Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008302.1 Hibiscus syriacus cultivar Beakdansim tig00110988_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: 3402722
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 17
Found at i:205439 original size:22 final size:21
Alignment explanation
Indices: 205380--205433 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
205370 AAAATTTAGT
* *
205380 GAAACCGAAAGTAACCCAAATC
1 GAAA-CGAAATTAACCCAAACC
205402 GAAACCGAAATTAACCCAAACC
1 GAAA-CGAAATTAACCCAAACC
205424 GAAA-GAAATT
1 GAAACGAAATT
205434 CGAACCGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 6 0.20
22 24 0.80
ACGTcount: A:0.52, C:0.24, G:0.13, T:0.11
Consensus pattern (21 bp):
GAAACGAAATTAACCCAAACC
Found at i:205471 original size:33 final size:31
Alignment explanation
Indices: 205404--205502 Score: 92
Period size: 32 Copynumber: 3.1 Consensus size: 31
205394 CCCAAATCGA
* **
205404 AACCGAAATTAACCCAAACCGAAAGA-AATTCG
1 AACCGAATTTAACCC-AACCGAAA-ACAACCCG
205436 AACCGAATTTTAACCCAATCCGAAAACAACCCG
1 AACCGAA-TTTAACCCAA-CCGAAAACAACCCG
* * *
205469 AACTGAATTTAACCCTACCTAAAAGCAACCCG
1 AACCGAATTTAACCCAACCGAAAA-CAACCCG
205501 AA
1 AA
205503 AAGAAATTAA
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
31 6 0.11
32 28 0.49
33 23 0.40
ACGTcount: A:0.45, C:0.29, G:0.10, T:0.15
Consensus pattern (31 bp):
AACCGAATTTAACCCAACCGAAAACAACCCG
Found at i:214031 original size:6 final size:6
Alignment explanation
Indices: 214014--214089 Score: 73
Period size: 6 Copynumber: 12.7 Consensus size: 6
214004 GGGTTTTTTA
* * ** *
214014 GGTTCG GGTTTG GATTTG GGTTCA GATTTG GGTTT- GGTTTG GGTTTG
1 GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG
* *
214061 GGTTTG AGTTTG GGTTTA GGTTTAG GGTT
1 GGTTTG GGTTTG GGTTTG GGTTT-G GGTT
214090 CAAGTTTAGG
Statistics
Matches: 55, Mismatches: 13, Indels: 3
0.77 0.18 0.04
Matches are distributed among these distances:
5 5 0.09
6 46 0.84
7 4 0.07
ACGTcount: A:0.08, C:0.03, G:0.42, T:0.47
Consensus pattern (6 bp):
GGTTTG
Found at i:214108 original size:19 final size:18
Alignment explanation
Indices: 214074--214120 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
214064 TTGAGTTTGG
* *
214074 GTTTAGGTTTAGGGTTCAA
1 GTTTAGGGTTAAGGTT-AA
214093 GTTTAGGGTTAAGGTTAA
1 GTTTAGGGTTAAGGTTAA
*
214111 GGTT-GGGTTA
1 GTTTAGGGTTA
214121 TAGAAGATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 6 0.24
18 5 0.20
19 14 0.56
ACGTcount: A:0.21, C:0.02, G:0.36, T:0.40
Consensus pattern (18 bp):
GTTTAGGGTTAAGGTTAA
Found at i:215188 original size:18 final size:18
Alignment explanation
Indices: 215165--215253 Score: 151
Period size: 18 Copynumber: 4.9 Consensus size: 18
215155 TTATAACACA
215165 TATGTCCCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
215183 TATGTCCCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
*
215201 TATGTCCCGAATGACCAC
1 TATGTCCCGAAGGACCAC
215219 ATATGTCCCGAAGGACCAC
1 -TATGTCCCGAAGGACCAC
*
215238 TATATCCCGAAGGACC
1 TATGTCCCGAAGGACC
215254 GCGTAGACCC
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
18 50 0.75
19 17 0.25
ACGTcount: A:0.29, C:0.33, G:0.20, T:0.18
Consensus pattern (18 bp):
TATGTCCCGAAGGACCAC
Found at i:215233 original size:37 final size:36
Alignment explanation
Indices: 215165--215253 Score: 151
Period size: 37 Copynumber: 2.4 Consensus size: 36
215155 TTATAACACA
215165 TATGTCCCGAAGGACCACTATGTCCCGAAGGACCAC
1 TATGTCCCGAAGGACCACTATGTCCCGAAGGACCAC
*
215201 TATGTCCCGAATGACCACATATGTCCCGAAGGACCAC
1 TATGTCCCGAAGGACCAC-TATGTCCCGAAGGACCAC
*
215238 TATATCCCGAAGGACC
1 TATGTCCCGAAGGACC
215254 GCGTAGACCC
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
36 17 0.35
37 32 0.65
ACGTcount: A:0.29, C:0.33, G:0.20, T:0.18
Consensus pattern (36 bp):
TATGTCCCGAAGGACCACTATGTCCCGAAGGACCAC
Found at i:215968 original size:24 final size:20
Alignment explanation
Indices: 215919--215976 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
215909 TTCCCATTGA
*
215919 AGTGCATCGGTGCATTCTAC
1 AGTGCATCGATGCATTCTAC
215939 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
215962 AGGTGCATCGATGCA
1 A-GTGCATCGATGCA
215977 CTACCATGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.29
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:218770 original size:18 final size:18
Alignment explanation
Indices: 218747--218811 Score: 105
Period size: 18 Copynumber: 3.7 Consensus size: 18
218737 GTAGAATTTG
218747 TCCCGAAGGACCACTATA
1 TCCCGAAGGACCACTATA
*
218765 TCCCGAAGGACCACTATG
1 TCCCGAAGGACCACTATA
*
218783 TCCTGAAGGACCACTATA
1 TCCCGAAGGACCACTATA
218801 T-CCGAAGGACC
1 TCCCGAAGGACC
218812 GCGTAGACCC
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
17 9 0.21
18 34 0.79
ACGTcount: A:0.31, C:0.32, G:0.20, T:0.17
Consensus pattern (18 bp):
TCCCGAAGGACCACTATA
Found at i:219548 original size:20 final size:20
Alignment explanation
Indices: 219523--219560 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
219513 TTCCCATTGA
*
219523 AGTGCATCGGTGCATTCTAC
1 AGTGCATCGATGCATTCTAC
219543 AGTGCATCGATGCATTCT
1 AGTGCATCGATGCATTCT
219561 TTAACACAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:219657 original size:19 final size:19
Alignment explanation
Indices: 219633--219684 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
219623 TTTTAAGGGG
*
219633 ATGCATCGATGCACTCCTT
1 ATGCATCGATGCACTCCTC
219652 ATGCATCGATGCACTCCTC
1 ATGCATCGATGCACTCCTC
*
219671 ATGAATCGATGCAC
1 ATGCATCGATGCAC
219685 CAACCGTACT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.27
Consensus pattern (19 bp):
ATGCATCGATGCACTCCTC
Found at i:222660 original size:16 final size:17
Alignment explanation
Indices: 222629--222664 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
222619 ATTACTTAGG
*
222629 TTATATATATATATAGT
1 TTATATATATACATAGT
222646 TTATA-ATATACATAGT
1 TTATATATATACATAGT
222662 TTA
1 TTA
222665 ACCATACATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.50
Consensus pattern (17 bp):
TTATATATATACATAGT
Found at i:222945 original size:13 final size:13
Alignment explanation
Indices: 222927--222959 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
222917 TAATTTACTT
222927 TATATAGTTTATA
1 TATATAGTTTATA
222940 TATATAGTTTATA
1 TATATAGTTTATA
222953 TACTATA
1 TA-TATA
222960 CATAGTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.52
Consensus pattern (13 bp):
TATATAGTTTATA
Found at i:222984 original size:18 final size:18
Alignment explanation
Indices: 222938--222980 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
222928 ATATAGTTTA
* *
222938 TATATATAGTTTATATAC
1 TATACATAGTTTATACAC
222956 TATACATAGTTTATACAC
1 TATACATAGTTTATACAC
222974 -ATACATA
1 TATACATA
222981 AGTTATTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.42
Consensus pattern (18 bp):
TATACATAGTTTATACAC
Found at i:223009 original size:13 final size:15
Alignment explanation
Indices: 222995--223032 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
222985 ATTATAAGTT
222995 TACATATATAGTTTA
1 TACATATATAGTTTA
**
223010 TACATATATA-CATA
1 TACATATATAGTTTA
223024 TACATATAT
1 TACATATAT
223033 TAACTATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.45, C:0.11, G:0.03, T:0.42
Consensus pattern (15 bp):
TACATATATAGTTTA
Found at i:223212 original size:2 final size:2
Alignment explanation
Indices: 223207--223336 Score: 105
Period size: 2 Copynumber: 67.5 Consensus size: 2
223197 TTATATAGTT
223207 TA TA TA TA TA TA TA TA TA TA TA T- TA TA T- TA TA TA 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
* * * * *
223246 TA TA T- TA GA TA AA T- TA TA -A TT TA TA AA CTA -A TA T- TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* * *
223284 TA TA GTT TA TA CA TA TA GTT TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
223328 TA TA TA TA T
1 TA TA TA TA T
223337 TAATATAAAT
Statistics
Matches: 102, Mismatches: 15, Indels: 22
0.73 0.11 0.16
Matches are distributed among these distances:
1 8 0.08
2 91 0.89
3 3 0.03
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:223362 original size:21 final size:21
Alignment explanation
Indices: 223338--223378 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
223328 TATATATATT
*
223338 AATATAAATTATAGTTTATAA
1 AATATAAATTATAATTTATAA
* *
223359 AATATTACTTATAATTTATA
1 AATATAAATTATAATTTATA
223379 CATATATAGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (21 bp):
AATATAAATTATAATTTATAA
Found at i:223371 original size:101 final size:98
Alignment explanation
Indices: 223199--223459 Score: 250
Period size: 97 Copynumber: 2.6 Consensus size: 98
223189 CTTTACACTT
*
223199 ATATAGTTTATATATATATATATATATATAT-TATAT-TA-TATATATAA-TATA-TTAGATAAA
1 ATATAGTTTATATATATATATATATATATATATATATATATTATATA-AATTATAGTT-TATAAA
* * **
223259 TTATAATTTATAAACTAATATTTTATATAGTTTATAC
64 ATATAACTTAT-AACTAATA-CATATATAGTTTATAC
223296 ATATAGTTTATATATATATATATATATATATATATATATATTAATATAAATTATAGTTTATAAAA
1 ATATAGTTTATATATATATATATATATATATATATATATATT-ATATAAATTATAGTTTATAAAA
* * * *
223361 TATTACTTATAATTTATACATATATAGTTTATAT
65 TATAACTTATAACTAATACATATATAGTTTATAC
* * * *
223395 ACATAGTTT-TATATATA-AT-TCATAAACATAATAATATATATTTATAATAATTATATAGTTTA
1 ATATAGTTTATATATATATATAT-ATATATAT-AT-ATATATA-TTAT-ATAAAT-TATAGTTTA
223457 TAA
60 TAA
223460 TAAACATAGT
Statistics
Matches: 139, Mismatches: 13, Indels: 20
0.81 0.08 0.12
Matches are distributed among these distances:
96 1 0.01
97 39 0.28
98 15 0.11
99 32 0.23
100 16 0.12
101 34 0.24
102 2 0.01
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (98 bp):
ATATAGTTTATATATATATATATATATATATATATATATATTATATAAATTATAGTTTATAAAAT
ATAACTTATAACTAATACATATATAGTTTATAC
Found at i:223408 original size:84 final size:83
Alignment explanation
Indices: 223195--223411 Score: 246
Period size: 84 Copynumber: 2.6 Consensus size: 83
223185 TATACTTTAC
* * *
223195 ACTTATATAGTTTATATATATATA-TATATATATATTATATTATATATATAATATATTAGATAAA
1 ACTTATATAGTTTATACATATATAGTTTATATATA-TATTTTATATATATAATATATTAGATAAA
*
223259 TTATAATTTATAAACTAAT
65 TTATAATTTATAAAATAAT
* *
223278 ATTTTATATAGTTTATAC--ATATAGTTTATATATATATATATATATATATATATATATATTAAT
1 A-CTTATATAGTTTATACATATATAGTTTATATATATAT-T-T-TATATATATA-ATATATT-AG
* *
223341 ATAAATTATAGTTTATAAAATATT
60 ATAAATTATAATTTATAAAATAAT
*
223365 ACTTATA-A-TTTATACATATATAGTTTATATACATAGTTTTATATATA
1 ACTTATATAGTTTATACATATATAGTTTATATATATA-TTTTATATATA
223412 ATTCATAAAC
Statistics
Matches: 114, Mismatches: 10, Indels: 19
0.80 0.07 0.13
Matches are distributed among these distances:
82 8 0.07
83 10 0.09
84 30 0.26
85 12 0.11
86 30 0.26
87 24 0.21
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (83 bp):
ACTTATATAGTTTATACATATATAGTTTATATATATATTTTATATATATAATATATTAGATAAAT
TATAATTTATAAAATAAT
Found at i:223450 original size:19 final size:18
Alignment explanation
Indices: 223422--223462 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
223412 ATTCATAAAC
223422 ATAATAATATATATTTATA
1 ATAATAATATA-ATTTATA
* *
223441 ATAATTATATAGTTTATA
1 ATAATAATATAATTTATA
223459 ATAA
1 ATAA
223463 ACATAGTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
ATAATAATATAATTTATA
Found at i:223458 original size:18 final size:17
Alignment explanation
Indices: 223422--223474 Score: 74
Period size: 16 Copynumber: 3.2 Consensus size: 17
223412 ATTCATAAAC
223422 ATAATAATATATA-TTT
1 ATAATAATATATAGTTT
223438 ATAATAATTATATAGTTT
1 ATAATAA-TATATAGTTT
*
223456 ATAATAA-ACATAGTTT
1 ATAATAATATATAGTTT
223472 ATA
1 ATA
223475 TAAACTTATA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
16 18 0.53
17 6 0.18
18 10 0.29
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (17 bp):
ATAATAATATATAGTTT
Found at i:223619 original size:2 final size:2
Alignment explanation
Indices: 223614--223660 Score: 53
Period size: 2 Copynumber: 24.5 Consensus size: 2
223604 TATGTACTTA
* * *
223614 AT AT AT AT AT AT AA AT CT -T AT AT AT AT -T AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
223654 AT AT AT A
1 AT AT AT A
223661 AATTACATAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:224207 original size:13 final size:13
Alignment explanation
Indices: 224191--224215 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
224181 TTATACATAT
224191 ATAGTTTATATAC
1 ATAGTTTATATAC
224204 ATAGTTTATATA
1 ATAGTTTATATA
224216 TAATCATATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (13 bp):
ATAGTTTATATAC
Found at i:224257 original size:19 final size:18
Alignment explanation
Indices: 224229--224274 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
224219 TCATATAAAC
224229 ATAAATATAGATATAATA
1 ATAAATATAGATATAATA
*
224247 ATAATATATAGTTATAAT-
1 ATAA-ATATAGATATAATA
*
224265 ATAAACATAG
1 ATAAATATAG
224275 TTTATATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 5 0.20
18 8 0.32
19 12 0.48
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.35
Consensus pattern (18 bp):
ATAAATATAGATATAATA
Found at i:224326 original size:26 final size:26
Alignment explanation
Indices: 224250--224327 Score: 69
Period size: 22 Copynumber: 3.1 Consensus size: 26
224240 TATAATAATA
* *
224250 ATATATAGTTATAATATAAACATAGTTT
1 ATATATAG-T-TAATATAAATATACTTT
224278 ATATATAGTT-ATAT--ATA-AC-TT
1 ATATATAGTTAATATAAATATACTTT
224299 ATATTATA-TTAATATAAATATACTTT
1 ATA-TATAGTTAATATAAATATACTTT
224325 ATA
1 ATA
224328 CTTTATATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 14
0.72 0.03 0.24
Matches are distributed among these distances:
21 7 0.17
22 9 0.21
23 2 0.05
24 3 0.07
25 6 0.14
26 6 0.14
27 1 0.02
28 8 0.19
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (26 bp):
ATATATAGTTAATATAAATATACTTT
Found at i:224480 original size:22 final size:22
Alignment explanation
Indices: 224438--224490 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
224428 TGTACTTAAT
224438 TATTATATACATAAATCTTATA
1 TATTATATACATAAATCTTATA
* *
224460 TATTATATATTATATAT-TTATA
1 TATTATATA-CATAAATCTTATA
*
224482 TAATATATA
1 TATTATATA
224491 AAACATAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 22 0.81
23 5 0.19
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (22 bp):
TATTATATACATAAATCTTATA
Found at i:224491 original size:7 final size:7
Alignment explanation
Indices: 224455--224489 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
224445 TACATAAATC
224455 TTATATA
1 TTATATA
224462 TTATATA
1 TTATATA
224469 TTATATA
1 TTATATA
224476 TT-TATA
1 TTATATA
*
224482 TAATATA
1 TTATATA
224489 T
1 T
224490 AAAACATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
6 5 0.19
7 21 0.81
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
TTATATA
Found at i:224924 original size:832 final size:829
Alignment explanation
Indices: 223340--225793 Score: 3843
Period size: 832 Copynumber: 3.0 Consensus size: 829
223330 TATATATTAA
*
223340 TATAAATTATAGTTTATAAAATAT-TAC---TTATAATTTATACATATATAGTTTATATACATAG
1 TATAAATTATAGTTTATAAACTATATACTTTTTATAATTTATACATATATAGTTTATATACATAG
223401 TTTTATATATAAT--TCATAAACATAATAATATATATTTATAATAATTATATAGTT-T-ATAATA
66 -TTTATATATAATCAT-ATAAACATAAT-ATA-ATA-TTATAATAA-TATATAGTTATAAT-ATA
* *
223462 AACATAGTTTATATAAACTTATAT-TAA-TTA-A--ATA-TAAT-T--A-ATACTTTA-A---TA
124 AACATAGTTTATATATAGTTATATATAACTTATATTATATTAATATAAATATACTTTATACTTTA
223513 T-TAATTTATATTATTGTTAACACATAG-TCATTAAAACTTTACGG-TTATATATAAACTTATAA
189 TATAATTTATA-TATTGTTAACACATAGTTCATTAAAACTTTACGGTTTATATATAAACTTATAA
*
223575 --TTTAATATAAACTATTATATAGTAATATATATGTACTTAA-TA-TATATATATAAATC--T-T
253 TTTTTAATATAAACTATTATATAGTAATATATATGTACTTAATTATTATATACATAAATCTATAT
223633 A-TATATATTATATATTTATAT-ATATATAAATTACATAATTTATTAATAAACTACATGTAAACT
318 ATTATATATTATATATTTATATAATATATAAA--ACATAATTTATTAATAAACTACATGTAAACT
*
223696 ACATAT-A-TATATTATATATTTGTCTTTATATATTATGTTATAATTGTTTTTTCAATTTTTTAT
381 ACATATAACTATATTATATATTTGTCTTTTTATATTATGTTATAATTG-TTTTTCAA-TTTTTAT
223759 ATTTGCAATTTACTATATTTTTTCATTATTTCTTTACATTTTGCA-TTATTTCGATTCCATCTTT
444 ATTTGCAATTTACTATA--TTTTCATTATTTCTTTACATTTTGCATTTATTTCGATTCCATCTTT
*
223823 TTTTGTTTTTTAATTTATTTAAATTTAAGCCTTTCACTTTTATAGTATTCAGTTTAGTCTTTAAA
507 TTGTGTTTTTTAATTTATTTAAATTTAAGCCTTTCACTTTTATAGTATTCAGTTTAGTCTTTAAA
223888 TTTATATTTGCATCTTCATTTGACCCATTGTTAGTTGTTATTTATATTTTTGTAATTGGCCCATA
572 TTTATATTTGCATCTTCATTTGACCCATTGTTAGTTGTTATTTATATTTTTGTAATTGGCCCAT-
223953 AACTTTTTAAATGAG--TAAATTAGTCC-TTTTTATATAATTTAAACCTCACATTTTAAATTGAT
636 AACTTTTTAAATGAGTATAAATTAGTCCTTTTTTATATAATTTAAACCTCACATTTTAAATTGAT
224015 TTCGA-TTGGTCCCTTACCTATGTGTGTTGTTTAATTTTTATTTTAAAATTTTATTTGTAATTTT
701 TTCGATTTGGTCCCTTACCTATGTGTGTTGTTTAATTTTTATTTTAAAATTTTATTTGTAATTTT
* *
224079 ACATTTCTTCAATTTTGTCCTTAAATTTATATTTTTTTACAAAATTGACCCATTATTATTTTTT
766 ACATTTCTTCAATTTTGTCCTTAAATTTATATTTTTTTACAAAATTGATCCATGATTATTTTTT
224143 TATAAATTATAGTTTATAAACTATATACTTTTTATAATTTATACATATATAGTTTATATACATAG
1 TATAAATTATAGTTTATAAACTATATACTTTTTATAATTTATACATATATAGTTTATATACATAG
*
224208 TTTATATATAATCATATAAACATAAATATAGATATAATAATAATATATAGTTATAATATAAACAT
66 TTTATATATAATCATATAAACAT-AATATA-ATATTATAATAATATATAGTTATAATATAAACAT
224273 AGTTTATATATAGTTATATATAACTTATATTATATTAATATAAATATACTTTATACTTTATATAA
129 AGTTTATATATAGTTATATATAACTTATATTATATTAATATAAATATACTTTATACTTTATATAA
224338 TTTATATATTGTTAACAC-TAGTTCATTAAAACTTTACGGTTTATATATAAACTTATAATTTTTA
194 TTTATATATTGTTAACACATAGTTCATTAAAACTTTACGGTTTATATATAAACTTATAATTTTTA
224402 ATATAAACTATTAT-TAGTAATATATATGTACTTAATTATTATATACATAAATCTTATATATTAT
259 ATATAAACTATTATATAGTAATATATATGTACTTAATTATTATATACATAAATC-TATATATTAT
224466 ATATTATATATTTATATAATATATAAAACATAATTTATTAATAAACTACATGTAAAACTACATAT
323 ATATTATATATTTATATAATATATAAAACATAATTTATTAATAAACTACATGT-AAACTACATAT
224531 AACTATATTATATATTTGTCTTTTTATATTATGTTATAATTGTTTTTCAATTTTTATATTTGCAA
387 AACTATATTATATATTTGTCTTTTTATATTATGTTATAATTGTTTTTCAATTTTTATATTTGCAA
*
224596 TTTACTATATTTTCATTATTTCTTTACATTTTGCATTTATTTCGTTTCCATCTTTTTGTGTTTTT
452 TTTACTATATTTTCATTATTTCTTTACATTTTGCATTTATTTCGATTCCATCTTTTTGTGTTTTT
224661 TAATTTATTTAAAGTTTAAGCCTTTCACTTTTATATGTATTCAGTTTAGTCTTTAAATTTATATT
517 TAATTTATTTAAA-TTTAAGCCTTTCACTTTTATA-GTATTCAGTTTAGTCTTTAAATTTATATT
*
224726 TGTATCTTCATTTGACCCATTGTTAGTTGTTATTTATATTTTTGTAATTGGCCCATAACTTTTTA
580 TGCATCTTCATTTGACCCATTGTTAGTTGTTATTTATATTTTTGTAATTGGCCCATAACTTTTTA
224791 AATGAGTATAAATTAGTCCTTTTTTATATAATTTAAACCTCACATTTTAAATTGATTTCGATTTG
645 AATGAGTATAAATTAGTCCTTTTTTATATAATTTAAACCTCACATTTTAAATTGATTTCGATTTG
224856 GTCCCTTACCTATGTGTG-TGTTTAATTTTTATTTTAAAATTTTATTTGTAATTTTACATTTCTT
710 GTCCCTTACCTATGTGTGTTGTTTAATTTTTATTTTAAAATTTTATTTGTAATTTTACATTTCTT
*
224920 CAATTTTGTCCTTAAATTTATATTTTTTTACAAAATTGATCCATGATTGTTTTTTT
775 CAATTTTGTCCTTAAATTTATATTTTTTTACAAAATTGATCCATGATT-ATTTTTT
224976 TATAAATTATAGTTTATAAACTATATACTTTTTATAATTTATACATATATAGTTTATATACATAG
1 TATAAATTATAGTTTATAAACTATATACTTTTTATAATTTATACATATATAGTTTATATACATAG
225041 TTTATATATAATTTCATATAAACATAATAT-ATATTAT-ATAATATATAGTTTATAATATAAACA
66 TTTATATATAA--TCATATAAACATAATATAATATTATAATAATATATAG-TTATAATATAAACA
225104 TAG-TT-TATATAGTTTATATATAAACTTATATTATATTAATATAAATTATATACTTTAATACTT
128 TAGTTTATATATAG-TTATATAT-AACTTATATTATATTAATAT-AA--ATATACTTT-ATACTT
225167 TATATAA-TT-TATATTGTTAACACATAGTTCATTAAAACTTTACGGTTTATATATAAACTTTAT
187 TATATAATTTATATATTGTTAACACATAGTTCATTAAAACTTTACGGTTTATATATAAAC-TTAT
*
225230 AATTTTTAATATAAACTATTTATATAGTAATA-ATA-G--GTTAATATATT-TATACATAAATCT
251 AATTTTTAATATAAACTA-TTATATAGTAATATATATGTACTTAAT-TATTATATACATAAATCT
**
225290 ATATATTATATTATATATATATATATATATATATATATATTACATAATTTATTAATAAACTACAT
314 ATATATTATA-TAT-TATATAT-T-TATATA-ATATATAAAACATAATTTATTAATAAACTACAT
*
225355 GTAAACTACATA-AAC--TA-TATATATTTGTCTTTTTATATATTTGTTATAATTGTTTTTCAAT
374 GTAAACTACATATAACTATATTATATATTTGTCTTTTTATAT-TATGTTATAATTGTTTTTCAAT
225416 TTTTATA-TTGCAATTTACTAT-TTTTCATTATTTC-TTACATTTTGCATTTATTTCGATTCCAT
438 TTTTATATTTGCAATTTACTATATTTTCATTATTTCTTTACATTTTGCATTTATTTCGATTCCAT
*
225478 CTTTTTGTGTTTTATAATTTA-TTAAATTTTAAGCCTTTCAC-TTTATAGTATTCAGTTTAGTCT
503 CTTTTTGTGTTTTTTAATTTATTTAAA-TTTAAGCCTTTCACTTTTATAGTATTCAGTTTAGTCT
225541 TTAAATTTATATTTGCATCTTCATTTGACCCA---TTAGTTGTTATTTATATTTTTGTAATTGGC
567 TTAAATTTATATTTGCATCTTCATTTGACCCATTGTTAGTTGTTATTTATATTTTTGTAATTGGC
225603 CCAT-AC-TTTTAAATGAGTATAAATTAGTCCTTTTTTATATAATTTAAACCTCACATTTTAAAT
632 CCATAACTTTTTAAATGAGTATAAATTAGTCCTTTTTTATATAATTTAAACCTCACATTTTAAAT
* *
225666 TCATTTCGATTT-GTCCCTTACCTATGTGTGTTGTTTAA--TTTATTTTAAATTTTTATTTGTAA
697 TGATTTCGATTTGGTCCCTTACCTATGTGTGTTGTTTAATTTTTATTTTAAAATTTTATTTGTAA
225728 TTTTACATTTCTTCAA-TTTGTCCTT-AATTTATA-TTTTTTACAAAATTGATCCATGATTATTT
762 TTTTACATTTCTTCAATTTTGTCCTTAAATTTATATTTTTTTACAAAATTGATCCATGATTATTT
225790 TTT
827 TTT
225793 T
1 T
225794 TTGTAATTTA
Statistics
Matches: 1558, Mismatches: 25, Indels: 122
0.91 0.01 0.07
Matches are distributed among these distances:
803 23 0.01
804 3 0.00
805 9 0.01
806 46 0.03
807 53 0.03
808 7 0.00
809 1 0.00
811 3 0.00
812 4 0.00
813 1 0.00
815 1 0.00
816 8 0.01
817 8 0.01
818 25 0.02
819 11 0.01
820 41 0.03
821 66 0.04
822 39 0.03
823 95 0.06
824 15 0.01
825 34 0.02
827 27 0.02
828 115 0.07
829 97 0.06
830 128 0.08
