Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005696.1 Hibiscus syriacus cultivar Beakdansim tig00013326_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: 101084
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:1908 original size:24 final size:24
Alignment explanation
Indices: 1881--1953 Score: 112
Period size: 24 Copynumber: 3.0 Consensus size: 24
1871 TTAGTTACAA
*
1881 AAGCTTGTGCTTTTGC-GACCGATG
1 AAGCTTGTGCTTTTGCAG-CAGATG
1905 AAGCTTGTGCTTTTGCAGCAGATG
1 AAGCTTGTGCTTTTGCAGCAGATG
*
1929 AAGTTTGTGCTTTTGCAGCAGATG
1 AAGCTTGTGCTTTTGCAGCAGATG
1953 A
1 A
1954 GTCTCCTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
24 45 0.98
25 1 0.02
ACGTcount: A:0.21, C:0.16, G:0.29, T:0.34
Consensus pattern (24 bp):
AAGCTTGTGCTTTTGCAGCAGATG
Found at i:6251 original size:18 final size:17
Alignment explanation
Indices: 6228--6261 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
6218 TTGGACCTGA
*
6228 AAATAATTAAATTAAATT
1 AAATAAATAAA-TAAATT
6246 AAATAAATAAATAAAT
1 AAATAAATAAATAAAT
6262 AAGGTAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AAATAAATAAATAAATT
Found at i:6341 original size:21 final size:22
Alignment explanation
Indices: 6311--6355 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
6301 TATATGTATT
*
6311 AAAACTATATAATATA-TTTCA
1 AAAACAATATAATATATTTTCA
*
6332 AAAACAATATAATTTATTTTCA
1 AAAACAATATAATATATTTTCA
6354 AA
1 AA
6356 GGTTATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (22 bp):
AAAACAATATAATATATTTTCA
Found at i:6503 original size:14 final size:15
Alignment explanation
Indices: 6484--6512 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
6474 AAACTATATT
6484 ATATGTTTTC-AAAA
1 ATATGTTTTCGAAAA
6498 ATATGTTTTCGAAAA
1 ATATGTTTTCGAAAA
6513 CTATATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.41
Consensus pattern (15 bp):
ATATGTTTTCGAAAA
Found at i:6531 original size:73 final size:74
Alignment explanation
Indices: 6396--6575 Score: 202
Period size: 73 Copynumber: 2.4 Consensus size: 74
6386 CCAGTTTTTT
* * *
6396 AAACTATATGTATATATATATTCAAAATAATATGTTTTTAAGAATTATATTATATATATTTTCAA
1 AAACTATAT-TATATGT-T-TTC-AAA-AATATGTTTTGAAGAACTATATTATATATATTTTCAA
*
6461 AATC-GCTTTTGAA
61 AAACTGCTTTTGAA
*
6474 AAACTATATTATATGTTTTCAAAAATATGTTTTCGAA-AACTATATTATATATGTTTTCAAAAAC
1 AAACTATATTATATGTTTTCAAAAATATGTTTT-GAAGAACTATATTATATATATTTTCAAAAAC
* *
6538 TGTTTTTTAA
65 TGCTTTTGAA
*
6548 AAACTATATATTGTATGTTTTCAAAAAT
1 AAAC--TATATTATATGTTTTCAAAAAT
6576 TATACCATAT
Statistics
Matches: 90, Mismatches: 8, Indels: 10
0.83 0.07 0.09
Matches are distributed among these distances:
73 34 0.38
74 16 0.18
75 3 0.03
76 22 0.24
77 6 0.07
78 9 0.10
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (74 bp):
AAACTATATTATATGTTTTCAAAAATATGTTTTGAAGAACTATATTATATATATTTTCAAAAACT
GCTTTTGAA
Found at i:6565 original size:38 final size:38
Alignment explanation
Indices: 6361--6574 Score: 131
Period size: 38 Copynumber: 5.6 Consensus size: 38
6351 TCAAAGGTTA
* *
6361 TATATATTATATACGTTTTCAAAAACCAGTTTTT--TAAAC
1 TATATATTATAT--GTTTTCAAAAA-CTGTTTTTCAAAAAC
* * * * * *
6400 TATATGTATATATATATTCAAAATAATATGTTTTT-AAGAAT
1 TATATAT-TATATGTTTTC-AAA-AA-CTGTTTTTCAAAAAC
* * * *
6441 TATAT-TATATATATTTTCAAAATC-GCTTTTGAAAAAC
1 TATATAT-TATATGTTTTCAAAAACTGTTTTTCAAAAAC
* *
6478 --TATATTATATGTTTTCAAAAA-TATGTTTTCGAAAAC
1 TATATATTATATGTTTTCAAAAACTGT-TTTTCAAAAAC
*
6514 TATAT-TATATATGTTTTCAAAAACTGTTTTTTAAAAAC
1 TATATAT-TATATGTTTTCAAAAACTGTTTTTCAAAAAC
*
6552 TATATATTGTATGTTTTCAAAAA
1 TATATATTATATGTTTTCAAAAA
6575 TTATACCATA
Statistics
Matches: 137, Mismatches: 25, Indels: 27
0.72 0.13 0.14
Matches are distributed among these distances:
35 17 0.12
36 15 0.11
37 5 0.04
38 53 0.39
39 15 0.11
40 25 0.18
41 7 0.05
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.45
Consensus pattern (38 bp):
TATATATTATATGTTTTCAAAAACTGTTTTTCAAAAAC
Found at i:6621 original size:2 final size:2
Alignment explanation
Indices: 6616--6665 Score: 75
Period size: 2 Copynumber: 25.0 Consensus size: 2
6606 TTGAAATTAT
*
6616 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6657 TA CTA TA TA
1 TA -TA TA TA
6666 ATGTAAAAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
1 1 0.02
2 42 0.93
3 2 0.04
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8491 original size:35 final size:35
Alignment explanation
Indices: 8451--8522 Score: 108
Period size: 35 Copynumber: 2.1 Consensus size: 35
8441 TTAAAAAAGA
* * *
8451 AGAATTAAATTAGGACTCAAATATTAGTTTAAAAT
1 AGAATTAAATTAAGACTCAAATACTAATTTAAAAT
*
8486 AGAATTGAATTAAGACTCAAATACTAATTTAAAAT
1 AGAATTAAATTAAGACTCAAATACTAATTTAAAAT
8521 AG
1 AG
8523 GATTTTTTAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.50, C:0.07, G:0.11, T:0.32
Consensus pattern (35 bp):
AGAATTAAATTAAGACTCAAATACTAATTTAAAAT
Found at i:8780 original size:17 final size:18
Alignment explanation
Indices: 8754--8793 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
8744 ATTATATGGA
8754 TATT-TTATTCAT-TTAT
1 TATTATTATTCATGTTAT
*
8770 TTTTATTATTCATGTTAT
1 TATTATTATTCATGTTAT
8788 TATTAT
1 TATTAT
8794 ACGTATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 3 0.15
17 8 0.40
18 9 0.45
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (18 bp):
TATTATTATTCATGTTAT
Found at i:8934 original size:2 final size:2
Alignment explanation
Indices: 8927--9011 Score: 65
Period size: 2 Copynumber: 44.5 Consensus size: 2
8917 TTTATCTAGT
* * *
8927 TA TA TA TA TA TA TA TA TA TA T- TT TA TA CT- TT TA -A TA GTT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA
* *
8968 TT TA TA TA TC TA T- TA T- TA -A 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
9007 TA TA T
1 TA TA T
