Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008464.1 Hibiscus syriacus cultivar Beakdansim tig00111277_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: 593006
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:321438 original size:42 final size:42
Alignment explanation
Indices: 321392--321502 Score: 204
Period size: 42 Copynumber: 2.6 Consensus size: 42
321382 CATGTTACTA
*
321392 GGAAAACGAATTACGTGAAACAAACACGGGAAAACGTTTTCC
1 GGAAAACGAATTACGTGAAACAAACACGGGAAAACATTTTCC
321434 GGAAAACGAATTACGTGAAACAAACACGGGAAAACATTTTCC
1 GGAAAACGAATTACGTGAAACAAACACGGGAAAACATTTTCC
*
321476 GAAAAACGAATTACGTGAAACAAACAC
1 GGAAAACGAATTACGTGAAACAAACAC
321503 TGAAATTCGG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 67 1.00
ACGTcount: A:0.47, C:0.19, G:0.19, T:0.15
Consensus pattern (42 bp):
GGAAAACGAATTACGTGAAACAAACACGGGAAAACATTTTCC
Found at i:325792 original size:24 final size:24
Alignment explanation
Indices: 325765--325848 Score: 57
Period size: 24 Copynumber: 3.4 Consensus size: 24
325755 CAAAGCTGGG
*
325765 CTCATACTTTGAATTTCCATGAAT
1 CTCATAATTTGAATTTCCATGAAT
* * *
325789 CTCAAAAATTT-AA-TTCAAT-ATT
1 CTC-ATAATTTGAATTTCCATGAAT
*
325811 CGGCTCATAGTTTGAATTTCCATGAAT
1 ---CTCATAATTTGAATTTCCATGAAT
325838 CTCATATATTT
1 CTCATA-ATTT
325849 TTTTCTAATT
Statistics
Matches: 43, Mismatches: 9, Indels: 15
0.64 0.13 0.22
Matches are distributed among these distances:
22 2 0.05
23 5 0.12
24 16 0.37
25 13 0.30
26 5 0.12
27 2 0.05
ACGTcount: A:0.32, C:0.18, G:0.08, T:0.42
Consensus pattern (24 bp):
CTCATAATTTGAATTTCCATGAAT
Found at i:327953 original size:10 final size:10
Alignment explanation
Indices: 327938--328038 Score: 67
Period size: 10 Copynumber: 9.1 Consensus size: 10
327928 GTGTTTGTGT
327938 TGTTCGTTTA
1 TGTTCGTTTA
327948 TGTTCGTTTA
1 TGTTCGTTTA
*
327958 TTGTGTTAGTTTA
1 ---TGTTCGTTTA
*
327971 TGTTCATTTATTA
1 TGTTC--GT-TTA
327984 TGTTCGTTTA
1 TGTTCGTTTA
*
327994 TGTTCGTTCGTTTG
1 ---T-GTTCGTTTA
*
328008 TGTTCGCTTA
1 TGTTCGTTTA
*
328018 CGTTCGTTTA
1 TGTTCGTTTA
328028 TGTTCGTTTA
1 TGTTCGTTTA
328038 T
1 T
328039 CATTTAAATG
Statistics
Matches: 71, Mismatches: 10, Indels: 20
0.70 0.10 0.20
Matches are distributed among these distances:
10 42 0.59
11 2 0.03
12 1 0.01
13 18 0.25
14 8 0.11
ACGTcount: A:0.11, C:0.11, G:0.20, T:0.58
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:327964 original size:13 final size:12
Alignment explanation
Indices: 327937--328006 Score: 58
Period size: 13 Copynumber: 5.8 Consensus size: 12
327927 TGTGTTTGTG
327937 TTGTTCGTTTA-
1 TTGTTCGTTTAT
327948 -TGTTCGTTTAT
1 TTGTTCGTTTAT
*
327959 TGTGTTAGTTTA-
1 T-TGTTCGTTTAT
*
327971 -TGTTCATTTAT
1 TTGTTCGTTTAT
327982 TATGTTCGTTTAT
1 T-TGTTCGTTTAT
327995 GTTCGTTCGTTT
1 -TT-GTTCGTTT
328007 GTGTTCGCTT
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
10 18 0.38
13 20 0.43
14 9 0.19
ACGTcount: A:0.11, C:0.09, G:0.19, T:0.61
Consensus pattern (12 bp):
TTGTTCGTTTAT
Found at i:327964 original size:23 final size:23
Alignment explanation
Indices: 327938--328028 Score: 112
Period size: 23 Copynumber: 3.9 Consensus size: 23
327928 GTGTTTGTGT
327938 TGTTCGTTTATGTTCGTTTATTG
1 TGTTCGTTTATGTTCGTTTATTG
* * *
327961 TGTTAGTTTATGTTCATTTATTA
1 TGTTCGTTTATGTTCGTTTATTG
327984 TGTTCGTTTATGTTCGTTCGT-TTG
1 TGTTCGTTTATGTTCGTT--TATTG
* *
328008 TGTTCGCTTACGTTCGTTTAT
1 TGTTCGTTTATGTTCGTTTAT
328029 GTTCGTTTAT
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
22 1 0.02
23 37 0.65
24 18 0.32
25 1 0.02
ACGTcount: A:0.11, C:0.11, G:0.20, T:0.58
Consensus pattern (23 bp):
TGTTCGTTTATGTTCGTTTATTG
Found at i:334059 original size:2 final size:2
Alignment explanation
Indices: 334052--334155 Score: 78
Period size: 2 Copynumber: 55.0 Consensus size: 2
334042 TTGGGCTGGG
* * * *
334052 TA TA TA TA TT TA AA T- TA AA TA TA TA AA TA T- TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
334092 TA TA TA TA TA TA TA TA TA TA TA T- TA -A TT TA AA TGA AA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA
334133 T- TA -A TA T- TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
334156 AAATAATTAT
Statistics
Matches: 78, Mismatches: 16, Indels: 16
0.71 0.15 0.15
Matches are distributed among these distances:
1 7 0.09
2 70 0.90
3 1 0.01
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:334290 original size:42 final size:42
Alignment explanation
Indices: 334226--334311 Score: 145
Period size: 42 Copynumber: 2.0 Consensus size: 42
334216 TACTAAACCT
*
334226 GTCCCCGTCCCCGTTTAACATAAACAGTTTTTCCCCGTCTCC
1 GTCCCCATCCCCGTTTAACATAAACAGTTTTTCCCCGTCTCC
* *
334268 GTCCCCATCCCCGTTTAGCATAAACGGTTTTTCCCCGTCTCC
1 GTCCCCATCCCCGTTTAACATAAACAGTTTTTCCCCGTCTCC
334310 GT
1 GT
334312 TTAATTCAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.15, C:0.40, G:0.14, T:0.31
Consensus pattern (42 bp):
GTCCCCATCCCCGTTTAACATAAACAGTTTTTCCCCGTCTCC
Found at i:334401 original size:21 final size:21
Alignment explanation
Indices: 334375--334415 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
334365 CCAAGAACAG
334375 TGCTACAGTGCATCGATGCAT
1 TGCTACAGTGCATCGATGCAT
334396 TGCTACAGTGCATCGATGCA
1 TGCTACAGTGCATCGATGCA
334416 CTAAAATTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.27
Consensus pattern (21 bp):
TGCTACAGTGCATCGATGCAT
Found at i:341606 original size:23 final size:23
Alignment explanation
Indices: 341576--341619 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
341566 AATACATTTA
341576 TGTCCCGAATGACCACGTAGAAT
1 TGTCCCGAATGACCACGTAGAAT
*
341599 TGTCCCGAATGACCGCGTAGA
1 TGTCCCGAATGACCACGTAGA
341620 CCCTCGACTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.27, G:0.25, T:0.20
Consensus pattern (23 bp):
TGTCCCGAATGACCACGTAGAAT
Found at i:342627 original size:160 final size:159
Alignment explanation
Indices: 342363--342683 Score: 617
Period size: 160 Copynumber: 2.0 Consensus size: 159
342353 GATACCATTA
342363 AATGTAACACCCCCAACCGTATCTGACCCGGATACGAGTCCGAGATGACACATTGACATTTCAAA
1 AATGTAACACCCCCAACCGTATCTGACCCGGATACGAGTCCGAGATGACACATTGACATTTCAAA
342428 ACCTTTATTCTTACAAAATAACATAATATTTGAACTTATATTAAGAAAATACGATCATATATTGT
66 ACCTTTATTCTTACAAAATAACATAATATTTGAACTTATATTAAGAAAATACGATCATATATTGT
342493 TGAATTGTATTTGTTGTGAAAATTTTGAGG
131 TGAATTGTATTTGTTGTG-AAATTTTGAGG
342523 AATGTAACA-CCCCAACCCGTATCTGACCCGGATACGAGTCCGAGATGACACATTGACATTTCAA
1 AATGTAACACCCCCAA-CCGTATCTGACCCGGATACGAGTCCGAGATGACACATTGACATTTCAA
342587 AACCTTTATTCTTACAAAATAACATAATATTTGAACTTATATTAAGAAAATACGATCATATATTG
65 AACCTTTATTCTTACAAAATAACATAATATTTGAACTTATATTAAGAAAATACGATCATATATTG
342652 TTGAATTGTATTTGTTGTGAAATTTTGAGG
130 TTGAATTGTATTTGTTGTGAAATTTTGAGG
342682 AA
1 AA
342684 AAAACGTATT
Statistics
Matches: 160, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
159 19 0.12
160 141 0.88
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.32
Consensus pattern (159 bp):
AATGTAACACCCCCAACCGTATCTGACCCGGATACGAGTCCGAGATGACACATTGACATTTCAAA
ACCTTTATTCTTACAAAATAACATAATATTTGAACTTATATTAAGAAAATACGATCATATATTGT
TGAATTGTATTTGTTGTGAAATTTTGAGG
Found at i:342845 original size:20 final size:21
Alignment explanation
Indices: 342806--342849 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
342796 AAGCAAAATT
*
342806 GTGCATCTATGCACTACTACA
1 GTGCATCGATGCACTACTACA
*
342827 GTGCATCGA-GCACTGCTACA
1 GTGCATCGATGCACTACTACA
342847 GTG
1 GTG
342850 ATTTTCGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (21 bp):
GTGCATCGATGCACTACTACA
Found at i:343653 original size:23 final size:23
Alignment explanation
Indices: 343617--343660 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
343607 AATACATATA
343617 TGTCCCGAAGGACCATGTAGAAT
1 TGTCCCGAAGGACCATGTAGAAT
* * *
343640 TGTCCTGAATGACCGTGTAGA
1 TGTCCCGAAGGACCATGTAGA
343661 CCCTCGACTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.25
Consensus pattern (23 bp):
TGTCCCGAAGGACCATGTAGAAT
Found at i:348138 original size:14 final size:14
Alignment explanation
Indices: 348119--348145 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
348109 GGTTGGAATC
348119 TGATTTAGTTGATA
1 TGATTTAGTTGATA
348133 TGATTTAGTTGAT
1 TGATTTAGTTGAT
348146 TGTAATATAC
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:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (14 bp):
TGATTTAGTTGATA
Found at i:353879 original size:16 final size:16
Alignment explanation
Indices: 353858--353891 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
353848 TTACTATTCA
*
353858 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
353874 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
353890 CG
1 CG
353892 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:361581 original size:14 final size:15
Alignment explanation
Indices: 361564--361601 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
361554 AATATTCAAA
361564 AAAAAATTAAGTA-T
1 AAAAAATTAAGTATT
* *
361578 AAAAAATAAATTATT
1 AAAAAATTAAGTATT
361593 AAAAAATTA
1 AAAAAATTA
361602 GAAATATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 11 0.55
15 9 0.45
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (15 bp):
AAAAAATTAAGTATT
Found at i:361783 original size:5 final size:6
Alignment explanation
Indices: 361754--361783 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
361744 TACTAAATTT
361754 TTTAAA TTTAAA TTTAAA TTTAAA -TTAAA T
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T
361784 AAATTTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:361881 original size:14 final size:16
Alignment explanation
Indices: 361859--361900 Score: 56
Period size: 14 Copynumber: 2.9 Consensus size: 16
361849 ATTATCATGA
361859 AATTATATAATTAAA-
1 AATTATATAATTAAAT
361874 AA-TATATAA--AAAT
1 AATTATATAATTAAAT
361887 AATTATATAATTAA
1 AATTATATAATTAA
361901 GAAGAACATT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
12 3 0.13
13 2 0.09
14 14 0.61
15 2 0.09
16 2 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AATTATATAATTAAAT
Found at i:368557 original size:17 final size:19
Alignment explanation
Indices: 368534--368609 Score: 79
Period size: 18 Copynumber: 4.1 Consensus size: 19
368524 TTTTTGTCCG
