 TTATATCCGG
113650106 TTGTATTCCG
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
39 4 0.05
40 73 0.95
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.23
Consensus pattern (39 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCAGTGG
Found at i:113671611 original size:15 final size:15
Alignment explanation
Indices: 113671591--113671646 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
113671581 TAAATCTTAA
113671591 CCAAATTTCCATTAC
1 CCAAATTTCCATTAC
*
113671606 CCAAATTTTAAATCATTA-
1 CCAAA-TTT---CCATTAC
*
113671624 CCGAATTTCCATTAC
1 CCAAATTTCCATTAC
113671639 CCAAATTT
1 CCAAATTT
113671647 GAAATCATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
14 5 0.16
15 12 0.38
16 3 0.09
17 3 0.09
18 4 0.12
19 5 0.16
ACGTcount: A:0.36, C:0.27, G:0.02, T:0.36
Consensus pattern (15 bp):
CCAAATTTCCATTAC
Found at i:113671631 original size:33 final size:34
Alignment explanation
Indices: 113671581--113671655 Score: 118
Period size: 33 Copynumber: 2.3 Consensus size: 34
113671571 TCAAAGAACA
113671581 TAAATC-TTAACCAAATTTCCATTACCCAAATTT
1 TAAATCATTAACCAAATTTCCATTACCCAAATTT
*
113671614 TAAATCATT-ACCGAATTTCCATTACCCAAATTT
1 TAAATCATTAACCAAATTTCCATTACCCAAATTT
*
113671647 GAAATCATT
1 TAAATCATT
113671656 TTGTCTTATA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
33 37 0.95
34 2 0.05
ACGTcount: A:0.39, C:0.23, G:0.03, T:0.36
Consensus pattern (34 bp):
TAAATCATTAACCAAATTTCCATTACCCAAATTT
Done.