Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008355.1 Hibiscus syriacus cultivar Beakdansim tig00111092_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: 983659
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 6
Found at i:324256 original size:20 final size:21
Alignment explanation
Indices: 324231--324280 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
324221 GAAGATTTTA
* *
324231 AAAATTTTATTTTAAAAAA-T
1 AAAATTTTAATTAAAAAAACT
*
324251 AAAATTATAATTAAAAAAACCT
1 AAAATTTTAATTAAAAAAA-CT
324273 AAAATTTT
1 AAAATTTT
324281 CTTAAATGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 16 0.67
22 8 0.33
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAATTTTAATTAAAAAAACT
Found at i:326241 original size:13 final size:13
Alignment explanation
Indices: 326223--326248 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
326213 AATTTTTTTT
326223 AAATTATTATATA
1 AAATTATTATATA
326236 AAATTATTATATA
1 AAATTATTATATA
326249 TTTTAATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AAATTATTATATA
Found at i:326248 original size:40 final size:42
Alignment explanation
Indices: 326192--326278 Score: 142
Period size: 40 Copynumber: 2.1 Consensus size: 42
326182 TTCCTAAAAT
326192 TATAAAATTATCATATATTTTAA-TTTTTTT-TAAATTATTA
1 TATAAAATTATCATATATTTTAATTTTTTTTCTAAATTATTA
*
326232 TATAAAATTATTATATATTTTAATTTTTTTTTCTAAATTATTA
1 TATAAAATTATCATATATTTTAA-TTTTTTTTCTAAATTATTA
326275 TATA
1 TATA
326279 TTTTTAATTT
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
40 22 0.51
42 7 0.16
43 14 0.33
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (42 bp):
TATAAAATTATCATATATTTTAATTTTTTTTCTAAATTATTA
Found at i:326253 original size:30 final size:30
Alignment explanation
Indices: 326219--326294 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 30
326209 TTTTAATTTT
*
326219 TTTTAAATTATTATAT-AAAATTATTATATA
1 TTTT-AATTTTTATATCAAAATTATTATATA
* * *
326249 TTTTAATTTTTTTTTCTAAATTATTATATA
1 TTTTAATTTTTATATCAAAATTATTATATA
326279 TTTTTAATTTTTATAT
1 -TTTTAATTTTTATAT
326295 TTTTTACTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.21
30 17 0.45
31 13 0.34
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (30 bp):
TTTTAATTTTTATATCAAAATTATTATATA
Found at i:326299 original size:40 final size:43
Alignment explanation
Indices: 326205--326299 Score: 101
Period size: 43 Copynumber: 2.2 Consensus size: 43
326195 AAAATTATCA
*
326205 TATATTTTAATTTTTTTTAAATTATTATATAAAATTATTATATATTT
1 TATATTTT--TTTTTTCTAAATTATTATAT--AATTATTATATATTT
*
326252 TA-A-TTTTTTTTTCTAAATTATTATAT-ATTTTTA-AT-TTT
1 TATATTTTTTTTTTCTAAATTATTATATAATTATTATATATTT
326290 TATATTTTTT
1 TATATTTTTT
326300 ACTAAAAATT
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
38 5 0.11
39 3 0.07
40 11 0.25
43 19 0.43
45 3 0.07
46 1 0.02
47 2 0.05
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (43 bp):
TATATTTTTTTTTTCTAAATTATTATATAATTATTATATATTT
Found at i:329372 original size:15 final size:15
Alignment explanation
Indices: 329352--329381 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
329342 ATATGGATTT
*
329352 AAAATTATTAAATTA
1 AAAATTAATAAATTA
329367 AAAATTAATAAATTA
1 AAAATTAATAAATTA
329382 GTCAAGTGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AAAATTAATAAATTA
Found at i:330428 original size:2 final size:2
Alignment explanation
Indices: 330417--330446 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
330407 ATATTCAAGT
330417 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
330447 TAGTTAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:333479 original size:31 final size:31
Alignment explanation
Indices: 333405--333491 Score: 99
Period size: 31 Copynumber: 2.8 Consensus size: 31
333395 AAATAAATTG
* *
333405 AGTTGAGCTCAACTTGACTCGAA-AAGTTCAA
1 AGTTGAGCTCGACCTGACTC-AAGAAGTTCAA
*
333436 AGCTGAGCTCGACCTGACTCAAGAAGTTCAA
1 AGTTGAGCTCGACCTGACTCAAGAAGTTCAA
*
333467 AGTTGAGATCGA-CTCGACTC-AGAAG
1 AGTTGAGCTCGACCT-GACTCAAGAAG
333492 CAGGCAAGCT
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
30 9 0.18
31 40 0.82
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.22
Consensus pattern (31 bp):
AGTTGAGCTCGACCTGACTCAAGAAGTTCAA
Found at i:335877 original size:18 final size:18
Alignment explanation
Indices: 335854--335890 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
335844 TACACAATAA
335854 AATCTTTCTTCAAATGAT
1 AATCTTTCTTCAAATGAT
335872 AATCTTTCTTCAAATGAT
1 AATCTTTCTTCAAATGAT
335890 A
1 A
335891 GAAATTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.16, G:0.05, T:0.43
Consensus pattern (18 bp):
AATCTTTCTTCAAATGAT
Found at i:336499 original size:14 final size:14
Alignment explanation
Indices: 336477--336521 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
336467 TGGAGAACAT
*
336477 AAACAAACATAAAC
1 AAACGAACATAAAC
336491 AAACGAACATAAAC
1 AAACGAACATAAAC
* *
336505 GAACGAA-ATAAAT
1 AAACGAACATAAAC
336518 AAAC
1 AAAC
336522 ATAAATGAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
13 8 0.30
14 19 0.70
ACGTcount: A:0.67, C:0.18, G:0.07, T:0.09
Consensus pattern (14 bp):
AAACGAACATAAAC
Found at i:336522 original size:37 final size:37
Alignment explanation
Indices: 336475--336546 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
336465 TTTGGAGAAC
336475 ATAAACAAACATAAACAAACGAACATAAACGAACGAA
1 ATAAACAAACATAAACAAACGAACATAAACGAACGAA
* **
336512 ATAAATAAACATAAATGAACGAACATAAACGAACG
1 ATAAACAAACATAAACAAACGAACATAAACGAACG
336547 TATAATCGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.62, C:0.17, G:0.10, T:0.11
Consensus pattern (37 bp):
ATAAACAAACATAAACAAACGAACATAAACGAACGAA
Found at i:336526 original size:23 final size:24
Alignment explanation
Indices: 336496--336540 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
336486 TAAACAAACG
336496 AACATAAACGAACGAA-ATAAATA
1 AACATAAACGAACGAACATAAATA
*
336519 AACATAAATGAACGAACATAAA
1 AACATAAACGAACGAACATAAA
336541 CGAACGTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.64, C:0.13, G:0.09, T:0.13
Consensus pattern (24 bp):
AACATAAACGAACGAACATAAATA
Found at i:336536 original size:14 final size:14
Alignment explanation
Indices: 336482--336546 Score: 68
Period size: 14 Copynumber: 5.0 Consensus size: 14
336472 AACATAAACA
*
336482 AACATAAACAAACG
1 AACATAAACGAACG
336496 AACATAAACGAACG
1 AACATAAACGAACG
*
336510 AA-ATAAA--TA--
1 AACATAAACGAACG
*
336519 AACATAAATGAACG
1 AACATAAACGAACG
336533 AACATAAACGAACG
1 AACATAAACGAACG
336547 TATAATCGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
9 2 0.05
10 5 0.12
11 1 0.02
12 1 0.02
13 5 0.12
14 28 0.67
ACGTcount: A:0.62, C:0.17, G:0.11, T:0.11
Consensus pattern (14 bp):
AACATAAACGAACG
Found at i:344858 original size:39 final size:39
Alignment explanation
Indices: 344815--344933 Score: 154
Period size: 39 Copynumber: 3.1 Consensus size: 39
344805 TTTAAAAAGT
*
344815 AATTTAGAATGTTAGT-GTAAAATAATTTAAGAAATTAAG
1 AATTTAGAATGTTA-TAGTGAAATAATTTAAGAAATTAAG
* *
344854 AATTTAGAATGTTATGGTCGCAA-AATTTAAGAAATTAAG
1 AATTTAGAATGTTATAGT-GAAATAATTTAAGAAATTAAG
* *
344893 AATTTAGAATGTTATAGTGAAATAATTTGAG-AATTATG
1 AATTTAGAATGTTATAGTGAAATAATTTAAGAAATTAAG
344931 AAT
1 AAT
344934 AAAAATTTAA
Statistics
Matches: 71, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
38 13 0.18
39 56 0.79
40 2 0.03
ACGTcount: A:0.45, C:0.02, G:0.17, T:0.36
Consensus pattern (39 bp):
AATTTAGAATGTTATAGTGAAATAATTTAAGAAATTAAG
Found at i:346273 original size:36 final size:36
Alignment explanation
Indices: 346213--346283 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
346203 TATTGCTGAG
*
346213 CTCGACTCGACTCGAAAACTCTGAAATGGAGCTCGA
1 CTCGACTCGACTCGAAAACTCTGAAATGAAGCTCGA
* *
346249 CTCGACTCGAACTCGAAATC-CTGAACTGAAGCTCG
1 CTCGACTCG-ACTCGAAAACTCTGAAATGAAGCTCG
346284 TGAGCAGCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
36 22 0.71
37 9 0.29
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.20
Consensus pattern (36 bp):
CTCGACTCGACTCGAAAACTCTGAAATGAAGCTCGA
Found at i:348690 original size:20 final size:19
Alignment explanation
Indices: 348661--348796 Score: 121
Period size: 20 Copynumber: 6.8 Consensus size: 19
348651 AAATGACCAA
348661 CAAATTCGCAACGCGAATT
1 CAAATTCGCAACGCGAATT
* **
348680 CAAATTTCGCAACTCAGGTTT
1 CAAA-TTCGCAACGC-GAATT
*
348701 CAAATTCGCAACGCGAAAAT
1 CAAATTCGCAACGCG-AATT
* *
348721 CAAATTCGCAACACAGAAGT
1 CAAATTCGCAACGC-GAATT
* *
348741 CAAATTCGCAATGCGAAAGT
1 CAAATTCGCAACGCG-AATT
348761 CGAAATTCGCAACGCG-ATT
1 C-AAATTCGCAACGCGAATT
*
348780 TAAGATTCGCAACGCGA
1 CAA-ATTCGCAACGCGA
348797 TGCTCCAAAA
Statistics
Matches: 95, Mismatches: 14, Indels: 15
0.77 0.11 0.12
Matches are distributed among these distances:
18 2 0.02
19 20 0.21
20 52 0.55
21 21 0.22
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.21
Consensus pattern (19 bp):
CAAATTCGCAACGCGAATT
Found at i:348716 original size:40 final size:40
Alignment explanation
Indices: 348661--348796 Score: 152
Period size: 40 Copynumber: 3.4 Consensus size: 40
348651 AAATGACCAA
* * *
348661 CAAATTCGCAACGCG-AATTCAAATTTCGCAACTCAGGTTT
1 CAAATTCGCAACGCGAAAATCAAA-TTCGCAACACAGATTT
**
348701 CAAATTCGCAACGCGAAAATCAAATTCGCAACACAGAAGT
1 CAAATTCGCAACGCGAAAATCAAATTCGCAACACAGATTT