831 117 0.08
832 189 0.12
833 151 0.10
834 69 0.04
835 68 0.04
836 40 0.03
837 23 0.01
838 41 0.03
ACGTcount: A:0.35, C:0.09, G:0.06, T:0.51
Consensus pattern (829 bp):
TATAAATTATAGTTTATAAACTATATACTTTTTATAATTTATACATATATAGTTTATATACATAG
TTTATATATAATCATATAAACATAATATAATATTATAATAATATATAGTTATAATATAAACATAG
TTTATATATAGTTATATATAACTTATATTATATTAATATAAATATACTTTATACTTTATATAATT
TATATATTGTTAACACATAGTTCATTAAAACTTTACGGTTTATATATAAACTTATAATTTTTAAT
ATAAACTATTATATAGTAATATATATGTACTTAATTATTATATACATAAATCTATATATTATATA
TTATATATTTATATAATATATAAAACATAATTTATTAATAAACTACATGTAAACTACATATAACT
ATATTATATATTTGTCTTTTTATATTATGTTATAATTGTTTTTCAATTTTTATATTTGCAATTTA
CTATATTTTCATTATTTCTTTACATTTTGCATTTATTTCGATTCCATCTTTTTGTGTTTTTTAAT
TTATTTAAATTTAAGCCTTTCACTTTTATAGTATTCAGTTTAGTCTTTAAATTTATATTTGCATC
TTCATTTGACCCATTGTTAGTTGTTATTTATATTTTTGTAATTGGCCCATAACTTTTTAAATGAG
TATAAATTAGTCCTTTTTTATATAATTTAAACCTCACATTTTAAATTGATTTCGATTTGGTCCCT
TACCTATGTGTGTTGTTTAATTTTTATTTTAAAATTTTATTTGTAATTTTACATTTCTTCAATTT
TGTCCTTAAATTTATATTTTTTTACAAAATTGATCCATGATTATTTTTT
Found at i:225040 original size:13 final size:13
Alignment explanation
Indices: 225024--225048 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
225014 TTATACATAT
225024 ATAGTTTATATAC
1 ATAGTTTATATAC
225037 ATAGTTTATATA
1 ATAGTTTATATA
225049 TAATTTCATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (13 bp):
ATAGTTTATATAC
Found at i:225083 original size:14 final size:14
Alignment explanation
Indices: 225064--225099 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
225054 TCATATAAAC
225064 ATAATATATA-TTAT
1 ATAATATATAGTT-T
225078 ATAATATATAGTTT
1 ATAATATATAGTTT
225092 ATAATATA
1 ATAATATA
225100 AACATAGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 19 0.90
15 2 0.10
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (14 bp):
ATAATATATAGTTT
Found at i:225137 original size:26 final size:27
Alignment explanation
Indices: 225076--225139 Score: 87
Period size: 26 Copynumber: 2.4 Consensus size: 27
225066 AATATATATT
*
225076 ATATAATATATAGTTTATAATATAAAC
1 ATATATTATATAGTTTATAATATAAAC
225103 ATAGT-TTATATAGTTTAT-ATATAAAC
1 ATA-TATTATATAGTTTATAATATAAAC
*
225129 TTATATTATAT
1 ATATATTATAT
225140 TAATATAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
25 1 0.03
26 16 0.48
27 15 0.45
28 1 0.03
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (27 bp):
ATATATTATATAGTTTATAATATAAAC
Found at i:225163 original size:66 final size:65
Alignment explanation
Indices: 225030--225163 Score: 143
Period size: 66 Copynumber: 2.0 Consensus size: 65
225020 ATATATAGTT
* *
225030 TATATACATAGTTTATATATAATTTCATATAAACATAATATATATTATATAATATATAGTTTATA
1 TATAAACATAGTTTATATAT-ATTTCATATAAACATAATATATATTATATAATATATAGCTTATA
225095 A
65 A
*
225096 TATAAACATAGTTTATATAGT-TTAT-ATATAAAC-TTATATTATATTAATATAAATTATATA-C
1 TATAAACATAGTTTATATA-TATT-TCATATAAACATAATA-TATATT-ATAT-AA-TATATAGC
225157 TT-TAA
60 TTATAA
225162 TA
1 TA
225164 CTTTATATAA
Statistics
Matches: 59, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
64 4 0.07
65 16 0.27
66 28 0.47
67 5 0.08
68 6 0.10
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.46
Consensus pattern (65 bp):
TATAAACATAGTTTATATATATTTCATATAAACATAATATATATTATATAATATATAGCTTATAA
Found at i:225294 original size:2 final size:2
Alignment explanation
Indices: 225270--225329 Score: 70
Period size: 2 Copynumber: 31.0 Consensus size: 2
225260 TAATAGGTTA
* * * *
225270 AT AT AT TT AT AC AT AA AT CT AT AT AT -T AT AT -T 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
225310 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
225330 TACATAATTT
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
1 2 0.04
2 46 0.96
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:225463 original size:19 final size:21
Alignment explanation
Indices: 225430--225469 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
225420 ATATTGCAAT
*
225430 TTACTATTTTTCA-TTATTTC
1 TTACTATTTTGCATTTATTTC
225450 TTAC-ATTTTGCATTTATTTC
1 TTACTATTTTGCATTTATTTC
225470 GATTCCATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.20, C:0.15, G:0.03, T:0.62
Consensus pattern (21 bp):
TTACTATTTTGCATTTATTTC
Found at i:232488 original size:19 final size:19
Alignment explanation
Indices: 232453--232491 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
232443 TGTCTCTGAT
*
232453 AATATAATTTAGGAATTCA
1 AATATAATTTAGCAATTCA
232472 AATATAATTTTA-CAATTCA
1 AATATAA-TTTAGCAATTCA
232491 A
1 A
232492 TTATTCCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.49, C:0.08, G:0.05, T:0.38
Consensus pattern (19 bp):
AATATAATTTAGCAATTCA
Found at i:238789 original size:3 final size:3
Alignment explanation
Indices: 238781--238833 Score: 99
Period size: 3 Copynumber: 18.0 Consensus size: 3
238771 TTCAGACCTG
238781 TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
238828 TAA TAA
1 TAA TAA
238834 ACAACAAACA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 47 0.96
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:239648 original size:218 final size:217
Alignment explanation
Indices: 239285--240116 Score: 1308
Period size: 218 Copynumber: 3.8 Consensus size: 217
239275 AGGTCTTATG
* * * *
239285 AATCAAGAAACCCCCAAAGGCTTAGTTTCTTAATTATCAAGAAACCCCTTTGTTAGGCTTAGCTT
1 AATCAAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAA-CCCTTTGTTAGGCTTAGCTT
* * *
239350 CCTTTAACAACTCTTTTGAGATAATTAGGAAACCCCAGAAGGCTTAATTTCTAAAATCTCATTTG
65 CCTTTAACATCTCTTTTGAGATAATTAGGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTG
** *
239415 AAAACAT-TCTGCACTGAAGGTCTTATGGATGACTTGAAGGCTTTATCATCTATCTCGAAAAGCT
130 AAAACATCT-TGCACTGAAGGTCTTATGGATGACCCGAAGGCTTTATCATCTAGCTCGAAAAGCT
*
239479 TAGAGATGACCCGAAGGATTTAAA
194 TACAGATGACCCGAAGGATTTAAA
*
239503 AATCAAGAAACCCTCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCTCTTTGTTAGGCTTAGCTT
1 AATCAAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACC-CTTTGTTAGGCTTAGCTT
*
239568 CCTTTAACATCTCTTTTGAGATATTTAGGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTG
65 CCTTTAACATCTCTTTTGAGATAATTAGGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTG
* *
239633 AAAACATCTTGCACTGAAGGTCTTACGGATGACCCTAAGGCTTTATCATCTAGCTCGAAAAGCTT
130 AAAACATCTTGCACTGAAGGTCTTATGGATGACCCGAAGGCTTTATCATCTAGCTCGAAAAGCTT
*
239698 ACAGATGACCGGAAGGATTTAAA
195 ACAGATGACCCGAAGGATTTAAA
* *
239721 AATCAAGAAACCACCGAAGACTTAGTTTCTTAGTTGTCAAGGAACCCTTTGTTAGGCTTAGCTTC
1 AATCAAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCTTTGTTAGGCTTAGCTTC
* * * *
239786 CTTTAACATCTCTGTTGAGATATTTAAGAAACCCTCGAAGGCTTAGTTTCTAAAATCTCATTTGA
66 CTTTAACATCTCTTTTGAGATAATTAGGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTGA
* * *
239851 AAACATC-TGAACTAAAGGTCTTATGGATGACCCGAAGGCTTTATCATCTAGCTCGAAATGCTTA
131 AAACATCTTGCACTGAAGGTCTTATGGATGACCCGAAGGCTTTATCATCTAGCTCGAAAAGCTTA
*
239915 CAGATAACCCGAAGGATTTAAAA
196 CAGATGACCCGAAGGATTT-AAA
*
239938 AATCAAGAAACCCCCGAAGGCTTAGTTTATTAGTTGTCAAGGAATCCCTTTGTTAGGCTTAGCTT
1 AATCAAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAA-CCCTTTGTTAGGCTTAGCTT
* * *
240003 CCTTTAACAGCTCTTTTGAGATAATTAGGAAACCCCTGAAGGCTTAGTTTCTAAATTCTCATTTG
65 CCTTTAACATCTCTTTTGAGATAATTAGGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTG
* * *
240068 AAAACATCCTGCATTGAAGGTCTTATGGATGAACCGAAGGCTTTATCAT
130 AAAACATCTTGCACTGAAGGTCTTATGGATGACCCGAAGGCTTTATCAT
240117 ATAGGGAAAT
Statistics
Matches: 566, Mismatches: 43, Indels: 9
0.92 0.07 0.01
Matches are distributed among these distances:
216 69 0.12
217 134 0.24
218 326 0.58
219 37 0.07
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31
Consensus pattern (217 bp):
AATCAAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCTTTGTTAGGCTTAGCTTC
CTTTAACATCTCTTTTGAGATAATTAGGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTGA
AAACATCTTGCACTGAAGGTCTTATGGATGACCCGAAGGCTTTATCATCTAGCTCGAAAAGCTTA
CAGATGACCCGAAGGATTTAAA
Found at i:240851 original size:22 final size:22
Alignment explanation
Indices: 240784--240875 Score: 78
Period size: 22 Copynumber: 4.1 Consensus size: 22
240774 GTAGAAATCC
* * *
240784 AATAAAGCTTTCATCTTTGAAA
1 AATAAATCTATCATCTTTGAAG
* * * *
240806 AAGAGAATCTGTTATCTTTAAAG
1 AATA-AATCTATCATCTTTGAAG
*
240829 AGA-AAATCTATCATTTTTGAAG
1 A-ATAAATCTATCATCTTTGAAG
*
240851 AATGAATCTATCATCTTTGAAG
1 AATAAATCTATCATCTTTGAAG
240873 AAT
1 AAT
240876 GTATCTAGAT
Statistics
Matches: 55, Mismatches: 12, Indels: 6
0.75 0.16 0.08
Matches are distributed among these distances:
21 1 0.02
22 38 0.69
23 15 0.27
24 1 0.02
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (22 bp):
AATAAATCTATCATCTTTGAAG
Found at i:240876 original size:22 final size:22
Alignment explanation
Indices: 240833--240882 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
240823 TTAAAGAGAA
*
240833 AATCTATCATTTTTGAAGAATG
1 AATCTATCATCTTTGAAGAATG
240855 AATCTATCATCTTTGAAGAATG
1 AATCTATCATCTTTGAAGAATG
*
240877 TATCTA
1 AATCTA
240883 GATATGCCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (22 bp):
AATCTATCATCTTTGAAGAATG
Found at i:245529 original size:42 final size:42
Alignment explanation
Indices: 245470--245553 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 42
245460 TTAATTTTTT
* * * *
245470 CATTTGCTCTTTTGAATCATCTTGGAA-TTTTTTCGCTTGATC
1 CATTTGCTCATTTGAATCACCCTGGAACTTTTTT-ACTTGATC
*
245512 CATTTGTTCATTTGAATCACCCTGGAACTTTTTTACTTGATC
1 CATTTGCTCATTTGAATCACCCTGGAACTTTTTTACTTGATC
245554 AATCATCTCT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
42 30 0.83
43 6 0.17
ACGTcount: A:0.19, C:0.20, G:0.13, T:0.48
Consensus pattern (42 bp):
CATTTGCTCATTTGAATCACCCTGGAACTTTTTTACTTGATC
Found at i:245874 original size:21 final size:21
Alignment explanation
Indices: 245834--245879 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
245824 ATGTGGATGT
* *
245834 AAAATGAAAATGCAAATATGC
1 AAAATGAAAATACAAATATGA
**
245855 AAAATGAAAATACATGTATGA
1 AAAATGAAAATACAAATATGA
245876 AAAA
1 AAAA
245880 GGTGTTACTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.61, C:0.07, G:0.13, T:0.20
Consensus pattern (21 bp):
AAAATGAAAATACAAATATGA
Found at i:246491 original size:36 final size:36
Alignment explanation
Indices: 246451--246522 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
246441 CCTTATCGTT
*
246451 GAATACTTTTGGTATCAATCTAATAGGATCTTTGTG
1 GAATACTTTTGGTATCAATCTAACAGGATCTTTGTG
*
246487 GAATACTTTTGGTATCAATTTAACAGGATCTTTGTG
1 GAATACTTTTGGTATCAATCTAACAGGATCTTTGTG
246523 TGCATAGCTC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (36 bp):