9012 TCTTAAATAT
Statistics
Matches: 67, Mismatches: 8, Indels: 16
0.74 0.09 0.18
Matches are distributed among these distances:
1 6 0.09
2 59 0.88
3 2 0.03
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.55
Consensus pattern (2 bp):
TA
Found at i:9373 original size:40 final size:37
Alignment explanation
Indices: 9296--9374 Score: 106
Period size: 40 Copynumber: 2.1 Consensus size: 37
9286 AGTGAGAGGG
*
9296 TAGCTTTTATATTTTAAATATTTGTTGTATATATATA
1 TAGCTTTTATATTTTAAATATTTGATGTATATATATA
9333 TAGCTTATT-TATTTTATTAATACTTTGATGTATATATATA
1 TAGCTT-TTATATTTTA--AATA-TTTGATGTATATATATA
9373 TA
1 TA
9375 TATATATATT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
37 13 0.35
38 2 0.05
39 4 0.11
40 18 0.49
ACGTcount: A:0.33, C:0.04, G:0.08, T:0.56
Consensus pattern (37 bp):
TAGCTTTTATATTTTAAATATTTGATGTATATATATA
Found at i:9456 original size:9 final size:9
Alignment explanation
Indices: 9434--9485 Score: 52
Period size: 9 Copynumber: 5.6 Consensus size: 9
9424 ATTTTTTTCC
*
9434 TTATCTTATC
1 TTAT-TTATT
9444 TTATTTATT
1 TTATTTATT
9453 TTATTTATT
1 TTATTTATT
9462 TTATTT-TT
1 TTATTTATT
*
9470 TTCCTTTTATT
1 TT--ATTTATT
9481 TTATT
1 TTATT
9486 CTCTTTATCT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
8 4 0.11
9 21 0.58
10 7 0.19
11 4 0.11
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.75
Consensus pattern (9 bp):
TTATTTATT
Found at i:9456 original size:14 final size:14
Alignment explanation
Indices: 9434--9485 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
9424 ATTTTTTTCC
*
9434 TTATCTTATCTTA-T
1 TTATTTTAT-TTATT
9448 TTATTTTATTTATT
1 TTATTTTATTTATT
*
9462 TTATTTT-TTTCCTT
1 TTATTTTATTT-ATT
9476 TTATTTTATT
1 TTATTTTATT
9486 CTCTTTATCT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
13 6 0.18
14 25 0.76
15 2 0.06
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.75
Consensus pattern (14 bp):
TTATTTTATTTATT
Found at i:20677 original size:106 final size:106
Alignment explanation
Indices: 20487--21252 Score: 905
Period size: 106 Copynumber: 7.4 Consensus size: 106
20477 GATTTTAGCT
* *
20487 AGAGTCAATTTCAACTTCACA--GTAATGGATATTGGACTCAAGACAACACAAGTTCAACTTCAC
1 AGAGCCAATTTCAACTTCACATCG-AA-GGATATTGGACTCGAGACAACACAAGTTCAACTTCAC
* * *
20550 AACGAAGGGACGGCTAGTTGTCAACAAACAATCTCCCAATTTC
64 AACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCAATTTC
* *
20593 AGAGCCAATTTCAACTTCACATCGAAGGATGTTGGACTCGGGACAACACAAGTTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACATCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
20658 CGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCAATTTC
66 CGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCAATTTC
* * *
20699 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACATCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
* * *
20764 CGAAGGGATGACTGGTTGTCAACAAATAATCTCCCAATTTC
66 CGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCAATTTC
** ** * * * *
20805 AGAGCCAATAGCGAA--GGATAT---TGGACTCATTGGACTCGAGACGAGACAAGTTCAACTTCA
1 AGAGCCAATTTC-AACTTCACATCGAAGGA-T-ATTGGACTCGAGACAACACAAGTTCAACTTCA
*
20865 CAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCTAATTTC
63 CAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCAATTTC
* * *
20909 AGGGTCAATTTCAACTTCACATCGAAGGATATTGGACTTGAGAC--CACAAGTTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACATCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
*
20972 CGAAGGAACGGCTGGTTGTCAACAAATAA--T-----TTT-
66 CGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCAATTTC
*
21005 ----CCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGA-AGACACAAGTTCAACTTCACA
1 AGAGCCAATTTCAACTTCACATCGAAGGATATTGGACTCGAGACA-ACACAAGTTCAACTTCACA
21065 ACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCAATTTC
65 ACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCAATTTC
* * * * * * * * *
21107 AGGGTCAATTTCAACTTCACATCGAATGATATTAGACTCAAGACATCACAAGCTCAACTTCATAG
1 AGAGCCAATTTCAACTTCACATCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
* * * * * * *
21172 CGAAGGGGCGGTTGGCTGTCAACAAACAATTTTCCAGTTCC
66 CGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCAATTTC
21213 AGAGCCAATTTCAACTTCACGA-CGGAA-GATATTGGACTCG
1 AGAGCCAATTTCAACTTCAC-ATC-GAAGGATATTGGACTCG
21253 GAACAATACA
Statistics
Matches: 567, Mismatches: 65, Indels: 56
0.82 0.09 0.08
Matches are distributed among these distances:
92 36 0.06
94 47 0.08
96 1 0.00
97 3 0.01
101 3 0.01
102 4 0.01
103 3 0.01
104 123 0.22
105 5 0.01
106 328 0.58
107 10 0.02
108 4 0.01
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.24
Consensus pattern (106 bp):
AGAGCCAATTTCAACTTCACATCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
CGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCAATTTC
Found at i:21079 original size:94 final size:92
Alignment explanation
Indices: 20914--21107 Score: 325
Period size: 94 Copynumber: 2.1 Consensus size: 92
20904 ATTTCAGGGT
* * *
20914 CAATTTCAACTTCACATCGAAGGATATTGGACTTGAGACCACAAGTTCAACTTCACAACGAAGGA
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGAACACAAGTTCAACTTCACAACGAAGGA
*
20979 ACGGCTGGTTGTCAACAAATAATTTTC
66 ACGGCTGGTTGTCAACAAATAATTTCC
21006 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGAAGACACAAGTTCAACTTCACAACGAAG
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAG-A-ACACAAGTTCAACTTCACAACGAAG
*
21071 GGACGGCTGGTTGTCAACAAATAATTTCC
64 GAACGGCTGGTTGTCAACAAATAATTTCC
21100 CAATTTCA
1 CAATTTCA
21108 GGGTCAATTT
Statistics
Matches: 95, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
92 35 0.37
93 1 0.01
94 59 0.62
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (92 bp):
CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGAACACAAGTTCAACTTCACAACGAAGGA
ACGGCTGGTTGTCAACAAATAATTTCC
Found at i:21829 original size:35 final size:35
Alignment explanation
Indices: 21739--21808 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
21729 AAAAAAGAAT
21739 AGTTGGATTAGGACTCAAATACTAGTCTAAAATAG
1 AGTTGGATTAGGACTCAAATACTAGTCTAAAATAG
21774 AGTTGGATTAGGACTCAAATACTAGTCTAAAATAG
1 AGTTGGATTAGGACTCAAATACTAGTCTAAAATAG
21809 GGTTTTTTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.29
Consensus pattern (35 bp):
AGTTGGATTAGGACTCAAATACTAGTCTAAAATAG
Found at i:22209 original size:17 final size:18
Alignment explanation
Indices: 22183--22222 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
22173 ATTATAGGGA
22183 TATT-TTATTCAT-TTAT
1 TATTATTATTCATGTTAT
*
22199 TTTTATTATTCATGTTAT
1 TATTATTATTCATGTTAT
22217 TATTAT
1 TATTAT
22223 ACGTATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 3 0.15
17 8 0.40
18 9 0.45
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (18 bp):
TATTATTATTCATGTTAT
Found at i:22479 original size:2 final size:2
Alignment explanation
Indices: 22474--22498 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
22464 CTTATAACTT
22474 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
22499 TGTTTTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22786 original size:2 final size:2
Alignment explanation
Indices: 22781--22821 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
22771 TTGATGTGTG
22781 TA TA TA 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 TA TA TA T
22822 CCTTTTTCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:22893 original size:18 final size:18
Alignment explanation
Indices: 22870--22935 Score: 66
Period size: 18 Copynumber: 3.7 Consensus size: 18
22860 TATTTTTTTC
*
22870 TTATTTTATTTATTTATT
1 TTATTTTCTTTATTTATT
22888 TTATTTT-TTCCT-TTTATT
1 TTATTTTCTT--TATTTATT
*
22906 TTATTCTCTTTATCTTA-T
1 TTATTTTCTTTAT-TTATT
22924 TTATTTTCTTTA
1 TTATTTTCTTTA
22936 CCTTGTTTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
17 3 0.07
18 32 0.78
19 6 0.15
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (18 bp):
TTATTTTCTTTATTTATT
Found at i:22944 original size:18 final size:18
Alignment explanation
Indices: 22905--22947 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
22895 TTCCTTTTAT
* *
22905 TTTATTCTCTTTATCTTA
1 TTTATTTTCTTTACCTTA
*
22923 TTTATTTTCTTTACCTTG
1 TTTATTTTCTTTACCTTA
22941 TTTATTT
1 TTTATTT
22948 AACAAATTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.02, T:0.70
Consensus pattern (18 bp):
TTTATTTTCTTTACCTTA
Found at i:25895 original size:15 final size:16
Alignment explanation
Indices: 25871--25913 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
25861 AGATGATTTC
*
25871 ATGAAGAGATGTTAAT
1 ATGAAAAGATGTTAAT
*
25887 -TGAAAAGATATTAAT
1 ATGAAAAGATGTTAAT
*
25902 ATGAATAGATGT
1 ATGAAAAGATGT
25914 GATGTTAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.47, C:0.00, G:0.21, T:0.33
Consensus pattern (16 bp):
ATGAAAAGATGTTAAT
Found at i:31658 original size:20 final size:20
Alignment explanation
Indices: 31633--31674 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
31623 TAATAATCAC
*
31633 TTAAAATCATAATGTAATAT
1 TTAAAAACATAATGTAATAT
*
31653 TTAAAAACATAATTTAATAT
1 TTAAAAACATAATGTAATAT
31673 TT
1 TT
31675 GTACTATTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (20 bp):
TTAAAAACATAATGTAATAT
Found at i:41512 original size:21 final size:22
Alignment explanation
Indices: 41445--41536 Score: 125
Period size: 22 Copynumber: 4.3 Consensus size: 22
41435 ATTTTTTTGG
41445 GTCTTGTTTGGGATCTCCCGGC
1 GTCTTGTTTGGGATCTCCCGGC
*
41467 GTCTTGCTTGGGATCTCCCGGC
1 GTCTTGTTTGGGATCTCCCGGC
* *
41489 GTCTTGTTTGGGAT-TTCTGGC
1 GTCTTGTTTGGGATCTCCCGGC
* *
41510 GTCTTGTTTGGGAT-TTCCGAC
1 GTCTTGTTTGGGATCTCCCGGC
41531 GTCTTG
1 GTCTTG
41537 AGGGTGTTGG
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
21 30 0.47
22 34 0.53
ACGTcount: A:0.05, C:0.23, G:0.32, T:0.40
Consensus pattern (22 bp):
GTCTTGTTTGGGATCTCCCGGC
Found at i:41521 original size:43 final size:43
Alignment explanation
Indices: 41445--41536 Score: 123
Period size: 43 Copynumber: 2.1 Consensus size: 43
41435 ATTTTTTTGG
*
41445 GTCTTGTTTGGGATCTCCCGGCGTCTTGCTTGGGATCTCCCGGC
1 GTCTTGTTTGGGATCTCCCGGCGTCTTGCTTGGGAT-TCCCGAC
* * * *
41489 GTCTTGTTTGGGAT-TTCTGGCGTCTTGTTTGGGATTTCCGAC
1 GTCTTGTTTGGGATCTCCCGGCGTCTTGCTTGGGATTCCCGAC
41531 GTCTTG
1 GTCTTG
41537 AGGGTGTTGG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
42 11 0.26
43 18 0.42
44 14 0.33
ACGTcount: A:0.05, C:0.23, G:0.32, T:0.40
Consensus pattern (43 bp):
GTCTTGTTTGGGATCTCCCGGCGTCTTGCTTGGGATTCCCGAC
Found at i:42164 original size:20 final size:20
Alignment explanation
Indices: 42142--42394 Score: 249
Period size: 20 Copynumber: 12.5 Consensus size: 20
42132 TAAGTTTCCA
* * *
42142 AAATCGCAACGCGAATATGA
1 AAATCGCAACGAGAATCTGT
* * *
42162 AAATCGCAACGCGAATATGA
1 AAATCGCAACGAGAATCTGT
* *
42182 AAATCGCAACGCGAA-CATAT
1 AAATCGCAACGAGAATC-TGT
* *
42202 AAATCGCAACGAGTATCCGT
1 AAATCGCAACGAGAATCTGT
* * *
42222 AAAAATCGCAACGCGTATCCGT
1 --AAATCGCAACGAGAATCTGT
*
42244 AAATCGCAACGAAAATAC-GT
1 AAATCGCAACGAGAAT-CTGT
* * *
42264 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGAGAATCTGT
* *
42285 AAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCTGT
42305 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGAGAATCTGT
*
42325 AAATCGCAACGATAATCTGT
1 AAATCGCAACGAGAATCTGT
* *
42345 AAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCTGT
42365 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGAGAATCTGT
42385 AAATCGCAAC
1 AAATCGCAAC
42395 ACTAAAATTT
Statistics
