Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 19 of 185
Found at i:5262814 original size:20 final size:20
Alignment explanation
Indices: 5262778--5262821 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
5262768 AACCGATATA
*
5262778 AATAAATAATACCAAAAATG
1 AATAAATAATACAAAAAATG
* *
5262798 AATAAATAATATAAAAAATT
1 AATAAATAATACAAAAAATG
5262818 AATA
1 AATA
5262822 TAAGTATGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.25
Consensus pattern (20 bp):
AATAAATAATACAAAAAATG
Found at i:5276873 original size:21 final size:21
Alignment explanation
Indices: 5276840--5276879 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
5276830 CCTAAACTCG
** *
5276840 AAACCTCGTACTCGAAACCCA
1 AAACCTCAAACTCAAAACCCA
5276861 AAACCTCAAACTCAAAACC
1 AAACCTCAAACTCAAAACC
5276880 TTAAGCTCGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.38, G:0.05, T:0.12
Consensus pattern (21 bp):
AAACCTCAAACTCAAAACCCA
Found at i:5279066 original size:16 final size:17
Alignment explanation
Indices: 5279039--5279070 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
5279029 GCCCGGCCCG
5279039 TTTTTAATTAAAATTAT
1 TTTTTAATTAAAATTAT
5279056 TTTTTAA-TAAAATTA
1 TTTTTAATTAAAATTA
5279071 AAACTAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTTAATTAAAATTAT
Found at i:5279106 original size:16 final size:16
Alignment explanation
Indices: 5279069--5279108 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
5279059 TTAATAAAAT
* *
5279069 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
5279085 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
5279101 TAAAATTA
1 TAAAATTA
5279109 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:5279108 original size:22 final size:22
Alignment explanation
Indices: 5279044--5279093 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
5279034 GCCCGTTTTT
* * *
5279044 AATTAAAATTATTTTTTAATAA
1 AATTAAAACTAATTGTTAATAA
*
5279066 AATTAAAACTAATTGTTATTAA
1 AATTAAAACTAATTGTTAATAA
5279088 AATTAA
1 AATTAA
5279094 TTGTTAGTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (22 bp):
AATTAAAACTAATTGTTAATAA
Found at i:5279187 original size:59 final size:59
Alignment explanation
Indices: 5279119--5279258 Score: 271
Period size: 59 Copynumber: 2.4 Consensus size: 59
5279109 TCAAATTATT
*
5279119 AATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
5279178 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
5279237 AATTATTAATTGTATTAATTGT
1 AATTATTAATTGTATTAATTGT
5279259 ATTAATTGTT
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
59 80 1.00
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.47
Consensus pattern (59 bp):
AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
Found at i:5279252 original size:9 final size:9
Alignment explanation
Indices: 5279240--5279267 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
5279230 TTTATCAAAT
5279240 TATTAATTG
1 TATTAATTG
5279249 TATTAATTG
1 TATTAATTG
5279258 TATTAATTG
1 TATTAATTG
5279267 T
1 T
5279268 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:5279407 original size:22 final size:24
Alignment explanation
Indices: 5279367--5279410 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
5279357 AAATAAACTT
5279367 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
5279391 AAAATAAAAAA-TA-TATATTT
1 AAAATAAAAAACTATTATATTT
5279411 AATATTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 2 0.10
24 11 0.55
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:5280360 original size:22 final size:22
Alignment explanation
Indices: 5280334--5280379 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
5280324 TTTTGCTGAG
* *
5280334 TTTTTG-TTCCTTCTGGTTTTTC
1 TTTTTGCTTCATTC-GGTTTCTC
5280356 TTTTTGCTTCATTCGGTTTCTC
1 TTTTTGCTTCATTCGGTTTCTC
5280378 TT
1 TT
5280380 GTTTCTCTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.02, C:0.20, G:0.13, T:0.65
Consensus pattern (22 bp):
TTTTTGCTTCATTCGGTTTCTC
Found at i:5286281 original size:7 final size:7
Alignment explanation
Indices: 5286269--5286302 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
5286259 ACTATTGTGA
5286269 CAGTTAG
1 CAGTTAG
5286276 CAGTTAG
1 CAGTTAG
*
5286283 TAGTTAG
1 CAGTTAG
*
5286290 TAGTTAG
1 CAGTTAG
5286297 CAGTTA
1 CAGTTA
5286303 TGGTAGTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.26, T:0.35
Consensus pattern (7 bp):
CAGTTAG
Found at i:5286296 original size:21 final size:21
Alignment explanation
Indices: 5286270--5286318 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
5286260 CTATTGTGAC
5286270 AGTTAGCAGTTA-GTAGTTAGT
1 AGTTAGCAGTTAGGTAGTTA-T
5286291 AGTTAGCAGTTATGGTAGTTAT
1 AGTTAGCAGTTA-GGTAGTTAT
5286313 AGTTAG
1 AGTTAG
5286319 TTAACTGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.46
22 7 0.27
23 7 0.27
ACGTcount: A:0.29, C:0.04, G:0.29, T:0.39
Consensus pattern (21 bp):
AGTTAGCAGTTAGGTAGTTAT
Found at i:5286481 original size:14 final size:14
Alignment explanation
Indices: 5286464--5286496 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
5286454 GTCTTCTTTG
5286464 TGTTTTCTTGTTTA
1 TGTTTTCTTGTTTA
*
5286478 TGTTTTCTTGTTTG
1 TGTTTTCTTGTTTA
5286492 TGTTT
1 TGTTT
5286497 CTGCCATGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.03, C:0.06, G:0.18, T:0.73
Consensus pattern (14 bp):
TGTTTTCTTGTTTA
Found at i:5290997 original size:21 final size:21
Alignment explanation
Indices: 5290971--5291019 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
5290961 TTGTTGTAAC
5290971 AGTTAGCAGTTA-GTAGTTAAT
1 AGTTAGCAGTTAGGTAGTT-AT
5290992 AGTTAGCAGTTATGGTAGTTAT
1 AGTTAGCAGTTA-GGTAGTTAT
5291014 AGTTAG
1 AGTTAG
5291020 TTAACTGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.46
22 8 0.31
23 6 0.23
ACGTcount: A:0.31, C:0.04, G:0.27, T:0.39
Consensus pattern (21 bp):
AGTTAGCAGTTAGGTAGTTAT
Found at i:5298668 original size:31 final size:31
Alignment explanation
Indices: 5298625--5298691 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
5298615 TCAATTTAAC
*
5298625 CACTAACATTTTAGATCAGTTT-TACTTTGGT
1 CACTCACATTTTAGATC-GTTTCTACTTTGGT
*
5298656 CACTCACATTTTAGATCGTTTCTATTTTGGT
1 CACTCACATTTTAGATCGTTTCTACTTTGGT
5298687 CACTC
1 CACTC
5298692 TCCGCTAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 4 0.12
31 29 0.88
ACGTcount: A:0.22, C:0.21, G:0.12, T:0.45
Consensus pattern (31 bp):
CACTCACATTTTAGATCGTTTCTACTTTGGT
Found at i:5300285 original size:30 final size:31
Alignment explanation
Indices: 5300231--5300306 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 31
5300221 TTAAAAAAAG
*
5300231 TAACTATTTTTAAAAGACTGATGGTCAAATT
1 TAACTCTTTTTAAAAGACTGATGGTCAAATT
* *
5300262 TAACTCTTTTTGAAAG-TTGATGGTCAAATT
1 TAACTCTTTTTAAAAGACTGATGGTCAAATT
* * *
5300292 TGATTCTTTTAAAAA
1 TAACTCTTTTTAAAA
5300307 AAATTGAGGA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 24 0.63
31 14 0.37
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42
Consensus pattern (31 bp):
TAACTCTTTTTAAAAGACTGATGGTCAAATT
Found at i:5309366 original size:27 final size:27
Alignment explanation
Indices: 5309328--5309419 Score: 141
Period size: 27 Copynumber: 3.4 Consensus size: 27
5309318 CTTATCTGGA
*
5309328 AGGCGCCAATGGTGGTGCCTATTTGGG
1 AGGCGCCAATGGTGGTGCCTATTTAGG
*
5309355 AGGCGCCAATGGTGGTGCCTATCTAGG
1 AGGCGCCAATGGTGGTGCCTATTTAGG
*
5309382 AGGCGCCAATGGTGGTGCC-ATATTAGA
1 AGGCGCCAATGGTGGTGCCTAT-TTAGG
5309409 AGGCGCCAATG
1 AGGCGCCAATG
5309420 CTGTGATTTT
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
26 2 0.03
27 58 0.97
ACGTcount: A:0.21, C:0.21, G:0.37, T:0.22
Consensus pattern (27 bp):
AGGCGCCAATGGTGGTGCCTATTTAGG
Found at i:5309523 original size:18 final size:20
Alignment explanation
Indices: 5309481--5309527 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 20
5309471 AAAACGGAAG
5309481 AAAGAAGAAGGAAGGAAGCA
1 AAAGAAGAAGGAAGGAAGCA
* *
5309501 GAAGAA-AA-GAAGGAAGGA
1 AAAGAAGAAGGAAGGAAGCA
5309519 AAAGAAGAA
1 AAAGAAGAA
5309528 AAAAATTAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 14 0.61
19 4 0.17
20 5 0.22
ACGTcount: A:0.64, C:0.02, G:0.34, T:0.00
Consensus pattern (20 bp):
AAAGAAGAAGGAAGGAAGCA
Found at i:5309530 original size:22 final size:23
Alignment explanation
Indices: 5309477--5309530 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
5309467 TACAAAAACG
*
5309477 GAAGAAAGAAGAAGGAAGGAAGCA
1 GAAGAAA-AAGAAGGAAGGAAGAA
5309501 GAAG-AAAAGAAGGAAGGAA-AA
1 GAAGAAAAAGAAGGAAGGAAGAA
5309522 GAAGAAAAA
1 GAAGAAAAA
5309531 AATTAGGTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 5 0.18
22 17 0.61
23 2 0.07
24 4 0.14
ACGTcount: A:0.65, C:0.02, G:0.33, T:0.00
Consensus pattern (23 bp):
GAAGAAAAAGAAGGAAGGAAGAA
Found at i:5310346 original size:19 final size:19
Alignment explanation
Indices: 5310324--5310659 Score: 88
Period size: 19 Copynumber: 18.5 Consensus size: 19
5310314 ATTGCAAAAT
*
5310324 TACAATATTACAATATTCA
1 TACAAAATTACAATATTCA
*
5310343 TACAAAAAAATTGCAATATTCA
1 TAC---AAAATTACAATATTCA
*
5310365 TACAAAATTATAATA-T--
1 TACAAAATTACAATATTCA
*
5310381 TACAACATT-C-ATA--CA
1 TACAAAATTACAATATTCA
* *
5310396 -A-AAAAATATAATATTCA
1 TACAAAATTACAATATTCA
*
5310413 TACAAAATTACAA-AAT--