368534 AAAAAAATCCGG-TTTTTT
1 AAAAAAATCCGGTTTTTTT
*
368552 AAAAAAAT-TGGATTTTTATCT
1 AAAAAAATCCGG-TTTTT-T-T
*
368573 GAAAAAATCCGGTTTTTTT
1 AAAAAAATCCGGTTTTTTT
368592 -AAAAAA-CCGGTTTTTTT
1 AAAAAAATCCGGTTTTTTT
368609 A
1 A
368610 CAAACCGAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
17 13 0.27
18 14 0.29
19 5 0.10
20 2 0.04
21 13 0.27
22 2 0.04
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.41
Consensus pattern (19 bp):
AAAAAAATCCGGTTTTTTT
Found at i:368609 original size:40 final size:40
Alignment explanation
Indices: 368512--368607 Score: 131
Period size: 39 Copynumber: 2.4 Consensus size: 40
368502 TCAAACCGGA
*
368512 TAAAAAACCGGTTTTTTGTCCGAAAAAAATCCGGTTTTTT
1 TAAAAAACCGGTTTTTTATCCGAAAAAAATCCGGTTTTTT
* ** * *
368552 AAAAAAATTGGATTTTTATCTG-AAAAAATCCGGTTTTTT
1 TAAAAAACCGGTTTTTTATCCGAAAAAAATCCGGTTTTTT
368591 TAAAAAACCGGTTTTTT
1 TAAAAAACCGGTTTTTT
368608 TACAAACCGA
Statistics
Matches: 46, Mismatches: 10, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
39 30 0.65
40 16 0.35
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (40 bp):
TAAAAAACCGGTTTTTTATCCGAAAAAAATCCGGTTTTTT
Found at i:368616 original size:16 final size:17
Alignment explanation
Indices: 368512--368609 Score: 70
Period size: 18 Copynumber: 5.1 Consensus size: 17
368502 TCAAACCGGA
368512 TAAAAAACCGGTTTTTT
1 TAAAAAACCGGTTTTTT
368529 GTCCGAAAAAAATCCGGTTTTTT
1 -T----AAAAAA-CCGGTTTTTT
* **
368552 AAAAAAATTGGATTTTTAT
1 TAAAAAACCGG-TTTTT-T
368571 CTGAAAAAATCCGGTTTTTT
1 -T-AAAAAA-CCGGTTTTTT
368591 TAAAAAACCGGTTTTTT
1 TAAAAAACCGGTTTTTT
368608 TA
1 TA
368610 CAAACCGAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 21
0.70 0.07 0.23
Matches are distributed among these distances:
17 14 0.22
18 18 0.28
19 2 0.03
20 1 0.02
21 11 0.17
22 8 0.12
23 10 0.16
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (17 bp):
TAAAAAACCGGTTTTTT
Found at i:370911 original size:16 final size:17
Alignment explanation
Indices: 370882--370918 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
370872 TCGTACATTC
370882 CATGCCTGAAGGATAAT
1 CATGCCTGAAGGATAAT
370899 CATGCCT-AAGGATAAT
1 CATGCCTGAAGGATAAT
370915 CATG
1 CATG
370919 TATATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (17 bp):
CATGCCTGAAGGATAAT
Found at i:371366 original size:16 final size:16
Alignment explanation
Indices: 371345--371375 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
371335 GAATACCAAT
371345 TAAATTAAGAAATTAC
1 TAAATTAAGAAATTAC
*
371361 TAAATTAAGAGATTA
1 TAAATTAAGAAATTA
371376 AGATCTGACG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.10, T:0.32
Consensus pattern (16 bp):
TAAATTAAGAAATTAC
Found at i:379961 original size:11 final size:11
Alignment explanation
Indices: 379945--380014 Score: 54
Period size: 11 Copynumber: 6.1 Consensus size: 11
379935 GAAATAAATT
379945 ATTGAAGCTCG
1 ATTGAAGCTCG
*
379956 ATTGAAGCTAGAG
1 ATTGAAGCT--CG
*
379969 ACTCG-AGCTCG
1 A-TTGAAGCTCG
379980 ATTGAAGCTCG
1 ATTGAAGCTCG
379991 ATTTTG-AGCTCG
1 A--TTGAAGCTCG
*
380003 ATTCAAGCTCG
1 ATTGAAGCTCG
380014 A
1 A
380015 AATCAAACTC
Statistics
Matches: 47, Mismatches: 5, Indels: 14
0.71 0.08 0.21
Matches are distributed among these distances:
10 4 0.09
11 25 0.53
12 7 0.15
13 9 0.19
14 2 0.04
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (11 bp):
ATTGAAGCTCG
Found at i:382353 original size:18 final size:19
Alignment explanation
Indices: 382330--382365 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
382320 TTTCAATCAC
*
382330 ATTTG-TTTAAATTTTCAT
1 ATTTGTTTTAAATGTTCAT
382348 ATTTGTTTTAAATGTTCA
1 ATTTGTTTTAAATGTTCA
382366 GGTGTCATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.06, G:0.08, T:0.58
Consensus pattern (19 bp):
ATTTGTTTTAAATGTTCAT
Found at i:382881 original size:7 final size:7
Alignment explanation
Indices: 382865--382922 Score: 53
Period size: 7 Copynumber: 8.3 Consensus size: 7
382855 ATAAGTACAT
382865 TTTAGGG
1 TTTAGGG
*
382872 TTTAGTG
1 TTTAGGG
*
382879 TTTATGG
1 TTTAGGG
**
382886 TTTATAG
1 TTTAGGG
* *
382893 TTCAAGG
1 TTTAGGG
382900 TTTAGGG
1 TTTAGGG
382907 TTTAGGG
1 TTTAGGG
*
382914 TTTAAGG
1 TTTAGGG
382921 TT
1 TT
382923 CATTACAAAG
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
7 41 1.00
ACGTcount: A:0.19, C:0.02, G:0.31, T:0.48
Consensus pattern (7 bp):
TTTAGGG
Found at i:382920 original size:21 final size:21
Alignment explanation
Indices: 382865--382922 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
382855 ATAAGTACAT
*
382865 TTTAGGGTTT-AGTGTTTATGG
1 TTTAGGGTTTAAG-GTTTAGGG
** *
382886 TTTATAGTTCAAGGTTTAGGG
1 TTTAGGGTTTAAGGTTTAGGG
382907 TTTAGGGTTTAAGGTT
1 TTTAGGGTTTAAGGTT
382923 CATTACAAAG
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
21 27 0.93
22 2 0.07
ACGTcount: A:0.19, C:0.02, G:0.31, T:0.48
Consensus pattern (21 bp):
TTTAGGGTTTAAGGTTTAGGG
Found at i:384942 original size:40 final size:40
Alignment explanation
Indices: 384913--385008 Score: 138
Period size: 40 Copynumber: 2.4 Consensus size: 40
384903 GCGAAAGTCA
* * *
384913 AATTCGCAACGCGAATAGTTAAATTGCAACGATAATATGT
1 AATTCGCAACGCGAATAGGTAAATCGCAACGAGAATATGT
*
384953 AATTCGCAACGCGAATAGGTAAATCGCAACGATAATATGT
1 AATTCGCAACGCGAATAGGTAAATCGCAACGAGAATATGT
* *
384993 AAATCGCAACACGAAT
1 AATTCGCAACGCGAAT
385009 TCTCCAAATT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.23
Consensus pattern (40 bp):
AATTCGCAACGCGAATAGGTAAATCGCAACGAGAATATGT
Found at i:384989 original size:20 final size:20
Alignment explanation
Indices: 384893--385002 Score: 98
Period size: 20 Copynumber: 5.5 Consensus size: 20
384883 ACAGGTTCCA
*
384893 AAATCGCAACGCGAA-A-GT
1 AAATCGCAACGAGAATAGGT
* *
384911 CAAATTCGCAACGCGAATAGTT
1 -AAA-TCGCAACGAGAATAGGT
* * *
384933 AAATTGCAACGATAATATGT
1 AAATCGCAACGAGAATAGGT
* *
384953 AATTCGCAACGCGAATAGGT
1 AAATCGCAACGAGAATAGGT
* *
384973 AAATCGCAACGATAATATGT
1 AAATCGCAACGAGAATAGGT
384993 AAATCGCAAC
1 AAATCGCAAC
385003 ACGAATTCTC
Statistics
Matches: 73, Mismatches: 15, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 3 0.04
20 65 0.89
21 4 0.05
22 1 0.01
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.21
Consensus pattern (20 bp):
AAATCGCAACGAGAATAGGT
Found at i:385036 original size:14 final size:14
Alignment explanation
Indices: 385013--385052 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
385003 ACGAATTCTC
385013 CAAA-TTCGCAACT
1 CAAATTTCGCAACT
385026 CAAATTTCGCAACT
1 CAAATTTCGCAACT
**
385040 TGAATTTCGCAAC
1 CAAATTTCGCAAC
385053 GCTAATTACC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 4 0.17
14 20 0.83
ACGTcount: A:0.35, C:0.28, G:0.10, T:0.28
Consensus pattern (14 bp):
CAAATTTCGCAACT
Found at i:385149 original size:20 final size:20
Alignment explanation
Indices: 385126--385163 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
385116 TCGTAACGCG
385126 AATAGGTAAATCACAACGAT
1 AATAGGTAAATCACAACGAT
* *
385146 AATATGTAAATCGCAACG
1 AATAGGTAAATCACAACG
385164 CGAATTCTCC
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:0.47, C:0.16, G:0.16, T:0.21
Consensus pattern (20 bp):
AATAGGTAAATCACAACGAT
Found at i:385246 original size:20 final size:20
Alignment explanation
Indices: 385218--385271 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
385208 CGATATAGGT
* *
385218 AATTAGCGTTGCGAAAATGA
1 AATTCGCGTTGCGAAAACGA
*
385238 AATTCGCGTTGAGAAAACGA
1 AATTCGCGTTGCGAAAACGA
*
385258 AAATCGCGTTGCGA
1 AATTCGCGTTGCGA
385272 TAGTACTGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (20 bp):
AATTCGCGTTGCGAAAACGA
Found at i:385345 original size:20 final size:20
Alignment explanation
Indices: 385322--385391 Score: 113
Period size: 20 Copynumber: 3.5 Consensus size: 20
385312 TAACTTCTGT
385322 GTTGCGATTTACATATTATC
1 GTTGCGATTTACATATTATC
385342 GTTGCGATTTACATATTATC
1 GTTGCGATTTACATATTATC
* **
385362 GTTGCGATTTACCTATTCGC
1 GTTGCGATTTACATATTATC
385382 GTTGCGATTT
1 GTTGCGATTT
385392 TGGAACCTGT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.20, C:0.17, G:0.19, T:0.44
Consensus pattern (20 bp):
GTTGCGATTTACATATTATC
Found at i:388144 original size:34 final size:34
Alignment explanation
Indices: 388105--388171 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
388095 TAGCATCGTC
* * * *
388105 GTTAAATAATTAGTGATTGGTGATTAAAATAGAT
1 GTTAAATAAATAATGATCGATGATTAAAATAGAT
388139 GTTAAATAAATAATGATCGATGATTAAAATAGA
1 GTTAAATAAATAATGATCGATGATTAAAATAGA
388172 AAAAAAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.46, C:0.01, G:0.18, T:0.34
Consensus pattern (34 bp):
GTTAAATAAATAATGATCGATGATTAAAATAGAT
Found at i:388900 original size:70 final size:70
Alignment explanation
Indices: 388812--389001 Score: 292
Period size: 70 Copynumber: 2.7 Consensus size: 70
388802 AGTAAGGTGG
*
388812 GATGCTCTTCTATGTTTATTAGTCATGTGAGATTATTTTGTTCTCTTATTTTTATTCTTTAGACA
1 GATGCTCTTCTATGTTTATTAGTCATGTGAGATTGTTTTGTTCTCTTATTTTTATTCTTTAGACA
388877 TTTGA
66 TTTGA
**
388882 GATGCTCTTCTATGTTTATTAGTCATGTGAGATTGTTTTGTTCTCTTATTTTTATTCTTTAGATT
1 GATGCTCTTCTATGTTTATTAGTCATGTGAGATTGTTTTGTTCTCTTATTTTTATTCTTTAGACA
*
388947 TTTGG
66 TTTGA
* * *
388952 GATGCTCTTCTATATTTTTTTA-ACTATGTGAGATTGTTTTGTTCTCTTAT
1 GATGCTCTTCTAT-GTTTATTAGTC-ATGTGAGATTGTTTTGTTCTCTTAT
389002 ATTTGCTATT
Statistics
Matches: 111, Mismatches: 7, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
70 80 0.72
71 31 0.28
ACGTcount: A:0.18, C:0.11, G:0.15, T:0.56
Consensus pattern (70 bp):
GATGCTCTTCTATGTTTATTAGTCATGTGAGATTGTTTTGTTCTCTTATTTTTATTCTTTAGACA
TTTGA
Found at i:389003 original size:37 final size:35
Alignment explanation
Indices: 388906--389016 Score: 88
Period size: 37 Copynumber: 3.1 Consensus size: 35
388896 TTTATTAGTC
388906 ATGTGAGATTGTTTTGTTCTCTTAT-TTTTATTCT
1 ATGTGAGATTGTTTTGTTCTCTTATATTTTATTCT
* * *
388940 -T-T-AGATT-TTTGGGATGCTCTTCTATATTTTTTTAACT
1 ATGTGAGATTGTTT-TG-TTCTC-T-TATATTTTATT--CT
388977 ATGTGAGATTGTTTTGTTCTCTTATATTTGCTATTCT
1 ATGTGAGATTGTTTTGTTCTCTTATATTT--TATTCT
389014 ATG
1 ATG
389017 CTCTTTAGAC
Statistics
Matches: 58, Mismatches: 6, Indels: 23
0.67 0.07 0.26
Matches are distributed among these distances:
30 3 0.05
31 6 0.10