Matches: 203, Mismatches: 23, Indels: 14
0.85 0.10 0.06
Matches are distributed among these distances:
20 167 0.82
21 17 0.08
22 19 0.09
ACGTcount: A:0.41, C:0.23, G:0.17, T:0.18
Consensus pattern (20 bp):
AAATCGCAACGAGAATCTGT
Found at i:43128 original size:24 final size:24
Alignment explanation
Indices: 43084--43130 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
43074 AAATTTGGTC
* *
43084 TTGGTCAATACCCGGACTTTGATA
1 TTGGTCAATACACAGACTTTGATA
*
43108 TTGGTCAATACACAGATTTTGAT
1 TTGGTCAATACACAGACTTTGAT
43131 GATGTTTCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (24 bp):
TTGGTCAATACACAGACTTTGATA
Found at i:45710 original size:33 final size:34
Alignment explanation
Indices: 45587--45713 Score: 152
Period size: 33 Copynumber: 3.8 Consensus size: 34
45577 GTATTTGACT
* * *
45587 ATCGCAACACGGAAATTACAATCGCAACGAGAGA
1 ATCGCAATACGGAAATGAAAATCGCAACGAGAGA
* * *
45621 ATCGCAATGC-GAAATGAAAATCCCAAC-ATGAAA
1 ATCGCAATACGGAAATGAAAATCGCAACGA-GAGA
*
45654 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATACGGAAATGAAAATCGCAACGAGAGA
*
45688 ATCGCAATAC-GAAATTAAAATCGCAA
1 ATCGCAATACGGAAATGAAAATCGCAA
45714 TGCGAAATGA
Statistics
Matches: 80, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
32 1 0.01
33 42 0.52
34 36 0.45
35 1 0.01
ACGTcount: A:0.46, C:0.20, G:0.19, T:0.14
Consensus pattern (34 bp):
ATCGCAATACGGAAATGAAAATCGCAACGAGAGA
Found at i:45733 original size:52 final size:52
Alignment explanation
Indices: 45651--45770 Score: 222
Period size: 52 Copynumber: 2.3 Consensus size: 52
45641 TCCCAACATG
45651 AAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATACGAAATT
1 AAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATACGAAATT
*
45704 AAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATT
1 AAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATACGAAATT
45756 AAAATCGCAATGCGA
1 AAAATCGCAATGCGA
45771 TTCTCTCGTT
Statistics
Matches: 66, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
52 53 0.80
53 13 0.20
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (52 bp):
AAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATACGAAATT
Found at i:45767 original size:19 final size:19
Alignment explanation
Indices: 45620--45770 Score: 134
Period size: 19 Copynumber: 8.7 Consensus size: 19
45610 GCAACGAGAG
45620 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
45639 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
45653 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
45673 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
* *
45687 AATCGCAATACGAAATTAA
1 AATCGCAATGCGAAATGAA
45706 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
45725 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
45739 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
45758 AATCGCAATGCGA
1 AATCGCAATGCGA
45771 TTCTCTCGTT
Statistics
Matches: 106, Mismatches: 10, Indels: 32
0.72 0.07 0.22
Matches are distributed among these distances:
14 32 0.30
15 2 0.02
16 5 0.05
17 4 0.04
18 3 0.03
19 47 0.44
20 13 0.12
ACGTcount: A:0.46, C:0.19, G:0.20, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:45930 original size:14 final size:14
Alignment explanation
Indices: 45911--45947 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
45901 CATCAATTAA
45911 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
45925 ACAAATCATCTTTT
1 ACAAATCAACTTTT
45939 ACAAATCAA
1 ACAAATCAA
45948 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:46021 original size:14 final size:14
Alignment explanation
Indices: 45998--46031 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
45988 TCTACTATTG
45998 AATCAACTTTTACA
1 AATCAACTTTTACA
*
46012 AATCATCTTTTACA
1 AATCAACTTTTACA
46026 AATCAA
1 AATCAA
46032 TTAAACAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (14 bp):
AATCAACTTTTACA
Found at i:46272 original size:18 final size:18
Alignment explanation
Indices: 46251--46287 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
46241 GTAATTGGAG
46251 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
46269 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
46287 T
1 T
46288 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:46294 original size:24 final size:24
Alignment explanation
Indices: 46243--46295 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
46233 TTTCATATGT
* * *
46243 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
46267 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
46291 AATTT
1 AATTT
46296 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:46586 original size:39 final size:39
Alignment explanation
Indices: 46543--46629 Score: 165
Period size: 39 Copynumber: 2.2 Consensus size: 39
46533 TCCGATGCTC
46543 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
*
46582 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
46621 ATCAAAATC
1 ATCAAAATC
46630 TACAACTTGA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.47, C:0.21, G:0.15, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
Found at i:47469 original size:20 final size:19
Alignment explanation
Indices: 47446--47492 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
47436 CGATATACCA
47446 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
47466 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
47486 GGTAAAA
1 GGTAAAA
47493 CGTTACCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:47650 original size:20 final size:19
Alignment explanation
Indices: 47627--47673 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
47617 CGATATAACA
47627 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
47647 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