1 TACAAAATTACAATATTCA
*
5310429 TACAATATT-C-ATA--CA
1 TACAAAATTACAATATTCA
* *
5310444 -AAAAAATTGCAATATTCA
1 TACAAAATTACAATATTCA
* *
5310462 TACAAAACTATAATATT-A
1 TACAAAATTACAATATTCA
5310480 T------TT-CAATATTCA
1 TACAAAATTACAATATTCA
*
5310492 TACAAAAAATTTATAATATTCA
1 TAC--AAAA-TTACAATATTCA
5310514 TACAAAATTACAATATTCA
1 TACAAAATTACAATATTCA
* *
5310533 TACAAAAAATTACTA-ATCCAA
1 TAC--AAAATTACAATATTC-A
* *
5310554 AACTATAAA-TACAA-ATTTAA
1 TAC-A-AAATTACAATA-TTCA
* *
5310574 TTATAAAA-T--AAT-TACA
1 -TACAAAATTACAATATTCA
*
5310590 TACAACATTACAATATTCA
1 TACAAAATTACAATATTCA
* *
5310609 TAAAAAAATTATAATATTCA
1 T-ACAAAATTACAATATTCA
*
5310629 TACAAAAAATTTAAAATATTCA
1 TAC--AAAA-TTACAATATTCA
5310651 TACAAAATT
1 TACAAAATT
5310660 CTAATCTAAA
Statistics
Matches: 230, Mismatches: 42, Indels: 90
0.64 0.12 0.25
Matches are distributed among these distances:
11 6 0.03
12 3 0.01
13 4 0.02
14 11 0.05
15 11 0.05
16 22 0.10
17 4 0.02
18 11 0.05
19 58 0.25
20 35 0.15
21 23 0.10
22 42 0.18
ACGTcount: A:0.54, C:0.13, G:0.01, T:0.32
Consensus pattern (19 bp):
TACAAAATTACAATATTCA
Found at i:5310372 original size:49 final size:49
Alignment explanation
Indices: 5310318--5310530 Score: 304
Period size: 49 Copynumber: 4.3 Consensus size: 49
5310308 ATAAAAATTG
5310318 CAAAATTACAATATTACAATATTCATACAAAAAAATTGCAATATTCATA
1 CAAAATTACAATATTACAATATTCATACAAAAAAATTGCAATATTCATA
* *
5310367 CAAAATTATAATATTACAACATTCATACAAAAAAATAT--AATATTCATA
1 CAAAATTACAATATTACAATATTCATACAAAAAAAT-TGCAATATTCATA
*
5310415 CAAAATTACAAAATTACAATATTCATACAAAAAAATTGCAATATTCATA
1 CAAAATTACAATATTACAATATTCATACAAAAAAATTGCAATATTCATA
* * * **
5310464 CAAAACTATAATATTATTTCAATATTCATACAAAAAATTTATAATATTCATA
1 CAAAATTACAATATTA---CAATATTCATACAAAAAAATTGCAATATTCATA
5310516 CAAAATTACAATATT
1 CAAAATTACAATATT
5310531 CATACAAAAA
Statistics
Matches: 145, Mismatches: 13, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
47 1 0.01
48 43 0.30
49 57 0.39
50 1 0.01
52 43 0.30
ACGTcount: A:0.54, C:0.13, G:0.01, T:0.32
Consensus pattern (49 bp):
CAAAATTACAATATTACAATATTCATACAAAAAAATTGCAATATTCATA
Found at i:5310423 original size:97 final size:99
Alignment explanation
Indices: 5310318--5310530 Score: 358
Period size: 97 Copynumber: 2.2 Consensus size: 99
5310308 ATAAAAATTG
*
5310318 CAAAATTACAATATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAATTATAATATTA
1 CAAAATTACAATATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAACTATAATATTA
5310383 -CAACATTCATACAAAAAA-ATATAATATTCATA
66 TCAACATTCATACAAAAAATATATAATATTCATA
*
5310415 CAAAATTACAAAATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAACTATAATATTA
1 CAAAATTACAATATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAACTATAATATTA
* *
5310480 TTTCAATATTCATACAAAAAATTTATAATATTCATA
66 --TCAACATTCATACAAAAAATATATAATATTCATA
5310516 CAAAATTACAATATT
1 CAAAATTACAATATT
5310531 CATACAAAAA
Statistics
Matches: 107, Mismatches: 5, Indels: 4
0.92 0.04 0.03
Matches are distributed among these distances:
97 63 0.59
100 17 0.16
101 27 0.25
ACGTcount: A:0.54, C:0.13, G:0.01, T:0.32
Consensus pattern (99 bp):
CAAAATTACAATATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAACTATAATATTA
TCAACATTCATACAAAAAATATATAATATTCATA
Found at i:5310509 original size:22 final size:21
Alignment explanation
Indices: 5310484--5310549 Score: 91
Period size: 19 Copynumber: 3.1 Consensus size: 21
5310474 ATATTATTTC
5310484 AATATTCATACAAAAAATTTAT
1 AATATTCATACAAAAAA-TTAT
*
5310506 AATATTCATAC--AAAATTAC
1 AATATTCATACAAAAAATTAT
5310525 AATATTCATACAAAAAATTACT
1 AATATTCATACAAAAAATTA-T
5310547 AAT
1 AAT
5310550 CCAAAACTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
19 14 0.36
20 4 0.10
21 7 0.18
22 14 0.36
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (21 bp):
AATATTCATACAAAAAATTAT
Found at i:5310540 original size:41 final size:41
Alignment explanation
Indices: 5310483--5310657 Score: 129
Period size: 41 Copynumber: 4.4 Consensus size: 41
5310473 AATATTATTT
5310483 CAATATTCATACAAAAAATTTATAATATTCATAC-AAAATTA
1 CAATATTCATACAAAAAA-TTATAATATTCATACAAAAATTA
* * *
5310524 CAATATTCATACAAAAAATTACT-A-ATCCAAAACTATAAA-TA
1 CAATATTCATACAAAAAATTA-TAATATTC-ATAC-AAAAATTA
* ** * * *
5310565 CAA-ATTTA-ATTATAAA--ATAAT-TACATAC-AACATTA
1 CAATATTCATACAAAAAATTATAATATTCATACAAAAATTA
5310600 CAATATTCATA-AAAAAATTATAATATTCATACAAAAAATTTA
1 CAATATTCATACAAAAAATTATAATATTCATAC-AAAAA-TTA
*
5310642 AAATATTCATACAAAA
1 CAATATTCATACAAAA
5310658 TTCTAATCTA
Statistics
Matches: 101, Mismatches: 17, Indels: 30
0.68 0.11 0.20
Matches are distributed among these distances:
34 2 0.02
35 5 0.05
36 12 0.12
37 5 0.05
38 5 0.05
39 14 0.14
40 11 0.11
41 27 0.27
42 16 0.16
43 4 0.04
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (41 bp):
CAATATTCATACAAAAAATTATAATATTCATACAAAAATTA
Found at i:5310646 original size:22 final size:21
Alignment explanation
Indices: 5310596--5310657 Score: 90
Period size: 22 Copynumber: 3.0 Consensus size: 21
5310586 TACATACAAC
*
5310596 ATTACAATATTCATA-AAAAA
1 ATTAAAATATTCATACAAAAA
*
5310616 ATTATAATATTCATACAAAAA
1 ATTAAAATATTCATACAAAAA
5310637 ATTTAAAATATTCATACAAAA
1 A-TTAAAATATTCATACAAAA
5310658 TTCTAATCTA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.37
21 6 0.16
22 18 0.47
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.32
Consensus pattern (21 bp):
ATTAAAATATTCATACAAAAA
Found at i:5310702 original size:115 final size:116
Alignment explanation
Indices: 5310483--5310693 Score: 288
Period size: 115 Copynumber: 1.8 Consensus size: 116
5310473 AATATTATTT
*
5310483 CAATATTCATACAAAAAATTTATAATATTCATACAAAATTACAATATTCATACAAAAAATTACTA
1 CAATATTCATACAAAAAATTTATAATATTCATACAAAATTAAAATATTCATAC-AAAAATTACTA
* * *
5310548 ATCCAAAACTATAAATACAAATTTAATTATAAAATAATTACATACAACATTA
65 ATCCAAAACTATAAACACAAATATAATAATAAAATAATTACATACAACATTA
5310600 CAATATTCATA-AAAAAA-TTATAATATTCATACAAAAAATTTAAAATATTCATAC-AAAATT-C
1 CAATATTCATACAAAAAATTTATAATATTCATAC--AAAA-TTAAAATATTCATACAAAAATTAC
*
5310661 TAAT-CTAAACTATAAACACTAAATATAGATAAT
63 TAATCCAAAACTATAAACAC-AAATATA-ATAAT
5310694 TTATAATTAA
Statistics
Matches: 84, Mismatches: 5, Indels: 11
0.84 0.05 0.11
Matches are distributed among these distances:
114 13 0.15
115 26 0.31
116 16 0.19
117 15 0.18
118 14 0.17
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (116 bp):
CAATATTCATACAAAAAATTTATAATATTCATACAAAATTAAAATATTCATACAAAAATTACTAA
TCCAAAACTATAAACACAAATATAATAATAAAATAATTACATACAACATTA
Found at i:5310846 original size:14 final size:15
Alignment explanation
Indices: 5310823--5310860 Score: 60
Period size: 14 Copynumber: 2.5 Consensus size: 15
5310813 TTTTTTCTTT
5310823 CTTTCTTCTTCTTCTC
1 CTTTC-TCTTCTTCTC
5310839 C-TTCTCTTCTTCTC
1 CTTTCTCTTCTTCTC
5310853 CTTTCTCT
1 CTTTCTCT
5310861 CTTTTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 11 0.52
15 9 0.43
16 1 0.05
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (15 bp):
CTTTCTCTTCTTCTC
Found at i:5311147 original size:17 final size:16
Alignment explanation
Indices: 5311115--5311157 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
5311105 AAAAAAATAT
*
5311115 AAATTATATTTTATTA
1 AAATTTTATTTTATTA
5311131 AAATTTTATTATTATTA
1 AAATTTTATT-TTATTA
**
5311148 TTATTTTATT
1 AAATTTTATT
5311158 CATTGGCGCC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
AAATTTTATTTTATTA
Found at i:5324087 original size:3 final size:3
Alignment explanation
Indices: 5324079--5324115 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
5324069 ATGACCAGCC
5324079 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
5324116 AGGATTTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:5331931 original size:29 final size:29
Alignment explanation
Indices: 5331888--5331943 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
5331878 ATTAGTCATT
* * *
5331888 TACAAATATAGGAGAGCTTGGATAAAATC
1 TACAAATATAAGAGAGATGGGATAAAATC
5331917 TACAAATATAAGAGAGATGGGATAAAA
1 TACAAATATAAGAGAGATGGGATAAAA
5331944 CTCCATGCTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.50, C:0.07, G:0.21, T:0.21
Consensus pattern (29 bp):
TACAAATATAAGAGAGATGGGATAAAATC
Found at i:5332514 original size:14 final size:13
Alignment explanation
Indices: 5332485--5332532 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
5332475 AATAAATTGA
*
5332485 AAATTTTTTAAAT
1 AAATATTTTAAAT
5332498 AAATATTTTAAACT
1 AAATATTTTAAA-T
*
5332512 AAATTAATTTTAAGT
1 AAA-T-ATTTTAAAT
5332527 AAATAT
1 AAATAT
5332533 AAAATATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
13 13 0.43
14 5 0.17
15 5 0.17
16 7 0.23
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (13 bp):
AAATATTTTAAAT
Found at i:5333134 original size:3 final size:3
Alignment explanation
Indices: 5333120--5333164 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
5333110 GGAGAAGAGG
*
5333120 AGA AGG AGA AGA AGA AGA AG- AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
5333165 AGTTTATAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:5333137 original size:20 final size:20
Alignment explanation
Indices: 5333112--5333160 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
5333102 GAGAGAAAGG