* * *
348741 CAAATTCGCAATGCGAAAGTCGAAATTCGCAACGC-GATTT
1 CAAATTCGCAACGCGAAAATC-AAATTCGCAACACAGATTT
348781 -AAGATTCGCAACGCGA
1 CAA-ATTCGCAACGCGA
348797 TGCTCCAAAA
Statistics
Matches: 82, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
39 2 0.02
40 61 0.74
41 19 0.23
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.21
Consensus pattern (40 bp):
CAAATTCGCAACGCGAAAATCAAATTCGCAACACAGATTT
Found at i:356675 original size:38 final size:38
Alignment explanation
Indices: 356623--356711 Score: 133
Period size: 38 Copynumber: 2.3 Consensus size: 38
356613 TTTCGTACCT
* *
356623 CTAAATGATTCAGTGCTGATTAATTCAGCAAAACAGTG
1 CTAAATGATTCAGTGCTAACTAATTCAGCAAAACAGTG
* *
356661 TTAAATGATTCAGTGCTAACTGATTCAGCAAAACAGTG
1 CTAAATGATTCAGTGCTAACTAATTCAGCAAAACAGTG
*
356699 CTGAATGATTCAG
1 CTAAATGATTCAG
356712 CACAGAAGTA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 45 1.00
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (38 bp):
CTAAATGATTCAGTGCTAACTAATTCAGCAAAACAGTG
Found at i:358245 original size:19 final size:17
Alignment explanation
Indices: 358217--358260 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 17
358207 TAAGGTTTTT
*
358217 TTTTATAAATATAATAATA
1 TTTTAAAAATA-AATAA-A
358236 TTTTAAAAATAAATAAA
1 TTTTAAAAATAAATAAA
*
358253 TTTCAAAA
1 TTTTAAAA
358261 GCACTGAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 8 0.35
18 5 0.22
19 10 0.43
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
TTTTAAAAATAAATAAA
Found at i:358753 original size:23 final size:23
Alignment explanation
Indices: 358721--358769 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
358711 TGTAATTTTT
358721 TTAGAAATTATTTATTAAAAATA
1 TTAGAAATTATTTATTAAAAATA
*
358744 TTAGATATTATTTATTAAAAATA
1 TTAGAAATTATTTATTAAAAATA
358767 TTA
1 TTA
358770 TTATTTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (23 bp):
TTAGAAATTATTTATTAAAAATA
Found at i:358767 original size:16 final size:17
Alignment explanation
Indices: 358748--358786 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
358738 AAAATATTAG
358748 ATATTATT-TATTAAAA
1 ATATTATTATATTAAAA
* *
358764 ATATTATTATTTTTAAA
1 ATATTATTATATTAAAA
358781 ATATTA
1 ATATTA
358787 GAACAATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATATTATTATATTAAAA
Found at i:358783 original size:17 final size:19
Alignment explanation
Indices: 358727--358786 Score: 70
Period size: 23 Copynumber: 3.1 Consensus size: 19
358717 TTTTTTAGAA
358727 ATTATTTATTAAAAATATTAGAT
1 ATTATTTATTAAAAATA-T---T
358750 ATTATTTATTAAAAATATT
1 ATTATTTATTAAAAATATT
358769 ATTATTT-TT-AAAATATT
1 ATTATTTATTAAAAATATT
358786 A
1 A
358787 GAACAATTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
17 9 0.24
18 2 0.05
19 8 0.22
22 1 0.03
23 17 0.46
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
ATTATTTATTAAAAATATT
Found at i:358979 original size:17 final size:17
Alignment explanation
Indices: 358957--358994 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
358947 TATTAATTGT
*
358957 TTATTAAAATAATAATA
1 TTATTAAAATAATAAAA
*
358974 TTATTAAAATATTAAAA
1 TTATTAAAATAATAAAA
358991 TTAT
1 TTAT
358995 AATATTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TTATTAAAATAATAAAA
Found at i:358980 original size:37 final size:37
Alignment explanation
Indices: 358877--358988 Score: 111
Period size: 42 Copynumber: 2.9 Consensus size: 37
358867 ATTATTATAT
* *
358877 TTTATTAAAATAA-AATAATAATAAATTATATTAATTA
1 TTTATTAAAATAATAAT-ATTATTAATTATATTAATTA
* *
358914 TTTATTAGAATAAGAATAACATATTATTAATTATATTAATTG
1 TTTATT--AA-AATAAT-A-ATATTATTAATTATATTAATTA
*
358956 TTTATTAAAATAATAATATTATTAA-AATATTAA
1 TTTATTAAAATAATAATATTATTAATTATATTAA
358989 AATTATAATA
Statistics
Matches: 63, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
36 7 0.11
37 16 0.25
38 1 0.02
39 7 0.11
40 6 0.10
42 24 0.38
43 2 0.03
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.45
Consensus pattern (37 bp):
TTTATTAAAATAATAATATTATTAATTATATTAATTA
Found at i:358986 original size:25 final size:24
Alignment explanation
Indices: 358958--359008 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 24
358948 ATTAATTGTT
*
358958 TATTAAAATAATAATATTATTAAAA
1 TATTAAAATAATAATATT-TAAAAA
*
358983 TATTAAAATTATAATATTTAAAAA
1 TATTAAAATAATAATATTTAAAAA
359007 TA
1 TA
359009 GGAATACTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 7 0.29
25 17 0.71
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
TATTAAAATAATAATATTTAAAAA
Found at i:360379 original size:3 final size:3
Alignment explanation
Indices: 360371--360405 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
360361 GACTTTGACC
*
360371 GAA GAA GAA GAG GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
360406 GGAGAGTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:361498 original size:31 final size:31
Alignment explanation
Indices: 361460--361535 Score: 152
Period size: 31 Copynumber: 2.5 Consensus size: 31
361450 TGATTTTGAA
361460 AAAAATAATTAAATAACCAAAAGAGAATCAC
1 AAAAATAATTAAATAACCAAAAGAGAATCAC
361491 AAAAATAATTAAATAACCAAAAGAGAATCAC
1 AAAAATAATTAAATAACCAAAAGAGAATCAC
361522 AAAAATAATTAAAT
1 AAAAATAATTAAAT
361536 GACTAAATAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.66, C:0.11, G:0.05, T:0.18
Consensus pattern (31 bp):
AAAAATAATTAAATAACCAAAAGAGAATCAC
Found at i:363999 original size:15 final size:14
Alignment explanation
Indices: 363961--363999 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
363951 CGTTTTGATC
363961 TAAAATAAAATATT
1 TAAAATAAAATATT
*
363975 TAAGACTAAAATATT
1 TAA-AATAAAATATT
363990 ATAAAATAAA
1 -TAAAATAAA
364000 CATTAAAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 3 0.14
15 15 0.71
16 3 0.14
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (14 bp):
TAAAATAAAATATT
Found at i:364974 original size:23 final size:23
Alignment explanation
Indices: 364927--364971 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
364917 ATTTATTTAT
364927 TATTATAATATTAAAAAATATAA
1 TATTATAATATTAAAAAATATAA
* *
364950 TATTATATTATT-AGAAATATAA
1 TATTATAATATTAAAAAATATAA
364972 ATAAATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
TATTATAATATTAAAAAATATAA
Found at i:365343 original size:29 final size:30
Alignment explanation
Indices: 365311--365384 Score: 107
Period size: 29 Copynumber: 2.5 Consensus size: 30
365301 AAAATAATTA
*
365311 ACGTAAAATGAATTACCTGAAAA-T-TGTTT
1 ACGTAAAATGAATTACATGAAAACTAT-TTT
*
365340 ACGTAAAATGCATTACATGAAAACTATTTT
1 ACGTAAAATGAATTACATGAAAACTATTTT
365370 ACGTAAAATGAATTA
1 ACGTAAAATGAATTA
365385 TATTTTTCAA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
29 21 0.52
30 18 0.45
31 1 0.03
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (30 bp):
ACGTAAAATGAATTACATGAAAACTATTTT
Found at i:365835 original size:27 final size:27
Alignment explanation
Indices: 365774--365835 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
365764 AGTAGAAAGT
**
365774 TAAAAAAATGTTTTACAAAAAATCAAA
1 TAAAAAAATAATTTACAAAAAATCAAA
* *
365801 TAATAAAATAATTTACAGAAAATACAAA
1 TAAAAAAATAATTTACAAAAAAT-CAAA
365829 -AAAAAAA
1 TAAAAAAA
365836 CTTAAAATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
27 25 0.86
28 4 0.14
ACGTcount: A:0.68, C:0.06, G:0.03, T:0.23
Consensus pattern (27 bp):
TAAAAAAATAATTTACAAAAAATCAAA
Found at i:365860 original size:17 final size:19
Alignment explanation
Indices: 365838--365883 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
365828 AAAAAAAACT
*
365838 TAAAA-TAATT-CCATTAG
1 TAAAATTAATTACAATTAG
365855 TAAAATTAATTACAATTAG
1 TAAAATTAATTACAATTAG
365874 TAAACATTAA
1 TAAA-ATTAA
365884 AAAATATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 5 0.20
18 5 0.20
19 10 0.40
20 5 0.20
ACGTcount: A:0.52, C:0.09, G:0.04, T:0.35
Consensus pattern (19 bp):
TAAAATTAATTACAATTAG
Found at i:367294 original size:16 final size:17
Alignment explanation
Indices: 367275--367307 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
367265 TTTCTTTCAC
*
367275 TTTTCTTTTCG-ATTTT
1 TTTTCCTTTCGAATTTT
367291 TTTTCCTTTCGAATTTT
1 TTTTCCTTTCGAATTTT
367308 GAGCTTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.09, C:0.15, G:0.06, T:0.70
Consensus pattern (17 bp):
TTTTCCTTTCGAATTTT
Found at i:367887 original size:21 final size:21
Alignment explanation
Indices: 367861--367920 Score: 93
Period size: 21 Copynumber: 2.9 Consensus size: 21
367851 ATTTACCGTG
367861 ATTGCGGCCGTCGCGGGTGCT
1 ATTGCGGCCGTCGCGGGTGCT
* **
367882 ATTGCGGTCGTCGCGGACGCT
1 ATTGCGGCCGTCGCGGGTGCT
367903 ATTGCGGCCGTCGCGGGT
1 ATTGCGGCCGTCGCGGGT
367921 AACTCGGACA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.07, C:0.28, G:0.42, T:0.23
Consensus pattern (21 bp):
ATTGCGGCCGTCGCGGGTGCT
Found at i:369110 original size:31 final size:29
Alignment explanation
Indices: 369072--369139 Score: 84
Period size: 31 Copynumber: 2.3 Consensus size: 29
369062 TAATACAAAT
*
369072 TTCTAAATTCACACTTGTGTCTATACCTAA
1 TTCTAAATTCACACTTGTGTCCAT-CCTAA
* *
369102 TCTCTAAATCCACATTTGTGTCCATCCTAA
1 T-TCTAAATTCACACTTGTGTCCATCCTAA
369132 TT-TAAATT
1 TTCTAAATT
369140 GTAAGAAGCA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 5 0.15
29 1 0.03
30 7 0.21
31 20 0.61