GAATACTTTTGGTATCAATCTAACAGGATCTTTGTG
Found at i:249621 original size:3 final size:3
Alignment explanation
Indices: 249601--249688 Score: 95
Period size: 3 Copynumber: 29.0 Consensus size: 3
249591 TTCAGGCCTG
* * * *
249601 TAA TAA TTA TAA TTA TAA TAA TAA TAA TAA TAT TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
249649 TAA CAA TAA TAA TAT TTA TAA TAA TAA TAAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
249689 AAATGTGCAA
Statistics
Matches: 68, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
3 65 0.96
4 3 0.04
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:249649 original size:30 final size:30
Alignment explanation
Indices: 249609--249688 Score: 124
Period size: 30 Copynumber: 2.6 Consensus size: 30
249599 TGTAATAATT
* *
249609 ATAATTATAATAATAATAATAATATTTATA
1 ATAATAATAATAAAAATAATAATATTTATA
*
249639 ATAATAATAATAACAATAATAATATTTATA
1 ATAATAATAATAAAAATAATAATATTTATA
249669 ATAATAATAAATAAAAATAA
1 ATAATAAT-AATAAAAATAA
249689 AAATGTGCAA
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
30 36 0.78
31 10 0.22
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (30 bp):
ATAATAATAATAAAAATAATAATATTTATA
Found at i:252800 original size:10 final size:11
Alignment explanation
Indices: 252771--252805 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
252761 TGAGACAATT
252771 AAGATAAAAGA
1 AAGATAAAAGA
252782 AAGATAAAAGA
1 AAGATAAAAGA
252793 AA-ATAAAA-A
1 AAGATAAAAGA
252802 AAGA
1 AAGA
252806 CAATGAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 3 0.13
10 7 0.30
11 13 0.57
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (11 bp):
AAGATAAAAGA
Found at i:253293 original size:51 final size:51
Alignment explanation
Indices: 253192--253302 Score: 138
Period size: 51 Copynumber: 2.2 Consensus size: 51
253182 TTATTAAATA
* *
253192 AAATAATAATAAACTAAAAATAATGTTTTGATTCTATTGTACTTTCTAATG
1 AAATAATAATAAACTAAAAATAATGTTTTAATTCTATTGTACTCTCTAATG
* *
253243 AAATAATAATAAACTAAAGAA-CATGTTTTAATTCTATCT-TAAGTCT-TAATG
1 AAATAATAATAAACTAAA-AATAATGTTTTAATTCTAT-TGT-ACTCTCTAATG
253294 AAATAATAA
1 AAATAATAA
253303 ATCTAATATT
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
51 47 0.89
52 6 0.11
ACGTcount: A:0.47, C:0.08, G:0.07, T:0.38
Consensus pattern (51 bp):
AAATAATAATAAACTAAAAATAATGTTTTAATTCTATTGTACTCTCTAATG
Found at i:255084 original size:19 final size:20
Alignment explanation
Indices: 255060--255121 Score: 69
Period size: 19 Copynumber: 3.1 Consensus size: 20
255050 ATTTTGACCA
255060 TTTAGCCGCCCATGCATTG-
1 TTTAGCCGCCCATGCATTGT
255079 TTTAGCCGCCC---CACTTGT
1 TTTAGCCGCCCATGCA-TTGT
255097 TTTCAGCCGCCCATGCATTGAT
1 TTT-AGCCGCCCATGCATTG-T
255119 TTT
1 TTT
255122 CAACAATCTC
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
16 2 0.06
17 3 0.08
18 3 0.08
19 19 0.53
21 3 0.08
22 6 0.17
ACGTcount: A:0.15, C:0.32, G:0.18, T:0.35
Consensus pattern (20 bp):
TTTAGCCGCCCATGCATTGT
Found at i:259164 original size:17 final size:17
Alignment explanation
Indices: 259144--259184 Score: 66
Period size: 16 Copynumber: 2.5 Consensus size: 17
259134 CGTATCGCCG
259144 ACAAAATTTTACTATTA
1 ACAAAATTTTACTATTA
*
259161 ACAAAA-TTTACTATTT
1 ACAAAATTTTACTATTA
259177 ACAAAATT
1 ACAAAATT
259185 CACAACCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 15 0.68
17 7 0.32
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (17 bp):
ACAAAATTTTACTATTA
Found at i:264929 original size:27 final size:27
Alignment explanation
Indices: 264888--264947 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
264878 AATGGAAATG
264888 TTATA-TAAAAGTATA-ATAAAACATAAA
1 TTATATTAAAAGTATACAT-AAA-ATAAA
264915 TTATATTAAAA-TATACATAAAATAAA
1 TTATATTAAAAGTATACATAAAATAAA
264941 TTA-ATTA
1 TTATATTA
264948 TATATAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
25 4 0.13
26 8 0.26
27 12 0.39
28 7 0.23
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (27 bp):
TTATATTAAAAGTATACATAAAATAAA
Found at i:269093 original size:12 final size:12
Alignment explanation
Indices: 269073--269109 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
269063 TATCAAAACA
*
269073 ATATGTATGTAT
1 ATATATATGTAT
269085 ATATATATGTAT
1 ATATATATGTAT
*
269097 ATATATATATAT
1 ATATATATGTAT
269109 A
1 A
269110 AGGATGGAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (12 bp):
ATATATATGTAT
Found at i:269094 original size:16 final size:16
Alignment explanation
Indices: 269073--269108 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
269063 TATCAAAACA
*
269073 ATATGTATGTATATAT
1 ATATGTATATATATAT
269089 ATATGTATATATATAT
1 ATATGTATATATATAT
269105 ATAT
1 ATAT
269109 AAGGATGGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (16 bp):
ATATGTATATATATAT
Found at i:271666 original size:9 final size:9
Alignment explanation
Indices: 271654--271705 Score: 56
Period size: 9 Copynumber: 6.1 Consensus size: 9
271644 AATATTTTTA
271654 TATTTAATT
1 TATTTAATT
*
271663 TATTTAA-G
1 TATTTAATT
271671 TATTTAATT
1 TATTTAATT
271680 TATTTAA--
1 TATTTAATT
* *
271687 TATTTTACT
1 TATTTAATT
271696 TATTTAATT
1 TATTTAATT
271705 T
1 T
271706 TTTTGCAGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
7 6 0.17
8 7 0.20
9 22 0.63
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (9 bp):
TATTTAATT
Found at i:271685 original size:17 final size:16
Alignment explanation
Indices: 271641--271703 Score: 76
Period size: 16 Copynumber: 3.9 Consensus size: 16
271631 TTATTATATT
271641 TTTAATATT-TTT-ATA
1 TTTAAT-TTATTTAATA
271656 TTTAATTTATTTAAGTA
1 TTTAATTTATTTAA-TA
271673 TTTAATTTATTTAATA
1 TTTAATTTATTTAATA
* *
271689 TTTTACTTATTTAAT
1 TTTAATTTATTTAAT
271704 TTTTTTGCAG
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
14 2 0.05
15 9 0.21
16 16 0.37
17 16 0.37
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (16 bp):
TTTAATTTATTTAATA
Found at i:275458 original size:2 final size:2
Alignment explanation
Indices: 275453--275480 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
275443 CTCTCTTCTT
275453 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
275481 GTATTTCACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:278242 original size:80 final size:80
Alignment explanation
Indices: 278092--278395 Score: 438
Period size: 80 Copynumber: 3.8 Consensus size: 80
278082 TGCCATAGCA
* * *
278092 CACAGCAA-AAAGGGAGCCAACCTAAGGATATACCTT-GGATCTACCCAAGGA-ATCCTTAGATC
1 CACA-CAACAAAGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAA-GATATCCTTAGGTC
*
278154 CGTAGGGTTACCTTAAG
64 CGTAGGGTTACCTTATG
* * * *
278171 TACACAGCTAAGGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTCCG
1 CACACAACAAAGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCG
278236 TAGGGTTACCTTATG
66 TAGGGTTACCTTATG
278251 CACACAACAAAGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGT--G
1 CACACAACAAAGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCG
*
278314 TAGGGTTACCTTGTG
66 TAGGGTTACCTTATG
* * * *
278329 CACACAACAAAGGGAACCAATCTAAGGATATGCCTTGGTACCTACCCAAGATATCTTTAGGTCCG
1 CACACAACAAAGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCG
278394 TA
66 TA
278396 ATGACTTACA
Statistics
Matches: 203, Mismatches: 17, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
78 75 0.37
79 31 0.15
80 97 0.48
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (80 bp):
CACACAACAAAGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCG
TAGGGTTACCTTATG
Found at i:278389 original size:158 final size:158
Alignment explanation
Indices: 278092--278395 Score: 434
Period size: 158 Copynumber: 1.9 Consensus size: 158
278082 TGCCATAGCA
* *
278092 CACAGCAAAAAGGGAGCCAACCTAAGGATATACCTTGGATCTACCCAAGGAATCCTTAGATCCGT
1 CACAGCAAAAAGGGAACCAACCTAAGGATATACCTTGGACCTACCCAAGGAATCCTTAGAT-CGT
* * * *
278157 AGGGTTACCTTAAGTACACAGCTAAGGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGA
65 AGGGTTACCTTAAGCACACAACAAAGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGA
278222 TATCCTTAGGTCCGTAGGGTTACCTTATG
130 TATCCTTAGGTCCGTAGGGTTACCTTATG
*
278251 CACA-CAACAAAGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAA-GATATCCTTAGGT-
1 CACAGCAA-AAAGGGAACCAACCTAAGGATATACCTT-GGACCTACCCAAGGA-ATCCTTAGATC
** * * *
278313 GTAGGGTTACCTTGTGCACACAACAAAGGGAACCAATCTAAGGATATGCCTTGGTACCTACCCAA
63 GTAGGGTTACCTTAAGCACACAACAAAGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAA
*
278378 GATATCTTTAGGTCCGTA
128 GATATCCTTAGGTCCGTA
278396 ATGACTTACA
Statistics
Matches: 129, Mismatches: 13, Indels: 7
0.87 0.09 0.05
Matches are distributed among these distances:
158 76 0.59
159 33 0.26
160 20 0.16
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (158 bp):
CACAGCAAAAAGGGAACCAACCTAAGGATATACCTTGGACCTACCCAAGGAATCCTTAGATCGTA
GGGTTACCTTAAGCACACAACAAAGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGAT
ATCCTTAGGTCCGTAGGGTTACCTTATG
Found at i:280517 original size:17 final size:17
Alignment explanation
Indices: 280495--280530 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
280485 TCTTATGCAC
280495 ATCAATATATTTATCAG
1 ATCAATATATTTATCAG
* *
280512 ATCAATATGTTTTTCAG
1 ATCAATATATTTATCAG
280529 AT
1 AT
280531 TTATTAATCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.44
Consensus pattern (17 bp):
ATCAATATATTTATCAG
Found at i:296659 original size:16 final size:17
Alignment explanation
Indices: 296621--296661 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
296611 TCTTTTTAAT
* *
296621 AATTAATTTATTTTCTG
1 AATTAATATATTTTCTA
296638 AA-TAATATATTTT-TA
1 AATTAATATATTTTCTA
296653 AATTAATAT
1 AATTAATAT
296662 TATTCATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 3 0.14
16 16 0.76
17 2 0.10
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (17 bp):
AATTAATATATTTTCTA
Found at i:300808 original size:2 final size:2
Alignment explanation
Indices: 300803--300827 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
300793 TGTGTGTGTG
300803 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
300828 GTTATGTAGC
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:303517 original size:2 final size:2
Alignment explanation
Indices: 303512--303536 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
303502 AATGAATTAA
303512 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
303537 AGCATGATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:303746 original size:160 final size:158
Alignment explanation
Indices: 303381--303792 Score: 419
Period size: 160 Copynumber: 2.6 Consensus size: 158
303371 GTTTTGTAAA