* *
5333112 AGAAGAGGAGAAGGAGAAGA
1 AGAAGAAGAGAAGAAGAAGA
5333132 AGAAGAAGAGAAGAAGAAGA
1 AGAAGAAGAGAAGAAGAAGA
5333152 AGAAGAAGA
1 AGAAGAAGA
5333161 AGAAAGTTTA
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:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (20 bp):
AGAAGAAGAGAAGAAGAAGA
Found at i:5333138 original size:23 final size:23
Alignment explanation
Indices: 5333112--5333163 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
5333102 GAGAGAAAGG
* *
5333112 AGAAGAGGAGAAGGAGAAGAAGA
1 AGAAGAGAAGAAGAAGAAGAAGA
5333135 AGAAGAGAAGAAGAAGAAGAAGA
1 AGAAGAGAAGAAGAAGAAGAAGA
5333158 AGAAGA
1 AGAAGA
5333164 AAGTTTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (23 bp):
AGAAGAGAAGAAGAAGAAGAAGA
Found at i:5333362 original size:22 final size:21
Alignment explanation
Indices: 5333335--5333520 Score: 154
Period size: 22 Copynumber: 9.0 Consensus size: 21
5333325 TAGATTAGAA
*
5333335 TTTTGTATGAATATTTTAAATT
1 TTTTGTATGAATATTGT-AATT
*
5333357 TTTTGTATGAATATTATAATT
1 TTTTGTATGAATATTGTAATT
5333378 TTTT-TATGAATATTGTAA--
1 TTTTGTATGAATATTGTAATT
* *
5333396 TGTTGCATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
* *
5333417 ATTTTATAATTAA-ATTTGT-ATT
1 -TTTTGT-ATGAATA-TTGTAATT
* * * * *
5333439 TATAGTTTTGGAT-TAGTAATT
1 TTTTG-TATGAATATTGTAATT
5333460 TTTTGTATGAATATTGTAA--
1 TTTTGTATGAATATTGTAATT
*
5333479 TTTTGTATGAATATTATAAATT
1 TTTTGTATGAATATTGT-AATT
5333501 TTTTGTATGAATATTGTAAT
1 TTTTGTATGAATATTGTAAT
5333521 AATATTATAG
Statistics
Matches: 129, Mismatches: 22, Indels: 27
0.72 0.12 0.15
Matches are distributed among these distances:
18 3 0.02
19 29 0.22
20 23 0.18
21 26 0.20
22 40 0.31
23 8 0.06
ACGTcount: A:0.32, C:0.01, G:0.12, T:0.55
Consensus pattern (21 bp):
TTTTGTATGAATATTGTAATT
Found at i:5333501 original size:41 final size:40
Alignment explanation
Indices: 5333335--5333520 Score: 166
Period size: 41 Copynumber: 4.5 Consensus size: 40
5333325 TAGATTAGAA
*
5333335 TTTTGTATGAATATTTTAAATTTTTTGTATGAATATTATAATT
1 TTTTGTATGAATATTGT-AA--TTTTGTATGAATATTATAATT
* * *
5333378 TTTT-TATGAATATTGTAATGTTGCATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATTTTGTATGAATATTATAATT
* * * *
5333417 ATTTTATAATTAA-ATTTGT-ATTTATAGTTTTG--GATTAGTAATT
1 -TTTTGT-ATGAATA-TTGTAATTT-T-G-TATGAATATTA-TAATT
5333460 TTTTGTATGAATATTGTAATTTTGTATGAATATTATAAATT
1 TTTTGTATGAATATTGTAATTTTGTATGAATATTAT-AATT
5333501 TTTTGTATGAATATTGTAAT
1 TTTTGTATGAATATTGTAAT
5333521 AATATTATAG
Statistics
Matches: 116, Mismatches: 14, Indels: 28
0.73 0.09 0.18
Matches are distributed among these distances:
39 21 0.18
40 6 0.05
41 44 0.38
42 33 0.28
43 10 0.09
44 2 0.02
ACGTcount: A:0.32, C:0.01, G:0.12, T:0.55
Consensus pattern (40 bp):
TTTTGTATGAATATTGTAATTTTGTATGAATATTATAATT
Found at i:5333642 original size:19 final size:19
Alignment explanation
Indices: 5333618--5333675 Score: 53
Period size: 22 Copynumber: 2.9 Consensus size: 19
5333608 TGAATGTTGT
5333618 AATATTATAATTTTGTATG
1 AATATTATAATTTTGTATG
**
5333637 AATATTGCAATTTTTTTGTATG
1 AATATT---ATAATTTTGTATG
* *
5333659 AATATTGTAATATTGTA
1 AATATTATAATTTTGTA
5333676 ATTTTGCATG
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
19 13 0.43
22 17 0.57
ACGTcount: A:0.34, C:0.02, G:0.12, T:0.52
Consensus pattern (19 bp):
AATATTATAATTTTGTATG
Found at i:5333646 original size:97 final size:99
Alignment explanation
Indices: 5333469--5333691 Score: 369
Period size: 97 Copynumber: 2.3 Consensus size: 99
5333459 TTTTTGTATG
*
5333469 AATATTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGTAATAATATTATAGTTT
1 AATATTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTG--ATAATATTATAATTT
5333534 TGTATGAATATTGCAATTTTTTTGTATGAATATTGT
64 TGTATGAATATTGCAATTTTTTTGTATGAATATTGT
* * *
5333570 AATTTTGTAATTTTGTATGAATATTAT-ATTTTTTTGTATGAATGTTG-TAATATTATAATTTTG
1 AATATTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGATAATATTATAATTTTG
5333633 TATGAATATTGCAATTTTTTTGTATGAATATTGT
66 TATGAATATTGCAATTTTTTTGTATGAATATTGT
*
5333667 AATATTGTAATTTTGCATGAATATT
1 AATATTGTAATTTTGTATGAATATT
5333692 GTAATGTGAG
Statistics
Matches: 116, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
97 72 0.62
100 18 0.16
101 26 0.22
ACGTcount: A:0.32, C:0.01, G:0.13, T:0.53
Consensus pattern (99 bp):
AATATTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGATAATATTATAATTTTG
TATGAATATTGCAATTTTTTTGTATGAATATTGT
Found at i:5333692 original size:49 final size:49
Alignment explanation
Indices: 5333469--5333692 Score: 319
Period size: 49 Copynumber: 4.5 Consensus size: 49
5333459 TTTTTGTATG
** *
5333469 AATATTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGT
5333518 AATAATAT-TATAGTTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGT
1 AAT-AT-TGTA-A-TTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGT
* *
5333570 AATTTTGTAATTTTGTATGAATATT--ATATTTTTTTGTATGAATGTTGT
1 AATATTGTAATTTTGTATGAATATTGCA-ATTTTTTTGTATGAATATTGT
*
5333618 AATATTATAATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGT
*
5333667 AATATTGTAATTTTGCATGAATATTG
1 AATATTGTAATTTTGTATGAATATTG
5333693 TAATGTGAGG
Statistics
Matches: 157, Mismatches: 10, Indels: 16
0.86 0.05 0.09
Matches are distributed among these distances:
47 1 0.01
48 43 0.27
49 62 0.39
50 7 0.04
51 5 0.03
52 39 0.25
ACGTcount: A:0.32, C:0.01, G:0.13, T:0.53
Consensus pattern (49 bp):
AATATTGTAATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGT
Found at i:5333948 original size:37 final size:39
Alignment explanation
Indices: 5333892--5333965 Score: 125
Period size: 37 Copynumber: 1.9 Consensus size: 39
5333882 CATATAAAGT
5333892 TTATAAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
1 TTATAAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
*
5333931 TTAT-AAAAAAATT-AAAATCATTTTATTAAAAGTTT
1 TTATAAAAAAAATTAAAAATCATTTCATTAAAAGTTT
5333966 GGGTTTTTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
37 21 0.62
38 9 0.26
39 4 0.12
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (39 bp):
TTATAAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
Found at i:5335750 original size:6 final size:6
Alignment explanation
Indices: 5335739--5335791 Score: 70
Period size: 6 Copynumber: 8.8 Consensus size: 6
5335729 GCATCATGCA
* * *
5335739 CCAGAG CCAGAG CCAGGG CTAGAG CCAGAG CCAGAG CCAGAG CGAGAG
1 CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG
*
5335787 GCAGA
1 CCAGA
5335792 ACTACATTCT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.32, C:0.28, G:0.38, T:0.02
Consensus pattern (6 bp):
CCAGAG
Found at i:5339019 original size:19 final size:19
Alignment explanation
Indices: 5338997--5339336 Score: 151
Period size: 19 Copynumber: 18.5 Consensus size: 19
5338987 ATTGCAAAAT
*
5338997 TACAATATTACAATATTCA
1 TACAAAATTACAATATTCA
*
5339016 TACAAAAAATTGCAATATTCA
1 TAC--AAAATTACAATATTCA
*
5339037 TACAAAATTATAATA-T--
1 TACAAAATTACAATATTCA
*
5339053 TACAACATT-C-ATA--CA
1 TACAAAATTACAATATTCA
*
5339068 -A-AAAA-TATAATATTCA
1 TACAAAATTACAATATTCA
*
5339084 TACAAAATTACAA-AAT--
1 TACAAAATTACAATATTCA
*
5339100 TACAATATT-C-ATA--CA
1 TACAAAATTACAATATTCA
*
5339115 -AAAAAATTACAATATTCA
1 TACAAAATTACAATATTCA
* *
5339133 TACAAAACTATAATATT-A
1 TACAAAATTACAATATTCA
*
5339151 TTACAATATT-C-ATA--CA
1 -TACAAAATTACAATATTCA
*
5339167 -A-AAAATTTATAATATTCA
1 TACAAAA-TTACAATATTCA
5339185 TACAAAATTACAATATTCA
1 TACAAAATTACAATATTCA
* *
5339204 TACAAAAAATTACTA-ATCCAA
1 TAC--AAAATTACAATATTC-A
*
5339225 AACTATAAA-TACAAATTTAATT-A
1 TAC-A-AAATTAC-AA--T-ATTCA
*
5339248 TAAAATAATTACAATATTCA
1 TACAA-AATTACAATATTCA
*
5339268 TACAACATTACAATATTCA
1 TACAAAATTACAATATTCA
* *
5339287 TAAAAAATTATAATATTCA
1 TACAAAATTACAATATTCA
*
5339306 TACAAAAAAATTAAAATATTCA
1 TAC---AAAATTACAATATTCA
5339328 TACAAAATT
1 TACAAAATT
5339337 CTAATCTAAA
Statistics
Matches: 241, Mismatches: 37, Indels: 86
0.66 0.10 0.24
Matches are distributed among these distances:
12 1 0.00
13 6 0.02
14 17 0.07
15 3 0.01
16 25 0.10
17 4 0.02
18 12 0.05
19 92 0.38
20 17 0.07
21 34 0.14
22 23 0.10
23 5 0.02
25 2 0.01
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (19 bp):
TACAAAATTACAATATTCA
Found at i:5339110 original size:74 final size:75
Alignment explanation
Indices: 5339002--5339201 Score: 209
Period size: 74 Copynumber: 2.7 Consensus size: 75
5338992 AAAATTACAA
* *
5339002 TATTACAATATTCATACAAAAAATTGCAATATTCATACAAAATTATAATATTACAACATTCATAC
1 TATTACAATAAT-ATAC-AAAAATTACAATATTCATACAAAATTA-AATATTACAACATTCATAC
5339067 AAAAAATATAATAT
63 -AAAAATATAATAT
*
5339081 TCA-TACAA-AAT-TAC-AAAATTACAATATTCATAC-AAA--AAA-ATTACAATATTCATACAA
1 T-ATTACAATAATATACAAAAATTACAATATTCATACAAAATTAAATATTACAACATTCATACAA
*
5339138 AACTATAATAT
65 AAATATAATAT
* *
5339149 TATTACAATATTCATACAAAAAATTTATAATATTCATACAAAATTACAATATT
1 TATTACAATAAT-ATAC-AAAAA-TTACAATATTCATACAAAATTA-AATATT
5339202 CATACAAAAA
Statistics
Matches: 102, Mismatches: 6, Indels: 26
0.76 0.04 0.19
Matches are distributed among these distances:
67 1 0.01
68 18 0.18
69 17 0.17
70 2 0.02
71 4 0.04
73 7 0.07
74 32 0.31
75 3 0.03
76 3 0.03
77 1 0.01
78 4 0.04
79 9 0.09
80 1 0.01
ACGTcount: A:0.54, C:0.13, G:0.01, T:0.33