ACGTcount: A:0.29, C:0.24, G:0.06, T:0.41
Consensus pattern (29 bp):
TTCTAAATTCACACTTGTGTCCATCCTAA
Found at i:372352 original size:28 final size:30
Alignment explanation
Indices: 372300--372363 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 30
372290 GCGCCTTGAG
*
372300 TTTTTTCATCCTTGTAATTAGGGTCCCT-A
1 TTTTTTCATCCTTATAATTAGGGTCCCTAA
* *
372329 TTTTTTCATCTTTATAATTA-GGTCCTTAA
1 TTTTTTCATCCTTATAATTAGGGTCCCTAA
372358 TTTTTT
1 TTTTTT
372364 AAATCTTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
28 6 0.19
29 25 0.81
ACGTcount: A:0.19, C:0.16, G:0.09, T:0.56
Consensus pattern (30 bp):
TTTTTTCATCCTTATAATTAGGGTCCCTAA
Found at i:372384 original size:42 final size:39
Alignment explanation
Indices: 372338--372514 Score: 124
Period size: 43 Copynumber: 4.3 Consensus size: 39
372328 ATTTTTTCAT
372338 CTTTATAATTAGGTCCTTAATTTTTTAAATCTTATTTTTCAC
1 CTTTATAATTAGGT-CTTAATTTTTT-AATCTTATTTTT-AC
* * * * *
372380 CTTTATAATTGAGGTCATAATATTATTCAATCTAACTTGTTAT
1 CTTTATAATT-AGGTCTTAAT-TT-TTTAATCTTA-TTTTTAC
**
372423 CTTTATAATTGAAATCTCTAATTTTTTAATCTT-TTTTTAC
1 CTTTATAATT-AGGTCT-TAATTTTTTAATCTTATTTTTAC
* * * * *
372463 CTTTATAATT-GTGTCCCCTAATTTTGTAATCTCACTTTTAA
1 CTTTATAATTAG-GT--CTTAATTTTTTAATCTTATTTTTAC
372504 CTTTATAATTA
1 CTTTATAATTA
372515 AGGCTTTTAA
Statistics
Matches: 106, Mismatches: 19, Indels: 20
0.73 0.13 0.14
Matches are distributed among these distances:
39 1 0.01
40 28 0.26
41 16 0.15
42 22 0.21
43 29 0.27
44 10 0.09
ACGTcount: A:0.28, C:0.14, G:0.06, T:0.52
Consensus pattern (39 bp):
CTTTATAATTAGGTCTTAATTTTTTAATCTTATTTTTAC
Found at i:372706 original size:44 final size:43
Alignment explanation
Indices: 372483--372773 Score: 177
Period size: 43 Copynumber: 6.7 Consensus size: 43
372473 GTGTCCCCTA
* ***
372483 ATTTTGTAATCTCACTTT-TAACTTTATAATTAAGGCTTTTAAG
1 ATTTTTTAATCTCACTTTCT-ACTTTATAATTAAGGCCCCTAAG
* * *
372526 -TTTTTTCAATCACAGTTTCTACATTT-TCAATTAAGGCCTCTAAG
1 ATTTTTT-AATCTCACTTTCTAC-TTTAT-AATTAAGGCCCCTAAG
* * *
372570 -TTTTTCAATCTCAATTTCTACTTTTATAATTAACGCCCCT-A-
1 ATTTTTTAATCTCACTTTCTAC-TTTATAATTAAGGCCCCTAAG
* * **
372611 ATTTTTTAATCTCACTTTTTTAACTTTATAATTGAGGCCTTTAAG
1 ATTTTTTAATCTCAC-TTTCT-ACTTTATAATTAAGGCCCCTAAG
* * *
372656 TTTTTTTAATCTCACTTTCTAGCTTTCTAATTGAGGCCCCTAAG
1 ATTTTTTAATCTCACTTTCTA-CTTTATAATTAAGGCCCCTAAG
* * * * * *
372700 AATTTTTTTTATCTCA-ATTATACCTTTATAATTGAGACCCAT-A-
1 -A-TTTTTTAATCTCACTTTCTA-CTTTATAATTAAGGCCCCTAAG
* *
372743 TTTTTTTCAATCTCAATTTCTACCTTTATAA
1 ATTTTTT-AATCTCACTTTCTA-CTTTATAA
372774 ATAAAGCATC
Statistics
Matches: 198, Mismatches: 35, Indels: 30
0.75 0.13 0.11
Matches are distributed among these distances:
41 6 0.03
42 24 0.12
43 71 0.36
44 51 0.26
45 34 0.17
46 12 0.06
ACGTcount: A:0.27, C:0.18, G:0.07, T:0.48
Consensus pattern (43 bp):
ATTTTTTAATCTCACTTTCTACTTTATAATTAAGGCCCCTAAG
Found at i:372747 original size:130 final size:126
Alignment explanation
Indices: 372460--372773 Score: 319
Period size: 130 Copynumber: 2.4 Consensus size: 126
372450 AATCTTTTTT
* *
372460 TACCTTTATAATTGTGTCCCCTAATTTTGTAATCTCACTTTTAACTTTATAATTAAGGCTTTTAA
1 TACCTTTATAATTGAG-CCCCTAATTTT-TAATCTCACTTTTAACTTTATAATTAAGGCCTTTAA
* * *
372525 GTTTTTTCAATCACAGTTTCTACATTTTCAATTAAGGCCTCTAAGTTTTTCAATCTCAATTTC
64 GTTTTTTCAATCACACTTTCTACATTTTCAATTAAGGCCCCTAAGTTTTTCAATCTCAATTTA
* * *
372588 TACTTTTATAATTAACGCCCCTAATTTTTTAATCTCACTTTTTTAACTTTATAATTGAGGCCTTT
1 TACCTTTATAATTGA-GCCCCTAA-TTTTTAATCTCAC--TTTTAACTTTATAATTAAGGCCTTT
* * * **
372653 AAGTTTTTTTAATCTCACTTTCTAGC--TTTCTAATTGAGGCCCCTAAGAATTTTTTTTATCTCA
62 AAGTTTTTTCAATCACACTTTCTA-CATTTTC-AATTAAGGCCCCTAAG---TTTTTCAATCTCA
372716 A-TTA
122 ATTTA
* * * *
372720 TACCTTTATAATTGAGACCCATATTTTTTTCAATCTCAATTTCTACCTTTATAA
1 TACCTTTATAATTGAG-CCCCTA-ATTTTT-AATCTCACTTT-TAACTTTATAA
372774 ATAAAGCATC
Statistics
Matches: 154, Mismatches: 19, Indels: 22
0.79 0.10 0.11
Matches are distributed among these distances:
128 28 0.18
129 9 0.06
130 58 0.38
131 5 0.03
132 35 0.23
133 19 0.12
ACGTcount: A:0.27, C:0.19, G:0.07, T:0.47
Consensus pattern (126 bp):
TACCTTTATAATTGAGCCCCTAATTTTTAATCTCACTTTTAACTTTATAATTAAGGCCTTTAAGT
TTTTTCAATCACACTTTCTACATTTTCAATTAAGGCCCCTAAGTTTTTCAATCTCAATTTA
Found at i:372863 original size:16 final size:16
Alignment explanation
Indices: 372842--372872 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
372832 TCTCTCATTA
372842 ATTCATTTAATTTTGG
1 ATTCATTTAATTTTGG
372858 ATTCATTTAATTTTG
1 ATTCATTTAATTTTG
372873 AATTAAATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.06, G:0.10, T:0.58
Consensus pattern (16 bp):
ATTCATTTAATTTTGG
Found at i:373573 original size:130 final size:130
Alignment explanation
Indices: 373309--373559 Score: 380
Period size: 130 Copynumber: 1.9 Consensus size: 130
373299 TATTGGGCCC
* * *
373309 TCACTGATATGACTCATGTATCTTTGTGGTGCATGAGGTAGGGTGATAATTGAATATTGCACATA
1 TCACTGATATGACTCATGTATCTTTGTGGTGCATAAGGTAGGGTGATAATTGAATACTGCACAGA
* * *
373374 TCAATCATATGACTCATGTGCCTTTATGGTGCATGAGGTGGAGTGATAATTAAATACTGCACAAA
66 CCAATCATATGACTAATGTACCTTTATGGTGCATGAGGTGGAGTGATAATTAAATACTGCACAAA
*
373439 TCACTTATATGACTCATGTATCTTTGTGGTGCATAAGGT-GGAGTGATAATTGAATACTGCACAG
1 TCACTGATATGACTCATGTATCTTTGTGGTGCATAAGGTAGG-GTGATAATTGAATACTGCACAG
* * *
373503 ACCACTCATATGACTAATGTACCTTTGTGGTGCATG-GAGTGGAGTGATAATTGAATA
65 ACCAATCATATGACTAATGTACCTTTATGGTGCATGAG-GTGGAGTGATAATTAAATA
373560 TTGTATTGAT
Statistics
Matches: 109, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
129 3 0.03
130 106 0.97
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (130 bp):
TCACTGATATGACTCATGTATCTTTGTGGTGCATAAGGTAGGGTGATAATTGAATACTGCACAGA
CCAATCATATGACTAATGTACCTTTATGGTGCATGAGGTGGAGTGATAATTAAATACTGCACAAA
Found at i:373575 original size:65 final size:65
Alignment explanation
Indices: 373309--373559 Score: 344
Period size: 65 Copynumber: 3.9 Consensus size: 65
373299 TATTGGGCCC
* * * *
373309 TCACTGATATGACTCATGTATCTTTGTGGTGCATGAGGTAGG-GTGATAATTGAATATTGCACAT
1 TCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGT-GGAGTGATAATTGAATACTGCACAG
373373 A
65 A
* * * * *
373374 TCAATCATATGACTCATGTGCCTTTATGGTGCATGAGGTGGAGTGATAATTAAATACTGCACAAA
1 TCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACTGCACAGA
* * *
373439 TCACTTATATGACTCATGTATCTTTGTGGTGCATAAGGTGGAGTGATAATTGAATACTGCACAGA
1 TCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACTGCACAGA
* *
373504 CCACTCATATGACTAATGTACCTTTGTGGTGCATG-GAGTGGAGTGATAATTGAATA
1 TCACTCATATGACTCATGTACCTTTGTGGTGCATGAG-GTGGAGTGATAATTGAATA
373560 TTGTATTGAT
Statistics
Matches: 163, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
64 3 0.02
65 160 0.98
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (65 bp):
TCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACTGCACAGA
Found at i:373881 original size:26 final size:26
Alignment explanation
Indices: 373825--373874 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
373815 TAAACGGACT
373825 TATATTGTTATACGATGTTTTGTATA
1 TATATTGTTATACGATGTTTTGTATA
373851 TATATTGTTATACGATGTTTTGTA
1 TATATTGTTATACGATGTTTTGTA
373875 ATAATATACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.26, C:0.04, G:0.16, T:0.54
Consensus pattern (26 bp):
TATATTGTTATACGATGTTTTGTATA
Found at i:374252 original size:21 final size:21
Alignment explanation
Indices: 374226--374344 Score: 129
Period size: 21 Copynumber: 5.7 Consensus size: 21
374216 CCAACTTCGC
*
374226 AAGTTCGCATTACGATAGTCG
1 AAGTTCGCATTGCGATAGTCG
* *
374247 AAGTTCGCGTTGCGATAGTCC
1 AAGTTCGCATTGCGATAGTCG
374268 AAGTTCGCATTGCGATAGTCG
1 AAGTTCGCATTGCGATAGTCG
* *
374289 -ACTATCGCATTGCGAT-TTAC-
1 AAGT-TCGCATTGCGATAGT-CG
374309 ATA-TTCGCATTGCGATAGTCG
1 A-AGTTCGCATTGCGATAGTCG
*
374330 AAGTTCGCGTTGCGA
1 AAGTTCGCATTGCGA
374345 ATCTGGAAAC
Statistics
Matches: 82, Mismatches: 9, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
20 17 0.21
21 64 0.78
22 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (21 bp):
AAGTTCGCATTGCGATAGTCG
Found at i:374284 original size:42 final size:41
Alignment explanation
Indices: 374225--374344 Score: 154
Period size: 42 Copynumber: 2.9 Consensus size: 41
374215 TCCAACTTCG
* *
374225 CAAGTTCGCATTACGATAGTCGAAGTTCGCGTTGCGATAGTC
1 CAAGTTCGCATTGCGATAGTCGAAGTTCGCGTTGCGAT-GTA
* * *
374267 CAAGTTCGCATTGCGATAGTCG-ACTATCGCATTGCGATTTA
1 CAAGTTCGCATTGCGATAGTCGAAGT-TCGCGTTGCGATGTA
374308 CATA-TTCGCATTGCGATAGTCGAAGTTCGCGTTGCGA
1 CA-AGTTCGCATTGCGATAGTCGAAGTTCGCGTTGCGA
374345 ATCTGGAAAC
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
41 33 0.49
42 35 0.51
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (41 bp):
CAAGTTCGCATTGCGATAGTCGAAGTTCGCGTTGCGATGTA
Found at i:374396 original size:19 final size:19
Alignment explanation
Indices: 374372--374422 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
374362 CGATATCGGA
*
374372 GATCGCGTTGCGAATTATC
1 GATCGCATTGCGAATTATC
374391 GATCGCATTGCGAATTATC
1 GATCGCATTGCGAATTATC
374410 GATCGCATTGCGA
1 GATCGCATTGCGA
374423 TTTAGTTGGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (19 bp):
GATCGCATTGCGAATTATC
Found at i:379163 original size:91 final size:92
Alignment explanation
Indices: 379061--379246 Score: 329