32 5 0.09
33 2 0.03
34 3 0.05
35 6 0.10
37 14 0.24
38 2 0.03
39 8 0.14
40 6 0.10
41 3 0.05
ACGTcount: A:0.17, C:0.10, G:0.15, T:0.58
Consensus pattern (35 bp):
ATGTGAGATTGTTTTGTTCTCTTATATTTTATTCT
Found at i:397399 original size:27 final size:26
Alignment explanation
Indices: 397355--397407 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
397345 AAATATATTA
* * *
397355 ATTTTTATAAACATATATTTTTTTAT
1 ATTTTTATAAAAAGATATTTATTTAT
397381 ATTTTTATAAATAAGATATTTATTTAT
1 ATTTTTATAAA-AAGATATTTATTTAT
397408 TTAGAAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (26 bp):
ATTTTTATAAAAAGATATTTATTTAT
Found at i:397693 original size:17 final size:17
Alignment explanation
Indices: 397661--397698 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
397651 AAACATATTG
*
397661 AAATTTAAATAGTAAATT
1 AAATTAAAATAGTAAA-T
397679 AAATTAAAATA-TAAAT
1 AAATTAAAATAGTAAAT
397695 AAAT
1 AAAT
397699 AGTGACTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 4 0.21
18 10 0.53
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (17 bp):
AAATTAAAATAGTAAAT
Found at i:398946 original size:3 final size:3
Alignment explanation
Indices: 398940--398986 Score: 62
Period size: 3 Copynumber: 16.3 Consensus size: 3
398930 TTTGGTATGT
* *
398940 ATA ATA ATA ATA AAA ATA ATA ATA AT- ATA ATA A-A ATA AAA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
398986 A
1 A
398987 AAAAATATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 4 0.11
3 34 0.89
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:398957 original size:9 final size:9
Alignment explanation
Indices: 398940--399000 Score: 65
Period size: 9 Copynumber: 7.1 Consensus size: 9
398930 TTTGGTATGT
*
398940 ATAATAATA
1 ATAAAAATA
398949 ATAAAAATA
1 ATAAAAATA
*
398958 ATAATAAT-
1 ATAAAAATA
*
398966 ATAATAA-A
1 ATAAAAATA
398974 ATAAAAATA
1 ATAAAAATA
398983 ATAAAAA-A
1 ATAAAAATA
*
398991 ATATAAATA
1 ATAAAAATA
399000 A
1 A
399001 AAACAAATGG
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
8 20 0.44
9 25 0.56
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (9 bp):
ATAAAAATA
Found at i:398996 original size:10 final size:11
Alignment explanation
Indices: 398945--399002 Score: 57
Period size: 11 Copynumber: 5.2 Consensus size: 11
398935 TATGTATAAT
398945 AATAATAAAAA
1 AATAATAAAAA
* *
398956 TAATAATAATAT
1 -AATAATAAAAA
398968 AATAA-AATAAA
1 AATAATAA-AAA
398979 AATAATAAAAA
1 AATAATAAAAA
398990 AAT-ATAAATAA
1 AATAATAAA-AA
399001 AA
1 AA
399003 ACAAATGGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
10 7 0.18
11 21 0.54
12 11 0.28
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AATAATAAAAA
Found at i:403021 original size:31 final size:31
Alignment explanation
Indices: 402985--403045 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
402975 CTCATCTCGA
** *
402985 TGCCTAATATTTTCTCTGTTATTATTTTAGG
1 TGCCTAATATTTTCTCCATTACTATTTTAGG
* *
403016 TGCCTAGTGTTTTCTCCATTACTATTTTAG
1 TGCCTAATATTTTCTCCATTACTATTTTAG
403046 CTGCTCGAAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.18, C:0.16, G:0.13, T:0.52
Consensus pattern (31 bp):
TGCCTAATATTTTCTCCATTACTATTTTAGG
Found at i:404234 original size:47 final size:47
Alignment explanation
Indices: 404159--404266 Score: 189
Period size: 47 Copynumber: 2.3 Consensus size: 47
404149 CTATCGGATA
404159 TCTCGGCGTCTTCTATATATATTAGTTCAAAAGATGTTCATGGGAGC
1 TCTCGGCGTCTTCTATATATATTAGTTCAAAAGATGTTCATGGGAGC
* * *
404206 TCTCGGTGTCTTCTATATATGTTCGTTCAAAAGATGTTCATGGGAGC
1 TCTCGGCGTCTTCTATATATATTAGTTCAAAAGATGTTCATGGGAGC
404253 TCTCGGCGTCTTCT
1 TCTCGGCGTCTTCT
404267 TCAGCCTTGG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 57 1.00
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.38
Consensus pattern (47 bp):
TCTCGGCGTCTTCTATATATATTAGTTCAAAAGATGTTCATGGGAGC
Found at i:404332 original size:35 final size:32
Alignment explanation
Indices: 404248--404333 Score: 138
Period size: 32 Copynumber: 2.7 Consensus size: 32
404238 GATGTTCATG
*
404248 GGAGCTCTCGGCGTCTTCTTCAGCCTTGGGGT
1 GGAGTTCTCGGCGTCTTCTTCAGCCTTGGGGT
*
404280 GGAGTTCTTGGCGTCTTCTTCAGCCTTGGGGT
1 GGAGTTCTCGGCGTCTTCTTCAGCCTTGGGGT
404312 GGAGTT-TCCGGCGTCTTCTTCA
1 GGAGTTCT-CGGCGTCTTCTTCA
404334 TCAGCATCAT
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
31 1 0.02
32 49 0.98
ACGTcount: A:0.07, C:0.26, G:0.33, T:0.35
Consensus pattern (32 bp):
GGAGTTCTCGGCGTCTTCTTCAGCCTTGGGGT
Found at i:404776 original size:169 final size:166
Alignment explanation
Indices: 404455--404790 Score: 645
Period size: 166 Copynumber: 2.0 Consensus size: 166
404445 AGCACACTTT
404455 AAAATGTTGCAAAAGTATTGGGCCCTAGCAATAAACAAAAGCACATGTTTTATAAAAGAAAAGTT
1 AAAATGTTGCAAAAGTATTGGGCCCTAGCAATAAACAAAAGCACATGTTTTATAAAAGAAAAGTT
404520 TGGTCTTGGCAATAAACGAAAGCAAGAACATGTTTTAAAAAGAAAAGTTTGTGTTATTAGAAGAA
66 TGGTCTTGGCAATAAACGAAAGCAAGAACATGTTTTAAAAAGAAAAGTTTGTGTTATTAGAAGAA
404585 AATTTATAAAAGTATTAATTTTATAAAGTGAAAGAA
131 AATTTATAAAAGTATTAATTTTATAAAGTGAAAGAA
404621 AAAATGTTGCAAAAGTATTGGGCCCTAGCAATAAACAAAAGCACATGTTTTATAAAAGAAAAGTT
1 AAAATGTTGCAAAAGTATTGGGCCCTAGCAATAAACAAAAGCACATGTTTTATAAAAGAAAAGTT
404686 TGGTCTCTGGCAATAAACGAAAGCAAGAACATGTTTTATAAAAGAAAAGTTTGTTGTTATTAGAA
66 TGGTCT-TGGCAATAAACGAAAGCAAGAACATGTTTTA-AAAAGAAAAGTTTG-TGTTATTAGAA
404751 GAAAATTTATAAAAGTATTAATTTTATAAAGTGAAAGAA
128 GAAAATTTATAAAAGTATTAATTTTATAAAGTGAAAGAA
404790 A
1 A
404791 GAAAGGTGAC
Statistics
Matches: 167, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
166 71 0.43
167 31 0.19
168 14 0.08
169 51 0.31
ACGTcount: A:0.46, C:0.08, G:0.17, T:0.29
Consensus pattern (166 bp):
AAAATGTTGCAAAAGTATTGGGCCCTAGCAATAAACAAAAGCACATGTTTTATAAAAGAAAAGTT
TGGTCTTGGCAATAAACGAAAGCAAGAACATGTTTTAAAAAGAAAAGTTTGTGTTATTAGAAGAA
AATTTATAAAAGTATTAATTTTATAAAGTGAAAGAA
Found at i:406482 original size:14 final size:14
Alignment explanation
Indices: 406429--406835 Score: 290
Period size: 14 Copynumber: 32.1 Consensus size: 14
406419 TATTTCAATT
406429 ACTTTAATGA-TTA
1 ACTTTAATGATTTA
406442 ACTTTAATGA-TTA
1 ACTTTAATGATTTA
406455 A---TAAT-A-TT-
1 ACTTTAATGATTTA
406463 ACTTTAATGATTTA
1 ACTTTAATGATTTA
*
406477 ATTTTAATGATTTA
1 ACTTTAATGATTTA
*
406491 A---TAAT-AATT-
1 ACTTTAATGATTTA
406500 ACTTTAATGATTTA
1 ACTTTAATGATTTA
* * *
406514 A-TAATAATTACTTA
1 ACT-TTAATGATTTA
406528 ACTTTAATGATTTA
1 ACTTTAATGATTTA
*
406542 A---TAAT-AATT-
1 ACTTTAATGATTTA
406551 ACTTTAATGATTTA
1 ACTTTAATGATTTA
*
406565 ATTTTAATGATTTA
1 ACTTTAATGATTTA
*
406579 A---TAAT-AATTA
1 ACTTTAATGATTTA
406589 A-TTTAATGATTTA
1 ACTTTAATGATTTA
406602 ACTTTAATGATTTA
1 ACTTTAATGATTTA
*
406616 A---TAAT-AATT-
1 ACTTTAATGATTTA
406625 ACTTTAATGATTTA
1 ACTTTAATGATTTA
*
406639 ATTTTAATGATTTA
1 ACTTTAATGATTTA
*
406653 A---TAAT-AATT-
1 ACTTTAATGATTTA
406662 ACTTTAATGATTTA
1 ACTTTAATGATTTA
406676 ACTTTAATGATTTA
1 ACTTTAATGATTTA
*
406690 A-TATAATGATTTA
1 ACTTTAATGATTTA
406703 ACTTTAATGATTTA
1 ACTTTAATGATTTA
*
406717 ATTTTAATGA-TTA
1 ACTTTAATGATTTA
*
406730 A---TAAT-AATT-
1 ACTTTAATGATTTA
*
406739 ACTTTATTGATTTA
1 ACTTTAATGATTTA
406753 ACTTT-ATGATTTA
1 ACTTTAATGATTTA
* *
406766 A-TAATAATTA-TTA
1 ACT-TTAATGATTTA
406779 ACTTTAATGATTTA
1 ACTTTAATGATTTA
*** * *
406793 AAAATAATTACTTA
1 ACTTTAATGATTTA
406807 ACTTTAATGATTTA
1 ACTTTAATGATTTA
406821 ACTTTAATGATTTA
1 ACTTTAATGATTTA
406835 A
1 A
406836 AATAATTAAT
Statistics
Matches: 312, Mismatches: 39, Indels: 85
0.72 0.09 0.19
Matches are distributed among these distances:
8 1 0.00
9 9 0.03
10 27 0.09
11 24 0.08
12 25 0.08
13 71 0.23
14 154 0.49
15 1 0.00
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.49
Consensus pattern (14 bp):
ACTTTAATGATTTA
Found at i:406507 original size:23 final size:23
Alignment explanation
Indices: 406479--406640 Score: 173
Period size: 23 Copynumber: 6.6 Consensus size: 23
406469 ATGATTTAAT
406479 TTTAATGATTTAATAATAATTAC
1 TTTAATGATTTAATAATAATTAC
406502 TTTAATGATTTAATAATAATTACTTAAC
1 TTTAATGATTTAATAAT-A--A-TT-AC
406530 TTTAATGATTTAATAATAATTAC
1 TTTAATGATTTAATAATAATTAC
** *
406553 TTTAATGATTTAATTTTAATGA-
1 TTTAATGATTTAATAATAATTAC
* *
406575 TTTAATAATAATTAATTTAATGATTTAAC
1 TTTAATGAT--TTAA--TAAT-AATT-AC
406604 TTTAATGATTTAATAATAATTAC
1 TTTAATGATTTAATAATAATTAC
406627 TTTAATGATTTAAT
1 TTTAATGATTTAAT
406641 TTTAATGATT
Statistics
Matches: 117, Mismatches: 10, Indels: 24
0.77 0.07 0.16
Matches are distributed among these distances:
22 8 0.07
23 54 0.46
24 10 0.09
25 5 0.04
26 3 0.03
27 9 0.08
28 20 0.17
29 8 0.07
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (23 bp):
TTTAATGATTTAATAATAATTAC
Found at i:406508 original size:37 final size:36
Alignment explanation
Indices: 406425--406880 Score: 180
Period size: 37 Copynumber: 13.0 Consensus size: 36
406415 ATTATATTTC
*
406425 AATTACTTTAATGA-TTAACTTTAATGATTAATAAT
1 AATTACTTTAATGATTTAATTTTAATGATTAATAAT
406460 -ATTACTTTAATGATTTAATTTTAATGATTTAATAAT
1 AATTACTTTAATGATTTAATTTTAATGA-TTAATAAT
* *
406496 AATTACTTTAATGATTTAA---TAATAATTACT--T
1 AATTACTTTAATGATTTAATTTTAATGATTAATAAT
** *
406527 -A--ACTTTAATGATTTAATAATAATTACTT--TAAT
1 AATTACTTTAATGATTTAATTTTAATGA-TTAATAAT
* * *
406559 GATTTAATTTTAATGATTTAA---TAATAATTAATTTAAT
1 -AATT-ACTTTAATGATTTAATTTTAATGATTAA--TAAT
* ** *
406596 GATTTAACTTTAATGATTTAATAATAATTACTT--TAAT
1 -AATT-ACTTTAATGATTTAATTTTAATGA-TTAATAAT
* * ** *
406633 GATTTAATTTTAATGATTTAATAATAATTACTT--TAAT
1 -AATT-ACTTTAATGATTTAATTTTAATGA-TTAATAAT
* *
406670 GATTTAACTTTAATGATTTAA-TATAATGA-T--T--T
1 -AATT-ACTTTAATGATTTAATTTTAATGATTAATAAT
406702 -A--ACTTTAATGATTTAATTTTAATGATTAATAAT
1 AATTACTTTAATGATTTAATTTTAATGATTAATAAT
* *
406735 AATTACTTTATTGATTTAACTTT-ATGATTTAATAAT
1 AATTACTTTAATGATTTAATTTTAATGA-TTAATAAT
*
406771 AATTA--TTAA--CTTTAATGATTTAA--A--AATAATT
1 AATTACTTTAATGATTTAAT--TTTAATGATTAATAA-T
* *
406802 ACTTAACTTTAATGATTTAACTTTAATGATTTAAAATAATT
1 AATT-ACTTTAATGATTTAATTTTAATGA-TT--AATAA-T
406843 AATTGAC-TTAATGATTT-ATATTTAATGATATAATAAT
1 AATT-ACTTTAATGATTTAAT-TTTAATGAT-TAATAAT
406880 A
1 A
406881 GAAATATCGA
Statistics
Matches: 345, Mismatches: 26, Indels: 98
0.74 0.06 0.21
Matches are distributed among these distances:
27 15 0.04
28 22 0.06