Consensus pattern (75 bp):
TATTACAATAATATACAAAAATTACAATATTCATACAAAATTAAATATTACAACATTCATACAAA
AATATAATAT
Found at i:5339123 original size:22 final size:22
Alignment explanation
Indices: 5339003--5339334 Score: 151
Period size: 22 Copynumber: 14.9 Consensus size: 22
5338993 AAATTACAAT
5339003 ATTACAATATTCATAC-AAAAA
1 ATTACAATATTCATACAAAAAA
*
5339024 ATTGCAATATTCATACAAAATTATAA
1 ATTACAATATTCATAC-AAA--A-AA
*
5339050 TATTACAACATTCATAC-AAAAA
1 -ATTACAATATTCATACAAAAAA
*
5339072 A-TATAATATTCATACAAAATTACAAA
1 ATTACAATATTCATAC--AA--A-AAA
5339098 ATTACAATATTCATACAAAAAA
1 ATTACAATATTCATACAAAAAA
**
5339120 ATTACAATATTCATACAAAACT
1 ATTACAATATTCATACAAAAAA
* * *
5339142 ATAATATTATTACAATATTCATACAAAAA
1 ATTACAATATT-C-ATA--C--A-AAAAA
* * * *
5339171 ATT--TATAAT-ATTCATACAAA
1 ATTACAATATTCATACA-AAAAA
5339191 ATTACAATATTCATAC-AAAAA
1 ATTACAATATTCATACAAAAAA
* * *
5339212 ATTACTA-ATCCA-A-AACTATAA
1 ATTACAATATTCATACAA--AAAA
* * *
5339233 A-TACAA-ATTTAATTATAAAATA
1 ATTACAATA-TTCA-TACAAAAAA
*
5339255 ATTACAATATTCATAC---AAC
1 ATTACAATATTCATACAAAAAA
5339274 ATTACAATATTCAT---AAAAA
1 ATTACAATATTCATACAAAAAA
*
5339293 ATTATAATATTCATACAAAAAA
1 ATTACAATATTCATACAAAAAA
*
5339315 ATTAAAATATTCATACAAAA
1 ATTACAATATTCATACAAAA
5339335 TTCTAATCTA
Statistics
Matches: 235, Mismatches: 39, Indels: 73
0.68 0.11 0.21
Matches are distributed among these distances:
19 32 0.14
20 29 0.12
21 32 0.14
22 67 0.29
23 18 0.08
24 8 0.03
25 6 0.03
26 7 0.03
27 30 0.13
28 1 0.00
29 5 0.02
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (22 bp):
ATTACAATATTCATACAAAAAA
Found at i:5339138 original size:41 final size:42
Alignment explanation
Indices: 5339095--5339334 Score: 165
Period size: 41 Copynumber: 5.5 Consensus size: 42
5339085 ACAAAATTAC
5339095 AAAATTACAATATTCATACAAAAAAATTACAATATTCATACAAAACTA
1 AAAATTACAATATTCATACAAAAAAATTACAATATTCAT-----AC-A
* *
5339143 TAATATTATTACAATATTCATACAAAAAATTTATAATATTCATAC-
1 -AA-A--ATTACAATATTCATACAAAAAAATTACAATATTCATACA
* * *
5339188 AAAATTACAATATTCATAC-AAAAAATTACTA-ATCCAAAACTA
1 AAAATTACAATATTCATACAAAAAAATTACAATATTC-ATAC-A
* * * *
5339230 TAAA-TACAA-ATTTAATTATAAAATAATTACAATATTCATAC-
1 AAAATTACAATA-TTCA-TACAAAAAAATTACAATATTCATACA
* *
5339271 AACATTACAATATTCAT---AAAAAATTATAATATTCATACAAA
1 AAAATTACAATATTCATACAAAAAAATTACAATATTCATAC--A
*
5339312 AAAATTAAAATATTCATACAAAA
1 AAAATTACAATATTCATACAAAA
5339335 TTCTAATCTA
Statistics
Matches: 152, Mismatches: 21, Indels: 41
0.71 0.10 0.19
Matches are distributed among these distances:
38 19 0.12
39 3 0.02
40 13 0.09
41 42 0.28
42 13 0.09
43 15 0.10
44 8 0.05
47 2 0.01
49 2 0.01
50 1 0.01
52 34 0.22
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (42 bp):
AAAATTACAATATTCATACAAAAAAATTACAATATTCATACA
Found at i:5339139 original size:21 final size:21
Alignment explanation
Indices: 5339003--5339043 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
5338993 AAATTACAAT
5339003 ATTACAATATTCATACAAAAA
1 ATTACAATATTCATACAAAAA
*
5339024 ATTGCAATATTCATACAAAA
1 ATTACAATATTCATACAAAA
5339044 TTATAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.54, C:0.15, G:0.02, T:0.29
Consensus pattern (21 bp):
ATTACAATATTCATACAAAAA
Found at i:5339169 original size:52 final size:51
Alignment explanation
Indices: 5338991--5339201 Score: 271
Period size: 52 Copynumber: 4.3 Consensus size: 51
5338981 ATAAAAATTG
*
5338991 CAAAATTAC-A-A-TATTACAATATTCATACAAAAAATTGCAATATTCATA
1 CAAAATTACAATATTATTACAATATTCATACAAAAAATTACAATATTCATA
* * *
5339039 CAAAATT---ATAATATTACAACATTCATACAAAAAA-TATAATATTCATA
1 CAAAATTACAATATTATTACAATATTCATACAAAAAATTACAATATTCATA
5339086 CAAAATTACAA-A--ATTACAATATTCATACAAAAAAATTACAATATTCATA
1 CAAAATTACAATATTATTACAATATTCATAC-AAAAAATTACAATATTCATA
* * *
5339135 CAAAACTATAATATTATTACAATATTCATACAAAAAATTTATAATATTCATA
1 CAAAATTACAATATTATTACAATATTCATACAAAAAA-TTACAATATTCATA
5339187 CAAAATTACAATATT
1 CAAAATTACAATATT
5339202 CATACAAAAA
Statistics
Matches: 142, Mismatches: 10, Indels: 18
0.84 0.06 0.11
Matches are distributed among these distances:
46 1 0.01
47 34 0.24
48 35 0.25
49 22 0.15
50 2 0.01
51 6 0.04
52 42 0.30
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.32
Consensus pattern (51 bp):
CAAAATTACAATATTATTACAATATTCATACAAAAAATTACAATATTCATA
Found at i:5339208 original size:52 final size:48
Alignment explanation
Indices: 5338991--5339201 Score: 300
Period size: 48 Copynumber: 4.3 Consensus size: 48
5338981 ATAAAAATTG
*
5338991 CAAAATTACAATATTACAATATTCATACAAAAAATTGCAATATTCATA
1 CAAAATTACAATATTACAATATTCATACAAAAAATTACAATATTCATA
* * *
5339039 CAAAATTATAATATTACAACATTCATACAAAAAA-TATAATATTCATA
1 CAAAATTACAATATTACAATATTCATACAAAAAATTACAATATTCATA
*
5339086 CAAAATTACAAAATTACAATATTCATACAAAAAAATTACAATATTCATA
1 CAAAATTACAATATTACAATATTCATAC-AAAAAATTACAATATTCATA
*
5339135 CAAAACTATA-ATATTATTACAATATTCATACAAAAAATTTATAATATTCATA
1 CAAAA-T-TACA-A-TATTACAATATTCATACAAAAAA-TTACAATATTCATA
5339187 CAAAATTACAATATT
1 CAAAATTACAATATT
5339202 CATACAAAAA
Statistics
Matches: 145, Mismatches: 10, Indels: 15
0.85 0.06 0.09
Matches are distributed among these distances:
47 36 0.25
48 38 0.26
49 21 0.14
50 5 0.03
51 11 0.08
52 34 0.23
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.32
Consensus pattern (48 bp):
CAAAATTACAATATTACAATATTCATACAAAAAATTACAATATTCATA
Found at i:5339513 original size:3 final size:3
Alignment explanation
Indices: 5339505--5339561 Score: 98
Period size: 3 Copynumber: 19.3 Consensus size: 3
5339495 TTTATAAACT
5339505 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC -TC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
*
5339552 TTC TCC TTC T
1 TTC TTC TTC T
5339562 CCTCTTCTCC
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 49 0.96
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TTC
Found at i:5341315 original size:33 final size:34
Alignment explanation
Indices: 5341247--5341315 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 34
5341237 CAAGCTTCAA
* *
5341247 ATCAGGATATACATATCATTTCAATCTCTTTAAC
1 ATCAGGATATACATATCATTTCAATCTCATAAAC
*
5341281 ATCATGATATACATATCA-TTCAATCAT-ATAAAC
1 ATCAGGATATACATATCATTTCAATC-TCATAAAC
5341314 AT
1 AT
5341316 TTCATATCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 13 0.42
34 18 0.58
ACGTcount: A:0.41, C:0.19, G:0.04, T:0.36
Consensus pattern (34 bp):
ATCAGGATATACATATCATTTCAATCTCATAAAC
Found at i:5345629 original size:9 final size:9
Alignment explanation
Indices: 5345596--5345637 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
5345586 TAGAAATTTT
5345596 TATTTTTAA
1 TATTTTTAA
*
5345605 TAATTTTAA
1 TATTTTTAA
5345614 TAATTTTTAA
1 T-ATTTTTAA
*
5345624 TTTTTTTAA
1 TATTTTTAA
5345633 -ATTTT
1 TATTTT
5345638 AAAAAATTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
8 4 0.14
9 16 0.57
10 8 0.29
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TATTTTTAA
Found at i:5351644 original size:29 final size:29
Alignment explanation
Indices: 5351611--5351666 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
5351601 AAAGCCTTTT
5351611 TTTTTCAA-AATTTACCGAAATGGGCCACA
1 TTTTT-AATAATTTACCGAAATGGGCCACA
* * *
5351640 TTTTTAATTATTTATCGGAATGGGCCA
1 TTTTTAATAATTTACCGAAATGGGCCA
5351667 TTTCCGCGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 2 0.09
29 21 0.91
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (29 bp):
TTTTTAATAATTTACCGAAATGGGCCACA
Found at i:5351912 original size:48 final size:48
Alignment explanation
Indices: 5351830--5351923 Score: 129
Period size: 48 Copynumber: 2.0 Consensus size: 48
5351820 TTTCTTGGCT
* * *
5351830 TAAAAACGCCTAAGTTAGCCTAACTTCCACCAATAATGGATTCAACCG
1 TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
5351878 TAAAAACGCCTAAGTCAG-CTCAAC-TCGCAACAATAAAGGATTCAAC
1 TAAAAACGCCTAAGTCAGCCT-AACTTC-CAACAATAAAGGATTCAAC
5351924 AGAATTCCCT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
47 4 0.10
48 37 0.90
ACGTcount: A:0.40, C:0.27, G:0.13, T:0.20
Consensus pattern (48 bp):
TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
Found at i:5354428 original size:48 final size:48
Alignment explanation
Indices: 5354346--5354439 Score: 129
Period size: 48 Copynumber: 2.0 Consensus size: 48
5354336 TTTCTTGGCT
* *
5354346 TAAAAACGCCTAAGTCAGCCTAACTTCCACCAATAATGGATTCAACCG
1 TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
*
5354394 TAAAAATGCCTAAGTCAG-CTCAAC-TCGCAACAATAAAGGATTCAAC
1 TAAAAACGCCTAAGTCAGCCT-AACTTC-CAACAATAAAGGATTCAAC
5354440 AGAATTCCCT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
47 4 0.10
48 37 0.90
ACGTcount: A:0.40, C:0.27, G:0.13, T:0.20
Consensus pattern (48 bp):
TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
Found at i:5355783 original size:28 final size:28
Alignment explanation
Indices: 5355726--5355785 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
5355716 GATTTCACGG
*
5355726 AAAATGGCCCATTCCAGTAAATAATCAA
1 AAAATGGCCCATTCCAGTAAATAATAAA
* * *
5355754 AAAATCGGCCCATTTCGGTAAAT-TTAAA
1 AAAAT-GGCCCATTCCAGTAAATAATAAA
5355782 AAAA
1 AAAA
5355786 AGGGCTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 12 0.44
29 15 0.56
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.23