Period size: 91 Copynumber: 2.0 Consensus size: 92
379051 GTTTACCAAA
* *
379061 TTAAAAACATATAGGCAGTACTATTCTAATAAGATACCAACTTATAAAACCAT-AATTTTTATCA
1 TTAAAAACATATAAGCAGTACTATTCTAATAAAATACCAACTTATAAAACCATAAATTTTTATCA
*
379125 ATCGTATATAAAATGATAAAAGAACAT
66 ATCATATATAAAATGATAAAAGAACAT
*
379152 TTAAAAACATATAAGCAGTACTATTCTAATAAAATGCCAACTTATAAAACCATAAATTTTTATCA
1 TTAAAAACATATAAGCAGTACTATTCTAATAAAATACCAACTTATAAAACCATAAATTTTTATCA
379217 ATCATATATAAAATGATAAAAGAACAT
66 ATCATATATAAAATGATAAAAGAACAT
379244 TTA
1 TTA
379247 GAACCTTTAT
Statistics
Matches: 90, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
91 50 0.56
92 40 0.44
ACGTcount: A:0.49, C:0.13, G:0.06, T:0.31
Consensus pattern (92 bp):
TTAAAAACATATAAGCAGTACTATTCTAATAAAATACCAACTTATAAAACCATAAATTTTTATCA
ATCATATATAAAATGATAAAAGAACAT
Found at i:386502 original size:36 final size:36
Alignment explanation
Indices: 386455--386523 Score: 138
Period size: 36 Copynumber: 1.9 Consensus size: 36
386445 TGCGAACGAC
386455 GACTTTTGATATGAGTCCTCTTAAGGTCCCATGAGT
1 GACTTTTGATATGAGTCCTCTTAAGGTCCCATGAGT
386491 GACTTTTGATATGAGTCCTCTTAAGGTCCCATG
1 GACTTTTGATATGAGTCCTCTTAAGGTCCCATG
386524 GTTGGATAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (36 bp):
GACTTTTGATATGAGTCCTCTTAAGGTCCCATGAGT
Found at i:388530 original size:22 final size:22
Alignment explanation
Indices: 388490--388532 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
388480 TTTACTCAAT
* **
388490 TTGACTTGAAAAAGTTTCAAAC
1 TTGACTCGAAAAAAATTCAAAC
388512 TTGACTCGAAAAAAATTCAAA
1 TTGACTCGAAAAAAATTCAAA
388533 TTCAAATCGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.28
Consensus pattern (22 bp):
TTGACTCGAAAAAAATTCAAAC
Found at i:392910 original size:2 final size:2
Alignment explanation
Indices: 392897--392959 Score: 71
Period size: 2 Copynumber: 33.5 Consensus size: 2
392887 TGATTCGTGC
* *
392897 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
392938 A- AT A- AT AT AT TT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
392960 ATTTTTATAA
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
1 4 0.08
2 47 0.92
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:392969 original size:27 final size:29
Alignment explanation
Indices: 392908--392970 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
392898 TATACATATA
392908 TATATATATATATATATATAATATATATTT
1 TATA-ATATATATATATATAATATATATTT
* * *
392938 AATAATATATTTATATATTATA-AT-TTT
1 TATAATATATATATATATAATATATATTT
392965 TATAAT
1 TATAAT
392971 TAAGTACAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 8 0.28
28 2 0.07
29 16 0.55
30 3 0.10
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (29 bp):
TATAATATATATATATATAATATATATTT
Found at i:396192 original size:23 final size:24
Alignment explanation
Indices: 396154--396202 Score: 91
Period size: 23 Copynumber: 2.1 Consensus size: 24
396144 CCATTTATTC
396154 AATTTTTAAATAACATTTCTACTA
1 AATTTTTAAATAACATTTCTACTA
396178 AATTTTTAAAT-ACATTTCTACTA
1 AATTTTTAAATAACATTTCTACTA
396201 AA
1 AA
396203 AAGATTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 14 0.56
24 11 0.44
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.45
Consensus pattern (24 bp):
AATTTTTAAATAACATTTCTACTA
Found at i:396695 original size:21 final size:21
Alignment explanation
Indices: 396648--396696 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
396638 ATTTTTTATT
*
396648 CCGGACCCTAGACCACTGTCC
1 CCGGACCCTAGACCACTGACC
**
396669 TTGGACCC-AGGACCACTGACC
1 CCGGACCCTA-GACCACTGACC
396690 CCGGACC
1 CCGGACC
396697 ACTAATCTCA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.20, C:0.45, G:0.22, T:0.12
Consensus pattern (21 bp):
CCGGACCCTAGACCACTGACC
Found at i:398710 original size:18 final size:18
Alignment explanation
Indices: 398683--398731 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
398673 ATTCAAGCCA
398683 ATTTTCCTTTCAATATTC
1 ATTTTCCTTTCAATATTC
*
398701 ATTTTGCTTTCAATATTC
1 ATTTTCCTTTCAATATTC
*
398719 ATTTTTCTTTCAA
1 ATTTTCCTTTCAA
398732 GAACACCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.22, C:0.18, G:0.02, T:0.57
Consensus pattern (18 bp):
ATTTTCCTTTCAATATTC
Found at i:400350 original size:97 final size:97
Alignment explanation
Indices: 400205--400692 Score: 545
Period size: 97 Copynumber: 5.0 Consensus size: 97
400195 TCCGATAGAG
*
400205 GGAGAAGAAGTTCGTAATGAGAAGAACTTGTTCAACCTTTGTTCGATTCACGGCATTTCGAATCA
1 GGAGAAGAAGTTCGTAAT-A-AAGAACTTGTTCAACCTTTGCTCGATTCACGGCATTTCGAATCA
400270 GCGACGGCTCACTTGAGGGATTAACATTTCCAAT
64 GCGACGGCTCACTTGAGGGATTAACATTTCCAAT
* * *
400304 GGAGAAGAAGTTCGTAATAAAAAACTTGTTCAACCTTTGCTCGATTCACGGCATTTCGAACCAGT
1 GGAGAAGAAGTTCGTAATAAAGAACTTGTTCAACCTTTGCTCGATTCACGGCATTTCGAATCAGC
* * *
400369 GACGGCTCATTTGAAGGATTAATATTTCCAAT
66 GACGGCTCACTTGAGGGATTAACATTTCCAAT
* * * * *
400401 AGAGAAGAAGTTTGTAATGAATAACTTGTTCAACCTTTTCTCGATTCACGGCATTTCGAATCAGC
1 GGAGAAGAAGTTCGTAATAAAGAACTTGTTCAACCTTTGCTCGATTCACGGCATTTCGAATCAGC
* * * *
400466 GA-TGCTTCACTTGAGGGATTAATATTTTCAGT
66 GACGGC-TCACTTGAGGGATTAACATTTCCAAT
* * * ** * *
400498 GGAGAAGAAGTTCATAATGAAGAACTTATTCAACCTTTGCTCGATTCACATCATTTCAAATTAGC
1 GGAGAAGAAGTTCGTAATAAAGAACTTGTTCAACCTTTGCTCGATTCACGGCATTTCGAATCAGC
* ** **
400563 GACGCCTCACACGAGGGAGCAACATTTCC-A-
66 GACGGCTCACTTGAGGGATTAACATTTCCAAT
* * * * * *
400593 GTAG-AGAA-TTCATAATGAGAAGAACTTGTTCAACCTTTGCTAGATTCACGACATTTCAAATTA
1 GGAGAAGAAGTTCGTAAT-A-AAGAACTTGTTCAACCTTTGCTCGATTCACGGCATTTCGAATCA
* * ** *
400656 GCAACGCCTCACTCAAGGGATCAACATTTCCAAT
64 GCGACGGCTCACTTGAGGGATTAACATTTCCAAT
400690 GGA
1 GGA
400693 AAGTTAATGA
Statistics
Matches: 334, Mismatches: 49, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
93 8 0.02
94 4 0.01
95 70 0.21
96 3 0.01
97 229 0.69
98 2 0.01
99 18 0.05
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (97 bp):
GGAGAAGAAGTTCGTAATAAAGAACTTGTTCAACCTTTGCTCGATTCACGGCATTTCGAATCAGC
GACGGCTCACTTGAGGGATTAACATTTCCAAT
Found at i:402252 original size:22 final size:23
Alignment explanation
Indices: 402224--402268 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
402214 TTGGTCCTTG
402224 TTTATGTTATGTTT-TTTTATTC
1 TTTATGTTATGTTTCTTTTATTC
402246 TTTATGTTATGTTTCCTTTTATT
1 TTTATGTTATGTTT-CTTTTATT
402269 TATTTAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 14 0.67
24 7 0.33
ACGTcount: A:0.13, C:0.07, G:0.09, T:0.71
Consensus pattern (23 bp):
TTTATGTTATGTTTCTTTTATTC
Found at i:403711 original size:335 final size:332
Alignment explanation
Indices: 403107--403778 Score: 1048
Period size: 335 Copynumber: 2.0 Consensus size: 332
403097 GTGTAAAATG
403107 TGGATTAAAGGTATAAAGGATTTCATACTGGTTTTGTATCATATTGCGATATGTTGAAATTCTGA
1 TGGATTAAAGGTATAAAGGATTTCATACTGGTTTTGTATCATATTGCGATATGTTGAAATTCTGA
* *
403172 AAATAAGTTCGATAGAATAAGAATCTTTATATGTTTAATATTGTATTTAATGTTGAATTAGAGAT
66 AAATAAGTTCGATAGAATAAGAATATTTATATGTTTAATATTGTATTTAATGGTGAATTAGAGAT
** * * * * *
403237 TGATGATATTAATAGTGCATTTAGGTGTGTTGGTGATGGTAAAAGATTGTTATCAGTTACGCTAA
131 TGATGATATTAATAACGAATTTAGGTGTGTTGCTGATGGTAAAAGATTGGTATCAGTTAAGCCAA
* * *
403302 GAAATAATTGGTACGAAATGGATCCGTATTGTTTTGTAGTGAAATTTGGAGTCTTGTTTGGTTCA
196 GAAATAATTGGTACGAAATGGATCCATAGTGTTTTGTAGTGAAATTTGGAGTCATGTTTGGTTCA
403367 TGATTTAAGTTGAACTTCCAGCCAA-T-TTG-TAGTTGTGCATTGTGATGTGTTCTTGAAGCTCA
261 TGATTTAAGTTGAACTTCCAGCCAATTGTTGTTAGTTGTGCATTGTGATGTGTTCTTGAAGCTCA
403429 AGATTGT
326 AGATTGT
403436 TGGATTAAAGGTAT-AAGGATTTCATACTGGTTTTCGTATCATATTGCGATTATGTTGAAATTCT
1 TGGATTAAAGGTATAAAGGATTTCATACTGGTTTT-GTATCATATTGCGA-TATGTTGAAATTCT
*
403500 GAAATTAAGTTTCGATAGAATAAGAATATTTATATGTTTAATATTGTGATTTAA-GGTGAATTAG
64 GAAAATAAG-TTCGATAGAATAAGAATATTTATATGTTTAATATTGT-ATTTAATGGTGAATTAG
*
403564 AGATTCTTTATGATATTAATAACGAATTTAGGTGTGTTGCTGATGGTATAAAGATTGGTATCAGT
127 AGA---TTGATGATATTAATAACGAATTTAGGTGTGTTGCTGATGGTA-AAAGATTGGTATCAGT
** *
403629 TAAGCCAAGAAATCGTTGGTATGAAATGGATCCATAGTGTTTTGTAGTGAAATTTGGAGTCATGT
188 TAAGCCAAGAAATAATTGGTACGAAATGGATCCATAGTGTTTTGTAGTGAAATTTGGAGTCATGT
*
403694 TTGGTTCATGATTTAAGTTGAACTTCCAGCCAATTTTGTTGTTATTTGTGCATTGTGATGTGTTC
253 TTGGTTCATGATTTAAGTTGAACTTCCAGCCAA--TTGTTGTTAGTTGTGCATTGTGATGTGTTC
*
403759 TTGAATCTCAAGATTGT
316 TTGAAGCTCAAGATTGT
403776 TGG
1 TGG
403779 CGGCTTCCTC
Statistics
Matches: 311, Mismatches: 19, Indels: 15
0.90 0.06 0.04
Matches are distributed among these distances:
328 20 0.06
329 28 0.09
330 22 0.07
331 48 0.15
332 6 0.02
334 37 0.12
335 105 0.34
338 1 0.00
339 3 0.01
340 41 0.13
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.40
Consensus pattern (332 bp):
TGGATTAAAGGTATAAAGGATTTCATACTGGTTTTGTATCATATTGCGATATGTTGAAATTCTGA
AAATAAGTTCGATAGAATAAGAATATTTATATGTTTAATATTGTATTTAATGGTGAATTAGAGAT
TGATGATATTAATAACGAATTTAGGTGTGTTGCTGATGGTAAAAGATTGGTATCAGTTAAGCCAA
GAAATAATTGGTACGAAATGGATCCATAGTGTTTTGTAGTGAAATTTGGAGTCATGTTTGGTTCA
TGATTTAAGTTGAACTTCCAGCCAATTGTTGTTAGTTGTGCATTGTGATGTGTTCTTGAAGCTCA
AGATTGT
Found at i:414878 original size:33 final size:34
Alignment explanation
Indices: 414818--414883 Score: 107
Period size: 33 Copynumber: 1.9 Consensus size: 34
414808 TGCGAACGAC
414818 GACTTTTGATATGAGTCCTCTTAAGGTCCCATGAGT
1 GACTTTTGATATGAG--CTCTTAAGGTCCCATGAGT
414854 GACTTTTGATATGAG-TCTTAAGGTCCCATG