* * *
303381 TAGGATATTTATTTA--TTTACAAATATCAGAAA-ATGACATTTAGTTGCTTTAAGACTGTCTTT
1 TAGGATATTTATTTATTTTTA-AAATATCA-AAATAAGACATATAGTTGCTTTAAGACTGTCCTT
* * *
303443 TCTTTAATATTAATAAATAAATAAATATTAATAAGAATATAATAATTTTCTTAAAAAATAATGAA
64 TCTTAAATATTAATAAATAAATAAATATT-ATAAGAATATAATAAATTTCCTAAAAAATAATGAA
* * *
303508 TTAAATATATATATATATATATATATATAAG
128 ATAAAAAAATATATATATATATATATATAAG
* * *
303539 CATGATATTTATTTATTTTTAATATATCAAAATAAGACATATAGTTGCTTTAAGACTGTCCTTTC
1 TAGGATATTTATTTATTTTTAAAATATCAAAATAAGACATATAGTTGCTTTAAGACTGTCCTTTC
* * *
303604 TTAACATTTTTGGA-AAATAAATAAATA-T-TAA-AA-ATAATAAATTTCCTAAGAAAATAATTT
66 TTAA-A-TATT-AATAAATAAATAAATATTATAAGAATATAATAAATTTCCTAA-AAAATAA-TG
* * * * *
303664 AAATAAAAACAATATGTATTTCTGGTTTATATAAG
126 AAATAAAAA-AATATATATATAT-ATATATATAAG
* * * *
303699 TAGGATATTTATTTATTTTTAAAATATCATAATAGGACATCTAGTTGCTTTAAGACTGTCATTTT
1 TAGGATATTTATTTATTTTTAAAATATCAAAATAAGACATATAGTTGCTTTAAGACTGTC-CTTT
** *
303764 CTTTGATATTAA-AAATAAATAAACATTAT
65 CTTAAATATTAATAAATAAATAAATATTAT
303793 TATTTAATTA
Statistics
Matches: 209, Mismatches: 32, Indels: 24
0.79 0.12 0.09
Matches are distributed among these distances:
156 14 0.07
157 9 0.04
158 40 0.19
159 52 0.25
160 71 0.34
161 22 0.11
162 1 0.00
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.42
Consensus pattern (158 bp):
TAGGATATTTATTTATTTTTAAAATATCAAAATAAGACATATAGTTGCTTTAAGACTGTCCTTTC
TTAAATATTAATAAATAAATAAATATTATAAGAATATAATAAATTTCCTAAAAAATAATGAAATA
AAAAAATATATATATATATATATATAAG
Found at i:303847 original size:14 final size:15
Alignment explanation
Indices: 303828--303867 Score: 64
Period size: 14 Copynumber: 2.7 Consensus size: 15
303818 GACTAAGATG
303828 AAAATAATAATAA-T
1 AAAATAATAATAATT
303842 AAAATAATAATAATT
1 AAAATAATAATAATT
*
303857 AAAGTAATAAT
1 AAAATAATAAT
303868 TTAAACATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (15 bp):
AAAATAATAATAATT
Found at i:303943 original size:15 final size:15
Alignment explanation
Indices: 303925--303982 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
303915 AATAATTATC
*
303925 AAAATAAAAGAAATT
1 AAAATAAAAGATATT
*
303940 AAAATTAATA-ATATT
1 AAAA-TAAAAGATATT
303955 AAAATATAAAG-TATT
1 AAAATA-AAAGATATT
*
303970 AAAATTAAAGATA
1 AAAATAAAAGATA
303983 CTAATTCGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
14 6 0.17
15 25 0.71
16 4 0.11
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAATAAAAGATATT
Found at i:303971 original size:30 final size:31
Alignment explanation
Indices: 303910--303977 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 31
303900 ACAAAATTGC
*
303910 AAATAAATAATTATCAAAATAAAAGAAATTA
1 AAATTAATAATTATCAAAATAAAAGAAATTA
* *
303941 AAATTAATAA-TATTAAAATATAAAG-TATTA
1 AAATTAATAATTATCAAAATA-AAAGAAATTA
303971 AAATTAA
1 AAATTAA
303978 AGATACTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 20 0.61
31 13 0.39
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (31 bp):
AAATTAATAATTATCAAAATAAAAGAAATTA
Found at i:305553 original size:28 final size:25
Alignment explanation
Indices: 305522--305573 Score: 59
Period size: 28 Copynumber: 2.0 Consensus size: 25
305512 ATTTCAAAAT
305522 TATAATTATGAGAAAAAAATAATTTATG
1 TATAATTAT-A-AAAAAAAT-ATTTATG
* *
305550 TATATTTATAAATAAAATATTTAT
1 TATAATTATAAAAAAAATATTTAT
305574 TTAGTTAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 6 0.27
26 7 0.32
27 1 0.05
28 8 0.36
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (25 bp):
TATAATTATAAAAAAAATATTTATG
Found at i:305681 original size:17 final size:17
Alignment explanation
Indices: 305642--305688 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
305632 TATTAAATAT
*
305642 TAATATAATAATTTATA
1 TAATATTATAATTTATA
* * *
305659 TTATATTATATTTTTTA
1 TAATATTATAATTTATA
305676 TAATATT-TAATTT
1 TAATATTATAATTT
305689 TAAAATACCA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
16 5 0.21
17 19 0.79
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TAATATTATAATTTATA
Found at i:305689 original size:17 final size:19
Alignment explanation
Indices: 305653--305689 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
305643 AATATAATAA
*
305653 TTTATATTATATTATATTT
1 TTTATAATATATTATATTT
305672 TTTATAATAT-TTA-ATTT
1 TTTATAATATATTATATTT
305689 T
1 T
305690 AAAATACCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 5 0.29
18 3 0.18
19 9 0.53
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTATAATATATTATATTT
Found at i:307395 original size:17 final size:17
Alignment explanation
Indices: 307373--307452 Score: 81
Period size: 17 Copynumber: 4.6 Consensus size: 17
307363 AATGTTGAAT
307373 AAGTTCTTCTCATTACG
1 AAGTTCTTCTCATTACG
307390 AAGTTCTTCTCATTACG
1 AAGTTCTTCTCATTACG
* * *
307407 AACTTCTTCTTCTTCATATG
1 AAGTTCTTC-TCAT--TACG
*
307427 -AGTTCTTCTCATTATG
1 AAGTTCTTCTCATTACG
*
307443 AACTTCTTCT
1 AAGTTCTTCT
307453 GGCAAAGTTG
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
16 4 0.08
17 33 0.62
18 6 0.11
19 7 0.13
20 3 0.06
ACGTcount: A:0.21, C:0.24, G:0.09, T:0.46
Consensus pattern (17 bp):
AAGTTCTTCTCATTACG
Found at i:307660 original size:123 final size:120
Alignment explanation
Indices: 307390--307829 Score: 579
Period size: 123 Copynumber: 3.6 Consensus size: 120
307380 TCTCATTACG
* *
307390 AAGTTCTTCTCATTACGAACTTCTTC-T--TCTTCATATGAGTTCTTCTCATTATGAACT-TCTT
1 AAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTGTC-T
* *
307451 CTGGCAAAGTTGATGTTGA--TATACCTTATGTGATAGAATCAAGCAAAA-GTTGAAC
65 CTGG-AAAGTTGATGTTGATCTATTCCTTATG-GATAGAGTCAAGCAAAAGGTTGAAC
*
307506 AAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAGCTGTCTC
1 AAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTGTCTC
* *
307571 TGGAAATGTTGATGTTGATCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAAC
66 TGGAAA-GTTGATGTTGATCTAT-TCCTTATG-GATAGAGTCAAGCAAAAGGTTGAAC
* *
307629 AAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTGTCTC
* * * * *
307694 TGGAAATGTTGATGCTGGTCTATCTCCTTCTGGATAGAGTCGAGCAAAAGGTTTAAC
66 TGGAAA-GTTGATGTTGATCTAT-TCCTTATGGATAGAGTCAAGCAAAAGGTTGAAC
* * * *
307751 AAGTTCATCTTATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAGCTGTCT
1 AAGTTCTTCTCATTATGAACTTCTTCTTC-CTCTTCAGATGAGTTCTTCTCATTATGAACTGTCT
307816 CTGGAAATGTTGAT
65 CTGGAAA-GTTGAT
307830 CCATCGAATG
Statistics
Matches: 294, Mismatches: 20, Indels: 13
0.90 0.06 0.04
Matches are distributed among these distances:
116 25 0.09
117 1 0.00
118 3 0.01
119 44 0.15
120 2 0.01
121 3 0.01
122 71 0.24
123 145 0.49
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.40
Consensus pattern (120 bp):
AAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTGTCTC
TGGAAAGTTGATGTTGATCTATTCCTTATGGATAGAGTCAAGCAAAAGGTTGAAC
Found at i:307989 original size:114 final size:114
Alignment explanation
Indices: 307614--308151 Score: 669
Period size: 113 Copynumber: 4.7 Consensus size: 114
307604 GATAGAGTCG
*
307614 AGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * * * *** * *
307678 CATTATGAACTTTCTCTGGAAATGTTGATGCTGGTCTATCTCCTTCTGGAT-AGAGTCG
66 CATTATGAACTTTC-CT----ATGGTAATGCTGATCCA--T-CGAAT-GATGA-ATTCA
* * * *
307736 AGCAAAAGGTTTAACAAGTTCATCTTATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * * * *
307801 CATTATGAGCTGT-CTCTGGAAATGTTGATCCATCGAATGATGAATTCA
66 CATTATGAACTTTCCTATGGTAATGCTGATCCATCGAATGATGAATTCA
*
307849 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
*
307914 CATTATGAACTTTACCT-TCGTAATGCTGATCCATCGAATGATGAATTCA
66 CATTATGAACTTT-CCTATGGTAATGCTGATCCATCGAATGATGAATTCA
*
307963 AGCGAAAA-GTTGAACAAGTTCTTCTCATTAAGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AGC-AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
**
308027 TCATTATGAACTCGACC--TGGTAATGCTGATCCATCGAATGATGAATTCA
65 TCATTATGAACT-TTCCTATGGTAATGCTGATCCATCGAATGATGAATTCA
*
308076 AGCGAAAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTC
1 AGC-AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
308140 TCATTATGAACT
65 TCATTATGAACT
308152 CCTTCTTCAG
Statistics
Matches: 374, Mismatches: 36, Indels: 21
0.87 0.08 0.05
Matches are distributed among these distances:
113 182 0.49
114 103 0.28
115 7 0.02
117 10 0.03
121 2 0.01
122 40 0.11
123 30 0.08
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (114 bp):
AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
CATTATGAACTTTCCTATGGTAATGCTGATCCATCGAATGATGAATTCA
Found at i:308029 original size:227 final size:228
Alignment explanation
Indices: 307390--308151 Score: 798
Period size: 227 Copynumber: 3.3 Consensus size: 228
307380 TCTCATTACG
* *
307390 AAGTTCTTCTCATTACGAA---CTTCTT-CTTCTTCATATGAGTTCTTCTCATTATGAACTTCTT
1 AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-T-TT
* * * * ** ** *
307451 CTGGCAAAGTTGATGTTGATATAC-CTTATGTGATAGAATCAAGCAAAAGTTGAACAAGTTCTTC
64 CT--CTATGTTAATGCTGATCCACTCCGA-ATGAT-GAATCAAGCAAAAGTTGAACAAGTTCTTC
307515 TCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATTATGAGCTGTCTCTGGAAATG
125 TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAGCTGTCTCTGG-AA--
* *** * *
307579 TTGATGTTGATCTATCTCCTTCTGCGAT-AGAGTCGAGCAAAAGGTTGAAC
187 ---ATGTTGATCCA--T-CGAAT--GATGA-ATTCAAGCAAAAGGTTGAAC
*
307629 AAGCTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATTATGAACTTTCT
1 AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT
* * * *** * * * *
307693 CTGGAAATGTTGATGCTGGTCTATCTCCTTCTGGATAGAGTCGAGCAAAAGGTTTAACAAGTTCA
66 CT----ATGTTAATGCTGATCCA-CTCCGAAT-GAT-GAATCAAGCAAAA-GTTGAACAAGTTCT
* *
307758 TCTTATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAGCTGTCTCTGGAAA
123 TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAGCTGTCTCTGGAAA
307823 TGTTGATCCATCGAATGATGAATTCAAGCAAAAGGTTGAAC
188 TGTTGATCCATCGAATGATGAATTCAAGCAAAAGGTTGAAC
*
307864 AAGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAC
1 AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-C
307929 -CT-TCG-TAATGCTGATCCA-T-CGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTC
65 TCTAT-GTTAATGCTGATCCACTCCGAATGATGAA-TCAAGC-AAAAGTTGAACAAGTTCTTCTC
* * * * *
307989 ATTAAGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAC-CTGGTAATGC
127 ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAGCT-GTCTCTGGAAATGT
308053 TGATCCATCGAATGATGAATTCAAGCGAAAA-GTTGAAC
191 TGATCCATCGAATGATGAATTCAAGC-AAAAGGTTGAAC
*
308091 AAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACT
1 AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
308152 CCTTCTTCAG
Statistics
Matches: 458, Mismatches: 44, Indels: 54
0.82 0.08 0.10