29 1 0.00
30 7 0.02
31 11 0.03
32 10 0.03
33 8 0.02
34 41 0.12
35 17 0.05
36 50 0.14
37 118 0.34
38 5 0.01
39 2 0.01
40 24 0.07
41 14 0.04
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (36 bp):
AATTACTTTAATGATTTAATTTTAATGATTAATAAT
Found at i:406603 original size:74 final size:74
Alignment explanation
Indices: 406525--406880 Score: 441
Period size: 74 Copynumber: 4.8 Consensus size: 74
406515 TAATAATTAC
406525 TTAACTTTAATGATTTAATAATAATTACTTTAATGATTTAATTTTAATGATTTAATAATAATTAA
1 TTAACTTTAATGATTTAATAATAATTACTTTAATGATTTAATTTTAATGATTTAATAATAATTAA
406590 TTTAATGAT
66 TTTAATGAT
*
406599 TTAACTTTAATGATTTAATAATAATTACTTTAATGATTTAATTTTAATGATTTAATAATAATTAC
1 TTAACTTTAATGATTTAATAATAATTACTTTAATGATTTAATTTTAATGATTTAATAATAATTAA
406664 TTTAATGAT
66 TTTAATGAT
*
406673 TTAACTTTAATGATTTAATATAATGATTTAACTTTAATGATTTAATTTTAATGA-TTAATAATAA
1 TTAACTTTAATGATTT-A-ATAAT-AATT-ACTTTAATGATTTAATTTTAATGATTTAATAATAA
* *
406737 TTACTTTATTGAT
62 TTAATTTAATGAT
* *
406750 TTAACTTT-ATGATTTAATAATAATTA--TTAA--CTTTAATGATTTAA--A---AATAATTACT
1 TTAACTTTAATGATTTAATAATAATTACTTTAATGATTTAAT--TTTAATGATTTAATAA-TAAT
406805 TAACTTTAATGAT
63 TAA-TTTAATGAT
*
406818 TTAACTTTAATGATTTAAAATAATTAATTGAC-TTAATGATTT-ATATTTAATGATATAATAATA
1 TTAACTTTAATGATTT--AATAA-TAATT-ACTTTAATGATTTAAT-TTTAATGATTTAATAATA
406881 GAAATATCGA
Statistics
Matches: 252, Mismatches: 9, Indels: 38
0.84 0.03 0.13
Matches are distributed among these distances:
66 5 0.02
67 5 0.02
68 23 0.09
69 7 0.03
70 9 0.04
71 5 0.02
72 6 0.02
73 4 0.02
74 104 0.41
75 4 0.02
76 16 0.06
77 33 0.13
78 26 0.10
79 5 0.02
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.49
Consensus pattern (74 bp):
TTAACTTTAATGATTTAATAATAATTACTTTAATGATTTAATTTTAATGATTTAATAATAATTAA
TTTAATGAT
Found at i:406867 original size:40 final size:41
Alignment explanation
Indices: 406776--406880 Score: 142
Period size: 40 Copynumber: 2.5 Consensus size: 41
406766 ATAATAATTA
*
406776 TTAACTTTAATGATTTAAAAATAATTACTTAACTTTAATGAT
1 TTAACTTTAATGATTT-AAAATAATTAATTAACTTTAATGAT
*
406818 TTAACTTTAATGATTTAAAATAATTAATTGAC-TTAATGAT
1 TTAACTTTAATGATTTAAAATAATTAATTAACTTTAATGAT
*
406858 TTATA-TTTAATGATATAATAATA
1 TTA-ACTTTAATGATTTAA-AATA
406881 GAAATATCGA
Statistics
Matches: 58, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
40 23 0.40
41 19 0.33
42 16 0.28
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.46
Consensus pattern (41 bp):
TTAACTTTAATGATTTAAAATAATTAATTAACTTTAATGAT
Found at i:408636 original size:41 final size:41
Alignment explanation
Indices: 408579--408690 Score: 158
Period size: 41 Copynumber: 2.8 Consensus size: 41
408569 ATATATTACT
408579 ATTATTAT--ATCATTAAA-TATAAATCATTAAAGTCAAGTA
1 ATTATTATAAATCATTAAAGT-TAAATCATTAAAGTCAAGTA
*
408618 ATTATTATAAATCATTAAAGTTAAATCATTAAAGTTAAGTA
1 ATTATTATAAATCATTAAAGTTAAATCATTAAAGTCAAGTA
* *
408659 ATTATTTTTAAATCATTAAAGTTAAATAATTA
1 ATTA-TTATAAATCATTAAAGTTAAATCATTA
408691 TATTAATCAT
Statistics
Matches: 66, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
39 8 0.12
41 32 0.48
42 26 0.39
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.41
Consensus pattern (41 bp):
ATTATTATAAATCATTAAAGTTAAATCATTAAAGTCAAGTA
Found at i:408648 original size:27 final size:27
Alignment explanation
Indices: 408587--408649 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
408577 CTATTATTAT
408587 ATCATTAAATATAAATCATTAAAGTCAA
1 ATCATT-AATATAAATCATTAAAGTCAA
* * * *
408615 GTAATTATTATAAATCATTAAAGTTAA
1 ATCATTAATATAAATCATTAAAGTCAA
408642 ATCATTAA
1 ATCATTAA
408650 AGTTAAGTAA
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
27 24 0.86
28 4 0.14
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.37
Consensus pattern (27 bp):
ATCATTAATATAAATCATTAAAGTCAA
Found at i:408669 original size:28 final size:27
Alignment explanation
Indices: 408638--408987 Score: 187
Period size: 27 Copynumber: 13.6 Consensus size: 27
408628 ATCATTAAAG
* *
408638 TTAAATCATTAAAGTTAAGTAATTATTT
1 TTAAATCATTAAAGTTAAATAATTA-TA
408666 TTAAATCATTAAAGTTAAATAATTATA
1 TTAAATCATTAAAGTTAAATAATTATA
*
408693 TT-AATCATTAAAGTTAAATCATTA-A
1 TTAAATCATTAAAGTTAAATAATTATA
* * * *
408718 GT-AATTATT--A-TTAAATCATTAAA
1 TTAAATCATTAAAGTTAAATAATTATA
408741 TTAAATCATTAAAGTTAAATAA-TATTA
1 TTAAATCATTAAAGTTAAATAATTA-TA
* * *
408768 TTAAATCATTAAATTTAAATCATTAAA
1 TTAAATCATTAAAGTTAAATAATTATA
* * * *
408795 GT-AATTATT--A-TTAAATCATTAAAA
1 TTAAATCATTAAAGTTAAATAATT-ATA
*
408819 TTAAATCATTAAAG-T-AATTA-T-TA
1 TTAAATCATTAAAGTTAAATAATTATA
*
408842 TT-AATC-TT-AAGTTAAATAAAGTAATTATT
1 TTAAATCATTAAAG-T---TAAA-TAATTATA
*
408871 TTAAAT-ATTAAAGTTAAGTAATTATTA
1 TTAAATCATTAAAGTTAAATAATTA-TA
*
408898 TTAAATCATTTAAAG-T-AATTA-T-TA
1 TTAAATCA-TTAAAGTTAAATAATTATA
* * *
408922 TTAAATCATTAAAATTAAATCATTAAA
1 TTAAATCATTAAAGTTAAATAATTATA
* * * *
408949 GT-AATTATT--A-TTAAATCATTAAA
1 TTAAATCATTAAAGTTAAATAATTATA
408972 GTTAAATCATTAAAGT
1 -TTAAATCATTAAAGT
408988 AATTGAAATA
Statistics
Matches: 255, Mismatches: 31, Indels: 72
0.71 0.09 0.20
Matches are distributed among these distances:
20 3 0.01
21 2 0.01
22 15 0.06
23 34 0.13
24 24 0.09
25 26 0.10
26 50 0.20
27 53 0.21
28 30 0.12
29 9 0.04
30 6 0.02
31 3 0.01
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.42
Consensus pattern (27 bp):
TTAAATCATTAAAGTTAAATAATTATA
Found at i:408738 original size:8 final size:8
Alignment explanation
Indices: 408706--408831 Score: 67
Period size: 8 Copynumber: 16.6 Consensus size: 8
408696 ATCATTAAAG
408706 TTAAATCA
1 TTAAATCA
* *
408714 TTAAGTAA
1 TTAAATCA
*
408722 TT--ATTA
1 TTAAATCA
408728 TTAAATCA
1 TTAAATCA
408736 TT-AA--A
1 TTAAATCA
408741 TTAAATCA
1 TTAAATCA
*
408749 TTAAAGTTAA
1 TTAAA--TCA
* *
408759 ATAATATTA
1 TTAA-ATCA
408768 TTAAATCA
1 TTAAATCA
408776 TTAAAT--
1 TTAAATCA
408782 TTAAATCA
1 TTAAATCA
*
408790 TTAAAGTAA
1 TTAAA-TCA
*
408799 TT--ATTA
1 TTAAATCA
408805 TTAAATCA
1 TTAAATCA
408813 TTAAA--A
1 TTAAATCA
408819 TTAAATCA
1 TTAAATCA
408827 TTAAA
1 TTAAA
408832 GTAATTATTA
Statistics
Matches: 90, Mismatches: 13, Indels: 30
0.68 0.10 0.23
Matches are distributed among these distances:
5 3 0.03
6 22 0.24
7 3 0.03
8 47 0.52
9 9 0.10
10 5 0.06
11 1 0.01
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (8 bp):
TTAAATCA
Found at i:408753 original size:103 final size:103
Alignment explanation
Indices: 408613--408948 Score: 309
Period size: 102 Copynumber: 3.2 Consensus size: 103
408603 CATTAAAGTC
408613 AAGTAATTATTA-TAAATCATTAAAGTTAAATCATTAAAGTTAAGTAATTATTTTTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAA-TTAAATCATTAAAGTTAAGTAATTATTTTTAAATCATTA
408677 AAGTTAAATAATTATATTAATCATTAAAGTTAAATCATT
65 AAGTTAAATAATTATATTAATCATTAAAGTTAAATCATT
* *
408716 AAGTAATTATTATTAAATCATTAAATTAAATCATTAAAGTTAAATAA-TATTATTAAATCATTAA
1 AAGTAATTATTATTAAATCATTAAATTAAATCATTAAAGTTAAGTAATTATTTTTAAATCATTAA
* * * * *
408780 ATTTAAATCATTAAAGTAATTATT--A-TTAAATCATT
66 AGTTAAATAATTATATTAATCATTAAAGTTAAATCATT
* * * *
408815 AA--AATTAAATCATTAAAGTAATTATTATT-AATCTTAAGTTAAA-TAAAGTAATTA-TTTTAA
1 AAGTAATT--ATTATTAAA-TCATTA-AATTAAATC---A-TTAAAGTTAAGTAATTATTTTTAA
* *
408875 AT-ATTAAAGTTAAGTAATTATTATTAAATCATTTAAAG-TAATTATTATT
58 ATCATTAAAGTTAAATAATTA-TATT-AATCA-TTAAAGTTAA--ATCATT
* * **
408924 AAATCATTAAAATTAAATCATTAAA
1 AAGTAATTATTATTAAATCATTAAA
408949 GTAATTATTA
Statistics
Matches: 188, Mismatches: 25, Indels: 36
0.76 0.10 0.14
Matches are distributed among these distances:
97 4 0.02
99 20 0.11
100 10 0.05
101 3 0.02
102 50 0.27
103 49 0.26
104 23 0.12
105 2 0.01
107 5 0.03
108 5 0.03
109 14 0.07
111 3 0.02
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.42
Consensus pattern (103 bp):
AAGTAATTATTATTAAATCATTAAATTAAATCATTAAAGTTAAGTAATTATTTTTAAATCATTAA
AGTTAAATAATTATATTAATCATTAAAGTTAAATCATT
Found at i:408857 original size:77 final size:75
Alignment explanation
Indices: 408666--408887 Score: 288
Period size: 77 Copynumber: 3.1 Consensus size: 75
408656 GTAATTATTT
* *
408666 TTAAATCATTAAAGTTAAATA-ATTATATTAATCATTAAAGTTAAATCATTAAGTAATTATTATT
1 TTAAATCATTAAAGTTAAATATATTAT-TAAATCATTAAATTTAAATCATTAAGTAATTATTATT
408730 AAATCATTAAA
65 AAATCATTAAA
408741 TTAAATCATTAAAGTTAAATAATATTATTAAATCATTAAATTTAAATCATTAAAGTAATTATTAT
1 TTAAATCATTAAAGTTAAAT-ATATTATTAAATCATTAAATTTAAATCATT-AAGTAATTATTAT
408806 TAAATCATTAAAA
64 TAAATCATT-AAA
*
408819 TTAAATCATTAAAG-T-AAT-TATTATT-AATC-TT-AAGTTAAAT-A--AAGTAATTATT-TTA
1 TTAAATCATTAAAGTTAAATATATTATTAAATCATTAAATTTAAATCATTAAGTAATTATTATTA
408874 AAT-ATTAAA
66 AATCATTAAA
408883 GTTAA
1 -TTAA
408888 GTAATTATTA
Statistics
Matches: 139, Mismatches: 3, Indels: 20
0.86 0.02 0.12
Matches are distributed among these distances:
64 3 0.02
65 7 0.05
66 6 0.04
67 11 0.08
70 1 0.01
71 8 0.06
72 2 0.01
73 4 0.03
74 7 0.05
75 20 0.14
76 25 0.18
77 28 0.20
78 17 0.12
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.42
Consensus pattern (75 bp):
TTAAATCATTAAAGTTAAATATATTATTAAATCATTAAATTTAAATCATTAAGTAATTATTATTA
AATCATTAAA
Found at i:408915 original size:24 final size:24
Alignment explanation
Indices: 408886--408931 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
408876 TATTAAAGTT
408886 AAGTAATTATTATTAAATCATTTA
1 AAGTAATTATTATTAAATCATTTA
408910 AAGTAATTATTATTAAATCATT
1 AAGTAATTATTATTAAATCATT
408932 AAAATTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (24 bp):
AAGTAATTATTATTAAATCATTTA
Found at i:408955 original size:23 final size:23
Alignment explanation
Indices: 408921--408973 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
408911 AGTAATTATT
*
408921 ATTAAA-TCATTAAAATTAAATC
1 ATTAAAGTAATTAAAATTAAATC
**
408943 ATTAAAGTAATTATTATTAAATC
1 ATTAAAGTAATTAAAATTAAATC
408966 ATTAAAGT
1 ATTAAAGT
408974 TAAATCATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 6 0.22
23 21 0.78
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.40
Consensus pattern (23 bp):
ATTAAAGTAATTAAAATTAAATC
Found at i:408986 original size:14 final size:14
Alignment explanation
Indices: 408587--408987 Score: 205
Period size: 14 Copynumber: 30.8 Consensus size: 14
408577 CTATTATTAT
408587 ATCATTAAA-TATAA
1 ATCATTAAAGT-TAA
*