1 GACTTTTGATATGAGCTCTTAAGGTCCCATG
414884 GTTGGATAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
33 15 0.50
36 15 0.50
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (34 bp):
GACTTTTGATATGAGCTCTTAAGGTCCCATGAGT
Found at i:418616 original size:36 final size:36
Alignment explanation
Indices: 418569--418637 Score: 138
Period size: 36 Copynumber: 1.9 Consensus size: 36
418559 TGCGAAGGAC
418569 GACTTTTGATATGAGTCCTCTTAAGGTCCCATGAGT
1 GACTTTTGATATGAGTCCTCTTAAGGTCCCATGAGT
418605 GACTTTTGATATGAGTCCTCTTAAGGTCCCATG
1 GACTTTTGATATGAGTCCTCTTAAGGTCCCATG
418638 GGTGGATAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (36 bp):
GACTTTTGATATGAGTCCTCTTAAGGTCCCATGAGT
Found at i:428304 original size:24 final size:24
Alignment explanation
Indices: 428277--428326 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
428267 CAATTTATTC
428277 AATTTTTAAATAACATTTCTACTA
1 AATTTTTAAATAACATTTCTACTA
*
428301 AATTTTTAAATTACATTTCTACTA
1 AATTTTTAAATAACATTTCTACTA
428325 AA
1 AA
428327 AAGATTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.46
Consensus pattern (24 bp):
AATTTTTAAATAACATTTCTACTA
Found at i:428819 original size:14 final size:14
Alignment explanation
Indices: 428802--428835 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
428792 CCTTGGACCC
*
428802 CGGACCACTATTCT
1 CGGACCACTATCCT
428816 CGGACCACTATCCT
1 CGGACCACTATCCT
428830 CGGACC
1 CGGACC
428836 CAGGACTACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.21, C:0.41, G:0.18, T:0.21
Consensus pattern (14 bp):
CGGACCACTATCCT
Found at i:428820 original size:21 final size:21
Alignment explanation
Indices: 428769--428821 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
428759 GGATATTTTT
*
428769 TATTC-CGGACCCTAGACCAC
1 TATTCTCGGACCCCAGACCAC
* * * *
428789 TGTCCTTGGACCCCGGACCAC
1 TATTCTCGGACCCCAGACCAC
428810 TATTCTCGGACC
1 TATTCTCGGACC
428822 ACTATCCTCG
Statistics
Matches: 24, Mismatches: 8, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
20 3 0.12
21 21 0.88
ACGTcount: A:0.19, C:0.40, G:0.19, T:0.23
Consensus pattern (21 bp):
TATTCTCGGACCCCAGACCAC
Found at i:428856 original size:35 final size:35
Alignment explanation
Indices: 428783--428856 Score: 87
Period size: 35 Copynumber: 2.1 Consensus size: 35
428773 CCGGACCCTA
* * * *
428783 GACCACTGTCCTTGGACCCCGGACCACTATTCTCG
1 GACCACTATCCTCGGACCCAGGACCACTACTCTCG
*
428818 GACCACTATCCTCGGACCCAGGACTACTGACTCT-G
1 GACCACTATCCTCGGACCCAGGACCACT-ACTCTCG
428853 GACC
1 GACC
428857 CCGGGGTCCG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
35 29 0.88
36 4 0.12
ACGTcount: A:0.20, C:0.39, G:0.20, T:0.20
Consensus pattern (35 bp):
GACCACTATCCTCGGACCCAGGACCACTACTCTCG
Found at i:429882 original size:24 final size:24
Alignment explanation
Indices: 429855--429924 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 24
429845 ACATGTTCAT
* *
429855 GAACACATTCGTTAACATATAATC
1 GAACACGTTCGTTAACATATAAAC
* *
429879 GAACACGTTTGTGAACATATAAAC
1 GAACACGTTCGTTAACATATAAAC
429903 GAACACGTTC-TTAAACA-ATAAA
1 GAACACGTTCGTT-AACATATAAA
429925 TAAATGAACA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
23 6 0.15
24 33 0.85
ACGTcount: A:0.44, C:0.19, G:0.11, T:0.26
Consensus pattern (24 bp):
GAACACGTTCGTTAACATATAAAC
Found at i:430980 original size:19 final size:19
Alignment explanation
Indices: 430956--431045 Score: 180
Period size: 19 Copynumber: 4.7 Consensus size: 19
430946 AATGCATTTT
430956 ATGCATCGATGCACATACC
1 ATGCATCGATGCACATACC
430975 ATGCATCGATGCACATACC
1 ATGCATCGATGCACATACC
430994 ATGCATCGATGCACATACC
1 ATGCATCGATGCACATACC
431013 ATGCATCGATGCACATACC
1 ATGCATCGATGCACATACC
431032 ATGCATCGATGCAC
1 ATGCATCGATGCAC
431046 TTAGTGTATT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 71 1.00
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.21
Consensus pattern (19 bp):
ATGCATCGATGCACATACC
Found at i:433082 original size:97 final size:97
Alignment explanation
Indices: 432939--433426 Score: 518
Period size: 97 Copynumber: 5.0 Consensus size: 97
432929 TCCGATAGAG
*
432939 GGAGAAGAAGTTCGTAATGAGAAGAACTTGTTCAACCTTTGTTCGATTCACGGCATTTCGAATCA
1 GGAGAAGAAGTTCGTAAT-A-AAGAACTTGTTCAACCTTTGCTCGATTCACGGCATTTCGAATCA
* *
433004 CCGATGGCTCACTTGAGGGATTAACATTTCCAAT
64 GCGACGGCTCACTTGAGGGATTAACATTTCCAAT
* * *
433038 GGAGAAGAAGTTCGTAATAAAGAACTTGTTCAACCTTTGCTCGATTCATGGCATTTCGAACCAGT
1 GGAGAAGAAGTTCGTAATAAAGAACTTGTTCAACCTTTGCTCGATTCACGGCATTTCGAATCAGC
* * *
433103 GACGGCTCATTTGAAGGATTAATATTTCCAAT
66 GACGGCTCACTTGAGGGATTAACATTTCCAAT
* * * * * *
433135 AGAGAAGAAGTTTGTAATGAATAACTTGTTCAACCTTTTCTCGATTCACGGCATTTTGAATCAGC
1 GGAGAAGAAGTTCGTAATAAAGAACTTGTTCAACCTTTGCTCGATTCACGGCATTTCGAATCAGC
* * *
433200 GAC-GCTTCACTTGAGGGATTAATATTTTCAGT
66 GACGGC-TCACTTGAGGGATTAACATTTCCAAT
* * * * * ** * *
433232 GGATAAGAAGTTCATAATGAAGAACTTATTCAACATTTGCTCGATTCACATCATTTCAAATTAGC
1 GGAGAAGAAGTTCGTAATAAAGAACTTGTTCAACCTTTGCTCGATTCACGGCATTTCGAATCAGC
* ** **
433297 GACGCCTCACACGAGGGAGCAACATTTCC-A-
66 GACGGCTCACTTGAGGGATTAACATTTCCAAT
* * * * * *
433327 GTAG-AGAA-TTCATAATGAGAATAACTTTTTCAACCTTTGCTAGATTCACGGCATTTCGAATTA
1 GGAGAAGAAGTTCGTAAT-A-AAGAACTTGTTCAACCTTTGCTCGATTCACGGCATTTCGAATCA
* * * *
433390 GCAACGCCTCACTTAAGGGATCAACATTTCCAAT
64 GCGACGGCTCACTTGAGGGATTAACATTTCCAAT
433424 GGA
1 GGA
433427 AAGTTAATGA
Statistics
Matches: 324, Mismatches: 59, Indels: 14
0.82 0.15 0.04
Matches are distributed among these distances:
93 8 0.02
94 4 0.01
95 65 0.20
96 3 0.01
97 224 0.69
98 2 0.01
99 18 0.06
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Consensus pattern (97 bp):
GGAGAAGAAGTTCGTAATAAAGAACTTGTTCAACCTTTGCTCGATTCACGGCATTTCGAATCAGC
GACGGCTCACTTGAGGGATTAACATTTCCAAT
Found at i:435139 original size:26 final size:27
Alignment explanation
Indices: 435082--435139 Score: 77
Period size: 26 Copynumber: 2.2 Consensus size: 27
435072 TTGGTCCTTG
435082 TATTTATGTTTATGTTTATTTTTATTC
1 TATTTATGTTTATGTTTATTTTTATTC
*
435109 T-TTTATG-TTATGTTTCCTTTTTATT-
1 TATTTATGTTTATGTTT-ATTTTTATTC
435134 TATTTA
1 TATTTA
435140 ATTAGGTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 9 0.32
26 18 0.64
27 1 0.04
ACGTcount: A:0.17, C:0.05, G:0.07, T:0.71
Consensus pattern (27 bp):
TATTTATGTTTATGTTTATTTTTATTC
Found at i:436577 original size:344 final size:343
Alignment explanation
Indices: 435935--436628 Score: 1201
Period size: 344 Copynumber: 2.0 Consensus size: 343
435925 AAGTGTAAAA
435935 ATTG-TGGATTAAAGGTATAAAGGATTTCATACTGGTTTTCGTATCATATTGCGATTATGTTGAA
1 ATTGTTGGATTAAAGGTATAAAGGATTTCATACTGGTTTTCGTATCATATTGCGATTATGTTGAA
* * *
435999 ATTCTGAAAATTAAGTTTTGATAGAATAAGAATCTTTATATGTTTAATATTGTTATTTAATGTTG
66 ATTCTGAAAATTAAGTTTCGATAGAATAAGAATATTTATATGTTTAATATTGTGATTTAATGTTG
** * * *
436064 AATTAGAGATCTTGATGATATTAATAGTGCATTTAGGTGTTGTTGGTGATGGTATAAAGATTGTT
131 AATTAGAGATCTTGATGATATTAATAACGAATTTAGGTGTTGTTGCTGATGGTATAAAGATTGGT
* * * *
436129 ATCAGTTACGCTAAGAAATAATTGGTACGAAATGGATCCGTATTGTTTTGTAGTGAAATTTGGAG
196 ATCAGTTAAGCCAAGAAATAATTGGTACGAAATGGATCCATAGTGTTTTGTAGTGAAATTTGGAG
*
436194 TCTTGTTTGGTTCATGATTTAAGTTGAACTTCCAGCCAATTTTGTAGTTATTTGTGCATTGTGAT
261 TCATGTTTGGTTCATGATTTAAGTTGAACTTCCAGCCAATTTTGTAGTTATTTGTGCATTGTGAT
436259 GTGTTCTTGAAGCTCAAG
326 GTGTTCTTGAAGCTCAAG
436277 ATTGTTGGATTAAAGGTATAAAGGATTTCATACTGGTTTTCGTATCATATTGCGATTATGTTGAA
1 ATTGTTGGATTAAAGGTATAAAGGATTTCATACTGGTTTTCGTATCATATTGCGATTATGTTGAA
436342 ATTCTGAAAATTAAGTTTCGATAGAATAAGAATATTTATATGTTTAATATTGTGATTTAATGTTG
66 ATTCTGAAAATTAAGTTTCGATAGAATAAGAATATTTATATGTTTAATATTGTGATTTAATGTTG
*
436407 AATTAGAGATTCTTTATGATATTAATAACGAATTTAGGTGTTGTTGCTGATGGTATAAAGATTGG
131 AATTAGAGA-TCTTGATGATATTAATAACGAATTTAGGTGTTGTTGCTGATGGTATAAAGATTGG
** *
436472 TATCAGTTAAGCCAAGAAATCGTTGGTATGAAATGGATCCATAGTGTTTTGTAGTGAAATTTGGA
195 TATCAGTTAAGCCAAGAAATAATTGGTACGAAATGGATCCATAGTGTTTTGTAGTGAAATTTGGA
*
436537 GTCATGTTTGGTTCATGATTTAAGTTGAACTTCCAGCCAATTTTGTTGTTATTTGTGCATTGTGA
260 GTCATGTTTGGTTCATGATTTAAGTTGAACTTCCAGCCAATTTTGTAGTTATTTGTGCATTGTGA
*
436602 TGTGTTCTTGAATCTCAAG
325 TGTGTTCTTGAAGCTCAAG
436621 ATTGTTGG
1 ATTGTTGG
436629 CGGCTTCCTC
Statistics
Matches: 331, Mismatches: 19, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
342 4 0.01
343 131 0.40
344 196 0.59
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.42
Consensus pattern (343 bp):
ATTGTTGGATTAAAGGTATAAAGGATTTCATACTGGTTTTCGTATCATATTGCGATTATGTTGAA
ATTCTGAAAATTAAGTTTCGATAGAATAAGAATATTTATATGTTTAATATTGTGATTTAATGTTG
AATTAGAGATCTTGATGATATTAATAACGAATTTAGGTGTTGTTGCTGATGGTATAAAGATTGGT
ATCAGTTAAGCCAAGAAATAATTGGTACGAAATGGATCCATAGTGTTTTGTAGTGAAATTTGGAG
TCATGTTTGGTTCATGATTTAAGTTGAACTTCCAGCCAATTTTGTAGTTATTTGTGCATTGTGAT
GTGTTCTTGAAGCTCAAG
Found at i:443779 original size:20 final size:20
Alignment explanation
Indices: 443731--443786 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
443721 TCGATGCACC
*
443731 AGTGTATGGATACACTGCAT
1 AGTGTATGGATACACTGCAG
*
443751 AGTGCATGGATACACTGCAG
1 AGTGTATGGATACACTGCAG
* *
443771 GGTGTATGGATGCACT
1 AGTGTATGGATACACT
443787 TTGACACCCT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.27
Consensus pattern (20 bp):
AGTGTATGGATACACTGCAG
Found at i:444033 original size:21 final size:19
Alignment explanation