Matches are distributed among these distances:
226 2 0.00
227 170 0.37
228 12 0.03
229 1 0.00
231 11 0.02
232 1 0.00
235 49 0.11
236 35 0.08
237 3 0.01
238 2 0.00
239 17 0.04
240 14 0.03
241 1 0.00
242 47 0.10
243 3 0.01
244 17 0.04
245 35 0.08
246 38 0.08
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.39
Consensus pattern (228 bp):
AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT
CTATGTTAATGCTGATCCACTCCGAATGATGAATCAAGCAAAAGTTGAACAAGTTCTTCTCATTA
TGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAGCTGTCTCTGGAAATGTTGATC
CATCGAATGATGAATTCAAGCAAAAGGTTGAAC
Found at i:308136 original size:40 final size:35
Alignment explanation
Indices: 308092--308186 Score: 122
Period size: 33 Copynumber: 2.6 Consensus size: 35
308082 AAGTTGAACA
308092 AGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATG
1 AGTTCTTCTCATTATGAAC-TC-TC--C-TTCTTCAGATG
308132 AGTTCTTCTCATTATGAA--CTCCTTCTTCAGATG
1 AGTTCTTCTCATTATGAACTCTCCTTCTTCAGATG
*
308165 AGCTCTTCTCATTATGAACTCT
1 AGTTCTTCTCATTATGAACTCT
308187 ACCTGGAAAT
Statistics
Matches: 52, Mismatches: 1, Indels: 9
0.84 0.02 0.15
Matches are distributed among these distances:
33 28 0.54
34 1 0.02
35 2 0.04
36 2 0.04
37 1 0.02
40 18 0.35
ACGTcount: A:0.20, C:0.24, G:0.11, T:0.45
Consensus pattern (35 bp):
AGTTCTTCTCATTATGAACTCTCCTTCTTCAGATG
Found at i:308186 original size:16 final size:16
Alignment explanation
Indices: 308135--308186 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
308125 TCAGATGAGT
308135 TCTTCTCATTATGAAC
1 TCTTCTCATTATGAAC
* *
308151 TCCTTCTTCA-GATGAGC
1 T-CTTC-TCATTATGAAC
308168 TCTTCTCATTATGAAC
1 TCTTCTCATTATGAAC
308184 TCT
1 TCT
308187 ACCTGGAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
15 3 0.10
16 13 0.45
17 10 0.34
18 3 0.10
ACGTcount: A:0.21, C:0.27, G:0.10, T:0.42
Consensus pattern (16 bp):
TCTTCTCATTATGAAC
Found at i:308338 original size:76 final size:76
Alignment explanation
Indices: 308212--308393 Score: 267
Period size: 76 Copynumber: 2.4 Consensus size: 76
308202 AATAATAAAA
* * * *
308212 AAACATTC-TGCACTGTAGGGCTTACAGCTGACTCGAAGGTTTTGAAAACATCAAAAAGCTCCCA
1 AAACA-TCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCA
308276 AAGACTTTTTGG
65 AAGACTTTTTGG
* * *
308288 AAACATCATGCACTGTAGGACTTATAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCAA
*
308353 AGGCTTTTTGG
66 AGACTTTTTGG
*
308364 AAACATCATACACTGTAGGACTTACAGATG
1 AAACATCATGCACTGTAGGACTTACAGATG
308394 TGGGAAATAG
Statistics
Matches: 95, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
75 2 0.02
76 93 0.98
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (76 bp):
AAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCAA
AGACTTTTTGG
Found at i:309096 original size:22 final size:22
Alignment explanation
Indices: 309071--309125 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
309061 AATAAAGCTT
309071 TCATCTTTGAAAAGAGAATCCA
1 TCATCTTTGAAAAGAGAATCCA
* *
309093 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCCA
309115 TCATCTTTGAA
1 TCATCTTTGAA
309126 GAGTGTAGAT
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:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCCA
Found at i:315997 original size:20 final size:20
Alignment explanation
Indices: 315974--316012 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
315964 CGAACGTAAA
*
315974 AATGCAAATATAAAAATGTG
1 AATGCAAACATAAAAATGTG
* *
315994 AATGTAACCATAAAAATGT
1 AATGCAAACATAAAAATGT
316013 AAATTGTGCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.54, C:0.08, G:0.13, T:0.26
Consensus pattern (20 bp):
AATGCAAACATAAAAATGTG
Found at i:317597 original size:9 final size:8
Alignment explanation
Indices: 317570--317625 Score: 53
Period size: 9 Copynumber: 6.9 Consensus size: 8
317560 AATATTTGAA
317570 AATAAAAT
1 AATAAAAT
317578 AAT-AAAT
1 AATAAAAT
317585 AATAAATAT
1 AATAAA-AT
317594 AATAAATAT
1 AATAAA-AT
*
317603 TATGAAAAT
1 AAT-AAAAT
*
317612 AAT-AAGT
1 AATAAAAT
317619 AATAAAA
1 AATAAAA
317626 ATTTTGAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
7 13 0.32
8 7 0.17
9 17 0.43
10 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.29
Consensus pattern (8 bp):
AATAAAAT
Found at i:317633 original size:25 final size:22
Alignment explanation
Indices: 317585--317652 Score: 73
Period size: 25 Copynumber: 2.9 Consensus size: 22
317575 AATAATAAAT
*
317585 AATAAATATAATAAATATTATGAA
1 AATAAA-ATAATAAAAATTATG-A
*
317609 AATAATAAGTAATAAAAATTTTGA
1 AATAA-AA-TAATAAAAATTATGA
317633 AATAAAATAATTAAAAATTA
1 AATAAAATAA-TAAAAATTA
317653 AATAAATATG
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
22 3 0.08
23 10 0.26
24 12 0.32
25 13 0.34
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.32
Consensus pattern (22 bp):
AATAAAATAATAAAAATTATGA
Found at i:318146 original size:27 final size:25
Alignment explanation
Indices: 318111--318161 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
318101 ATTTCAAAAT
318111 TATAATTATGAGAA-AAAATAATTTATG
1 TATAATTAT-A-AATAAAAT-ATTTATG
*
318138 TATATTTATAAATAAAATATTTAT
1 TATAATTATAAATAAAATATTTAT
318162 TTAGTTAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
25 8 0.36
26 6 0.27
27 8 0.36
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (25 bp):
TATAATTATAAATAAAATATTTATG
Found at i:320306 original size:119 final size:122
Alignment explanation
Indices: 320105--320518 Score: 536
Period size: 119 Copynumber: 3.5 Consensus size: 122
320095 GTCGAATAAG
* *
320105 TTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTTTTCTGGA
1 TTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTGGA
320170 AATGTTGATGTTGATCTATCTCATTCTGTGATAGAGTCATGCAAAAGGTTGAACAAA
66 AATGTTGATGTTGATCTATCTCATTCTGTGATAGAGTCATGCAAAAGGTTGAACAAA
* *
320227 CTCTTCTCATTATGAAC-T-TT-TTCTTCTTCAGGTGAGTTCTTCTCATTATGAACTCTTCTGGA
1 TTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTGGA
* * *
320289 AATGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATACAAAAGGTTGAACAAT
66 AATGTTGATGTTGATCTATCTCATTCTGTGATAGAGTCATGCAAAAGGTTGAACAAA
* * *
320346 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTTTCATTATGAACTTTTCTCT
1 TTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAAC-TCT-TCT
* * * * *
320411 GGAAA---TGA---TGATCCATC-GA----GTGAT-GAAT-TTGAGCAAAAGGTTGAACAAG
63 GGAAATGTTGATGTTGATCTATCTCATTCTGTGATAGAGTCAT--GCAAAAGGTTGAACAAA
320460 TTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCT
1 TTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCT
320519 ACCTGGCAAA
Statistics
Matches: 262, Mismatches: 22, Indels: 26
0.85 0.07 0.08
Matches are distributed among these distances:
112 3 0.01
113 32 0.12
114 45 0.17
119 117 0.45
120 3 0.01
121 3 0.01
122 21 0.08
123 28 0.11
124 2 0.01
125 8 0.03
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.42
Consensus pattern (122 bp):
TTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTGGA
AATGTTGATGTTGATCTATCTCATTCTGTGATAGAGTCATGCAAAAGGTTGAACAAA
Found at i:320674 original size:100 final size:101
Alignment explanation
Indices: 320450--320729 Score: 427
Period size: 100 Copynumber: 2.8 Consensus size: 101
320440 TGAGCAAAAG
*
320450 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
* * *
320515 CTCTACCTGGCAAAGTTAATCCATCGATCAAGCTAAA
66 CTCTA-CTGGAAAAGTTAATACATCGATCAAGATAAA
* * * *
320552 GTTGAACAAGTTCTTCTTATTATGAACTTTTTATTCCTCTTCATATGAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
* *
320617 CTCT-CTGGAAAAGTTGATACATCGGTCAAGATAAA
66 CTCTACTGGAAAAGTTAATACATCGATCAAGATAAA
*
320652 GTTGAACAAGTTCTTCTCATTATAAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
*
320717 CTTTATCTGGAAA
66 CTCTA-CTGGAAA
320730 TGTTGACCCA
Statistics
Matches: 160, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
100 89 0.56
102 71 0.44
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.40
Consensus pattern (101 bp):
GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
CTCTACTGGAAAAGTTAATACATCGATCAAGATAAA
Found at i:321173 original size:22 final size:22
Alignment explanation
Indices: 321118--321174 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
321108 AATAAAGCTT
* * *
321118 TCATCTTTGAAAAGAGAATATA
1 TCATCTTTGAAGACAAAATATA
* *
321140 TCATATTTGAAGACAAAATCTA
1 TCATCTTTGAAGACAAAATATA
321162 TCATCTTTGAAGA
1 TCATCTTTGAAGA
321175 GTGTAGATGT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAGACAAAATATA
Found at i:322660 original size:74 final size:74
Alignment explanation
Indices: 322529--322668 Score: 194
Period size: 74 Copynumber: 1.9 Consensus size: 74
322519 ATGGATCTTC
* * *
322529 AGCATGTCCCAACATTGGCTAATACAAACGTTCAAAATATTCTAACATTCTTTATTATGATTGAA
1 AGCATGTCCCAACATTGACTAATACAAACGTTCAAAATATTCTAACATTCATGATTATGATTGAA
322594 AGGGGTTTT
66 AGGGGTTTT
* * *
322603 AGCATG-CCCTAACATTGACTAATACAAATGTTCAAAATGTGTC-AATATTCATGATTATGATTG
1 AGCATGTCCC-AACATTGACTAATACAAACGTTCAAAATAT-TCTAACATTCATGATTATGATTG
322666 AAA
64 AAA
322669 TAGGCTTTCA
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
73 3 0.05
74 53 0.91
75 2 0.03
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (74 bp):
AGCATGTCCCAACATTGACTAATACAAACGTTCAAAATATTCTAACATTCATGATTATGATTGAA
AGGGGTTTT
Found at i:322963 original size:28 final size:28
Alignment explanation
Indices: 322932--322991 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
322922 TTTCTGGTTG
*
322932 AAATGGGCCT-ACAAGAATTGGGCCTTCA
1 AAATGGACCTGACAA-AATTGGGCCTTCA
* * *
322960 AAATGGATCTGTCTAAATTGGGCCTTCA
1 AAATGGACCTGACAAAATTGGGCCTTCA
322988 AAAT
1 AAAT
322992 ACCCCAACAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 25 0.93
29 2 0.07
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (28 bp):
AAATGGACCTGACAAAATTGGGCCTTCA
Found at i:322991 original size:14 final size:14
Alignment explanation
Indices: 322935--322991 Score: 53
Period size: 15 Copynumber: 4.0 Consensus size: 14
322925 CTGGTTGAAA
*
322935 TGGGCCTACAAGAAT
1 TGGGCCTTCAA-AAT
322950 TGGGCCTTCAAAA-
1 TGGGCCTTCAAAAT
** *
322963 TGGATCTGTCTAAAT
1 TGGGCCT-TCAAAAT
322978 TGGGCCTTCAAAAT
1 TGGGCCTTCAAAAT
322992 ACCCCAACAT
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
13 5 0.15
14 13 0.39
15 15 0.45
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (14 bp):
TGGGCCTTCAAAAT
Found at i:325201 original size:8 final size:8
Alignment explanation
Indices: 325188--325248 Score: 61
Period size: 8 Copynumber: 7.8 Consensus size: 8
325178 CTTGATTCAA
325188 TTTTTTCC
1 TTTTTTCC
325196 TTTTTTCC
1 TTTTTTCC
*
325204 TTTTTTTC
1 TTTTTTCC
*
325212 -TTGTTCC
1 TTTTTTCC