47667 GGTAAAA
1 GGTAAAA
47674 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:47675 original size:17 final size:19
Alignment explanation
Indices: 47636--47678 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
47626 AGGTAAAAAT
47636 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
47656 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
47673 ATGATA
1 ATGATA
47679 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:49923 original size:21 final size:21
Alignment explanation
Indices: 49897--49961 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
49887 AAGACAATCA
*
49897 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
49918 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
49939 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
49960 AG
1 AG
49962 GCATAAAGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.42, C:0.11, G:0.31, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:50037 original size:33 final size:33
Alignment explanation
Indices: 49995--50060 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
49985 AAATAGATGG
*
49995 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
50028 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
50061 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:51879 original size:19 final size:19
Alignment explanation
Indices: 51855--51903 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
51845 AATGTAGGGT
51855 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
51874 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
51893 TATTTTTGTAT
1 TAATTTTGTAT
51904 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:52365 original size:200 final size:200
Alignment explanation
Indices: 52022--53000 Score: 1877
Period size: 200 Copynumber: 4.9 Consensus size: 200
52012 CAATATGGCC
*
52022 AACAGGGTGCAACCATAAAGTTTCGATCCATATATATAAAGTGTCGATCCCAAAAACATCGAAAC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATATAAAGTGTCGATCCCAAAAACATCGAAAC
52087 CCAAAAGTATAATGTATTAGGTAATTTTTCAATCTAACCGGTACAAGTGTACCGGTTTTATGAGA
66 CCAAAAGTATAATGTATTAGGTAATTTTTCAATCTAACCGGTACAAGTGTACCGGTTTTATGAGA
52152 TAATATGTCTAAATAATGTGTCGACACATTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
131 TAATATGTCTAAATAATGTGTCGACACATTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
52217 TGGAA
196 TGGAA
52222 AACAGGGTGCAACCATAAAGTGTCGATCCATATATATAAAGTGTCGATCCCAAAAACATCGAAAC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATATAAAGTGTCGATCCCAAAAACATCGAAAC
52287 CCAAAAGTATAATGTATTAGGTAATTTTTCAATCTAACCGGTACAAGTGTACCGGTTTTATGAGA
66 CCAAAAGTATAATGTATTAGGTAATTTTTCAATCTAACCGGTACAAGTGTACCGGTTTTATGAGA
*
52352 TAATATGTCTAAATAATGTGTCGACACATTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATAAA
131 TAATATGTCTAAATAATGTGTCGACACATTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
52417 TGGAA
196 TGGAA
*
52422 AACAGGGTGCAACCATAAAGTGTCGATCCATATATATAAAGTGTCGATCCCAAAAACATCAAAAC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATATAAAGTGTCGATCCCAAAAACATCGAAAC
52487 CCAAAAGTATAATGTATTAGGTAATTTTTCAATCTAACCGGTACAAGTGTACCGGTTTTATGAGA
66 CCAAAAGTATAATGTATTAGGTAATTTTTCAATCTAACCGGTACAAGTGTACCGGTTTTATGAGA
52552 TAATATGTCTAAATAATGTGTCGACACATTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
131 TAATATGTCTAAATAATGTGTCGACACATTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
**
52617 TGGCC
196 TGGAA
52622 AACAGGGTGCAACCATAAAGTGTCGATCCATATATATAAAGTGTCGATCCCAAAAACATCGAAAC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATATAAAGTGTCGATCCCAAAAACATCGAAAC
* * *
52687 CTAAAAGTATAATATATTAGGTAATTTTTCAATCTAACCGGTACAAGTGTACCAGTTTTATGAGA
66 CCAAAAGTATAATGTATTAGGTAATTTTTCAATCTAACCGGTACAAGTGTACCGGTTTTATGAGA
*
52752 TAATATGTCTAAATAATGTATCGACACATTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
131 TAATATGTCTAAATAATGTGTCGACACATTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
52817 TGGAA
196 TGGAA
52822 AACAGGGTGCAACCATAAAGTGTCGATCCATATATATAAAGTGTCGATCCCAAAAACATCGAAAC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATATAAAGTGTCGATCCCAAAAACATCGAAAC
52887 CCAAAAGTATAATGTATTAGGTAATTTTTCAATCTAACCGGTACAAGTGTACCGGTTTTATGAGA
66 CCAAAAGTATAATGTATTAGGTAATTTTTCAATCTAACCGGTACAAGTGTACCGGTTTTATGAGA
52952 TAATATGTCTAAATAATGTGTCGACACATTTTTAGTTTGTGTCGATATT
131 TAATATGTCTAAATAATGTGTCGACACATTTTTAGTTTGTGTCGATATT
53001 AATTTAAATA
Statistics
Matches: 762, Mismatches: 17, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
200 762 1.00
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (200 bp):
AACAGGGTGCAACCATAAAGTGTCGATCCATATATATAAAGTGTCGATCCCAAAAACATCGAAAC
CCAAAAGTATAATGTATTAGGTAATTTTTCAATCTAACCGGTACAAGTGTACCGGTTTTATGAGA
TAATATGTCTAAATAATGTGTCGACACATTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
TGGAA
Found at i:54457 original size:6 final size:6
Alignment explanation
Indices: 54446--54509 Score: 65
Period size: 6 Copynumber: 10.7 Consensus size: 6
54436 CAAGCGGTCA
* * * * *
54446 ATGAAG ATGAAG CTGACG ATGAAG ATGACG ATGATG ATGATG ATGAAG
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG
* *
54494 CTGACG ATGAAG ATGA
1 ATGAAG ATGAAG ATGA
54510 TGACGACGAC
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.39, C:0.08, G:0.33, T:0.20
Consensus pattern (6 bp):
ATGAAG
Found at i:54467 original size:18 final size:18
Alignment explanation
Indices: 54446--54509 Score: 92
Period size: 18 Copynumber: 3.6 Consensus size: 18
54436 CAAGCGGTCA
54446 ATGAAGATGAAGCTGACG
1 ATGAAGATGAAGCTGACG
* * *
54464 ATGAAGATGACGATGATG
1 ATGAAGATGAAGCTGACG
*
54482 ATGATGATGAAGCTGACG
1 ATGAAGATGAAGCTGACG
54500 ATGAAGATGA
1 ATGAAGATGA
54510 TGACGACGAC