Indices: 444007--444066 Score: 77
Period size: 18 Copynumber: 3.1 Consensus size: 19
443997 AAATGTTTAA
*
444007 TAAAAAAGATACCAATTGT
1 TAAAAAAGATATCAATTGT
*
444026 TAACAAAATGATATCGATTGT
1 TAA-AAAA-GATATCAATTGT
444047 T-AAAAAGATATCAATTGT
1 TAAAAAAGATATCAATTGT
444065 TA
1 TA
444067 CCAATTGTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
18 12 0.34
19 7 0.20
20 5 0.14
21 11 0.31
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.32
Consensus pattern (19 bp):
TAAAAAAGATATCAATTGT
Found at i:446692 original size:20 final size:20
Alignment explanation
Indices: 446664--446714 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
446654 GCACTAGTGT
*
446664 ATGGCTACACTGCAGAGTCC
1 ATGGATACACTGCAGAGTCC
* **
446684 ATGGATACACTGCAGTGTGT
1 ATGGATACACTGCAGAGTCC
446704 ATGGATACACT
1 ATGGATACACT
446715 TTGACACCCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.25
Consensus pattern (20 bp):
ATGGATACACTGCAGAGTCC
Found at i:454536 original size:21 final size:20
Alignment explanation
Indices: 454519--454569 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 20
454509 TTGTATTTGC
454519 ATTT-GCATTACATGTATTT
1 ATTTAGCATTACATGTATTT
454538 ATTTAAGCATTACATGTATTT
1 ATTT-AGCATTACATGTATTT
454559 ATTTAAGCATT
1 ATTT-AGCATT
454570 TTACATGCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 4 0.13
21 26 0.87
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.49
Consensus pattern (20 bp):
ATTTAGCATTACATGTATTT
Found at i:456209 original size:22 final size:22
Alignment explanation
Indices: 456192--456258 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
456182 CTCGTATAAA
456192 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
456214 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
456236 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
456258 T
1 T
456259 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:456519 original size:30 final size:31
Alignment explanation
Indices: 456478--456537 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
456468 TAGACATAGT
*
456478 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
*
456508 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATACCTTTAACACATAGTGCATAT
456538 AACTTTTCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:456595 original size:29 final size:29
Alignment explanation
Indices: 456553--456622 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
456543 TTCTGCATAA
**
456553 TCATGTCATGTAATACATACAATATGAAT
1 TCATGTCATGTAATACATACAATACAAAT
**
456582 TCATGTCATGTAATACATTTAATACAAAT
1 TCATGTCATGTAATACATACAATACAAAT
456611 TCATGTCATGTA
1 TCATGTCATGTA
456623 TCATAATATG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (29 bp):
TCATGTCATGTAATACATACAATACAAAT
Found at i:457044 original size:66 final size:66
Alignment explanation
Indices: 456929--457077 Score: 201
Period size: 66 Copynumber: 2.2 Consensus size: 66
456919 TTTTCTCATG
* * *
456929 GGGGAATCGGTTCCTCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTTATATACGAT
1 GGGGTATCGGTTCC-CCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCAT-TACGAT
456994 G-A
64 GAA
** * * *
456996 GGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCTTGCATTCTGGAAATTCATTTCGTTGA
1 GGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATTACGATGA
457061 A
66 A
457062 GGGGTATCGGTTCCCC
1 GGGGTATCGGTTCCCC
457078 TTGAATGGGT
Statistics
Matches: 73, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
65 5 0.07
66 55 0.75
67 13 0.18
ACGTcount: A:0.17, C:0.26, G:0.27, T:0.30
Consensus pattern (66 bp):
GGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATTACGATGA
A
Found at i:457087 original size:21 final size:21
Alignment explanation
Indices: 457057--457099 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
457047 ATTCATTTCG
* *
457057 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
457078 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
457099 T
1 T
457100 AACCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:463155 original size:22 final size:22
Alignment explanation
Indices: 463138--463204 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
463128 CTCGTATAAA
463138 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
463160 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
463182 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
463204 T
1 T
463205 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:463465 original size:30 final size:31
Alignment explanation
Indices: 463424--463483 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
463414 TAGACATAGT
*
463424 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
*
463454 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATACCTTTAACACATAGTGCATAT
463484 AACTTTTCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:463541 original size:29 final size:29
Alignment explanation
Indices: 463499--463568 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
463489 TTCTGCATAA
**
463499 TCATGTCATGTAATACATACAATATGAAT
1 TCATGTCATGTAATACATACAATACAAAT
**
463528 TCATGTCATGTAATACATTTAATACAAAT
1 TCATGTCATGTAATACATACAATACAAAT
463557 TCATGTCATGTA
1 TCATGTCATGTA
463569 TCATAATATG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (29 bp):
TCATGTCATGTAATACATACAATACAAAT
Found at i:464034 original size:21 final size:21
Alignment explanation
Indices: 464004--464046 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
463994 ATTCATTTCG
* *
464004 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
464025 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
464046 T
1 T
464047 AACCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:464046 original size:67 final size:67
Alignment explanation
Indices: 463875--464024 Score: 203
Period size: 67 Copynumber: 2.2 Consensus size: 67
463865 TTTTCTCATG
* * *
463875 GGGGAATCGGTTCCTCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTTATATACGAT
1 GGGGTATCGGTTCC-CCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
*
463940 GAG
65 GAA
** * * *
463943 GGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCTTGCATTCTGGAAATTCAT-TTCGTTG
1 GGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATATACGATG
464007 AA
66 AA
464009 GGGGTATCGGTTCCCC
1 GGGGTATCGGTTCCCC
464025 TTGAATGGGT
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
66 22 0.30
67 38 0.52
68 13 0.18
ACGTcount: A:0.17, C:0.25, G:0.27, T:0.30
Consensus pattern (67 bp):
GGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATATACGATG
AA
Found at i:468050 original size:13 final size:13
Alignment explanation
Indices: 468032--468056 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
468022 TGAAGCAAAT
468032 CCATCAGTAAGTG
1 CCATCAGTAAGTG
468045 CCATCAGTAAGT
1 CCATCAGTAAGT
468057 CTTTCGAGCA
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:0.24, G:0.20, T:0.24
Consensus pattern (13 bp):
CCATCAGTAAGTG
Found at i:468105 original size:42 final size:42
Alignment explanation
Indices: 468044--468313 Score: 344
Period size: 42 Copynumber: 6.5 Consensus size: 42
468034 ATCAGTAAGT
*
468044 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGG
1 GCCATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTCGG
* * *
468086 GTCATCAATAAGTCTTTCGAGCATGATGATGAAGTCCTTCGG
1 GCCATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTCGG
* *
468128 GCCATCAATAAGTCTTTCGAGCATGATGATGAAGTCCTTCGG
1 GCCATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTCGG
* *
468170 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGG
1 GCCATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTCGG
* * *
468212 GCCATCAGTAAGTCTTTTGAGCATGATGATTAAATCATTCGG
1 GCCATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTCGG
* *** * * *
468254 GTCATTTTTTAGTCTTTCGAGCAAGAT-AATAAATCCTTCGG
1 GCCATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTCGG
* * *
468295 GTCATCCATAAGTCCTTCG
1 GCCATCAATAAGTCTTTCG
468314 GGTAGGATGT
Statistics
Matches: 204, Mismatches: 24, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
41 26 0.13
42 178 0.87
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (42 bp):
GCCATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTCGG
Found at i:468801 original size:53 final size:53
Alignment explanation
Indices: 468734--468881 Score: 163
Period size: 53 Copynumber: 2.8 Consensus size: 53
468724 AGAATCACAC
* * *
468734 CAGAAGAATGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAG
1 CAGAAGATTATTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCAAACCCGTAAG
* * * ***
468787 CAGAAGATTATTCGAATTCTACTCCCTGAAGCAATAGGGAGCAAATCCGTTTT
1 CAGAAGATTATTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCAAACCCGTAAG
* * *
468840 TAGAAGATTATTCGAGTTCCTTAATCCATGAA-CAAGAGGGAG
1 CAGAAGATTATTCGAGTT-C-TACTCCCTGAAGCAAGAGGGAG
468882 TGGATCCGTC
Statistics
Matches: 79, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
53 60 0.76
54 10 0.13
55 9 0.11
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.24
Consensus pattern (53 bp):
CAGAAGATTATTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCAAACCCGTAAG
Found at i:474618 original size:16 final size:16
Alignment explanation