**
325219 TTTTTTTA
1 TTTTTTCC
* *
325227 TTTCTTCT
1 TTTTTTCC
325235 TTTTTTCC
1 TTTTTTCC
325243 TTTTTT
1 TTTTTT
325249 TTCTTTTTGT
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
7 5 0.12
8 36 0.88
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.79
Consensus pattern (8 bp):
TTTTTTCC
Found at i:325255 original size:8 final size:8
Alignment explanation
Indices: 325188--325268 Score: 60
Period size: 8 Copynumber: 10.1 Consensus size: 8
325178 CTTGATTCAA
*
325188 TTTTTTCC
1 TTTTTTTC
*
325196 TTTTTTCC
1 TTTTTTTC
325204 TTTTTTTC
1 TTTTTTTC
* *
325212 -TTGTTCC
1 TTTTTTTC
325219 TTTTTTT-
1 TTTTTTTC
* *
325226 ATTTCTTC
1 TTTTTTTC
325234 TTTTTTTCC
1 TTTTTTT-C
325243 TTTTTTTTC
1 -TTTTTTTC
325252 TTTTTGTT-
1 TTTTT-TTC
325260 TTTTTTTC
1 TTTTTTTC
325268 T
1 T
325269 GATGAATGAG
Statistics
Matches: 58, Mismatches: 9, Indels: 12
0.73 0.11 0.15
Matches are distributed among these distances:
7 12 0.21
8 35 0.60
9 4 0.07
10 7 0.12
ACGTcount: A:0.01, C:0.16, G:0.02, T:0.80
Consensus pattern (8 bp):
TTTTTTTC
Found at i:325255 original size:15 final size:13
Alignment explanation
Indices: 325196--325267 Score: 62
Period size: 13 Copynumber: 5.5 Consensus size: 13
325186 AATTTTTTCC
325196 TTTTTTCCTTTTT
1 TTTTTTCCTTTTT
325209 TTCTTGTTCCTTTTT
1 TT-TT-TTCCTTTTT
* *
325224 TTATTT-C-TTCT
1 TTTTTTCCTTTTT
325235 TTTTTTCCTTTTT
1 TTTTTTCCTTTTT
325248 TTTCTTT--TTGTTT
1 TTT-TTTCCTT-TTT
325261 TTTTTTC
1 TTTTTTC
325268 TGATGAATGA
Statistics
Matches: 48, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
11 8 0.17
12 7 0.15
13 16 0.33
14 6 0.12
15 11 0.23
ACGTcount: A:0.01, C:0.15, G:0.03, T:0.81
Consensus pattern (13 bp):
TTTTTTCCTTTTT
Found at i:327897 original size:43 final size:44
Alignment explanation
Indices: 327814--327900 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 44
327804 CCATGTATCA
* *
327814 AACAAAACTTTTACATGTAGGGGACAACTTTCAGTCCTAACTTC
1 AACAAAACTTTTACATATAGGGGACAACTTTCACTCCTAACTTC
* * * *
327858 AACAAAAC-TTTACATATATGGGATAACTTTCCCTTCTAACTTC
1 AACAAAACTTTTACATATAGGGGACAACTTTCACTCCTAACTTC
327901 TCTAAAGCCA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
43 29 0.78
44 8 0.22
ACGTcount: A:0.34, C:0.23, G:0.10, T:0.32
Consensus pattern (44 bp):
AACAAAACTTTTACATATAGGGGACAACTTTCACTCCTAACTTC
Found at i:328366 original size:36 final size:36
Alignment explanation
Indices: 328306--328374 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
328296 TCTTACCATA
* *
328306 GAATGCTTTTGGTATCAATCTAACAGGATCTTTGTG
1 GAATACTTTTGGTATCAATATAACAGGATCTTTGTG
* *
328342 GAATACTTTTGGTATTAATATAACATGATCTTT
1 GAATACTTTTGGTATCAATATAACAGGATCTTT
328375 ATGTGCATAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (36 bp):
GAATACTTTTGGTATCAATATAACAGGATCTTTGTG
Found at i:329271 original size:2 final size:2
Alignment explanation
Indices: 329264--329312 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
329254 ATAAAGAAGA
329264 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
329306 AT AT AT A
1 AT AT AT A
329313 ATAGTATAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:330032 original size:2 final size:2
Alignment explanation
Indices: 330027--330061 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
330017 AATGAATTAA
*
330027 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
330062 AGCAGGATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:330076 original size:168 final size:161
Alignment explanation
Indices: 329841--330315 Score: 517
Period size: 158 Copynumber: 2.9 Consensus size: 161
329831 TATGATATTT
* * * *
329841 CTAAGGAAAA-AATATTAAATATATATATATATATATATATTTAGGGTTTTGTAAATAGGACATT
1 CTAA-GAAAATAATATTAAATATATATATATATATATATATTTA-TGTTTTATAAGTAGGATATT
*
329905 TATTTATTTATAAATATCAGAAAATAACATCTAGTTGCTTTAAGACTG-CGTTTTCTTTAATATT
64 TATTTATTTTTAAATATCAGAAAA-AACATCTAGTTGCTTTAAGACTGTC-TTTTCTTTAATATT
329969 AATAAATAAATAAATATTAATAAAAATATAATAATTTTC
127 AA-AAATAAATAAATATT-AT-AAAA-ATAATAATTTTC
* * *
330008 CTAA-AAAATAATGAATTAAATATATATATATATATATATATATATATATTTATAAGCAGGATAT
1 CTAAGAAAATAAT--ATTAAATATATATATATATATATATATTTATGT-TTTATAAGTAGGATAT
* * *
330072 TTATTTATTTTTAATATATCAGAATAAGACATCTAGTTGCTTTAAGATTGTCATTTC-TTAATAT
63 TTATTTATTTTTAA-ATATCAGAA-AAAACATCTAGTTGCTTTAAGACTGTCTTTTCTTTAATA-
*
330136 TTGGAAAATAAATAAATA-T-TAAAAATAATAATTTTC
125 TT-AAAAATAAATAAATATTATAAAAATAATAATTTTC
* * *
330172 CTAAGAAAATAAT-TTAAATA-A-A-ACA-ATATGTAT-TTTCTGGTTTTTATAAGTAGGATATT
1 CTAAGAAAATAATATTAAATATATATATATATATATATATTTAT-G-TTTTATAAGTAGGATATT
* *
330231 TATTTATTTTTAAAATATCA-AAATAGAACATCTAGTTGCTTTAAAACTGTCCTTTTATTTAATA
64 TATTTATTTTT-AAATATCAGAAA-A-AACATCTAGTTGCTTTAAGACTGT-CTTTTCTTTAATA
330295 TTAAAAATAAATAAATATTAT
125 TTAAAAATAAATAAATATTAT
330316 TATTTAATTA
Statistics
Matches: 265, Mismatches: 24, Indels: 45
0.79 0.07 0.13
Matches are distributed among these distances:
156 1 0.00
157 6 0.02
158 75 0.28
159 12 0.05
160 8 0.03
161 1 0.00
162 7 0.03
164 16 0.06
165 16 0.06
166 4 0.02
167 5 0.02
168 61 0.23
169 49 0.18
170 4 0.02
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.42
Consensus pattern (161 bp):
CTAAGAAAATAATATTAAATATATATATATATATATATATTTATGTTTTATAAGTAGGATATTTA
TTTATTTTTAAATATCAGAAAAAACATCTAGTTGCTTTAAGACTGTCTTTTCTTTAATATTAAAA
ATAAATAAATATTATAAAAATAATAATTTTC
Found at i:330452 original size:15 final size:15
Alignment explanation
Indices: 330434--330491 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
330424 AATAATGATC
*
330434 AAAATAAAAGAAATT
1 AAAATAAAAGATATT
*
330449 AAAATTAATA-ATATT
1 AAAA-TAAAAGATATT
330464 AAAATATAAAG-TATT
1 AAAATA-AAAGATATT
*
330479 AAAATTAAAGATA
1 AAAATAAAAGATA
330492 CTAATTCGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
14 6 0.17
15 25 0.71
16 4 0.11
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAATAAAAGATATT
Found at i:330480 original size:30 final size:31
Alignment explanation
Indices: 330419--330486 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 31
330409 ATAAAATTGC
*
330419 AAATAAATAATGATCAAAATAAAAGAAATTA
1 AAATTAATAATGATCAAAATAAAAGAAATTA
* *
330450 AAATTAATAAT-ATTAAAATATAAAG-TATTA
1 AAATTAATAATGATCAAAATA-AAAGAAATTA
330480 AAATTAA
1 AAATTAA
330487 AGATACTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 19 0.58
31 14 0.42
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.29
Consensus pattern (31 bp):
AAATTAATAATGATCAAAATAAAAGAAATTA
Found at i:334676 original size:19 final size:19
Alignment explanation
Indices: 334632--334668 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
334622 CATGGGACTT
334632 ATTAAAAAATCATATACAA
1 ATTAAAAAATCATATACAA
*
334651 ATTAAAAAGTCA-ATACAA
1 ATTAAAAAATCATATACAA
334669 TTTTAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.62, C:0.11, G:0.03, T:0.24
Consensus pattern (19 bp):
ATTAAAAAATCATATACAA
Found at i:341446 original size:20 final size:21
Alignment explanation
Indices: 341421--341472 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
341411 TTTTCCCAAT
*
341421 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
341441 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
341462 TCGCAATGCGA
1 TCGCAATGCGA
341473 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:341516 original size:21 final size:21
Alignment explanation
Indices: 341482--341544 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 21
341472 ATACTGACTA
* * *
341482 TCGCAATGCAATTTTCCTAAT
1 TCGCATTGCGATTTTCATAAT
* *
341503 TCGCATTGCGATTTACGT-AT
1 TCGCATTGCGATTTTCATAAT
*
341523 TCGCGTTGCGATTTTCATAAT
1 TCGCATTGCGATTTTCATAAT
341544 T
1 T
341545 AGGAAAATCG
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
20 17 0.50
21 17 0.50
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (21 bp):
TCGCATTGCGATTTTCATAAT
Found at i:342162 original size:19 final size:19
Alignment explanation
Indices: 342138--342182 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
342128 GCAACGAGAG
*
342138 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
342157 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
342176 AATCGCA
1 AATCGCA
342183 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.49, C:0.27, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:342268 original size:20 final size:19
Alignment explanation
Indices: 342178--342276 Score: 135
Period size: 19 Copynumber: 5.1 Consensus size: 19
342168 GAAACCAAAA
*
342178 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
342197 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
342216 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
342235 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
342255 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
342275 TC
1 TC
342277 AACCAAAAGA
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
19 38 0.54
20 32 0.45
21 1 0.01
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:344355 original size:42 final size:42
Alignment explanation
Indices: 344279--344397 Score: 102
Period size: 42 Copynumber: 2.8 Consensus size: 42
344269 GACTCGCCTG
* * * *
344279 TCATCCCTC-AAGA-GTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCAT-CCTCGAAGAGGTCC-CTCCCACCGTTCAAGAGGCCACTA
*
344321 TCATTCCTCG-AGA-GTCTCCTCCCACCGTTCAAGAGGCCACTG
1 TCA-TCCTCGAAGAGGTC-CCTCCCACCGTTCAAGAGGCCACTA
* * *
344363 TCATCGTTGAAGAGGTCCCTCCCACCATTCAAGAG
1 TCATCCTCGAAGAGGTCCCTCCCACCGTTCAAGAG
344398 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
41 4 0.06
42 55 0.86
43 5 0.08
ACGTcount: A:0.23, C:0.35, G:0.18, T:0.24
Consensus pattern (42 bp):
TCATCCTCGAAGAGGTCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:345771 original size:14 final size:14
Alignment explanation
Indices: 345752--345787 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
345742 ATTGTTTAAT
345752 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
345766 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
345780 TGATTTGT
1 TGATTTGT
345788 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:345976 original size:19 final size:19
Alignment explanation
Indices: 345954--345995 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
345944 AAATCGCAAC
345954 GCGAATTTAATTTCGCGTT
1 GCGAATTTAATTTCGCGTT
* *
345973 GCGATTTTCATTTCGCGTT
1 GCGAATTTAATTTCGCGTT
345992 GCGA
1 GCGA
345996 TTCCCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.17, C:0.19, G:0.24, T:0.40
Consensus pattern (19 bp):
GCGAATTTAATTTCGCGTT
Found at i:345996 original size:19 final size:19
Alignment explanation
Indices: 345963--346115 Score: 93