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.39, C:0.08, G:0.33, T:0.20
Consensus pattern (18 bp):
ATGAAGATGAAGCTGACG
Found at i:54468 original size:12 final size:12
Alignment explanation
Indices: 54446--54509 Score: 83
Period size: 12 Copynumber: 5.3 Consensus size: 12
54436 CAAGCGGTCA
*
54446 ATGAAGATGAAG
1 ATGACGATGAAG
*
54458 CTGACGATGAAG
1 ATGACGATGAAG
*
54470 ATGACGATGATG
1 ATGACGATGAAG
*
54482 ATGATGATGAAG
1 ATGACGATGAAG
*
54494 CTGACGATGAAG
1 ATGACGATGAAG
54506 ATGA
1 ATGA
54510 TGACGACGAC
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 43 1.00
ACGTcount: A:0.39, C:0.08, G:0.33, T:0.20
Consensus pattern (12 bp):
ATGACGATGAAG
Found at i:54483 original size:3 final size:3
Alignment explanation
Indices: 54463--54537 Score: 69
Period size: 3 Copynumber: 25.0 Consensus size: 3
54453 TGAAGCTGAC
* * * * * *
54463 GAT GAA GAT GAC GAT GAT GAT GAT GAT GAA GCT GAC GAT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* * *
54511 GAC GAC GAC GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT
54538 ACAAACAAGT
Statistics
Matches: 58, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.36, C:0.08, G:0.33, T:0.23
Consensus pattern (3 bp):
GAT
Found at i:54502 original size:21 final size:21
Alignment explanation
Indices: 54472--54533 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
54462 CGATGAAGAT
*
54472 GACGATGATGATGATGATGAA
1 GACGACGATGATGATGATGAA
* *
54493 G-CTGACGATGAAGATGATGAC
1 GAC-GACGATGATGATGATGAA
54514 GACGACGATGATGATGATGA
1 GACGACGATGATGATGATGA
54534 TGATACAAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 1 0.03
21 33 0.94
22 1 0.03
ACGTcount: A:0.35, C:0.10, G:0.34, T:0.21
Consensus pattern (21 bp):
GACGACGATGATGATGATGAA
Found at i:54517 original size:18 final size:19
Alignment explanation
Indices: 54446--54518 Score: 82
Period size: 18 Copynumber: 4.1 Consensus size: 19
54436 CAAGCGGTCA
54446 ATGAAGATGAAG-CTGACG
1 ATGAAGATGAAGACTGACG
* *
54464 ATGAAGATGACGA-TGATG
1 ATGAAGATGAAGACTGACG
*
54482 ATGATGATGAAG-CTGACG
1 ATGAAGATGAAGACTGACG
*
54500 ATGAAGATGATGAC-GACG
1 ATGAAGATGAAGACTGACG
54518 A
1 A
54519 CGATGATGAT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
18 44 0.98
19 1 0.02
ACGTcount: A:0.38, C:0.10, G:0.33, T:0.19
Consensus pattern (19 bp):
ATGAAGATGAAGACTGACG
Found at i:57275 original size:19 final size:19
Alignment explanation
Indices: 57233--57343 Score: 142
Period size: 19 Copynumber: 6.0 Consensus size: 19
57223 GCCGCACCGC
57233 AATGAAAATCGCAATGCAGA
1 AATGAAAATCGCAATGC-GA
*
57253 AATGAAAATCGCAATACGA
1 AATGAAAATCGCAATGCGA
57272 AATGAAAATCGCAA--CG-
1 AATGAAAATCGCAATGCGA
*
57288 -A-GAGAATCGCAATGCGGA
1 AATGAAAATCGCAATGC-GA
57306 AATGAAAATCGCAATGCGA
1 AATGAAAATCGCAATGCGA
*
57325 AATGAAAATCGCATTGCGA
1 AATGAAAATCGCAATGCGA
57344 TTCTCTCGTT
Statistics
Matches: 81, Mismatches: 4, Indels: 13
0.83 0.04 0.13
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
16 1 0.01
17 3 0.04
19 37 0.46
20 29 0.36
ACGTcount: A:0.47, C:0.16, G:0.22, T:0.15
Consensus pattern (19 bp):
AATGAAAATCGCAATGCGA
Found at i:57370 original size:33 final size:33
Alignment explanation
Indices: 57333--57410 Score: 147
Period size: 33 Copynumber: 2.4 Consensus size: 33
57323 GAAATGAAAA
57333 TCGCATTGCGATTCTCTCGTTGCGATTTTCAGT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCAGT
*
57366 TCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCAGT
57399 TCGCATTGCGAT
1 TCGCATTGCGAT
57411 AGTCATTTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.13, C:0.24, G:0.21, T:0.42
Consensus pattern (33 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCAGT
Found at i:57376 original size:19 final size:18
Alignment explanation
Indices: 57333--57410 Score: 64
Period size: 14 Copynumber: 4.7 Consensus size: 18
57323 GAAATGAAAA
*
57333 TCGCATTGCGATTCTC--
1 TCGCATTGCGATTTTCAT
57349 TCG--TTGCGATTTTCAGT
1 TCGCATTGCGATTTTCA-T
*
57366 TCGCATTGCGATTCTC--
1 TCGCATTGCGATTTTCAT
57382 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCA-T
57399 TCGCATTGCGAT
1 TCGCATTGCGAT
57411 AGTCATTTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 17
0.71 0.04 0.25
Matches are distributed among these distances:
14 20 0.41
16 6 0.12
17 6 0.12
19 17 0.35
ACGTcount: A:0.13, C:0.24, G:0.21, T:0.42
Consensus pattern (18 bp):
TCGCATTGCGATTTTCAT
Found at i:57536 original size:14 final size:14
Alignment explanation
Indices: 57517--57553 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
57507 CATCAATTAA
57517 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
57531 ACAAATCATCTTTT
1 ACAAATCAACTTTT
57545 ACAAATCAA
1 ACAAATCAA
57554 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:59479 original size:19 final size:19
Alignment explanation
Indices: 59435--59500 Score: 87
Period size: 19 Copynumber: 3.4 Consensus size: 19
59425 TAGTTTACTT
* *
59435 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
59455 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
* *
59474 TTGCAACGAGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
59493 TCGCAACG
1 TCGCAACG
59501 ACAGAATCGC
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
19 28 0.68
20 13 0.32
ACGTcount: A:0.47, C:0.27, G:0.15, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:59529 original size:19 final size:19
Alignment explanation
Indices: 59505--59569 Score: 86
Period size: 19 Copynumber: 3.7 Consensus size: 19
59495 GCAACGACAG
59505 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
59524 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
59538 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
59557 AATCGCAATGCGA
1 AATCGCAATGCGA
59570 TTTTGGTTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 23 0.59