408601 ATCATTAAAGTCAA
1 ATCATTAAAGTTAA
* * *
408615 GTAATT--ATTATAA
1 ATCATTAAAGT-TAA
408628 ATCATTAAAGTTAA
1 ATCATTAAAGTTAA
408642 ATCATTAAAGTTAA
1 ATCATTAAAGTTAA
* * ***
408656 GTAATTATTTTTAA
1 ATCATTAAAGTTAA
408670 ATCATTAAAGTTAA
1 ATCATTAAAGTTAA
* *
408684 ATAATTATA-TT-A
1 ATCATTAAAGTTAA
408696 ATCATTAAAGTTAA
1 ATCATTAAAGTTAA
408710 ATCATT-AAG-T-A
1 ATCATTAAAGTTAA
*
408721 ATTATT--A-TTAA
1 ATCATTAAAGTTAA
408732 ATCATTAAA-TTAA
1 ATCATTAAAGTTAA
408745 ATCATTAAAGTTAA
1 ATCATTAAAGTTAA
* *
408759 AT-AATATTA-TTAA
1 ATCATTA-AAGTTAA
*
408772 ATCATTAAATTTAA
1 ATCATTAAAGTTAA
408786 ATCATTAAAG-T-A
1 ATCATTAAAGTTAA
*
408798 ATTATT--A-TTAA
1 ATCATTAAAGTTAA
*
408809 ATCATTAAAATTAA
1 ATCATTAAAGTTAA
408823 ATCATTAAAG-T-A
1 ATCATTAAAGTTAA
*
408835 ATTATT--A-TT-A
1 ATCATTAAAGTTAA
408845 ATC-TT-AAGTTAA
1 ATCATTAAAGTTAA
* * *
408857 ATAAAGTAATTATTTTAA
1 AT-CATTAA--A-GTTAA
408875 AT-ATTAAAGTTAA
1 ATCATTAAAGTTAA
* * *
408888 GTAATTATTA-TTAA
1 ATCATTA-AAGTTAA
408902 ATCATTTAAAG-T-A
1 ATCA-TTAAAGTTAA
*
408915 ATTATT--A-TTAA
1 ATCATTAAAGTTAA
*
408926 ATCATTAAAATTAA
1 ATCATTAAAGTTAA
408940 ATCATTAAAG-T-A
1 ATCATTAAAGTTAA
*
408952 ATTATT--A-TTAA
1 ATCATTAAAGTTAA
408963 ATCATTAAAGTTAA
1 ATCATTAAAGTTAA
408977 ATCATTAAAGT
1 ATCATTAAAGT
408988 AATTGAAATA
Statistics
Matches: 295, Mismatches: 49, Indels: 86
0.69 0.11 0.20
Matches are distributed among these distances:
9 2 0.01
10 14 0.05
11 32 0.11
12 34 0.12
13 52 0.18
14 142 0.48
15 8 0.03
16 4 0.01
17 1 0.00
18 6 0.02
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (14 bp):
ATCATTAAAGTTAA
Found at i:408991 original size:37 final size:37
Alignment explanation
Indices: 408666--408887 Score: 268
Period size: 37 Copynumber: 6.1 Consensus size: 37
408656 GTAATTATTT
* *
408666 TTAAATCATTAAAGTTAAATAATTATATTAATCATTAAAG
1 TTAAATCATTAAAG-T-AATTATTAT-TAAATCATTAAAG
408706 TTAAATCATT-AAGTAATTATTATTAAATCATTAAA-
1 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
*
408741 TTAAATCATTAAAGTTAAATAATATTATTAAATCATTAAAT
1 TTAAATCATTAAAG-T-AAT--TATTATTAAATCATTAAAG
*
408782 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAA
1 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
408819 TTAAATCATTAAAGTAATTATTATT-AATC-TT-AAG
1 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
408853 TT-AA--A-TAAAGTAATTATT-TTAAAT-ATTAAAG
1 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
408884 TTAA
1 TTAA
408888 GTAATTATTA
Statistics
Matches: 168, Mismatches: 4, Indels: 28
0.84 0.02 0.14
Matches are distributed among these distances:
29 2 0.01
30 18 0.11
31 6 0.04
32 1 0.01
33 2 0.01
34 4 0.02
35 12 0.07
36 18 0.11
37 52 0.31
38 4 0.02
39 6 0.04
40 29 0.17
41 14 0.08
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.42
Consensus pattern (37 bp):
TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
Found at i:410966 original size:32 final size:32
Alignment explanation
Indices: 410927--411012 Score: 145
Period size: 32 Copynumber: 2.7 Consensus size: 32
410917 ATGATGCTGA
*
410927 TGAAGAAGACTCCGAGAACTCCACCCCAAGGC
1 TGAAGAAGACGCCGAGAACTCCACCCCAAGGC
*
410959 TGAAGAAGACGCCAAGAACTCCACCCCAAGGC
1 TGAAGAAGACGCCGAGAACTCCACCCCAAGGC
*
410991 TGAAGAAGACGCCGAGAGCTCC
1 TGAAGAAGACGCCGAGAACTCC
411013 CATGAACATT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.35, C:0.33, G:0.24, T:0.08
Consensus pattern (32 bp):
TGAAGAAGACGCCGAGAACTCCACCCCAAGGC
Found at i:411060 original size:43 final size:44
Alignment explanation
Indices: 410999--411084 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 44
410989 GCTGAAGAAG
410999 ACGCCGAGAGCTCCCATGAACA-TTTTGAACGAACATATATAGA
1 ACGCCGAGAGCTCCCATGAACACTTTTGAACGAACATATATAGA
*
411042 ACGCCGAGAGCTCCCATGAACATCTTTTGAACTAACATATATA
1 ACGCCGAGAGCTCCCATGAACA-CTTTTGAACGAACATATATA
411085 AAAGACGCCG
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
43 22 0.55
45 18 0.45
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.23
Consensus pattern (44 bp):
ACGCCGAGAGCTCCCATGAACACTTTTGAACGAACATATATAGA
Found at i:413840 original size:22 final size:20
Alignment explanation
Indices: 413815--413867 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
413805 CCTCTAAGTT
413815 TTTTTATTTTCTTTAATTATTA
1 TTTTTATTTTC-TTAA-TATTA
*
413837 TTTTT-TCTTTCTTAATATTT
1 TTTTTAT-TTTCTTAATATTA
413857 TTCTTTATTTT
1 TT-TTTATTTT
413868 ATTGCTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
20 6 0.22
21 11 0.41
22 10 0.37
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTTTATTTTCTTAATATTA
Found at i:413855 original size:17 final size:17
Alignment explanation
Indices: 413821--413863 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
413811 AGTTTTTTTA
*
413821 TTTTCTTTAATTATTATT
1 TTTTCTTTAATTAATA-T
*
413839 TTTTCTTT-CTTAATAT
1 TTTTCTTTAATTAATAT
413855 TTTTCTTTA
1 TTTTCTTTA
413864 TTTTATTGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 9 0.41
17 5 0.23
18 8 0.36
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTCTTTAATTAATAT
Found at i:413955 original size:4 final size:4
Alignment explanation
Indices: 413941--413999 Score: 68
Period size: 4 Copynumber: 15.0 Consensus size: 4
413931 TTCCCTTTTG
* **
413941 ATTT A-TT ATTT ATTT ATTTT ATTT ACTT A-AC ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT A-TTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
413988 ATTT ATTT ATTT
1 ATTT ATTT ATTT
414000 GTATAACATT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
3 4 0.09
4 39 0.83
5 4 0.09
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.69
Consensus pattern (4 bp):
ATTT
Found at i:413980 original size:35 final size:34
Alignment explanation
Indices: 413941--414024 Score: 109
Period size: 35 Copynumber: 2.4 Consensus size: 34
413931 TTCCCTTTTG
413941 ATTTATTATTTATTTATTTTATTTACT-TAACATTT
1 ATTTATTATTTATTTA-TTTATTT-CTATAACATTT
*
413976 ATTTATTTATTTATTTATTTATTTGTATAACATTT
1 ATTTA-TTATTTATTTATTTATTTCTATAACATTT
*
414011 -TTTATTTTTTATTT
1 ATTTATTATTTATTT
414025 TCTAATTTGA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
33 9 0.20
34 5 0.11
35 20 0.44
36 11 0.24
ACGTcount: A:0.26, C:0.04, G:0.01, T:0.69
Consensus pattern (34 bp):
ATTTATTATTTATTTATTTATTTCTATAACATTT
Found at i:414053 original size:14 final size:14
Alignment explanation
Indices: 414034--414062 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
414024 TTCTAATTTG
414034 AATCAAAGGTAAAC
1 AATCAAAGGTAAAC
414048 AATCAAAGGTAAAC
1 AATCAAAGGTAAAC
414062 A
1 A
414063 TTTTTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.14, G:0.14, T:0.14
Consensus pattern (14 bp):
AATCAAAGGTAAAC
Found at i:417891 original size:46 final size:47
Alignment explanation
Indices: 417834--417949 Score: 182
Period size: 46 Copynumber: 2.5 Consensus size: 47
417824 ATTAACATAG
*
417834 TATTTTTATTTTTCAATGATGATGTGATTAACATAATATTTTTA-TA
1 TATTTTTATTTTTCAATGATGATGTGATTAACAAAATATTTTTATTA
* *
417880 TATTATTATTTTTCAATGATGATGTGATTAATAAAATATTTTTATTA
1 TATTTTTATTTTTCAATGATGATGTGATTAACAAAATATTTTTATTA
417927 TATTTTTATTTTTTCAATG-TGAT
1 TATTTTTA-TTTTTCAATGATGAT
417950 ATTATTTTGT
Statistics
Matches: 64, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
46 41 0.64
47 13 0.20
48 10 0.16
ACGTcount: A:0.32, C:0.03, G:0.09, T:0.56
Consensus pattern (47 bp):
TATTTTTATTTTTCAATGATGATGTGATTAACAAAATATTTTTATTA
Found at i:419150 original size:12 final size:12
Alignment explanation
Indices: 419123--419192 Score: 54
Period size: 12 Copynumber: 5.8 Consensus size: 12
419113 GCGAAGATAT
* *
419123 CAGAAATCAAAA
1 CAGAATTCAGAA
*
419135 CAGAATTCAGAT
1 CAGAATTCAGAA
419147 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
*
419159 CAGAATCCA-AA
1 CAGAATTCAGAA
*
419170 TCAGAAATCAGAA
1 -CAGAATTCAGAA
*
419183 CAAAATTCAG
1 CAGAATTCAG
419193 GTCATGTATC
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
11 4 0.09
12 37 0.82
13 4 0.09
ACGTcount: A:0.53, C:0.19, G:0.13, T:0.16
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:419155 original size:24 final size:24
Alignment explanation
Indices: 419121--419215 Score: 102
Period size: 24 Copynumber: 4.0 Consensus size: 24
419111 AAGCGAAGAT
419121 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * *
419145 ATCAGATATCAGAACAGAATCCAA
1 ATCAGAAATCAAAACAGAATTCAG
* *
419169 ATCAGAAATCAGAACAAAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* *
419193 GTCATG-TATCAAAACAGAATTCA
1 ATCA-GAAATCAAAACAGAATTCA
419216 AGTCAAAAAT
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
24 57 0.98
25 1 0.02
ACGTcount: A:0.51, C:0.18, G:0.13, T:0.19
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:419192 original size:48 final size:48
Alignment explanation
Indices: 419121--419229 Score: 139
Period size: 48 Copynumber: 2.3 Consensus size: 48
419111 AAGCGAAGAT
* * *
419121 ATCAGAAATCAAAACAGAATTCAGATCA-GATATCAGAACAGAATCCAA
1 ATCAGAAATCAGAACAAAATTCAGATCATG-TATCAAAACAGAATCCAA
* *
419169 ATCAGAAATCAGAACAAAATTCAGGTCATGTATCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAAAATTCAGATCATGTATCAAAACAGAATCCAA
* *
419217 GTCAAAAATCAGA
1 ATCAGAAATCAGA
419230 TAAAATATTT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
48 52 0.98
49 1 0.02
ACGTcount: A:0.51, C:0.17, G:0.13, T:0.18
Consensus pattern (48 bp):
ATCAGAAATCAGAACAAAATTCAGATCATGTATCAAAACAGAATCCAA
Found at i:419227 original size:24 final size:24
Alignment explanation
Indices: 419122--419227 Score: 99
Period size: 24 Copynumber: 4.4 Consensus size: 24
419112 AGCGAAGATA
419122 TCAGAAATCAAAACAGAATTC-AG
1 TCAGAAATCAAAACAGAATTCAAG
* * * *
419145 ATCAGATATCAGAACAGAATCCAAA
1 -TCAGAAATCAAAACAGAATTCAAG
* * *
419170 TCAGAAATCAGAACAAAATTCAGG
1 TCAGAAATCAAAACAGAATTCAAG
*
419194 TCATG-TATCAAAACAGAATTCAAG
1 TCA-GAAATCAAAACAGAATTCAAG
*
419218 TCAAAAATCA
1 TCAGAAATCA
419228 GATAAAATAT
Statistics
Matches: 64, Mismatches: 15, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
24 62 0.97
25 2 0.03
ACGTcount: A:0.51, C:0.18, G:0.12, T:0.19
Consensus pattern (24 bp):
TCAGAAATCAAAACAGAATTCAAG
Found at i:434813 original size:7 final size:8
Alignment explanation
Indices: 434796--434820 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