Consensus pattern (28 bp):
AAAATGGCCCATTCCAGTAAATAATAAA
Found at i:5379861 original size:5 final size:5
Alignment explanation
Indices: 5379851--5379885 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
5379841 AAATAAACAA
5379851 AAATT AAATT AAATT AAATT AAATT AAATT AAATT
1 AAATT AAATT AAATT AAATT AAATT AAATT AAATT
5379886 TAAAAATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AAATT
Found at i:5382967 original size:6 final size:6
Alignment explanation
Indices: 5382958--5382983 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
5382948 AAATTTATTT
5382958 AATATC AATATC AATATC AATATC AA
1 AATATC AATATC AATATC AATATC AA
5382984 ATTTAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (6 bp):
AATATC
Found at i:5386132 original size:18 final size:18
Alignment explanation
Indices: 5386109--5386144 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
5386099 TTCAAAAATT
5386109 AGTCATTTCACATCTATA
1 AGTCATTTCACATCTATA
5386127 AGTCATTTCACATCTATA
1 AGTCATTTCACATCTATA
5386145 TATTCATCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.39
Consensus pattern (18 bp):
AGTCATTTCACATCTATA
Found at i:5386356 original size:25 final size:25
Alignment explanation
Indices: 5386328--5386380 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
5386318 TCATGTATTC
*
5386328 CATGTAGTTTATAAACCATGTAAAT
1 CATGTAATTTATAAACCATGTAAAT
* *
5386353 CATGTAATTTATAATCCTTGTAAAT
1 CATGTAATTTATAAACCATGTAAAT
5386378 CAT
1 CAT
5386381 ATAGCTCTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (25 bp):
CATGTAATTTATAAACCATGTAAAT
Found at i:5386587 original size:23 final size:24
Alignment explanation
Indices: 5386561--5386625 Score: 91
Period size: 23 Copynumber: 2.8 Consensus size: 24
5386551 TCTGGAAAAT
*
5386561 GGTAAGCTCCGT-AGAGCTGAAAC
1 GGTAAGCTCCATAAGAGCTGAAAC
5386584 GGTAAGCT-CATAAGAGCTGAAAC
1 GGTAAGCTCCATAAGAGCTGAAAC
*
5386607 GGTAAGCT-CATACGAGCTG
1 GGTAAGCTCCATAAGAGCTG
5386626 TGGTGAGTCC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
22 2 0.05
23 37 0.95
ACGTcount: A:0.32, C:0.20, G:0.29, T:0.18
Consensus pattern (24 bp):
GGTAAGCTCCATAAGAGCTGAAAC
Found at i:5387783 original size:8 final size:8
Alignment explanation
Indices: 5387769--5387838 Score: 54
Period size: 8 Copynumber: 9.0 Consensus size: 8
5387759 ATAATAAAAT
5387769 AATATATA
1 AATATATA
*
5387777 AAAATATA
1 AATATATA
* *
5387785 CATATATT
1 AATATATA
*
5387793 AATATGTA
1 AATATATA
*
5387801 AAAATATA
1 AATATATA
5387809 AATATATA
1 AATATATA
* *
5387817 AGTATGT-
1 AATATATA
*
5387824 -ACATATA
1 AATATATA
5387831 AATATATA
1 AATATATA
5387839 CTTATAAAAT
Statistics
Matches: 44, Mismatches: 16, Indels: 4
0.69 0.25 0.06
Matches are distributed among these distances:
6 3 0.07
8 41 0.93
ACGTcount: A:0.57, C:0.03, G:0.04, T:0.36
Consensus pattern (8 bp):
AATATATA
Found at i:5387822 original size:24 final size:23
Alignment explanation
Indices: 5387767--5387838 Score: 85
Period size: 24 Copynumber: 3.1 Consensus size: 23
5387757 TTATAATAAA
* *
5387767 ATAATATATAAAAATATACATAT
1 ATAATATGTAAAAATATAAATAT
5387790 ATTAATATGTAAAAATATAAATAT
1 A-TAATATGTAAAAATATAAATAT
*
5387814 ATAAGTATGT--ACATATAAATAT
1 ATAA-TATGTAAAAATATAAATAT
5387836 ATA
1 ATA
5387839 CTTATAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
22 14 0.32
23 4 0.09
24 26 0.59
ACGTcount: A:0.57, C:0.03, G:0.04, T:0.36
Consensus pattern (23 bp):
ATAATATGTAAAAATATAAATAT
Found at i:5395679 original size:5 final size:5
Alignment explanation
Indices: 5395649--5395697 Score: 53
Period size: 5 Copynumber: 9.4 Consensus size: 5
5395639 AAATATATGT
* * *
5395649 TAAAA GTAAAA TAAAA CTTAAG TAAAA TAAAA TAAAA TAAAA CAAAA TA
1 TAAAA -TAAAA TAAAA -TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TA
5395698 CTATCATCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
5 28 0.78
6 8 0.22
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:5396092 original size:12 final size:12
Alignment explanation
Indices: 5396075--5396100 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5396065 ACTGTCCTAG
5396075 TTTGTGAATAAA
1 TTTGTGAATAAA
5396087 TTTGTGAATAAA
1 TTTGTGAATAAA
5396099 TT
1 TT
5396101 CGGCTAGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (12 bp):
TTTGTGAATAAA
Found at i:5404215 original size:21 final size:20
Alignment explanation
Indices: 5404172--5404220 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
5404162 AAAAACAAAG
*
5404172 AAAATAACAAAATAAAAAATT
1 AAAATAA-AGAATAAAAAATT
* *
5404193 AAGAATAAAGAATAAATATTT
1 AA-AATAAAGAATAAAAAATT
5404214 AAAATAA
1 AAAATAA
5404221 TAAATAACTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 5 0.21
21 14 0.58
22 5 0.21
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.22
Consensus pattern (20 bp):
AAAATAAAGAATAAAAAATT
Found at i:5404226 original size:20 final size:20
Alignment explanation
Indices: 5404180--5404227 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
5404170 AGAAAATAAC
5404180 AAAATAAAAAATTAAGAATA
1 AAAATAAAAAATTAAGAATA
* *
5404200 AAGAATAAATATTTAA-AATA
1 AA-AATAAAAAATTAAGAATA
5404220 ATAAATAA
1 A-AAATAA
5404228 CTAAAGAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (20 bp):
AAAATAAAAAATTAAGAATA
Found at i:5407045 original size:14 final size:14
Alignment explanation
Indices: 5407026--5407069 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
5407016 TTGATTGCCA
5407026 GTAAAATGTTTTCT
1 GTAAAATGTTTTCT
*
5407040 GTAAAATGATTTACT
1 GTAAAATG-TTTTCT
* *
5407055 GGAAAATATTTTCT
1 GTAAAATGTTTTCT
5407069 G
1 G
5407070 GTGTTTGATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
14 14 0.56
15 11 0.44
ACGTcount: A:0.34, C:0.07, G:0.16, T:0.43
Consensus pattern (14 bp):
GTAAAATGTTTTCT
Found at i:5409196 original size:20 final size:21
Alignment explanation
Indices: 5409155--5409200 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
5409145 ACAACCCAAG
*
5409155 AAAATAAAATACAACAGGCCC
1 AAAATAAAATACAACAGACCC
5409176 AAAA-AAAATACAA-ATGACCC
1 AAAATAAAATACAACA-GACCC
5409196 AAAAT
1 AAAAT
5409201 TTAAACCCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 1 0.05
20 17 0.77
21 4 0.18
ACGTcount: A:0.63, C:0.20, G:0.07, T:0.11
Consensus pattern (21 bp):
AAAATAAAATACAACAGACCC
Found at i:5411296 original size:109 final size:109
Alignment explanation
Indices: 5411084--5411297 Score: 245
Period size: 109 Copynumber: 2.0 Consensus size: 109
5411074 AGTTTTAAAT
* * *
5411084 TAAGGCAATATTTCGCGTTTGGAAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATTTC
1 TAAGGCAATATTTCGCGTTTGGAAAATTCGAGAAAACGTACCCTAACGTACTGGGTCTCGATTTC
* ** * *
5411149 TCGTTCGACCAAATGGCCAAATACCCTTTTAAACTTTCAATAAC
66 TCATTAAACCAAATAGCAAAATACCCTTTTAAACTTTCAATAAC
* * * ** *
5411193 TAAGGCAATATTTTGCATTTTGG-AAATTCGATAAATTGTACCCTAACTTACTGGGTCTCGATTT
1 TAAGGCAATATTTCGC-GTTTGGAAAATTCGAGAAAACGTACCCTAACGTACTGGGTCTCGA-TT
*
5411257 TCTCATTAAACCCAAATAGCAAAATA-TCTTTTAAA-TTTCAA
64 TCTCATTAAA-CCAAATAGCAAAATACCCTTTTAAACTTTCAA
5411298 ACACATAAAA
Statistics
Matches: 87, Mismatches: 15, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
109 52 0.60
110 22 0.25
111 13 0.15
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.34
Consensus pattern (109 bp):
TAAGGCAATATTTCGCGTTTGGAAAATTCGAGAAAACGTACCCTAACGTACTGGGTCTCGATTTC
TCATTAAACCAAATAGCAAAATACCCTTTTAAACTTTCAATAAC
Found at i:5411320 original size:15 final size:16
Alignment explanation
Indices: 5411289--5411321 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5411279 AATATCTTTT
*
5411289 AAATTTCAAACACATA
1 AAATTTCAAACAAATA
5411305 AAATTTCAAA-AAATA
1 AAATTTCAAACAAATA
5411320 AA
1 AA
5411322 TGCAATATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (16 bp):
AAATTTCAAACAAATA
Found at i:5415828 original size:16 final size:16
Alignment explanation
Indices: 5415801--5415838 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
5415791 TCATTAAAAA
**
5415801 AATATA-AATAAATTT
1 AATATATAATAAAAGT
5415816 AATATATAATAAAAGT
1 AATATATAATAAAAGT
5415832 AATATAT
1 AATATAT
5415839 TACTAAGGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (16 bp):
AATATATAATAAAAGT
Found at i:5417909 original size:20 final size:20
Alignment explanation
Indices: 5417884--5417923 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5417874 CATGACGGAA
5417884 GCAGC-AACAGAAACAGAAAC
1 GCAGCAAACAGAAACA-AAAC
*
5417904 GCAGCAAACAGTAACAAAAC
1 GCAGCAAACAGAAACAAAAC
5417924 AACAATAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.55, C:0.25, G:0.17, T:0.03
Consensus pattern (20 bp):
GCAGCAAACAGAAACAAAAC
Found at i:5420370 original size:20 final size:20
Alignment explanation
Indices: 5420347--5420387 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
5420337 TGTCAACAAT
5420347 AATTAA-ATTTATTTTCTTTA
1 AATTAAGATTTATTTT-TTTA
5420367 AATTAAGATTTATTTTTTTA
1 AATTAAGATTTATTTTTTTA
5420387 A
1 A
5420388 CAAATTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (20 bp):
AATTAAGATTTATTTTTTTA
Found at i:5422189 original size:6 final size:6
Alignment explanation
Indices: 5422178--5422209 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
5422168 TAATTTAATA
5422178 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TT