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:59531 original size:33 final size:33
Alignment explanation
Indices: 59489--59564 Score: 143
Period size: 33 Copynumber: 2.3 Consensus size: 33
59479 ACGAGAAACC
59489 AAAATCGCAACGACAGAATCGCAATGCGAAATG
1 AAAATCGCAACGACAGAATCGCAATGCGAAATG
*
59522 AAAATCGCAACGAGAGAATCGCAATGCGAAATG
1 AAAATCGCAACGACAGAATCGCAATGCGAAATG
59555 AAAATCGCAA
1 AAAATCGCAA
59565 TGCGATTTTG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.47, C:0.20, G:0.21, T:0.12
Consensus pattern (33 bp):
AAAATCGCAACGACAGAATCGCAATGCGAAATG
Found at i:59587 original size:19 final size:19
Alignment explanation
Indices: 59565--59731 Score: 156
Period size: 19 Copynumber: 9.3 Consensus size: 19
59555 AAAATCGCAA
*
59565 TGCGATTTTGGTTTCGAGT
1 TGCGATTTTGGTTTCGCGT
59584 TGCGATTTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
59598 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
59617 TGCGA--TT-CTAT--CGT
1 TGCGATTTTGGTTTCGCGT
**
59631 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
59650 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
59669 TGCGATTTTGGTTTCTCGT
1 TGCGATTTTGGTTTCGCGT
* **
59688 TGCGATTCTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
59707 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
59727 TGCGA
1 TGCGA
59732 AAGTAAACTA
Statistics
Matches: 121, Mismatches: 16, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
14 19 0.16
15 1 0.01
16 5 0.04
17 5 0.04
18 1 0.01
19 78 0.64
20 12 0.10
ACGTcount: A:0.10, C:0.17, G:0.27, T:0.47
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:59601 original size:14 final size:14
Alignment explanation
Indices: 59582--59639 Score: 53
Period size: 14 Copynumber: 3.8 Consensus size: 14
59572 TTGGTTTCGA
59582 GTTGCGATTTTGTC
1 GTTGCGATTTTGTC
59596 GTTGCGATTTTGGTTTCGC
1 GTTGCGATTTT-G--T--C
* *
59615 GTTGCGATTCTATC
1 GTTGCGATTTTGTC
59629 GTTGCGATTTT
1 GTTGCGATTTT
59640 CATTTCGCGT
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
14 22 0.61
15 1 0.03
16 1 0.03
17 1 0.03
19 11 0.31
ACGTcount: A:0.09, C:0.16, G:0.28, T:0.48
Consensus pattern (14 bp):
GTTGCGATTTTGTC
Found at i:59607 original size:33 final size:33
Alignment explanation
Indices: 59565--59694 Score: 161
Period size: 33 Copynumber: 3.8 Consensus size: 33
59555 AAAATCGCAA
*
59565 TGCGATTTTGGTTTCGAGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
* *
59598 TGCGATTTTGGTTTCGCGTTGCGATTCTATCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
**
59631 TGCGATTTTCATTTCGCGTTGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTTT-G--T--CGT
*
59669 TGCGATTTTGGTTTCTCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
59695 CTCATTTCGC
Statistics
Matches: 82, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
33 55 0.67
36 1 0.01
38 26 0.32
ACGTcount: A:0.08, C:0.16, G:0.28, T:0.48
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
Found at i:59689 original size:38 final size:35
Alignment explanation
Indices: 59565--59731 Score: 153
Period size: 33 Copynumber: 4.7 Consensus size: 35
59555 AAAATCGCAA
*
59565 TGCGATTTTGGTTTCGAGTTGCGATTTTG--TCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTTTGTTTCGT
* *
59598 TGCGATTTTGGTTTCGCGTTGCGA--TTCTATCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTTTGTTTCGT
**
59631 TGCGATTTTCATTTCGCGTTGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTTT-GTTT--CGT
* **
59669 TGCGATTTTGGTTTCTCGTTGCGATTCTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGTTGCGATT-TTGTTT--CGT
* *
59707 TGCGATTTTAAGTTTCGTGTTGCGA
1 TGCGATTTT-GGTTTCGCGTTGCGA
59732 AAGTAAACTA
Statistics
Matches: 111, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
31 2 0.02
33 49 0.44
35 2 0.02
36 2 0.02
38 43 0.39
39 13 0.12
ACGTcount: A:0.10, C:0.17, G:0.27, T:0.47
Consensus pattern (35 bp):
TGCGATTTTGGTTTCGCGTTGCGATTTTGTTTCGT
Found at i:61677 original size:20 final size:20
Alignment explanation
Indices: 61647--61708 Score: 90
Period size: 20 Copynumber: 3.1 Consensus size: 20
61637 TTTTGGTTGA
61647 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
** *
61667 AATGACTATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
61686 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
61706 AAT
1 AAT
61709 CGCAACGCGA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 16 0.46
20 19 0.54
ACGTcount: A:0.47, C:0.18, G:0.23, T:0.13
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:61696 original size:19 final size:19
Alignment explanation
Indices: 61645--61737 Score: 97
Period size: 19 Copynumber: 5.1 Consensus size: 19
61635 TCTTTTGGTT
*
61645 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
**
61664 GAGAATGACTATCGCAACGC
1 GA-AATGAAAATCGCAACGC
61684 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
61701 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
61717 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
61736 GA
1 GA
61738 TTTTGGTTTC
Statistics
Matches: 60, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
14 10 0.17
15 1 0.02
16 2 0.03
17 2 0.03
18 1 0.02
19 28 0.47
20 16 0.27
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:61716 original size:33 final size:37
Alignment explanation
Indices: 61645--61732 Score: 130
Period size: 33 Copynumber: 2.4 Consensus size: 37
61635 TCTTTTGGTT
61645 GAAATGAAAATCGCAACGAGAGAATGACTATCGCAACGC
1 GAAATGAAAATCGCAAC-AGAGAATGAC-ATCGCAACGC
61684 GAAATGAAAATCGCAAC-GAG-A-GA-ATCGCAACGC
1 GAAATGAAAATCGCAACAGAGAATGACATCGCAACGC
61717 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
61733 TGCGATTTTG
Statistics
Matches: 49, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