434786 ATTTTTTAAT
434796 AAAAATAA
1 AAAAATAA
434804 AAAAATAA
1 AAAAATAA
434812 AAAAATAA
1 AAAAATAA
434820 A
1 A
434821 TCCCCACCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAATAA
Found at i:447351 original size:21 final size:21
Alignment explanation
Indices: 447327--447371 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
447317 GGAGTACGGA
447327 GGACGGTGGACGGCAAGCGAC
1 GGACGGTGGACGGCAAGCGAC
*
447348 GGACGGTGGATGGCAAGCGAC
1 GGACGGTGGACGGCAAGCGAC
447369 GGA
1 GGA
447372 TGACGATGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.24, C:0.20, G:0.49, T:0.07
Consensus pattern (21 bp):
GGACGGTGGACGGCAAGCGAC
Found at i:459363 original size:33 final size:33
Alignment explanation
Indices: 459321--459391 Score: 142
Period size: 33 Copynumber: 2.2 Consensus size: 33
459311 TAAAATTTGA
459321 GCTCAATTGAAGCGAAAGAATAGTTCGCTCTGT
1 GCTCAATTGAAGCGAAAGAATAGTTCGCTCTGT
459354 GCTCAATTGAAGCGAAAGAATAGTTCGCTCTGT
1 GCTCAATTGAAGCGAAAGAATAGTTCGCTCTGT
459387 GCTCA
1 GCTCA
459392 CCAAAAGACT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.27
Consensus pattern (33 bp):
GCTCAATTGAAGCGAAAGAATAGTTCGCTCTGT
Found at i:462034 original size:37 final size:36
Alignment explanation
Indices: 461992--462063 Score: 117
Period size: 37 Copynumber: 2.0 Consensus size: 36
461982 AAAATAAATT
*
461992 TTAAGGGCAACTTCGTAATAATAAGTATTGAAAAAAA
1 TTAAGGGCAACTTCATAATAATAAGTATT-AAAAAAA
*
462029 TTAAGGGTAACTTCATAATAATAAGTATTAAAAAA
1 TTAAGGGCAACTTCATAATAATAAGTATTAAAAAA
462064 TGAGTTTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
36 6 0.18
37 27 0.82
ACGTcount: A:0.50, C:0.07, G:0.14, T:0.29
Consensus pattern (36 bp):
TTAAGGGCAACTTCATAATAATAAGTATTAAAAAAA
Found at i:467341 original size:28 final size:28
Alignment explanation
Indices: 467282--467346 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
467272 CAACAGAGTC
* * *
467282 GACCATATATCAATCAGGCGGTAAAACC
1 GACCATATATCAATCAGACGGCAAAACA
* * *
467310 GACCATATGTCAATCAGACGGCAGAGCA
1 GACCATATATCAATCAGACGGCAAAACA
467338 GACCATATA
1 GACCATATA
467347 ACAAAACTAA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.38, C:0.25, G:0.20, T:0.17
Consensus pattern (28 bp):
GACCATATATCAATCAGACGGCAAAACA
Found at i:467833 original size:2 final size:2
Alignment explanation
Indices: 467826--467903 Score: 156
Period size: 2 Copynumber: 39.0 Consensus size: 2
467816 ACTAACTAAC
467826 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
467868 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
467904 GGGTTAAAGT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 76 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:477720 original size:39 final size:39
Alignment explanation
Indices: 477694--477785 Score: 148
Period size: 39 Copynumber: 2.4 Consensus size: 39
477684 GCCAAACTTA
* *
477694 AAGACTCCAGGAGTGCACGGCATCTTTAGATCAATGGAT
1 AAGACTCCAGGAGTGCACGACATCTTTAGACCAATGGAT
* *
477733 AAGACTCCAGGAGTGCACGACGTCTTTAGATCAATGGAT
1 AAGACTCCAGGAGTGCACGACATCTTTAGACCAATGGAT
477772 AAGACTCCAGGAGT
1 AAGACTCCAGGAGT
477786 ACTTAGCGTC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 51 1.00
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.22
Consensus pattern (39 bp):
AAGACTCCAGGAGTGCACGACATCTTTAGACCAATGGAT
Found at i:478138 original size:60 final size:60
Alignment explanation
Indices: 478074--478191 Score: 182
Period size: 60 Copynumber: 2.0 Consensus size: 60
478064 TATTTTTATC
* *
478074 TTGATAGTTGATCGTCCATATTCATCTTTATTATTATTTTTAGTTTGCTATCTTTTCATG
1 TTGATAGTTAATCGTCCATATTCATCTTTATTATCATTTTTAGTTTGCTATCTTTTCATG
** * *
478134 TTGATAGTTAATCGTCTGTATTTATCTTTATTATCATTTTTAGTTTGTTATCTTTTCA
1 TTGATAGTTAATCGTCCATATTCATCTTTATTATCATTTTTAGTTTGCTATCTTTTCA
478192 GTTTTTATTC
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.20, C:0.12, G:0.11, T:0.57
Consensus pattern (60 bp):
TTGATAGTTAATCGTCCATATTCATCTTTATTATCATTTTTAGTTTGCTATCTTTTCATG
Found at i:480517 original size:20 final size:20
Alignment explanation
Indices: 480492--480565 Score: 130
Period size: 20 Copynumber: 3.7 Consensus size: 20
480482 GCGTAGCTAG
* *
480492 GCACTGAAGATGACGCTCAA
1 GCACTGAAGGTGGCGCTCAA
480512 GCACTGAAGGTGGCGCTCAA
1 GCACTGAAGGTGGCGCTCAA
480532 GCACTGAAGGTGGCGCTCAA
1 GCACTGAAGGTGGCGCTCAA
480552 GCACTGAAGGTGGC
1 GCACTGAAGGTGGC
480566 ATCCGCCTGG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.27, C:0.24, G:0.34, T:0.15
Consensus pattern (20 bp):
GCACTGAAGGTGGCGCTCAA
Found at i:480917 original size:12 final size:12
Alignment explanation
Indices: 480900--480934 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
480890 GAAATGAAAA
480900 TGACAGTGGATG
1 TGACAGTGGATG
480912 TGACAGTGGATG
1 TGACAGTGGATG
480924 TGACAGTGGAT
1 TGACAGTGGAT
480935 AGTGCACATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.26, C:0.09, G:0.40, T:0.26
Consensus pattern (12 bp):
TGACAGTGGATG
Found at i:498351 original size:23 final size:23
Alignment explanation
Indices: 498321--498473 Score: 272
Period size: 23 Copynumber: 6.7 Consensus size: 23
498311 ACAGCAACCG
* *
498321 ACAAGCATCACTGTATCAATTCA
1 ACAAGCATCATTGCATCAATTCA
498344 ACAAGCATCATTGCATCAATTCA
1 ACAAGCATCATTGCATCAATTCA
498367 ACAAGCATCATTGCATCAATTCA
1 ACAAGCATCATTGCATCAATTCA
*
498390 GCAAGCATCATTGCATCAATTCA
1 ACAAGCATCATTGCATCAATTCA
498413 ACAAGCATCATTGCATCAATTCA
1 ACAAGCATCATTGCATCAATTCA
498436 ACAAGCATCATTGCATCAATTCA
1 ACAAGCATCATTGCATCAATTCA
498459 ACAAGCATCA-TGCAT
1 ACAAGCATCATTGCAT
498474 TCAGAAAACA
Statistics
Matches: 126, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
22 5 0.04
23 121 0.96
ACGTcount: A:0.39, C:0.26, G:0.10, T:0.25
Consensus pattern (23 bp):
ACAAGCATCATTGCATCAATTCA
Found at i:498592 original size:20 final size:20
Alignment explanation
Indices: 498559--498609 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
498549 AACCCTTACA
**
498559 AATATCAAGTAGAAG-AAAGC
1 AATATCAAACAGAAGCAAA-C
498579 AATATCAAACAGAAGCAAAC
1 AATATCAAACAGAAGCAAAC
*
498599 AATATAAAACA
1 AATATCAAACA
498610 TAATCAAGCG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 24 0.89
21 3 0.11
ACGTcount: A:0.61, C:0.14, G:0.12, T:0.14
Consensus pattern (20 bp):
AATATCAAACAGAAGCAAAC
Found at i:498623 original size:20 final size:20
Alignment explanation
Indices: 498600--498637 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
498590 GAAGCAAACA
498600 ATATAAAACATAATCAAGCG
1 ATATAAAACATAATCAAGCG
* *
498620 ATATCAAGCATAATCAAG
1 ATATAAAACATAATCAAG
498638 TATCAACTAT
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:0.53, C:0.16, G:0.11, T:0.21
Consensus pattern (20 bp):
ATATAAAACATAATCAAGCG
Found at i:501236 original size:18 final size:18
Alignment explanation
Indices: 501209--501341 Score: 88
Period size: 18 Copynumber: 7.4 Consensus size: 18
501199 ATAGTTTTGA
*
501209 TTCGGTTTTGGATTTGGG
1 TTCGGGTTTGGATTTGGG
* *
501227 TTCGGGTTTGGATTTAGA
1 TTCGGGTTTGGATTTGGG
**
501245 TTCAAGTTTGGA-TTGGG
1 TTCGGGTTTGGATTTGGG
* *
501262 TTCGGGTTTAGATTCGGG
1 TTCGGGTTTGGATTTGGG
** * *
501280 TTTAGGTTTGGGTTTGGT
1 TTCGGGTTTGGATTTGGG
* * * * *
501298 TTCAGGTTCGGGTTCGAG
1 TTCGGGTTTGGATTTGGG
* *
501316 TTTGGATTTGGATTTGGG
1 TTCGGGTTTGGATTTGGG
*
501334 TTCTGGTT
1 TTCGGGTT
501342 AGGTTTAGAG
Statistics
Matches: 82, Mismatches: 32, Indels: 2
0.71 0.28 0.02
Matches are distributed among these distances:
17 12 0.15
18 70 0.85
ACGTcount: A:0.11, C:0.07, G:0.37, T:0.46
Consensus pattern (18 bp):
TTCGGGTTTGGATTTGGG
Found at i:501795 original size:103 final size:104
Alignment explanation
Indices: 501656--501847 Score: 350
Period size: 103 Copynumber: 1.9 Consensus size: 104
501646 GATGAATTTT
*
501656 TGGGTGTTTGATCCAAAAAAACACTAAATGATTTGGGTTTTGGTGTTTGTGAAGATCAAATGAGG
1 TGGGTGTTTGATCCAAAAAAACACGAAATGATTTGGGTTTTGGTGTTTGTGAAGATCAAATGAGG
*
501721 GTTTTTGGGATCAACACGGATGAACAATGGTTGAAATTA
66 GGTTTTGGGATCAACACGGATGAACAATGGTTGAAATTA
501760 TGGGTGTTTGATCC-AAAAAACACGAAATGATTTGGGTTTTGGTGTTTGTGAAGATCAAATGAGG
1 TGGGTGTTTGATCCAAAAAAACACGAAATGATTTGGGTTTTGGTGTTTGTGAAGATCAAATGAGG
*
501824 GGTTTTGGGATGAACACGGATGAA
66 GGTTTTGGGATCAACACGGATGAA
501848 AACTTATGAA
Statistics
Matches: 85, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
103 71 0.84
104 14 0.16
ACGTcount: A:0.31, C:0.08, G:0.29, T:0.32
Consensus pattern (104 bp):
TGGGTGTTTGATCCAAAAAAACACGAAATGATTTGGGTTTTGGTGTTTGTGAAGATCAAATGAGG
GGTTTTGGGATCAACACGGATGAACAATGGTTGAAATTA
Found at i:502135 original size:29 final size:29
Alignment explanation
Indices: 502097--502195 Score: 80
Period size: 28 Copynumber: 3.3 Consensus size: 29
502087 CAATGCAATG
502097 TATT-AATTTAAGCTTCATATTTAAAATT
1 TATTCAATTTAAGCTTCATATTTAAAATT
* * *
502125 TCTTCAATTT-AG-TCCAAATATAATGTTACAATT
1 TATTCAATTTAAGCTTC----AT-AT-TTAAAATT
502158 TATT-AATTTAAGCTTCATATTTAAAATT
1 TATTCAATTTAAGCTTCATATTTAAAATT
*
502186 TGTTCAATTT
1 TATTCAATTT
502196 TATCCTTATA
Statistics
Matches: 54, Mismatches: 7, Indels: 19
0.68 0.09 0.24
Matches are distributed among these distances:
27 2 0.04
28 15 0.28
29 12 0.22
30 2 0.04
31 2 0.04
32 7 0.13
33 12 0.22
34 2 0.04
ACGTcount: A:0.36, C:0.10, G:0.05, T:0.48
Consensus pattern (29 bp):
TATTCAATTTAAGCTTCATATTTAAAATT
Found at i:502207 original size:61 final size:61
Alignment explanation
Indices: 502057--502195 Score: 201
Period size: 61 Copynumber: 2.3 Consensus size: 61
502047 GTTTCTTACT
* *** *
502057 TTTAAAA-TT-TTCAATTTAGTCCAAATTTAACAATGCAATGTATTAATTTAAGCTTCATA
1 TTTAAAATTTCTTCAATTTAGTCCAAATATAATGTTACAATGTATTAATTTAAGCTTCATA
*
502116 TTTAAAATTTCTTCAATTTAGTCCAAATATAATGTTACAATTTATTAATTTAAGCTTCATA
1 TTTAAAATTTCTTCAATTTAGTCCAAATATAATGTTACAATGTATTAATTTAAGCTTCATA
*
502177 TTTAAAATTTGTTCAATTT
1 TTTAAAATTTCTTCAATTT
502196 TATCCTTATA
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
59 7 0.10
60 2 0.03
61 62 0.87
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46
Consensus pattern (61 bp):
TTTAAAATTTCTTCAATTTAGTCCAAATATAATGTTACAATGTATTAATTTAAGCTTCATA
Found at i:502325 original size:13 final size:13
Alignment explanation
Indices: 502309--502339 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
502299 TGTATATACC