5422210 AGATTCTAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTAT
Found at i:5422191 original size:18 final size:19
Alignment explanation
Indices: 5422170--5422210 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
5422160 TAAATTTATA
5422170 ATTTAATA-TTTTATTTTT
1 ATTTAATATTTTTATTTTT
*
5422188 ATTT-TTATTTTTATTTTT
1 ATTTAATATTTTTATTTTT
5422206 ATTTA
1 ATTTA
5422211 GATTCTAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (19 bp):
ATTTAATATTTTTATTTTT
Found at i:5431660 original size:24 final size:24
Alignment explanation
Indices: 5431604--5431674 Score: 81
Period size: 24 Copynumber: 2.9 Consensus size: 24
5431594 ATCTTAATTA
5431604 ACAGTATTTTTTTCTGCTTTGTAGC
1 ACAGT-TTTTTTTCTGCTTTGTAGC
* *
5431629 ACGGTTTTTTTTCTGTTTTGTAGC
1 ACAGTTTTTTTTCTGCTTTGTAGC
*
5431653 ACATTTTTCCTTTTCT-CTTTGT
1 ACAGTTTT--TTTTCTGCTTTGT
5431675 TCTAGTTTCA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
24 24 0.62
25 9 0.23
26 6 0.15
ACGTcount: A:0.11, C:0.17, G:0.14, T:0.58
Consensus pattern (24 bp):
ACAGTTTTTTTTCTGCTTTGTAGC
Found at i:5437116 original size:21 final size:21
Alignment explanation
Indices: 5437090--5437130 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
5437080 AGACGAGCAA
*
5437090 TACTCCACAACAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
5437111 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
5437131 TTGAGCAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:5451071 original size:18 final size:15
Alignment explanation
Indices: 5451043--5451106 Score: 65
Period size: 15 Copynumber: 4.1 Consensus size: 15
5451033 GTGTTGCATG
5451043 CATCACCATCACCAT
1 CATCACCATCACCAT
*
5451058 CATCACTTCCATCATCAT
1 CATCA---CCATCACCAT
5451076 CATCACCATCACCAT
1 CATCACCATCACCAT
* * *
5451091 CAGCCCCATCATCAT
1 CATCACCATCACCAT
5451106 C
1 C
5451107 TTCATCTTCA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
15 27 0.66
18 14 0.34
ACGTcount: A:0.30, C:0.45, G:0.02, T:0.23
Consensus pattern (15 bp):
CATCACCATCACCAT
Found at i:5451106 original size:6 final size:6
Alignment explanation
Indices: 5451043--5451120 Score: 50
Period size: 6 Copynumber: 13.0 Consensus size: 6
5451033 GTGTTGCATG
* * * * *
5451043 CATCAC CATCAC CATCAT CA-CTT CCATCAT CATCAT CACCAT CACCAT
1 CATCAT CATCAT CATCAT CATCAT -CATCAT CATCAT CATCAT CATCAT
* ** * *
5451091 CAGCCC CATCAT CATCTT CATCTT CATCAT
1 CATCAT CATCAT CATCAT CATCAT CATCAT
5451121 AAACAATGCC
Statistics
Matches: 58, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
5 2 0.03
6 54 0.93
7 2 0.03
ACGTcount: A:0.28, C:0.42, G:0.01, T:0.28
Consensus pattern (6 bp):
CATCAT
Found at i:5451111 original size:9 final size:9
Alignment explanation
Indices: 5451043--5451120 Score: 50
Period size: 9 Copynumber: 8.7 Consensus size: 9
5451033 GTGTTGCATG
*
5451043 CATCACCAT
1 CATCATCAT
*
5451052 CACCATCAT
1 CATCATCAT
*
5451061 CA-CTTCCAT
1 CATCAT-CAT
5451070 CATCATCAT
1 CATCATCAT
* *
5451079 CACCATCAC
1 CATCATCAT
* **
5451088 CATCAGCCC
1 CATCATCAT
5451097 CATCATCAT
1 CATCATCAT
* *
5451106 CTTCATCTT
1 CATCATCAT
5451115 CATCAT
1 CATCAT
5451121 AAACAATGCC
Statistics
Matches: 52, Mismatches: 15, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
8 2 0.04
9 48 0.92
10 2 0.04
ACGTcount: A:0.28, C:0.42, G:0.01, T:0.28
Consensus pattern (9 bp):
CATCATCAT
Found at i:5455466 original size:72 final size:72
Alignment explanation
Indices: 5455349--5455492 Score: 270
Period size: 72 Copynumber: 2.0 Consensus size: 72
5455339 AGAAGTCAGA
5455349 TTTTTGTGGAAACAGTAAGCATTTTACAGATAAACCCAAGAAGTTTCCAAGATTTTAGCAGGGGC
1 TTTTTGTGGAAACAGTAAGCATTTTACAGATAAACCCAAGAAGTTTCCAAGATTTTAGCAGGGGC
5455414 AATTGGT
66 AATTGGT
* *
5455421 TTTTTGTGGAAACAGTAAGCATTTTATAGATAAACCCAAGAAGTTTCCAGGATTTTAGCAGGGGC
1 TTTTTGTGGAAACAGTAAGCATTTTACAGATAAACCCAAGAAGTTTCCAAGATTTTAGCAGGGGC
5455486 AATTGGT
66 AATTGGT
5455493 CCTACTACTC
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.31
Consensus pattern (72 bp):
TTTTTGTGGAAACAGTAAGCATTTTACAGATAAACCCAAGAAGTTTCCAAGATTTTAGCAGGGGC
AATTGGT
Found at i:5465989 original size:44 final size:44
Alignment explanation
Indices: 5465926--5466139 Score: 205
Period size: 44 Copynumber: 4.5 Consensus size: 44
5465916 AGTACTTCTA
*
5465926 ATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTG
1 ATCAGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTG
*
5465970 ATCAGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTA
1 ATCAGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTG
* *
5466014 ATCAGTGACAAGTGACAAGTGACAAGTGATAAG-TGGTAACTTTAACTACACTTATCTG
1 ATCAGTGACAAGTG---A-T---AAGTGAT-AGCT--T---TA--GCTACACTTATCTG
* *
5466072 ATCAGTGACAAGTGATGAGTGGTAGCTTTAGCTACACTTATCTG
1 ATCAGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTG
* * *
5466116 ATCTGGGACAAGTGACAAGTGATA
1 ATCAGTGACAAGTGATAAGTGATA
5466140 AATGTGATCC
Statistics
Matches: 140, Mismatches: 14, Indels: 32
0.75 0.08 0.17
Matches are distributed among these distances:
44 88 0.63
46 1 0.01
47 1 0.01
48 1 0.01
49 1 0.01
50 2 0.01
51 14 0.10
52 2 0.01
53 1 0.01
54 1 0.01
55 1 0.01
56 1 0.01
58 26 0.19
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.29
Consensus pattern (44 bp):
ATCAGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTG
Found at i:5466029 original size:7 final size:7
Alignment explanation
Indices: 5466017--5466048 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
5466007 TTATCTAATC
5466017 AGTGACA
1 AGTGACA
5466024 AGTGACA
1 AGTGACA
5466031 AGTGACA
1 AGTGACA
*
5466038 AGTGATA
1 AGTGACA
5466045 AGTG
1 AGTG
5466049 GTAACTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.41, C:0.09, G:0.31, T:0.19
Consensus pattern (7 bp):
AGTGACA
Found at i:5466043 original size:58 final size:58
Alignment explanation
Indices: 5465973--5466086 Score: 192
Period size: 58 Copynumber: 2.0 Consensus size: 58
5465963 TTATCTGATC
* *
5465973 AGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTAATCAGTGACAAGTGACA
1 AGTGACAAGTGATAAGTGATAACTTTAACTACACTTATCTAATCAGTGACAAGTGACA
* *
5466031 AGTGACAAGTGATAAGTGGTAACTTTAACTACACTTATCTGATCAGTGACAAGTGA
1 AGTGACAAGTGATAAGTGATAACTTTAACTACACTTATCTAATCAGTGACAAGTGA
5466087 TGAGTGGTAG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (58 bp):
AGTGACAAGTGATAAGTGATAACTTTAACTACACTTATCTAATCAGTGACAAGTGACA
Found at i:5466098 original size:102 final size:102
Alignment explanation
Indices: 5465929--5466137 Score: 355
Period size: 102 Copynumber: 2.0 Consensus size: 102
5465919 ACTTCTAATC
* *
5465929 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGATAAGTGATA
1 AGTGACAAGTGATAAGTGGTAACTTTAACTACACTTATCTGATCAGTGACAAGTGATAAGTGATA
*
5465994 GCTTTAGCTACACTTATCTAATCAGTGACAAGTGACA
66 GCTTTAGCTACACTTATCTAATCAGGGACAAGTGACA
* *
5466031 AGTGACAAGTGATAAGTGGTAACTTTAACTACACTTATCTGATCAGTGACAAGTGATGAGTGGTA
1 AGTGACAAGTGATAAGTGGTAACTTTAACTACACTTATCTGATCAGTGACAAGTGATAAGTGATA
* *
5466096 GCTTTAGCTACACTTATCTGATCTGGGACAAGTGACA
66 GCTTTAGCTACACTTATCTAATCAGGGACAAGTGACA
5466133 AGTGA
1 AGTGA
5466138 TAAATGTGAT
Statistics
Matches: 100, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
102 100 1.00
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (102 bp):
AGTGACAAGTGATAAGTGGTAACTTTAACTACACTTATCTGATCAGTGACAAGTGATAAGTGATA
GCTTTAGCTACACTTATCTAATCAGGGACAAGTGACA
Found at i:5467382 original size:31 final size:31
Alignment explanation
Indices: 5467345--5467416 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 31
5467335 TATAGAATAT
*
5467345 AATTTAGTCACCCTTATTAGATAAGTTGT-C
1 AATTTAGTCACCCTCATTAGATAAGTTGTCC
*
5467375 AATTTTAGTCA-CCTCGTTAGATAAGTTGTCC
1 AA-TTTAGTCACCCTCATTAGATAAGTTGTCC
5467406 AATTTAGTCAC
1 AATTTAGTCAC
5467417 TCTACTGTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
30 26 0.70
31 11 0.30
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (31 bp):
AATTTAGTCACCCTCATTAGATAAGTTGTCC
Found at i:5468241 original size:7 final size:7
Alignment explanation
Indices: 5468229--5468258 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
5468219 GATCCCAATT
5468229 CAATCCA
1 CAATCCA
5468236 CAATCCA
1 CAATCCA
5468243 CAATCCA
1 CAATCCA
*
5468250 CAATTCA
1 CAATCCA
5468257 CA
1 CA
5468259 TTTCATTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.43, C:0.40, G:0.00, T:0.17
Consensus pattern (7 bp):
CAATCCA
Found at i:5477076 original size:13 final size:13
Alignment explanation
Indices: 5477058--5477082 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5477048 ATTTTTTTAA
5477058 TTTTTAATTAATG
1 TTTTTAATTAATG
5477071 TTTTTAATTAAT
1 TTTTTAATTAAT
5477083 AAATATTTTT
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:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
TTTTTAATTAATG
Found at i:5491211 original size:24 final size:24
Alignment explanation
Indices: 5491179--5491226 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
5491169 TCGATTCAAA
*
5491179 TGGTACCAAATAAATCCACTAAGT
1 TGGTACCAAATAAATCCACCAAGT
*
5491203 TGGTACCAAATAAATTCACCAAGT
1 TGGTACCAAATAAATCCACCAAGT
5491227 AAAATGACGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.42, C:0.21, G:0.12, T:0.25
Consensus pattern (24 bp):