Period size: 19 Copynumber: 8.8 Consensus size: 19
345953 CGCGAATTTA
345963 ATTTCGCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
345982 ATTTCGCGTTGCGA--TTC
1 ATTTCGCGTTGCGATTTTC
* *
345999 ---CCTCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
*
346015 ATTTCGCATTGCGA-----
1 ATTTCGCGTTGCGATTTTC
*
346029 AATTCGCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
*
346048 ATTTCGCATTGCGA--TTC
1 ATTTCGCGTTGCGATTTTC
* *
346065 ---TCTCGTTACGATTTTC
1 ATTTCGCGTTGCGATTTTC
* ** *
346081 ATTTCGCATTGCGATAGTA
1 ATTTCGCGTTGCGATTTTC
346100 ATTTCCGCGTTGCGAT
1 ATTT-CGCGTTGCGAT
346116 AGACATTAAG
Statistics
Matches: 99, Mismatches: 19, Indels: 31
0.66 0.13 0.21
Matches are distributed among these distances:
14 29 0.29
16 6 0.06
17 6 0.06
19 48 0.48
20 10 0.10
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.42
Consensus pattern (19 bp):
ATTTCGCGTTGCGATTTTC
Found at i:346011 original size:33 final size:32
Alignment explanation
Indices: 345969--346095 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
345959 TTTAATTTCG
*
345969 CGTTGCGATTTTCATTTCGCGTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
*
346002 CGTTGCGATTTTCATTTCGCATTGCGAAATT-CG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
346035 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
*
346068 CGTTACGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
346096 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
31 3 0.03
33 80 0.93
35 3 0.03
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:346060 original size:66 final size:66
Alignment explanation
Indices: 345965--346094 Score: 233
Period size: 66 Copynumber: 2.0 Consensus size: 66
345955 CGAATTTAAT
* *
345965 TTCGCGTTGCGATTTTCATTTCGCGTTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGAA
1 TTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTACGATTTTCATTTCGCATTGCGAA
346030 A
66 A
*
346031 TTCGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTACGATTTTCATTTCGCATTGCGA
1 TTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTACGATTTTCATTTCGCATTGCGA
346095 TAGTAATTTC
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.42
Consensus pattern (66 bp):
TTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTACGATTTTCATTTCGCATTGCGAA
A
Found at i:348398 original size:12 final size:12
Alignment explanation
Indices: 348381--348415 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
348371 TCTTCGGGGA
348381 CTTTTTCTTCTT
1 CTTTTTCTTCTT
348393 CTTTTTCTTCTT
1 CTTTTTCTTCTT
348405 CTTTTTCTTCT
1 CTTTTTCTTCT
348416 CAGGATTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:348619 original size:24 final size:24
Alignment explanation
Indices: 348585--348638 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
348575 CTGAAACATC
*
348585 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
348609 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
348633 ATCAAA
1 ATCAAA
348639 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:349436 original size:20 final size:21
Alignment explanation
Indices: 349411--349462 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
349401 TTTTCCTAAT
*
349411 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
349431 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
349452 TCGCAATGCGA
1 TCGCAATGCGA
349463 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:349791 original size:20 final size:20
Alignment explanation
Indices: 349727--349795 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
349717 ATTCATTTGA
349727 CTATCGCAACGC-AAAATGG
1 CTATCGCAACGCGAAAATGG
** *
349746 CTATCGCAATTCG-AAATGAA
1 CTATCGCAACGCGAAAATG-G
**
349766 AAATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
349786 CTATCGCAAC
1 CTATCGCAAC
349796 TAGAAAATCG
Statistics
Matches: 37, Mismatches: 10, Indels: 5
0.71 0.19 0.10
Matches are distributed among these distances:
19 15 0.41
20 17 0.46
21 5 0.14
ACGTcount: A:0.39, C:0.25, G:0.19, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:349846 original size:14 final size:16
Alignment explanation
Indices: 349826--349899 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 16
349816 TGAAAATCGC
349826 ATTGCGATTTTC-TCG
1 ATTGCGATTTTCTTCG
349841 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC--TTCG
349858 CATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
349877 CATTGCGATTTTC-TCG
1 -ATTGCGATTTTCTTCG
349893 -TTGCGAT
1 ATTGCGAT
349900 AGTCAGTTTC
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
14 18 0.33
16 3 0.06
17 3 0.06
19 30 0.56
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (16 bp):
ATTGCGATTTTCTTCG
Found at i:349863 original size:19 final size:19
Alignment explanation
Indices: 349822--349889 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
349812 GAAATGAAAA
349822 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
349838 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
349855 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
349874 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
349890 TCGTTGCGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.23
16 3 0.06
17 3 0.06
19 30 0.64
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:349915 original size:20 final size:20
Alignment explanation
Indices: 349892--349948 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
349882 CGATTTTCTC
349892 GTTGCGATAGTCAGTTTCGT
1 GTTGCGATAGTCAGTTTCGT
349912 GTTGCGATAGTCAGTTTCGT
1 GTTGCGATAGTCAGTTTCGT
*
349932 GTTGCGATAGTCTGTTT
1 GTTGCGATAGTCAGTTT
349949 TGCCTTCAAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.14, C:0.14, G:0.30, T:0.42
Consensus pattern (20 bp):
GTTGCGATAGTCAGTTTCGT
Found at i:351971 original size:20 final size:20
Alignment explanation
Indices: 351946--351994 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
351936 CGAAACTTAA
351946 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
351966 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGAAAATGACT
351986 ATCGCAACG
1 ATCGCAACG
351995 ATGAAATCGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.35, C:0.27, G:0.24, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:352000 original size:20 final size:20
Alignment explanation
Indices: 351946--352001 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
351936 CGAAACTTAA
* *
351946 ATCGCAACGCGAAAATGACT
1 ATCGCAACGAGGAAATGACT
* *
351966 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGAGGAAATGACT
*
351986 ATCGCAACGATGAAAT
1 ATCGCAACGAGGAAAT
352002 CGCAATGCGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (20 bp):
ATCGCAACGAGGAAATGACT
Found at i:352005 original size:14 final size:14
Alignment explanation
Indices: 351986--352073 Score: 59
Period size: 14 Copynumber: 5.6 Consensus size: 14
351976 GGAAATGGCT
351986 ATCGCAACGATGAA
1 ATCGCAACGATGAA
352000 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--ATG-AA
**
352019 ATCGCAACGACAAA
1 ATCGCAACGATGAA
352033 ATCGCAATGCGAAATGAA
1 ATCGCAA--CG--ATGAA
**
352051 ATCGCAACGACAAA
1 ATCGCAACGATGAA
352065 ATCGCAACG
1 ATCGCAACG
352074 CGAAACACAA
Statistics
Matches: 59, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
14 28 0.47
15 1 0.02
16 6 0.10
17 2 0.03
18 13 0.22
19 9 0.15
ACGTcount: A:0.45, C:0.23, G:0.19, T:0.12
Consensus pattern (14 bp):
ATCGCAACGATGAA
Found at i:352018 original size:18 final size:18
Alignment explanation
Indices: 351995--352057 Score: 80
Period size: 18 Copynumber: 3.7 Consensus size: 18
351985 TATCGCAACG
351995 ATGAAATCGCAATGCGAA
1 ATGAAATCGCAATGCGAA
*
352013 ATGAAAATCGCAA--CGAC
1 ATG-AAATCGCAATGCGAA
352030 A--AAATCGCAATGCGAA
1 ATGAAATCGCAATGCGAA
352046 ATGAAATCGCAA
1 ATGAAATCGCAA
352058 CGACAAAATC
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 9 0.24
16 4 0.11
17 4 0.11
18 12 0.32
19 9 0.24
ACGTcount: A:0.48, C:0.19, G:0.19, T:0.14
Consensus pattern (18 bp):
ATGAAATCGCAATGCGAA
Found at i:352022 original size:19 final size:19
Alignment explanation
Indices: 351998--352057 Score: 69
Period size: 14 Copynumber: 3.5 Consensus size: 19
351988 CGCAACGATG
351998 AAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGA
*
352017 AAATCGCAA--CG--A-CA
1 AAATCGCAATGCGAAATGA
352031 AAATCGCAATGCGAAATG-
1 AAATCGCAATGCGAAATGA
352049 AAATCGCAA
1 AAATCGCAA
352058 CGACAAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
14 10 0.29
15 1 0.03
16 2 0.06
17 2 0.06
18 10 0.29
19 9 0.26
ACGTcount: A:0.48, C:0.20, G:0.18, T:0.13
Consensus pattern (19 bp):
AAATCGCAATGCGAAATGA
Found at i:352058 original size:32 final size:33
Alignment explanation
Indices: 351986--352078 Score: 152
Period size: 32 Copynumber: 2.8 Consensus size: 33
351976 GGAAATGGCT
**
351986 ATCGCAACGATGAAATCGCAATGCGAAATGAAA
1 ATCGCAACGACAAAATCGCAATGCGAAATGAAA
352019 ATCGCAACGACAAAATCGCAATGCGAAATG-AA
1 ATCGCAACGACAAAATCGCAATGCGAAATGAAA
*
352051 ATCGCAACGACAAAATCGCAACGCGAAA
1 ATCGCAACGACAAAATCGCAATGCGAAA
352079 CACAAATCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 29 0.51
33 28 0.49
ACGTcount: A:0.46, C:0.23, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAACGACAAAATCGCAATGCGAAATGAAA
Found at i:352107 original size:19 final size:18
Alignment explanation
Indices: 352085--352181 Score: 84
Period size: 19 Copynumber: 5.7 Consensus size: 18
352075 GAAACACAAA
352085 TCGCATTGCGACTTTCATT
1 TCGCATTGCGA-TTTCATT
*
352104 TCGCATTGCGATTT--TA
1 TCGCATTGCGATTTCATT
352120 T--CATTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
* *
352137 TTGCATTGCGATTT--TG
1 TCGCATTGCGATTTCATT
352153 TCG--TTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
352170 TCGCATTGCGAT
1 TCGCATTGCGAT
352182 AGCCATTTCC
Statistics
Matches: 63, Mismatches: 5, Indels: 21
0.71 0.06 0.24
Matches are distributed among these distances:
14 14 0.22
15 6 0.10
16 5 0.08
17 6 0.10
18 7 0.11
19 25 0.40
ACGTcount: A:0.15, C:0.20, G:0.19, T:0.46
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:352126 original size:14 final size:14
Alignment explanation
Indices: 352107--352165 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
352097 TTTCATTTCG
352107 CATTGCGATTTTAT
1 CATTGCGATTTTAT
352121 CATTGCGATTTTCATTTT
1 CATTGCGATTTT-A---T
*
352139 GCATTGCGATTTTGT
1 -CATTGCGATTTTAT
*
352154 CGTTGCGATTTT
1 CATTGCGATTTT
352166 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 23 0.61
15 2 0.05
18 1 0.03
19 12 0.32
ACGTcount: A:0.15, C:0.15, G:0.19, T:0.51
Consensus pattern (14 bp):
CATTGCGATTTTAT
Done.