*
502309 ATATACTTTATAT
1 ATATACTTCATAT
502322 ATATACTTCATAT
1 ATATACTTCATAT
502335 ATATA
1 ATATA
502340 GTTAATATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (13 bp):
ATATACTTCATAT
Found at i:502347 original size:13 final size:13
Alignment explanation
Indices: 502309--502347 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
502299 TGTATATACC
*
502309 ATATACTTTATAT
1 ATATACTTAATAT
*
502322 ATATACTTCATAT
1 ATATACTTAATAT
*
502335 ATATAGTTAATAT
1 ATATACTTAATAT
502348 GTAAACTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.49
Consensus pattern (13 bp):
ATATACTTAATAT
Found at i:502370 original size:18 final size:18
Alignment explanation
Indices: 502349--502395 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
502339 AGTTAATATG
502349 TAAACTATATAGTCTA-TA
1 TAAACTATATA-TCTAGTA
*
502367 TAAACTATATATGTAGTA
1 TAAACTATATATCTAGTA
*
502385 TATACTATATA
1 TAAACTATATA
502396 AATAGTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 3 0.12
18 23 0.88
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.40
Consensus pattern (18 bp):
TAAACTATATATCTAGTA
Found at i:502509 original size:27 final size:27
Alignment explanation
Indices: 502474--502545 Score: 108
Period size: 27 Copynumber: 2.7 Consensus size: 27
502464 TAGTATAAGT
*
502474 TATATTATATAGTATATAAATATCAAC
1 TATACTATATAGTATATAAATATCAAC
* *
502501 TATAGTATATACTATATAAATATCAAC
1 TATACTATATAGTATATAAATATCAAC
*
502528 TATACTATATAGTTTATA
1 TATACTATATAGTATATA
502546 TGGTTTTTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (27 bp):
TATACTATATAGTATATAAATATCAAC
Found at i:502615 original size:20 final size:20
Alignment explanation
Indices: 502590--502782 Score: 68
Period size: 20 Copynumber: 8.9 Consensus size: 20
502580 TATTTAGTAA
502590 ATATAGTTTATATATATAAT
1 ATATAGTTTATATATATAAT
* *
502610 ATATAGTATATAAATATCAACT
1 ATATAGTTTATATATAT-AA-T
* *
502632 ATGGTATGTAGTGTATAAATATAA-
1 A---TA--TAGTTTATATATATAAT
*
502656 ACTATAGTTTATATATATAGT
1 A-TATAGTTTATATATATAAT
* * * *
502677 ATATACTATATAAATAGT-TT
1 ATATAGTTTATATATA-TAAT
* *
502697 ATATAGTTCACTATTAAACTATAT
1 ATATAGTTTA-TA-TATA-TA-AT
* *
502721 ATATAGTTCAGTATTAAACTATAT
1 ATATAGTTTA-TA-TATA-TA-AT
*
502745 ATATAGTTCATATATA-AACT
1 ATATAGTTTATATATATAA-T
*
502765 ATATAATTTATATATATA
1 ATATAGTTTATATATATA
502783 GTTCATATGT
Statistics
Matches: 136, Mismatches: 22, Indels: 29
0.73 0.12 0.16
Matches are distributed among these distances:
19 1 0.01
20 64 0.47
21 7 0.05
22 10 0.07
23 2 0.01
24 35 0.26
25 2 0.01
26 2 0.01
27 13 0.10
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.43
Consensus pattern (20 bp):
ATATAGTTTATATATATAAT
Found at i:502686 original size:18 final size:18
Alignment explanation
Indices: 502665--502699 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
502655 AACTATAGTT
*
502665 TATATATATAGTATATAC
1 TATATAAATAGTATATAC
*
502683 TATATAAATAGTTTATA
1 TATATAAATAGTATATA
502700 TAGTTCACTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.46
Consensus pattern (18 bp):
TATATAAATAGTATATAC
Found at i:502723 original size:24 final size:24
Alignment explanation
Indices: 502712--502769 Score: 100
Period size: 24 Copynumber: 2.4 Consensus size: 24
502702 GTTCACTATT
502712 AAACTATATATATAGTTCAGTAT-T
1 AAACTATATATATAGTTCA-TATAT
502736 AAACTATATATATAGTTCATATAT
1 AAACTATATATATAGTTCATATAT
502760 AAACTATATA
1 AAACTATATA
502770 ATTTATATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 3 0.09
24 30 0.91
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.40
Consensus pattern (24 bp):
AAACTATATATATAGTTCATATAT
Found at i:502758 original size:33 final size:33
Alignment explanation
Indices: 502735--502813 Score: 99
Period size: 33 Copynumber: 2.4 Consensus size: 33
502725 AGTTCAGTAT
502735 TAAACTATATATATAGTTCATATATAAACTATA
1 TAAACTATATATATAGTTCATATATAAACTATA
** * *
502768 TAATTTATATATATAGTTCATATGT-AA-TAATG
1 TAAACTATATATATAGTTCATATATAAACT-ATA
502800 TAAACTATATATAT
1 TAAACTATATATAT
502814 TATATAGTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
31 1 0.03
32 16 0.41
33 22 0.56
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.43
Consensus pattern (33 bp):
TAAACTATATATATAGTTCATATATAAACTATA
Found at i:502812 original size:2 final size:2
Alignment explanation
Indices: 502805--502932 Score: 61
Period size: 2 Copynumber: 62.0 Consensus size: 2
502795 TAATGTAAAC
* *
502805 TA TA TA TA T- TA TA TA GTA TA TA AA TA TCA -A CTA TA GTA CA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA T-A TA -TA TA -TA TA TA
* * *
502847 GTT TA TA TA TA TA TA -A T- TCA TA TG TA AA T- TA TA TA GTA TA
1 -TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA -TA TA
* *
502887 TA TA CTT TA TA TA TA TA TA GTT TA TA TA TA TA TA T- TA TA TA CTA
1 TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA
502931 TA
1 TA
502933 AAAATAGTTT
Statistics
Matches: 96, Mismatches: 14, Indels: 32
0.68 0.10 0.23
Matches are distributed among these distances:
1 6 0.06
2 76 0.79
3 14 0.15
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.47
Consensus pattern (2 bp):
TA
Found at i:502826 original size:9 final size:8
Alignment explanation
Indices: 502805--502932 Score: 61
Period size: 9 Copynumber: 15.5 Consensus size: 8
502795 TAATGTAAAC
502805 TATATATA
1 TATATATA
502813 T-TATATA
1 TATATATA
*
502820 GTATATAAA
1 -TATATATA
502829 TATCA-ACTA
1 TAT-ATA-TA
*
502838 TAGTACATA
1 TA-TATATA
*
502847 GTTTATATA
1 -TATATATA
502856 TATATA-A
1 TATATATA
*
502863 T-TCATATG
1 TAT-ATATA
*
502871 TAAAT-TA
1 TATATATA
502878 TATAGTATA
1 TATA-TATA
*
502887 TATACTTTA
1 TATA-TATA
502896 TATATATA
1 TATATATA
*
502904 TAGTTTATA
1 TA-TATATA
502913 TATATATA
1 TATATATA
502921 T-TATATA
1 TATATATA
502928 CTATA
1 -TATA
502933 AAAATAGTTT
Statistics
Matches: 91, Mismatches: 14, Indels: 29
0.68 0.10 0.22
Matches are distributed among these distances:
6 1 0.01
7 21 0.23
8 27 0.30
9 39 0.43
10 3 0.03
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.47
Consensus pattern (8 bp):
TATATATA
Found at i:502905 original size:17 final size:16
Alignment explanation
Indices: 502875--502932 Score: 68
Period size: 15 Copynumber: 3.7 Consensus size: 16
502865 CATATGTAAA
502875 TTATATAGTATATATAC
1 TTATATA-TATATATAC
*
502892 TT-TATATATATATAG
1 TTATATATATATATAC
502907 TT-TATATATATATA-
1 TTATATATATATATAC
502921 TTATATACTATA
1 TTATATA-TATA
502933 AAAATAGTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
14 2 0.05
15 26 0.68
16 8 0.21
17 2 0.05
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.52
Consensus pattern (16 bp):
TTATATATATATATAC
Found at i:509180 original size:22 final size:22
Alignment explanation
Indices: 509120--509182 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 22
509110 TTGGTGCAGA
*
509120 GGGAATTGATACCCCCCTTGAAG
1 GGGAATCGATACCCCCC-TGAAG
* * *
509143 GGGAACCGAT-TCCCCCTGTAG
1 GGGAATCGATACCCCCCTGAAG
509164 GGGAATCGATACCCCCCTG
1 GGGAATCGATACCCCCCTG
509183 GGGTTATGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
21 13 0.39
22 12 0.36
23 8 0.24
ACGTcount: A:0.22, C:0.32, G:0.27, T:0.19
Consensus pattern (22 bp):
GGGAATCGATACCCCCCTGAAG
Found at i:511075 original size:17 final size:16
Alignment explanation
Indices: 511046--511111 Score: 64
Period size: 16 Copynumber: 4.1 Consensus size: 16
511036 CATTTTGGAT
*
511046 ATTTTGGAATGTTTGA
1 ATTTTGGATTGTTTGA
511062 ATTTGTGGATTGTTTG-
1 ATTT-TGGATTGTTTGA
* *
511078 ACTTTGAATTTGTTTGA
1 ATTTTGGA-TTGTTTGA
511095 ATTTATGGA-TGTTTGA
1 ATTT-TGGATTGTTTGA
511111 A
1 A
511112 CTTATATTTC
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
15 3 0.07
16 22 0.54
17 13 0.32
18 3 0.07
ACGTcount: A:0.23, C:0.02, G:0.24, T:0.52
Consensus pattern (16 bp):
ATTTTGGATTGTTTGA
Found at i:512584 original size:22 final size:22
Alignment explanation
Indices: 512552--512609 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
512542 CTATATATAA
512552 TATATTATATAGTTTACATAGTT
1 TATA-TATATAGTTTACATAGTT
* *
512575 TATATATATATTTTATATAGTT
1 TATATATATAGTTTACATAGTT
*
512597 TATAGATATAGTT
1 TATATATATAGTT
512610 CATATGTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 27 0.87
23 4 0.13
ACGTcount: A:0.36, C:0.02, G:0.09, T:0.53
Consensus pattern (22 bp):
TATATATATAGTTTACATAGTT
Found at i:512766 original size:2 final size:2
Alignment explanation
Indices: 512754--513043 Score: 62
Period size: 2 Copynumber: 147.5 Consensus size: 2
512744 CCCTAAATCG
* *
512754 TA TA TA CTA TA TA TA TA TA -A AA TA TA TA GTT TA TA T- TA -A TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * * * *
512795 CA CTA TA TA -A TT TA CA CA TA GTA TA TA T- TA -A TA AA CTA TA
1 TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA
* * * *
512835 TA -A TT TA TA CA TA GTA TA TA T- TA TT TA TA -A T- TA TA CA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
512874 -A TA TA TA AA TA TA AA T- TA TA TA GTT TA TA TA TA -A T- TCA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA T-A TA
* * * *
512914 TA TA -A TT TA TA TA TA AA CTA TA TA GTA T- TA TA GTT TA TA CA
1 TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA -TA TA TA TA
* * * *
512955 TG TA TA TA TA GTT TA TA CA TA -A TA TA TA TA GTT TA TA TA TA GTA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA
* * * * *
512999 TA TA -A TA -A TA TA AA TA TA AA CA T- TA TA GTT TT TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
513039 TA TA T
1 TA TA T
513044 TGTTTCATTT
Statistics
Matches: 205, Mismatches: 48, Indels: 70
0.63 0.15 0.22
Matches are distributed among these distances:
1 20 0.10
2 165 0.80
3 20 0.10
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (2 bp):
TA
Found at i:512816 original size:33 final size:33
Alignment explanation
Indices: 512779--512857 Score: 131
Period size: 33 Copynumber: 2.4 Consensus size: 33
512769 TATAAAATAT
* *
512779 ATAGTTTATATTAATACACTATATAATTTACAC
1 ATAGTATATATTAATAAACTATATAATTTACAC
*
512812 ATAGTATATATTAATAAACTATATAATTTATAC
1 ATAGTATATATTAATAAACTATATAATTTACAC
512845 ATAGTATATATTA
1 ATAGTATATATTA
512858 TTTATAATTA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.43