TGGTACCAAATAAATCCACCAAGT
Found at i:5491729 original size:16 final size:18
Alignment explanation
Indices: 5491702--5491735 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
5491692 AAAAGTTAAA
5491702 AGTGGTTAATT-ATTTTT
1 AGTGGTTAATTAATTTTT
5491719 AGTGG-TAATTAATTTTT
1 AGTGGTTAATTAATTTTT
5491736 TATAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.26, C:0.00, G:0.18, T:0.56
Consensus pattern (18 bp):
AGTGGTTAATTAATTTTT
Found at i:5509435 original size:13 final size:13
Alignment explanation
Indices: 5509419--5509455 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
5509409 TTTAAATCAA
5509419 ACTTTTCAAAAAC
1 ACTTTTCAAAAAC
* *
5509432 ACTTCTCAAAAAT
1 ACTTTTCAAAAAC
5509445 ACTTTTCAAAA
1 ACTTTTCAAAA
5509456 GCATTGTGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (13 bp):
ACTTTTCAAAAAC
Found at i:5515361 original size:96 final size:96
Alignment explanation
Indices: 5515197--5515392 Score: 383
Period size: 96 Copynumber: 2.0 Consensus size: 96
5515187 ATTCCTATTT
5515197 CAACATGCAGAATTTTCTAACGATGCCTGCACAGTTTCTATTGTTTTAACAATTAGAAACTATGC
1 CAACATGCAGAATTTTCTAACGATGCCTGCACAGTTTCTATTGTTTTAACAATTAGAAACTATGC
5515262 CCACTACTCCAAAAGTGGCCTAAGTAATAGG
66 CCACTACTCCAAAAGTGGCCTAAGTAATAGG
5515293 CAACATGCAGAATTTTCTAACGATGCCTGCACAGTTTCTATTGTTTTAACAATTAGAAACTATGC
1 CAACATGCAGAATTTTCTAACGATGCCTGCACAGTTTCTATTGTTTTAACAATTAGAAACTATGC
*
5515358 CCACTACTCCAAAAGTGGCCTAAGTAGTAGG
66 CCACTACTCCAAAAGTGGCCTAAGTAATAGG
5515389 CAAC
1 CAAC
5515393 CAATTAATTG
Statistics
Matches: 99, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 99 1.00
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (96 bp):
CAACATGCAGAATTTTCTAACGATGCCTGCACAGTTTCTATTGTTTTAACAATTAGAAACTATGC
CCACTACTCCAAAAGTGGCCTAAGTAATAGG
Found at i:5520958 original size:22 final size:24
Alignment explanation
Indices: 5520915--5520958 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
5520905 TGATAATATA
5520915 TTTTGATATAACAAATTAAAGTGT
1 TTTTGATATAACAAATTAAAGTGT
*
5520939 TTTTGA-ATAA-AAGTTAAAGT
1 TTTTGATATAACAAATTAAAGT
5520959 TAAACAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.43, C:0.02, G:0.14, T:0.41
Consensus pattern (24 bp):
TTTTGATATAACAAATTAAAGTGT
Found at i:5521218 original size:97 final size:97
Alignment explanation
Indices: 5521047--5521238 Score: 348
Period size: 97 Copynumber: 2.0 Consensus size: 97
5521037 ATCAACTTTA
*
5521047 AAATAAAGTTAAAATGATTTTAATCAAGTAATAATTATTTCAACTAGTCAAACTGTTTTTAAAAC
1 AAATAAAGTTAAAATGAGTTTAATCAAGTAATAATTATTTCAACTAGTCAAACTGTTTTTAAAAC
*
5521112 AAGTCAGTATAGCTCCAGGCCAAAAAGTATTG
66 AAGTCAGTATAGCTCCAAGCCAAAAAGTATTG
* *
5521144 AAATCAAGTTAAAATGAGTTTAATCAAGTAATAATTCTTTCAACTAGTCAAACTGTTTTTAAAAC
1 AAATAAAGTTAAAATGAGTTTAATCAAGTAATAATTATTTCAACTAGTCAAACTGTTTTTAAAAC
5521209 AAGTCAGTATAGCTCCAAGCCAAAAAGTAT
66 AAGTCAGTATAGCTCCAAGCCAAAAAGTAT
5521239 CGATAGTTTT
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
97 91 1.00
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (97 bp):
AAATAAAGTTAAAATGAGTTTAATCAAGTAATAATTATTTCAACTAGTCAAACTGTTTTTAAAAC
AAGTCAGTATAGCTCCAAGCCAAAAAGTATTG
Found at i:5521367 original size:20 final size:20
Alignment explanation
Indices: 5521326--5521369 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
5521316 TATCAATACT
*
5521326 GTATCGATACTTTTCATATG
1 GTATCGATAATTTTCATATG
*
5521346 GTATCGATAAATTTT-ATCTG
1 GTATCGAT-AATTTTCATATG
5521366 GTAT
1 GTAT
5521370 TGGCGGTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.27, C:0.11, G:0.16, T:0.45
Consensus pattern (20 bp):
GTATCGATAATTTTCATATG
Found at i:5522930 original size:27 final size:27
Alignment explanation
Indices: 5522894--5522984 Score: 112
Period size: 27 Copynumber: 3.4 Consensus size: 27
5522884 ATTTGATAGA
* *
5522894 CGCGATTAGTTGAGCCTATCTCAGAGG
1 CGCGACTAGTTGAGCCTATCTCAAAGG
*
5522921 CGTGACTAGTTGAGCCTATCT-AACAGG
1 CGCGACTAGTTGAGCCTATCTCAA-AGG
*
5522948 CGCGACTAGTTGAGCCTAACTCAAAGG
1 CGCGACTAGTTGAGCCTATCTCAAAGG
* *
5522975 CACGAATAGT
1 CGCGACTAGT
5522985 GGGGCCCACT
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
26 1 0.02
27 52 0.95
28 2 0.04
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.23
Consensus pattern (27 bp):
CGCGACTAGTTGAGCCTATCTCAAAGG
Found at i:5523318 original size:20 final size:20
Alignment explanation
Indices: 5523283--5523320 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5523273 ATTTTTTTGC
*
5523283 ATTTCGAAACTGTTTTAAGA
1 ATTTCGAAAATGTTTTAAGA
*
5523303 ATTTCGAAAATTTTTTAA
1 ATTTCGAAAATGTTTTAA
5523321 CAGATCTAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.45
Consensus pattern (20 bp):
ATTTCGAAAATGTTTTAAGA
Found at i:5528364 original size:60 final size:60
Alignment explanation
Indices: 5528290--5528408 Score: 193
Period size: 60 Copynumber: 2.0 Consensus size: 60
5528280 ATACTAAACT
* * * * *
5528290 AAACACAATAATTTATAACTTTATCCTAAATTACTAATAAATTAATTTTAAAATGATTAC
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTAC
5528350 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
5528409 TAAAAAGCAA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.52, C:0.12, G:0.01, T:0.35
Consensus pattern (60 bp):
AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTAC
Found at i:5528442 original size:60 final size:59
Alignment explanation
Indices: 5528312--5528429 Score: 139
Period size: 60 Copynumber: 2.0 Consensus size: 59
5528302 TTATAACTTT
* * * * *
5528312 ATCCTAAATTACTAATAAATTAATTTTAAAATGATTACAAACACAAAAATTTATAACATA
1 ATCCAAAATTACTAACAAATTAATTTTAAAATAATTACAAAAACAAAAA-TAATAACATA
* * *
5528372 ATCCTAAATTACTAACAAATTAATTTTAAAATAATTATAAAAAGCAAAAA-AATTACAT
1 ATCCAAAATTACTAACAAATTAATTTTAAAATAATTACAAAAA-CAAAAATAATAACAT
5528430 TCATTCAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
59 6 0.12
60 39 0.76
61 6 0.12
ACGTcount: A:0.55, C:0.11, G:0.02, T:0.32
Consensus pattern (59 bp):
ATCCAAAATTACTAACAAATTAATTTTAAAATAATTACAAAAACAAAAATAATAACATA
Found at i:5528730 original size:27 final size:27
Alignment explanation
Indices: 5528660--5528731 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 27
5528650 GCACCATTCA
* * * *
5528660 CGCCTACTTGTCAGGCGCGATTAGTAG
1 CGCCTATTTGACAGGCTCAATTAGTAG
* * *
5528687 CGCCTATCTGGCAGGCTCAATTAGTCG
1 CGCCTATTTGACAGGCTCAATTAGTAG
*
5528714 TGCCTATTTGACAGGCTC
1 CGCCTATTTGACAGGCTC
5528732 GACTCGTTTT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.18, C:0.28, G:0.26, T:0.28
Consensus pattern (27 bp):
CGCCTATTTGACAGGCTCAATTAGTAG
Found at i:5529592 original size:3 final size:3
Alignment explanation
Indices: 5529584--5529647 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
5529574 TTTGTTTAGT
5529584 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
5529632 GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA G
5529648 TTATTGGTTG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:5563053 original size:60 final size:59
Alignment explanation
Indices: 5562954--5563096 Score: 196
Period size: 60 Copynumber: 2.4 Consensus size: 59
5562944 AGTAGTTTTA
* * *
5562954 AATCTGATGAAGAAAAAACTTCATCAGATCAGAAAGAAGACATAAATGTTACTAGTAAT
1 AATCTGATGAAGAAAAAACTTCAACAGATCAGAAAGAAGACATAAAAGTCACTAGTAAT
* * *
5563013 CAATCTGATGAAGAAAAAACTTCAACAGATCAGGATGAAGACATAAAAGTCACTAGTTAT
1 -AATCTGATGAAGAAAAAACTTCAACAGATCAGAAAGAAGACATAAAAGTCACTAGTAAT
* *
5563073 AATTTTGATGAAGAAAACACTTCA
1 AA-TCTGATGAAGAAAAAACTTCA
5563097 TCTGAAGATG
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
59 2 0.03
60 72 0.97
ACGTcount: A:0.48, C:0.13, G:0.15, T:0.24
Consensus pattern (59 bp):
AATCTGATGAAGAAAAAACTTCAACAGATCAGAAAGAAGACATAAAAGTCACTAGTAAT
Found at i:5582126 original size:57 final size:56
Alignment explanation
Indices: 5582005--5582134 Score: 133
Period size: 57 Copynumber: 2.3 Consensus size: 56
5581995 TGGTTTTTTT
*
5582005 TTCTTTTTTAGTCACCAACTGCGAAAAAGTATAAAATGGTCACCTAACTATTAGTAAG
1 TTCTTTTTT-GTCACCAACTACGAAAAAGTATAAAATGGTCACCTAACTATTA-TAAG
* * *
5582063 TT-TTTTTTGTCACCTAACTATG-AAAAGTTTCAAAATGGTCA-CTCAACTATT-TAAT
1 TTCTTTTTTGTCACC-AACTACGAAAAAGTAT-AAAATGGTCACCT-AACTATTATAAG
5582118 TATCTTTTTTGATCACC
1 T-TCTTTTTTG-TCACC
5582135 CATCTATCTT
Statistics
Matches: 62, Mismatches: 4, Indels: 12
0.79 0.05 0.15
Matches are distributed among these distances:
55 4 0.06
56 16 0.26
57 35 0.56
58 7 0.11
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (56 bp):
TTCTTTTTTGTCACCAACTACGAAAAAGTATAAAATGGTCACCTAACTATTATAAG
Found at i:5592668 original size:19 final size:19
Alignment explanation
Indices: 5592638--5592687 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
5592628 TAAAATATAA
5592638 ATTTTGGAATTTCAAAAATT
1 ATTTT-GAATTTCAAAAATT
**
5592658 ATTTTGAATTTTTGAAAATT
1 ATTTTGAA-TTTCAAAAATT
5592678 ATTTTGAATT
1 ATTTTGAATT
5592688 ATTTTTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 5 0.19
20 22 0.81
ACGTcount: A:0.36, C:0.02, G:0.10, T:0.52
Consensus pattern (19 bp):
ATTTTGAATTTCAAAAATT
Found at i:5601124 original size:97 final size:97
Alignment explanation
Indices: 5600954--5601148 Score: 363
Period size: 97 Copynumber: 2.0 Consensus size: 97
5600944 TCACATGACC
5600954 TAATCTAGCATGCCACATGTCAATGGATTCAGCAATATAAGTAGAAGTGATGGCTGTATTATTAT