Indices: 474585--474618 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
474575 TTTACCGGAT
**
474585 AAAAAACCGGTTTGAA
1 AAAAAACCGGTTAAAA
474601 AAAAAACCGGTTAAAA
1 AAAAAACCGGTTAAAA
474617 AA
1 AA
474619 CCGGTTTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.59, C:0.12, G:0.15, T:0.15
Consensus pattern (16 bp):
AAAAAACCGGTTAAAA
Found at i:476953 original size:21 final size:21
Alignment explanation
Indices: 476929--476968 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
476919 TTTATTTTAT
476929 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
476950 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
476969 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:477016 original size:33 final size:33
Alignment explanation
Indices: 476963--477061 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
476953 TTTGTTTCAA
476963 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
476995 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
477028 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
477061 T
1 T
477062 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:477090 original size:13 final size:13
Alignment explanation
Indices: 477047--477101 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
477037 TTGGAAGTAT
477047 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
477060 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
477074 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
477087 TTAAGTATTTGAA
1 TTAAGTATTTCAA
477100 TT
1 TT
477102 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:477323 original size:21 final size:21
Alignment explanation
Indices: 477297--477346 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
477287 TGGAGCGTGG
477297 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTACCCTCTCATA
**
477318 GGGAATCGGTTTCCTCTCATA
1 GGGAATCGGTACCCTCTCATA
477339 GGGAATCG
1 GGGAATCG
477347 ATTCCCTAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.22, C:0.24, G:0.28, T:0.26
Consensus pattern (21 bp):
GGGAATCGGTACCCTCTCATA
Found at i:477691 original size:15 final size:17
Alignment explanation
Indices: 477665--477696 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
477655 TTCTATGAGA
477665 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
477681 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
477697 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:478269 original size:9 final size:9
Alignment explanation
Indices: 478255--478281 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
478245 TGAGATTTTA
478255 ATTTTATTT
1 ATTTTATTT
478264 ATTTTATTT
1 ATTTTATTT
478273 ATTTTATTT
1 ATTTTATTT
478282 GGAGTATGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (9 bp):
ATTTTATTT
Found at i:478806 original size:2 final size:2
Alignment explanation
Indices: 478799--478836 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
478789 GAAATTCATA
478799 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
478837 TGTATTGGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:486034 original size:14 final size:14
Alignment explanation
Indices: 486015--486042 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
486005 TCTATTTAGA
486015 AAAATGATACTAAT
1 AAAATGATACTAAT
486029 AAAATGATACTAAT
1 AAAATGATACTAAT
486043 CTCTCTCTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (14 bp):
AAAATGATACTAAT
Found at i:493425 original size:45 final size:45
Alignment explanation
Indices: 493361--493451 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 45
493351 TTATCATGCA
* * *
493361 CATCACATTACAAATTTATGGTAATTTCTATTATTATTCATTCTT
1 CATCACATTACAAATTTATGATAATGTCTATTATCATTCATTCTT
*
493406 CATCATATTACAAATTTATGATAATGTCTATTATCATTCATTCTT
1 CATCACATTACAAATTTATGATAATGTCTATTATCATTCATTCTT
493451 C
1 C
493452 TGTAGTTTCA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.32, C:0.16, G:0.04, T:0.47
Consensus pattern (45 bp):
CATCACATTACAAATTTATGATAATGTCTATTATCATTCATTCTT
Found at i:494404 original size:22 final size:21
Alignment explanation
Indices: 494358--494410 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
494348 ATAATTATTT
*
494358 AAAAAATTAAATAAAAATACCA
1 AAAAAATTTAATAAAAATA-CA
*
494380 AAAACATTTAATAAAAAATA-A
1 AAAAAATTTAAT-AAAAATACA
494401 AAAAAATTTA
1 AAAAAATTTA
494411 GGTTGGACCG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 10 0.37
22 10 0.37
23 7 0.26
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAAAATTTAATAAAAATACA
Found at i:494405 original size:23 final size:21
Alignment explanation
Indices: 494358--494406 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
494348 ATAATTATTT
*
494358 AAAAAATTAAATAAAAATACCA
1 AAAAAATTAAATAAAAATA-AA
* *
494380 AAAACATTTAATAAAAAATAAA
1 AAAAAATTAAAT-AAAAATAAA
494402 AAAAA
1 AAAAA
494407 TTTAGGTTGG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATAAA
Found at i:497960 original size:17 final size:17
Alignment explanation
Indices: 497938--497976 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
497928 ACAAGAATCT
* *
497938 TCTTCCGCCTTACTGCC
1 TCTTCCGCCTAACAGCC
497955 TCTTCCGCCTAACAGCC
1 TCTTCCGCCTAACAGCC
497972 TCTTC
1 TCTTC
497977 TAGCTCGACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.10, C:0.46, G:0.10, T:0.33
Consensus pattern (17 bp):
TCTTCCGCCTAACAGCC
Found at i:499954 original size:176 final size:177
Alignment explanation
Indices: 499656--500010 Score: 676
Period size: 176 Copynumber: 2.0 Consensus size: 177
499646 AATCTTATGC
499656 ATCTTATTAATGAAGTATAAGGCACTCTTTTCCTCCTTCCTTTGATAAAGGAACTCATTGAGTTC
1 ATCTTATTAATGAAGTATAAGGCACTCTTTTCCTCCTTCCTTTGATAAAGGAACTC--T-AGTTC
499721 CTCATCATGAAGGGGGTTTTTAGTGAGGCCTTCAATTCCTATCCAAAAAAAATAGTACAACAGAT
63 CTCATCATGAAGGGGGTTTTTAGTGAGGCCTTCAATTCCTATCCAAAAAAAATAGTACAACAGAT
499786 TGTTTATCCCAACCAAAAATCTTAACCCCTACAACAGAAAGCACCCAAAA
128 TGTTTATCCCAACCAAAAATCTTAACCCCTACAACAGAAAGCACCCAAAA
499836 ATCTTATTAATGAAGTATAAGGCACTCTTTTCCTCCTTCCTTTGATAAAGGAACTC-AGTTCCTC
1 ATCTTATTAATGAAGTATAAGGCACTCTTTTCCTCCTTCCTTTGATAAAGGAACTCTAGTTCCTC
499900 ATCATGAAGGGGGTTTTTAGTGAGGCCTTCAATTCCTATCCAAAAAAAATAGTACAACAGATTGT
66 ATCATGAAGGGGGTTTTTAGTGAGGCCTTCAATTCCTATCCAAAAAAAATAGTACAACAGATTGT
499965 TTATCCCAACCAAAAATCTTAACCCCTACAACAGAAAGCACCCAAA
131 TTATCCCAACCAAAAATCTTAACCCCTACAACAGAAAGCACCCAAA
500011 TCCTAGATAG
Statistics
Matches: 175, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
176 119 0.68
180 56 0.32
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.29
Consensus pattern (177 bp):
ATCTTATTAATGAAGTATAAGGCACTCTTTTCCTCCTTCCTTTGATAAAGGAACTCTAGTTCCTC
ATCATGAAGGGGGTTTTTAGTGAGGCCTTCAATTCCTATCCAAAAAAAATAGTACAACAGATTGT
TTATCCCAACCAAAAATCTTAACCCCTACAACAGAAAGCACCCAAAA
Found at i:502496 original size:18 final size:18
Alignment explanation
Indices: 502473--502507 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
502463 GAGTACAAGC
502473 TATTGTAACTAAGAGGGT
1 TATTGTAACTAAGAGGGT
502491 TATTGTAACTAAGAGGG
1 TATTGTAACTAAGAGGG
502508 CTTCTGTGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.06, G:0.29, T:0.31
Consensus pattern (18 bp):
TATTGTAACTAAGAGGGT
Found at i:503694 original size:18 final size:19
Alignment explanation
Indices: 503666--503702 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
503656 AATACAACAT
*
503666 TCCGAGTAATCTTATTCCC
1 TCCGAGTAATCCTATTCCC
503685 TCCG-GTAATCCTATTCCC
1 TCCGAGTAATCCTATTCCC
503703 GTTAGTAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.19, C:0.35, G:0.11, T:0.35
Consensus pattern (19 bp):
TCCGAGTAATCCTATTCCC
Found at i:507888 original size:28 final size:28
Alignment explanation
Indices: 507856--507978 Score: 110
Period size: 26 Copynumber: 4.5 Consensus size: 28
507846 TTTGAAAAGG
*
507856 ACATAATTTTAAATAAACAAACACCAAC
1 ACATAATTTTAAATAAACGAACACCAAC
* *
507884 ACATATAATTTTAAATAAATGAGCA-CAA-
1 AC--ATAATTTTAAATAAACGAACACCAAC
* * *
507912 ACATAATTTTAAATAAATGAGCACGAAC
1 ACATAATTTTAAATAAACGAACACCAAC
* * **
507940 ACATAATTTTAAATTAACTAACATTAAC
1 ACATAATTTTAAATAAACGAACACCAAC
507968 AC--AATTTTAAA
1 ACATAATTTTAAA
507979 ATTCTAAAGG
Statistics
Matches: 81, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
26 30 0.37
27 2 0.02
28 28 0.35
29 3 0.04
30 18 0.22
ACGTcount: A:0.53, C:0.15, G:0.04, T:0.28
Consensus pattern (28 bp):
ACATAATTTTAAATAAACGAACACCAAC
Found at i:507917 original size:26 final size:27
Alignment explanation
Indices: 507856--507953 Score: 126
Period size: 26 Copynumber: 3.5 Consensus size: 27
507846 TTTGAAAAGG
** *
507856 ACATAATTTTAAATAAACAAACACCAAC
1 ACATAATTTTAAATAAATGAGCA-CAAC
507884 ACATATAATTTTAAATAAATGAGCACAA-
1 AC--ATAATTTTAAATAAATGAGCACAAC
507912 ACATAATTTTAAATAAATGAGCACGAAC
1 ACATAATTTTAAATAAATGAGCAC-AAC
507940 ACATAATTTTAAAT
1 ACATAATTTTAAAT
507954 TAACTAACAT
Statistics
Matches: 63, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
26 22 0.35
27 2 0.03
28 18 0.29
29 3 0.05
30 18 0.29
ACGTcount: A:0.53, C:0.14, G:0.05, T:0.28
Consensus pattern (27 bp):
ACATAATTTTAAATAAATGAGCACAAC
Found at i:512893 original size:16 final size:17
Alignment explanation
Indices: 512872--512906 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
512862 ACTCGATATC
512872 ATTATATTA-ATTTTAT