Consensus pattern (33 bp):
ATAGTATATATTAATAAACTATATAATTTACAC
Found at i:512894 original size:9 final size:10
Alignment explanation
Indices: 512849--513017 Score: 62
Period size: 11 Copynumber: 15.7 Consensus size: 10
512839 TTATACATAG
512849 TATAT-ATTA
1 TATATAATTA
*
512858 TTTATAATTA
1 TATATAATTA
*
512868 TACATAATATA
1 TATATAAT-TA
512879 TAAATATAAATTA
1 T--ATAT-AATTA
512892 TATAGT--TTA
1 TATA-TAATTA
512901 TATATAATTCA
1 TATATAATT-A
512912 TATATAATTTA
1 TATATAA-TTA
*
512923 TATATAAACTA
1 TATAT-AATTA
512934 TATAGT-ATTA
1 TATA-TAATTA
512944 TAGTTTATACATGTA
1 TA---TATA-AT-TA
*
512959 TATATAGTTTA
1 TATATA-ATTA
*
512970 TACATAA-TA
1 TATATAATTA
*
512979 TATATAGTT-
1 TATATAATTA
*
512988 TATATATAGTA
1 TATATA-ATTA
512999 TATAATAATATA
1 TAT-ATAAT-TA
*
513011 AATATAA
1 TATATAA
513018 ACATTATAGT
Statistics
Matches: 121, Mismatches: 16, Indels: 44
0.67 0.09 0.24
Matches are distributed among these distances:
8 1 0.01
9 24 0.20
10 19 0.16
11 41 0.34
12 19 0.16
13 8 0.07
14 5 0.04
15 4 0.03
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (10 bp):
TATATAATTA
Found at i:512906 original size:11 final size:11
Alignment explanation
Indices: 512890--513002 Score: 68
Period size: 11 Copynumber: 11.2 Consensus size: 11
512880 AAATATAAAT
512890 TATATAGTTTA
1 TATATAGTTTA
* *
512901 TATATAATTCA
1 TATATAGTTTA
*
512912 TATATAATTTA
1 TATATAGTTTA
*
512923 TATATA---AA
1 TATATAGTTTA
512931 CTATATAG--TA
1 -TATATAGTTTA
512941 T-TATAGTTTA
1 TATATAGTTTA
*
512951 TACAT-G--TA
1 TATATAGTTTA
512959 TATATAGTTTA
1 TATATAGTTTA
* *
512970 TACATA--ATA
1 TATATAGTTTA
512979 TATATAGTTTA
1 TATATAGTTTA
*
512990 TATATAGTATA
1 TATATAGTTTA
513001 TA
1 TA
513003 ATAATATAAA
Statistics
Matches: 80, Mismatches: 12, Indels: 20
0.71 0.11 0.18
Matches are distributed among these distances:
8 12 0.15
9 15 0.19
10 5 0.06
11 48 0.60
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (11 bp):
TATATAGTTTA
Found at i:512907 original size:20 final size:21
Alignment explanation
Indices: 512882--513043 Score: 109
Period size: 20 Copynumber: 7.6 Consensus size: 21
512872 TAATATATAA
512882 ATATAAAT-TATATAGTTTAT
1 ATATAAATATATATAGTTTAT
* *
512902 ATATAATTCATATATAATTTAT
1 ATATAAAT-ATATATAGTTTAT
512924 ATATAAACTATATAGTA-TTATAGT
1 ATATAAA-TATATA-TAGTT-TA-T
* *
512948 TTATACATGTATATATAGTTTAT
1 ATATA-A-ATATATATAGTTTAT
*
512971 ACAT-AATATATATAGTTTAT
1 ATATAAATATATATAGTTTAT
* * * *
512991 ATAT-AGTATATAATAATATAA
1 ATATAAATATAT-ATAGTTTAT
* *
513012 ATATAAACAT-TATAGTTTTT
1 ATATAAATATATATAGTTTAT
*
513032 ATATATATATAT
1 ATATAAATATAT
513044 TGTTTCATTT
Statistics
Matches: 109, Mismatches: 21, Indels: 23
0.71 0.14 0.15
Matches are distributed among these distances:
20 43 0.39
21 13 0.12
22 27 0.25
23 8 0.07
24 9 0.08
25 9 0.08
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (21 bp):
ATATAAATATATATAGTTTAT
Found at i:515633 original size:25 final size:25
Alignment explanation
Indices: 515572--515638 Score: 64
Period size: 25 Copynumber: 2.6 Consensus size: 25
515562 AATTGGAATG
* * *
515572 ATTAATATATTAATTGTATTAAAAATT
1 ATTAAT-TATT-ATTATTTTAAAAATA
*
515599 ATTAATTATTTTTATTTTAAAATATA
1 ATTAATTATTATTATTTTAAAA-ATA
515625 ATTAA-TATTATTAT
1 ATTAATTATTATTAT
515639 AATTTTATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
25 17 0.50
26 11 0.32
27 6 0.18
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (25 bp):
ATTAATTATTATTATTTTAAAAATA
Found at i:516475 original size:33 final size:33
Alignment explanation
Indices: 516429--516522 Score: 134
Period size: 33 Copynumber: 2.8 Consensus size: 33
516419 TGGGAAATTG
* *
516429 GGAAAATTAATCTTGGTTGGTGGTCAACTTATT
1 GGAAAATTCATCTTGGTTGGTGGCCAACTTATT
* *
516462 GGAAATTTCATCTTGGTTAGTGGCCAACTTATT
1 GGAAAATTCATCTTGGTTGGTGGCCAACTTATT
*
516495 GGAAAATTCATCTTTGGTAGGTGGCCAA
1 GGAAAATTCATC-TTGGTTGGTGGCCAA
516523 TTTTGCACAT
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
33 40 0.75
34 13 0.25
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.36
Consensus pattern (33 bp):
GGAAAATTCATCTTGGTTGGTGGCCAACTTATT
Found at i:521405 original size:32 final size:32
Alignment explanation
Indices: 521355--521439 Score: 127
Period size: 32 Copynumber: 2.7 Consensus size: 32
521345 TCTGCATCAG
*
521355 GATGTTAAATC-CCTAAAGATGCCCCAACATTC
1 GATGTTGAATCTCC-AAAGATGCCCCAACATTC
*
521387 GATGTTGAATCTCCAAAGATGCCCCAACATTT
1 GATGTTGAATCTCCAAAGATGCCCCAACATTC
*
521419 GATGTTGAATCTTCAAAGATG
1 GATGTTGAATCTCCAAAGATG
521440 TCTTCATTGC
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
32 47 0.96
33 2 0.04
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.28
Consensus pattern (32 bp):
GATGTTGAATCTCCAAAGATGCCCCAACATTC
Found at i:522509 original size:14 final size:14
Alignment explanation
Indices: 522487--522541 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
522477 CTTCTTGTCC
*
522487 TTTTTTCTTTTTTA
1 TTTTCTCTTTTTTA
522501 TTTTCTCTTTTTCTA
1 TTTTCTCTTTTT-TA
*
522516 TTTGT-TGTTTTTT-
1 TTT-TCTCTTTTTTA
*
522529 TTTGCTCTTTTTT
1 TTTTCTCTTTTTT
522542 TGCTTCTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
13 10 0.29
14 12 0.35
15 11 0.32
16 1 0.03
ACGTcount: A:0.04, C:0.11, G:0.05, T:0.80
Consensus pattern (14 bp):
TTTTCTCTTTTTTA
Found at i:525155 original size:13 final size:13
Alignment explanation
Indices: 525137--525161 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
525127 AAAAGGGTTC
525137 AGAGCTCATGTCT
1 AGAGCTCATGTCT
525150 AGAGCTCATGTC
1 AGAGCTCATGTC
525162 ATGCAATTGC
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:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (13 bp):
AGAGCTCATGTCT
Found at i:528160 original size:12 final size:12
Alignment explanation
Indices: 528143--528178 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
528133 CTATACGGTA
528143 TGAACAGTACCG
1 TGAACAGTACCG
*
528155 TGAACAGTACCA
1 TGAACAGTACCG
*
528167 TGAACTGTACCG
1 TGAACAGTACCG
528179 AATGCTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.33, C:0.25, G:0.22, T:0.19
Consensus pattern (12 bp):
TGAACAGTACCG
Found at i:528238 original size:21 final size:21
Alignment explanation
Indices: 528214--528270 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
528204 GCCATAGTAT
528214 CGATACCATGCTACAGGGTAC
1 CGATACCATGCTACAGGGTAC
528235 CGATACCATGCTACAGGGTAC
1 CGATACCATGCTACAGGGTAC
528256 CGATACCATGCTACA
1 CGATACCATGCTACA
528271 ATACTGATAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (21 bp):
CGATACCATGCTACAGGGTAC
Found at i:531883 original size:12 final size:13
Alignment explanation
Indices: 531847--531891 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
531837 TTATTAAAAC
*
531847 ATAACTTATAACTT
1 ATAAATTATAA-TT
*
531861 ATAATTTATAATT
1 ATAAATTATAATT
531874 -TAAATTATAATT
1 ATAAATTATAATT
531886 ATAAAT
1 ATAAAT
531892 ATTCCTGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 11 0.39
13 7 0.25
14 10 0.36
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (13 bp):
ATAAATTATAATT
Found at i:538837 original size:26 final size:27
Alignment explanation
Indices: 538798--538868 Score: 99
Period size: 26 Copynumber: 2.7 Consensus size: 27
538788 CTACACCACG
* **
538798 TGGGAGTGTTGCTGAAGAATCA-CTGC
1 TGGGAGTGGTGCTGAAGAATCATCCCC
*
538824 TGGGAGTGGGGCTGAAGAATCATCCCC
1 TGGGAGTGGTGCTGAAGAATCATCCCC
538851 TGGGAGTGGTGCTGAAGA
1 TGGGAGTGGTGCTGAAGA
538869 TACTGGTCAT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
26 20 0.51
27 19 0.49
ACGTcount: A:0.23, C:0.15, G:0.39, T:0.23
Consensus pattern (27 bp):
TGGGAGTGGTGCTGAAGAATCATCCCC
Found at i:541542 original size:29 final size:27
Alignment explanation
Indices: 541473--541546 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 27
541463 TTGTGATATG
*
541473 ATTTTAAAATTTAATAATTATTTTATA
1 ATTTTAAAATTTAATAATAATTTTATA
* *
541500 ATTTAAAAAGTTTAATAATAATTTTTTA
1 ATTTTAAAA-TTTAATAATAATTTTATA
541528 ACTTTTAAAATTTTAATAA
1 A-TTTTAAAA-TTTAATAA
541547 ATAAAAATCA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 8 0.20
28 17 0.43
29 15 0.38
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (27 bp):
ATTTTAAAATTTAATAATAATTTTATA
Found at i:569987 original size:19 final size:19
Alignment explanation
Indices: 569963--570033 Score: 106
Period size: 19 Copynumber: 3.6 Consensus size: 19
569953 GAGTGGTCGT
*
569963 TCGACGATGACAAAGGCGA
1 TCGACGACGACAAAGGCGA
569982 TCGACGACGACAAAGGCGA
1 TCGACGACGACAAAGGCGA
570001 TCGACGACGACGACAAAGGCGA
1 T---CGACGACGACAAAGGCGA
570023 TCGACGACGAC
1 TCGACGACGAC
570034 TGGTAATGGG
Statistics
Matches: 48, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
19 29 0.60
22 19 0.40
ACGTcount: A:0.35, C:0.27, G:0.31, T:0.07
Consensus pattern (19 bp):
TCGACGACGACAAAGGCGA
Found at i:570033 original size:22 final size:22
Alignment explanation
Indices: 569964--570033 Score: 110
Period size: 22 Copynumber: 3.3 Consensus size: 22
569954 AGTGGTCGTT
*
569964 CGACGATGACAAAGGCGAT---
1 CGACGACGACAAAGGCGATCGA
569983 CGACGACGACAAAGGCGATCGA
1 CGACGACGACAAAGGCGATCGA
570005 CGACGACGACAAAGGCGATCGA
1 CGACGACGACAAAGGCGATCGA
570027 CGACGAC
1 CGACGAC
570034 TGGTAATGGG
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
19 18 0.38
22 29 0.62
ACGTcount: A:0.36, C:0.27, G:0.31, T:0.06
Consensus pattern (22 bp):
CGACGACGACAAAGGCGATCGA
Found at i:573641 original size:64 final size:64
Alignment explanation
Indices: 573572--573730 Score: 187
Period size: 64 Copynumber: 2.5 Consensus size: 64
573562 TTGAAGGTGT
** *** *
573572 ATCGATGCATTGGTAGTGCATCGATGCACT-CTTTTAA-AATAAAAACATCGAATGCAATTCATG
1 ATCGATGCATAAGTAGTGCATCGATGCA-TACCAATAATAAT-AAAACATCAAATGCAATTCATG
573635 C
64 C
* * *
573636 ATCGATGCATAAGTAGTGCATCGATGCATACCAATAATAATACAACATCAAATGCATTTTATGC
1 ATCGATGCATAAGTAGTGCATCGATGCATACCAATAATAATAAAACATCAAATGCAATTCATGC
* *
573700 ACCGATGCATCAGTAGTGCATCGATGCATAC
1 ATCGATGCATAAGTAGTGCATCGATGCATAC
573731 TTTCATTGAA
Statistics
Matches: 82, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
63 1 0.01
64 78 0.95
65 3 0.04
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (64 bp):
ATCGATGCATAAGTAGTGCATCGATGCATACCAATAATAATAAAACATCAAATGCAATTCATGC
Done.