1 TAATCTAGCATGCCACATGTCAATGGATTCAGCAATATAAGTAGAAGTGATGGCTGTATTATTAT
*
5601019 CATTAAACATGGTCTCAATCACAAATAAACCT
66 CATGAAACATGGTCTCAATCACAAATAAACCT
* *
5601051 TAATCTAGCATGCCACATGTCAATGGATTCAGCAATATAAGTAGAAGTGGTGGCTTTATTATTAT
1 TAATCTAGCATGCCACATGTCAATGGATTCAGCAATATAAGTAGAAGTGATGGCTGTATTATTAT
5601116 CATGAAACATGGTCTCAATCACAAATAAACCT
66 CATGAAACATGGTCTCAATCACAAATAAACCT
5601148 T
1 T
5601149 CACTCAGATA
Statistics
Matches: 95, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
97 95 1.00
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.30
Consensus pattern (97 bp):
TAATCTAGCATGCCACATGTCAATGGATTCAGCAATATAAGTAGAAGTGATGGCTGTATTATTAT
CATGAAACATGGTCTCAATCACAAATAAACCT
Found at i:5602870 original size:28 final size:27
Alignment explanation
Indices: 5602760--5602883 Score: 99
Period size: 28 Copynumber: 4.4 Consensus size: 27
5602750 TCGTTCAGAC
* *
5602760 GGACTTCCTCATTTAAGATTGTCTTGGA-
1 GGACTTCCACATTT-AGATAGTCTT-GAT
* *
5602788 CGACTTCCACATTTAAGATCGTCTTGA-
1 GGACTTCCACATTT-AGATAGTCTTGAT
* *
5602815 GGACTTCCTACATTTAGACAGTTTTGAT
1 GGACTTCC-ACATTTAGATAGTCTTGAT
* *
5602843 GGGCTTCGCACATTTAGATAGTCCTGAT
1 GGACTTC-CACATTTAGATAGTCTTGAT
*
5602871 GAACTTCCCACAT
1 GGACTT-CCACAT
5602884 ATCATATATT
Statistics
Matches: 79, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
27 18 0.23
28 59 0.75
29 2 0.03
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.35
Consensus pattern (27 bp):
GGACTTCCACATTTAGATAGTCTTGAT
Found at i:5602941 original size:22 final size:22
Alignment explanation
Indices: 5602915--5602979 Score: 67
Period size: 24 Copynumber: 2.9 Consensus size: 22
5602905 TGTCTTCCAT
*
5602915 ACGTCCCATAAAGGGCTCTCAT
1 ACGTCCCATAAAGGGCTCTCAA
* * *
5602937 GCGTCCTACATAAGGGGATCTCAA
1 ACGTCC--CATAAAGGGCTCTCAA
*
5602961 ACGTCCCTTAAAGGGCTCT
1 ACGTCCCATAAAGGGCTCT
5602980 ATATACTGGT
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
22 15 0.45
24 18 0.55
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (22 bp):
ACGTCCCATAAAGGGCTCTCAA
Found at i:5619491 original size:21 final size:21
Alignment explanation
Indices: 5619457--5619498 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5619447 ATTATTCCTA
* *
5619457 TATTGTTCATTGAACGTTATT
1 TATTGATCACTGAACGTTATT
*
5619478 TATTGATCACTGAATGTTATT
1 TATTGATCACTGAACGTTATT
5619499 GGAATATGCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.26, C:0.10, G:0.14, T:0.50
Consensus pattern (21 bp):
TATTGATCACTGAACGTTATT
Found at i:5623188 original size:15 final size:14
Alignment explanation
Indices: 5623164--5623195 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
5623154 CCACTCTTGG
5623164 TTTCTCTAACCCAA
1 TTTCTCTAACCCAA
5623178 TTTCTTCTAACCCAA
1 TTTC-TCTAACCCAA
5623193 TTT
1 TTT
5623196 TCAGGATGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.25, C:0.31, G:0.00, T:0.44
Consensus pattern (14 bp):
TTTCTCTAACCCAA
Found at i:5623936 original size:14 final size:16
Alignment explanation
Indices: 5623917--5623948 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5623907 AAATTTATTA
5623917 TTAAAT-TTA-ATTTT
1 TTAAATATTATATTTT
5623931 TTAAATATTATATTTT
1 TTAAATATTATATTTT
5623947 TT
1 TT
5623949 TTTAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 3 0.19
16 7 0.44
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTAAATATTATATTTT
Found at i:5623945 original size:21 final size:19
Alignment explanation
Indices: 5623915--5623954 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
5623905 AAAAATTTAT
5623915 TATTAAATTTAATTTTTTAAA
1 TATTAAATTT--TTTTTTAAA
*
5623936 TATTATATTTTTTTTTAAA
1 TATTAAATTTTTTTTTAAA
5623955 AAAAAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
21 9 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTAAATTTTTTTTTAAA
Found at i:5625872 original size:28 final size:26
Alignment explanation
Indices: 5625805--5625888 Score: 66
Period size: 28 Copynumber: 3.1 Consensus size: 26
5625795 AGGTTATTAG
5625805 TATTTTG-AAAATATAAAAAATATACA
1 TATTTTGAAAAATATAAAAAATATA-A
**
5625831 -A-TTAAAAAATATATAAAAAACCTATAA
1 TATTTTGAAAA-ATATAAAAAA--TATAA
*
5625858 TATTTTGAAAAATATATAAAATTTATAA
1 TATTTTGAAAAATATA-AAAA-ATATAA
5625886 TAT
1 TAT
5625889 ATAAACTATA
Statistics
Matches: 45, Mismatches: 5, Indels: 14
0.70 0.08 0.22
Matches are distributed among these distances:
24 2 0.04
25 4 0.09
26 10 0.22
27 1 0.02
28 18 0.40
29 10 0.22
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (26 bp):
TATTTTGAAAAATATAAAAAATATAA
Found at i:5639372 original size:2 final size:2
Alignment explanation
Indices: 5639365--5639396 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5639355 TTAAATAGTT
5639365 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5639397 TAAAGTTTGA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5639548 original size:23 final size:23
Alignment explanation
Indices: 5639518--5639568 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
5639508 TTTTCATCCA
*
5639518 TGCAAGTGATTGTGACACTTTAG
1 TGCAAGTGATAGTGACACTTTAG
* *
5639541 TGCAAGTGATAGTGGCACTTTGG
1 TGCAAGTGATAGTGACACTTTAG
5639564 TGCAA
1 TGCAA
5639569 ATTATTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.25, C:0.14, G:0.29, T:0.31
Consensus pattern (23 bp):
TGCAAGTGATAGTGACACTTTAG
Found at i:5652366 original size:18 final size:18
Alignment explanation
Indices: 5652345--5652382 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
5652335 CTTCTACCCT
5652345 TTCCCCTTTCCCTTCCCC
1 TTCCCCTTTCCCTTCCCC
*
5652363 TTCCCTTTTCCCTTCCCC
1 TTCCCCTTTCCCTTCCCC
5652381 TT
1 TT
5652383 GGATTGCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (18 bp):
TTCCCCTTTCCCTTCCCC
Found at i:5652490 original size:25 final size:25
Alignment explanation
Indices: 5652442--5652491 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
5652432 CAGGTAAGGC
*
5652442 TCCTTCTTCTTCTTCCGTTTTTCAT
1 TCCTTCTTCTTCTTCCGTTCTTCAT
* **
5652467 TCCTTTTTCTTCTTTTGTTCTTCAT
1 TCCTTCTTCTTCTTCCGTTCTTCAT
5652492 CTTCTCTTCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.04, C:0.28, G:0.04, T:0.64
Consensus pattern (25 bp):
TCCTTCTTCTTCTTCCGTTCTTCAT
Found at i:5655860 original size:15 final size:15
Alignment explanation
Indices: 5655821--5655873 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 15
5655811 GAACATTTGG
5655821 AATTTAATTAGATAAAA
1 AATTT-ATTA-ATAAAA
5655838 AACTTTTATTAATAAAA
1 AA--TTTATTAATAAAA
*
5655855 AATTTATTTATAAATA
1 AATTTATTAATAAA-A
5655871 AAT
1 AAT
5655874 CATTGCAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
15 11 0.34
16 4 0.12
17 10 0.31
18 4 0.12
19 3 0.09
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (15 bp):
AATTTATTAATAAAA
Found at i:5655947 original size:22 final size:20
Alignment explanation
Indices: 5655904--5655942 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
5655894 TAATTTAAAA
5655904 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
*
5655924 TATATAAATTTATTAATAT
1 TATAAAAATTTATTAATAT
5655943 ATGTAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:5662394 original size:71 final size:69
Alignment explanation
Indices: 5662280--5662422 Score: 259
Period size: 71 Copynumber: 2.0 Consensus size: 69
5662270 CTCTTCAAAA
*
5662280 TTACCAATCTTACCTATGCTATAATGCATTAAAACTTATCATTTTATATACATGTGAGCATTATA
1 TTACCAATCTTACCTATGCTATAATGCATTAAAACTTATCATTTTATATACATGTGAACATTATA
5662345 TACC
66 TACC
5662349 TTACCAATCTTACCTATATGCTATAATGCATTAAAACTTATCATTTTATATACATGTGAACATTA
1 TTACCAATCTTACC--TATGCTATAATGCATTAAAACTTATCATTTTATATACATGTGAACATTA
5662414 TATACC
64 TATACC
5662420 TTA
1 TTA
5662423 ATGATTTAAG
Statistics
Matches: 71, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
69 14 0.20
71 57 0.80
ACGTcount: A:0.36, C:0.18, G:0.06, T:0.40
Consensus pattern (69 bp):
TTACCAATCTTACCTATGCTATAATGCATTAAAACTTATCATTTTATATACATGTGAACATTATA
TACC
Found at i:5663951 original size:15 final size:15
Alignment explanation
Indices: 5663926--5663960 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
5663916 GACTCTATTT
*
5663926 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
5663940 TAATTAATATTAAGA
1 TAATTAATATTAAGA
5663955 TAATTA
1 TAATTA
5663961 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:5665816 original size:25 final size:25
Alignment explanation
Indices: 5665786--5665940 Score: 90
Period size: 26 Copynumber: 6.2 Consensus size: 25
5665776 AATAACGAGT
5665786 AGCTCCGAAGAGCCATTAATCAGGA
1 AGCTCCGAAGAGCCATTAATCAGGA
* * *
5665811 AGCTCCGGATAACCA-TATATCAGGA
1 AGCTCCGAAGAGCCATTA-ATCAGGA
* *
5665836 AG-TTC-AAGCAAG-C--TACATCGGGA
1 AGCTCCGAAG--AGCCATTA-ATCAGGA
* *
5665859 AGCTCTGGAGAGCCATTAATCAGGA
1 AGCTCCGAAGAGCCATTAATCAGGA
* * * *
5665884 AGCTCACAAAAAGCCTTTAATCGGGA
1 AGCTC-CGAAGAGCCATTAATCAGGA
5665910 AGCTCACGAAGAGCCATATAA-CAGGA
1 AGCTC-CGAAGAGCCAT-TAATCAGGA
*
5665936 CGCTC
1 AGCTC
5665941 ATAAGAGTTG
Statistics
Matches: 96, Mismatches: 24, Indels: 19
0.69 0.17 0.14
Matches are distributed among these distances:
23 13 0.14
24 7 0.07
25 35 0.36
26 38 0.40
27 3 0.03
ACGTcount: A:0.35, C:0.24, G:0.23, T:0.17
Consensus pattern (25 bp):
AGCTCCGAAGAGCCATTAATCAGGA
Done.