1 ATTATATTATATTTTAT
512888 ATTATATTATATTTTAT
1 ATTATATTATATTTTAT
512905 AT
1 AT
512907 GAATAAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
ATTATATTATATTTTAT
Found at i:513896 original size:31 final size:31
Alignment explanation
Indices: 513861--513933 Score: 110
Period size: 31 Copynumber: 2.4 Consensus size: 31
513851 TATTATAATG
*
513861 ATTAATCGACCGTTTAAACTTAAAAGATACA
1 ATTAATCGACCGTTGAAACTTAAAAGATACA
* * *
513892 ATTAATCAACCGTTGAAACTTAAATGATACG
1 ATTAATCGACCGTTGAAACTTAAAAGATACA
513923 ATTAATCGACC
1 ATTAATCGACC
513934 ATGAATACCT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.29
Consensus pattern (31 bp):
ATTAATCGACCGTTGAAACTTAAAAGATACA
Found at i:516411 original size:2 final size:2
Alignment explanation
Indices: 516404--516438 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
516394 ATGCATAAAT
516404 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
516439 TATTGACGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:516785 original size:16 final size:16
Alignment explanation
Indices: 516764--516795 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
516754 TATTCGGGTC
516764 GGGTCAAGTAGGGTGA
1 GGGTCAAGTAGGGTGA
516780 GGGTCAAGTAGGGTGA
1 GGGTCAAGTAGGGTGA
516796 AACATTGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.06, G:0.50, T:0.19
Consensus pattern (16 bp):
GGGTCAAGTAGGGTGA
Found at i:516984 original size:30 final size:30
Alignment explanation
Indices: 516923--516984 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
516913 TATGAGAACA
*
516923 TTTATTGAGAATAAAATAAAATAAAATATT
1 TTTATTGAGAATAAAATAAAATAAAACATT
* * *
516953 TTTATTGATAA-AAATTAAATTAATAACATT
1 TTTATTGAGAATAAAATAAAATAA-AACATT
516983 TT
1 TT
516985 AAAAAATGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.42
Consensus pattern (30 bp):
TTTATTGAGAATAAAATAAAATAAAACATT
Found at i:522235 original size:17 final size:17
Alignment explanation
Indices: 522210--522261 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
522200 CCGGTTTCGG
522210 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
* *
522227 TTTTTAAAAATCCGG-T
1 TTTTAAAAAAACCGGTT
* * *
522243 TATAAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
522260 TT
1 TT
522262 AATATTATTA
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
16 11 0.42
17 15 0.58
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.37
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:522341 original size:32 final size:33
Alignment explanation
Indices: 522305--522413 Score: 170
Period size: 33 Copynumber: 3.4 Consensus size: 33
522295 ACAAAGTTTA
*
522305 CGAT-AATTGAAATACTTAAATACTTCCAAGTT
1 CGATAAATTGAAATACTTAAAAACTTCCAAGTT
*
522337 CGATAAATTAAAATACTTAAAAACTTCCAAGTT
1 CGATAAATTGAAATACTTAAAAACTTCCAAGTT
*
522370 CGATAAATTCAAATACTTAAAAACTT-CAAGTT
1 CGATAAATTGAAATACTTAAAAACTTCCAAGTT
522402 CGAT-AATTGAAA
1 CGATAAATTGAAA
522414 CAAAGTTTAC
Statistics
Matches: 72, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
31 7 0.10
32 14 0.19
33 51 0.71
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (33 bp):
CGATAAATTGAAATACTTAAAAACTTCCAAGTT
Found at i:522426 original size:21 final size:21
Alignment explanation
Indices: 522402--522443 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
522392 ACTTCAAGTT
*
522402 CGATAATTGAAACAAAGTTTA
1 CGATAATTAAAACAAAGTTTA
*
522423 CGATAATTAAAATAAAGTTTA
1 CGATAATTAAAACAAAGTTTA
522444 AAAATAAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.31
Consensus pattern (21 bp):
CGATAATTAAAACAAAGTTTA
Found at i:524576 original size:23 final size:25
Alignment explanation
Indices: 524532--524577 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
524522 AAATTACAAA
*
524532 AATAAGATTTGAGAGAGTGTTGTGT
1 AATAAGATTTGAGAGAGAGTTGTGT
524557 AATAAGATTTGAGA-A-AGTTGT
1 AATAAGATTTGAGAGAGAGTTGT
524578 AATTAACCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 1 0.05
25 14 0.70
ACGTcount: A:0.37, C:0.00, G:0.28, T:0.35
Consensus pattern (25 bp):
AATAAGATTTGAGAGAGAGTTGTGT
Found at i:524753 original size:23 final size:24
Alignment explanation
Indices: 524703--524752 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 24
524693 TTTTAAACCC
*
524703 AAACCGATTTTTTTTTTCCGGATAA
1 AAACCGA-TTTTTTTATCCGGATAA
524728 AAACCGA-TTTTTTATCCGG-TAA
1 AAACCGATTTTTTTATCCGGATAA
524750 AAA
1 AAA
524753 AACCGGTCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 6 0.25
23 11 0.46
25 7 0.29
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (24 bp):
AAACCGATTTTTTTATCCGGATAA
Found at i:525214 original size:27 final size:25
Alignment explanation
Indices: 525171--525259 Score: 110
Period size: 24 Copynumber: 3.6 Consensus size: 25
525161 AAATTGAACG
* *
525171 ACCGATTTTTTT-ACCGGATTAAAA
1 ACCGGTTTTTTTAACCGGATAAAAA
525195 ACCGGTTTTTTTGAAACCGGATAAAAA
1 ACCGGTTTTTTT--AACCGGATAAAAA
* *
525222 ACC-GATTTTTTATCCGGATAAAAA
1 ACCGGTTTTTTTAACCGGATAAAAA
525246 ACCGGTTTTTTTAA
1 ACCGGTTTTTTTAA
525260 AAAACTGATT
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
24 26 0.47
25 8 0.15
26 7 0.13
27 14 0.25
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.36
Consensus pattern (25 bp):
ACCGGTTTTTTTAACCGGATAAAAA
Found at i:525262 original size:17 final size:17
Alignment explanation
Indices: 525240--525312 Score: 65
Period size: 17 Copynumber: 4.0 Consensus size: 17
525230 TTTATCCGGA
525240 TAAAAAACCGGTTTTTT
1 TAAAAAACCGGTTTTTT
* *
525257 TAAAAAACTGATTTTTT
1 TAAAAAACCGGTTTTTT
525274 ATCCGAAAAAATCCGGTTTTTT
1 -T---AAAAAA-CCGGTTTTTT
* *
525296 TTAAAAACCAGTTTTTT
1 TAAAAAACCGGTTTTTT
525313 ACAAACCGAA
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
17 24 0.53
18 6 0.13
21 7 0.16
22 8 0.18
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (17 bp):
TAAAAAACCGGTTTTTT
Found at i:525295 original size:39 final size:41
Alignment explanation
Indices: 525216--525313 Score: 139
Period size: 39 Copynumber: 2.4 Consensus size: 41
525206 TGAAACCGGA
525216 TAAAAAACCGATTTTTTATCCGGATAAAAAACCGGTTTTTT
1 TAAAAAACCGATTTTTTATCCGGATAAAAAACCGGTTTTTT
* *
525257 TAAAAAACTGATTTTTTATCC-GA-AAAAATCCGGTTTTTT
1 TAAAAAACCGATTTTTTATCCGGATAAAAAACCGGTTTTTT
*
525296 TTAAAAACC-AGTTTTTTA
1 TAAAAAACCGA-TTTTTTA
525314 CAAACCGAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
38 1 0.02
39 29 0.56
40 2 0.04
41 20 0.38
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (41 bp):
TAAAAAACCGATTTTTTATCCGGATAAAAAACCGGTTTTTT
Found at i:532738 original size:14 final size:14
Alignment explanation
Indices: 532719--532776 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
532709 AATCATCATA
532719 TATTATTTTATTAT
1 TATTATTTTATTAT
532733 TATTA-TTTATGTAT
1 TATTATTTTAT-TAT
* *
532747 GATGTGACATTTATTAT
1 TAT-T-A-TTTTATTAT
532764 TATTATTTTATTA
1 TATTATTTTATTA
532777 ATATATGATT
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
13 5 0.14
14 17 0.47
15 2 0.06
16 2 0.06
17 5 0.14
18 5 0.14
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.62
Consensus pattern (14 bp):
TATTATTTTATTAT
Found at i:533868 original size:14 final size:14
Alignment explanation
Indices: 533849--533875 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
533839 ATTTTTTATT
533849 TCATTTTATTTTAG
1 TCATTTTATTTTAG
533863 TCATTTTATTTTA
1 TCATTTTATTTTA
533876 ATTATTATCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.07, G:0.04, T:0.67
Consensus pattern (14 bp):
TCATTTTATTTTAG
Found at i:535564 original size:19 final size:19
Alignment explanation
Indices: 535514--535690 Score: 104
Period size: 19 Copynumber: 8.7 Consensus size: 19
535504 AATACAACGG
*
535514 TATTTTTTTATTTCAAATT
1 TATTTATTTATTTCAAATT
535533 TATTATGGATTTATTTCAAATT
1 TATT-T--ATTTATTTCAAATT
* *
535555 TATTTGTTTATTT-ATTTATT
1 TATTTATTTATTTCA--AATT
**
535575 TATTTATTTATTTTGGACTTATT
1 TATTTATTTA-TTT---CAAATT
*
535598 TGTTTATTTATTTCAAATT
1 TATTTATTTATTTCAAATT
*
535617 TATTTATTTATTTTGGACATATT
1 TATTTATTTA-TTT---CAAATT
* *** *
535640 TATTTATTCAACACGAATT
1 TATTTATTTATTTCAAATT
*
535659 CATTTATTTATTTCAAATT
1 TATTTATTTATTTCAAATT
*
535678 TATTTGTTTATTT
1 TATTTATTTATTT
535691 ATTTGTTTAG
Statistics
Matches: 120, Mismatches: 24, Indels: 28
0.70 0.14 0.16
Matches are distributed among these distances:
18 1 0.01
19 52 0.43
20 16 0.13
21 4 0.03
22 20 0.17
23 27 0.22
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.62
Consensus pattern (19 bp):
TATTTATTTATTTCAAATT
Found at i:535571 original size:23 final size:23
Alignment explanation
Indices: 535520--535629 Score: 94
Period size: 23 Copynumber: 5.1 Consensus size: 23
535510 ACGGTATTTT
*
535520 TTTATTTCAAATTTATTATG--GA
1 TTTATTTCAAATTTATT-TGTTTA
535542 TTTATTTCAAATTTATTTGTTTA
1 TTTATTTCAAATTTATTTGTTTA
535565 TTTATTT---ATTTA----TTTA
1 TTTATTTCAAATTTATTTGTTTA
*** *
535581 TTTATTTTGGACTTATTTGTTTA
1 TTTATTTCAAATTTATTTGTTTA
*
535604 TTTATTTCAAATTTATTTATTTA
1 TTTATTTCAAATTTATTTGTTTA
535627 TTT
1 TTT
535630 TGGACATATT
Statistics
Matches: 72, Mismatches: 7, Indels: 17
0.75 0.07 0.18
Matches are distributed among these distances:
16 11 0.15
19 4 0.06
20 5 0.07
21 2 0.03
22 17 0.24
23 33 0.46
ACGTcount: A:0.25, C:0.04, G:0.05, T:0.65
Consensus pattern (23 bp):
TTTATTTCAAATTTATTTGTTTA
Done.