33 26 0.53
35 2 0.04
36 1 0.02
37 3 0.06
39 17 0.35
ACGTcount: A:0.47, C:0.19, G:0.23, T:0.11
Consensus pattern (37 bp):
GAAATGAAAATCGCAACAGAGAATGACATCGCAACGC
Found at i:61783 original size:21 final size:21
Alignment explanation
Indices: 61757--61833 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
61747 CGCGTTGCGA
61757 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
* **
61778 TTCTCTCGTTGTAGATAGTCAT
1 TTCTCTCGTTG-CGATTTTCAT
*
61800 TT-TCGCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
61820 TTCTCTCGTTGCGA
1 TTCTCTCGTTGCGA
61834 CTCTTCTGCA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 9 0.20
21 28 0.61
22 9 0.20
ACGTcount: A:0.12, C:0.22, G:0.18, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:61955 original size:33 final size:33
Alignment explanation
Indices: 61913--61983 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
61903 AATACTAACT
*
61913 TGAAAATCGCAATGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
*
61946 TGAAAATCGCAACGAGAGAATCGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
61979 TGAAA
1 TGAAA
61984 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:61959 original size:19 final size:19
Alignment explanation
Indices: 61935--61983 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 19
61925 TGAGAGAATA
61935 GCAACGCGAAATGAAAATC
1 GCAACGCGAAATGAAAATC
*
61954 GCAA--CG--A-GAGAATC
1 GCAACGCGAAATGAAAATC
61968 GCAACGCGAAATGAAA
1 GCAACGCGAAATGAAA
61984 TCTAAGTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 10
0.66 0.06 0.29
Matches are distributed among these distances:
14 10 0.43
15 1 0.04
16 2 0.09
17 2 0.09
18 1 0.04
19 7 0.30
ACGTcount: A:0.47, C:0.20, G:0.24, T:0.08
Consensus pattern (19 bp):
GCAACGCGAAATGAAAATC
Found at i:62390 original size:20 final size:20
Alignment explanation
Indices: 62365--62518 Score: 220
Period size: 20 Copynumber: 7.5 Consensus size: 20
62355 CTTTAAAAAT
62365 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
62385 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
62405 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
62426 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
62446 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
62466 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
62486 CGCGTTGCGATTTTTACGGATA
1 CGCGTTGCGA--TTTACGGATA
*
62508 CTCGTTGCGAT
1 CGCGTTGCGAT
62519 AGTAAGAATC
Statistics
Matches: 122, Mismatches: 7, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
20 86 0.70
21 17 0.14
22 19 0.16
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.34
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:62539 original size:82 final size:80
Alignment explanation
Indices: 62362--62583 Score: 218
Period size: 82 Copynumber: 2.7 Consensus size: 80
62352 GCGCTTTAAA
* * * *
62362 AATCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGA--TTTACGGAT
1 AATCACGTTGCGATTTACGGATACGCATTGCGA-TTTACGGATCG-CGTTGCGATTTTTACGGAT
* *
62425 ACGCGTTGCGATTTACG
64 ACGCGTTGCGATGTAAG
*
62442 GAT-ACGCATTGCGATTTACGGATACGCATTGCGATTTACGGATACGCGTTGCGATTTTTACGGA
1 AATCACG--TTGCGATTTACGGATACGCATTGCGATTTACGGAT-CGCGTTGCGATTTTTACGGA
*
62506 TACTCGTTGCGATAGTAAG
63 TACGCGTTGCGAT-GTAAG
* * ** **
62525 AATCACGTTGCGATTT-TGGAAACTTATTTGCGATTCTGGGGATCGCGTTGCGATTTTTA
1 AATCACGTTGCGATTTACGGATACGCA-TTGCGATT-TACGGATCGCGTTGCGATTTTTA
62584 TTTCGCGTTG
Statistics
Matches: 118, Mismatches: 15, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
79 2 0.02
80 18 0.15
81 32 0.27
82 53 0.45
83 10 0.08
84 3 0.03
ACGTcount: A:0.21, C:0.18, G:0.27, T:0.35
Consensus pattern (80 bp):
AATCACGTTGCGATTTACGGATACGCATTGCGATTTACGGATCGCGTTGCGATTTTTACGGATAC
GCGTTGCGATGTAAG
Found at i:65961 original size:200 final size:199
Alignment explanation
Indices: 65620--66019 Score: 748
Period size: 200 Copynumber: 2.0 Consensus size: 199
65610 CTGAAGGAAT
*
65620 AGCGTAAGTGTTGGATCCAGTTTTCTTTTCTATTCGAACTCATTCTAAGAAAATGCTAACCCTCC
1 AGCGTAAGTGTTGGATCCAGTTTTCTTTTCTATTCGAACTCATTCTAAGAAAATGCTAACCCACC
65685 CTTTTTACTTGATCACTTCAGCTATCTCACCATCATCAACCCCACACATCATCCATAGAGACATC
66 CTTTTTACTTGATCACTTCAGCTATCTCACCATCATCAACCCCACACATCATCCATAGAGACATC
65750 AAAGCTAGTAATGTGTTGCTAGATTCAGATTTCCAGCCTCAGGTTGCGGATTTT-GGTTTGGAAA
131 AAAGCTAGTAATGTGTTGCTAGATTCAGATTTCCAGCCTCAGGTTGCGGATTTTGGGTTTGGAAA
65814 GCTC
196 GCTC
* *
65818 AGCGTAAGTGTTGGATCCAGTTTTCTTTTCTATTCTAACTCATTCTAAGGAAAATGCTAACCCAG
1 AGCGTAAGTGTTGGATCCAGTTTTCTTTTCTATTCGAACTCATTCTAA-GAAAATGCTAACCCAC
65883 CCTCTTTTACTTGATCACTTCAGCTATCTCACCATCATCAACCCCACACATCATCCATAGAGACA
65 CCT-TTTTACTTGATCACTTCAGCTATCTCACCATCATCAACCCCACACATCATCCATAGAGACA
65948 TCAAAGCTAGTAATGTGTTGCTAGATTCAGATTTCCAGCCTCAGGTTGCGGATTTTGGGTTTGGA
129 TCAAAGCTAGTAATGTGTTGCTAGATTCAGATTTCCAGCCTCAGGTTGCGGATTTTGGGTTTGGA
66013 AAGCTC
194 AAGCTC
66019 A
1 A
66020 TCCCTGACGG
Statistics
Matches: 196, Mismatches: 3, Indels: 3
0.97 0.01 0.01
Matches are distributed among these distances:
198 47 0.24
199 17 0.09
200 117 0.60
201 15 0.08
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.33
Consensus pattern (199 bp):
AGCGTAAGTGTTGGATCCAGTTTTCTTTTCTATTCGAACTCATTCTAAGAAAATGCTAACCCACC
CTTTTTACTTGATCACTTCAGCTATCTCACCATCATCAACCCCACACATCATCCATAGAGACATC
AAAGCTAGTAATGTGTTGCTAGATTCAGATTTCCAGCCTCAGGTTGCGGATTTTGGGTTTGGAAA
GCTC
Found at i:66664 original size:52 final size:53
Alignment explanation
Indices: 66585--66691 Score: 191
Period size: 52 Copynumber: 2.0 Consensus size: 53
66575 GAATTAGATG
66585 TCAAAATTTGTATCTTTGATATTATAAATATATATTAT-TGTTTTCTTTTGCTT
1 TCAAAATTTGTATCTTTGATATTATAAATATATATTATGTG-TTTCTTTTGCTT
66638 TCAAAATTT-TATCTTTGATATTATAAATATATATTATGTGTTTCTTTTGCTT
1 TCAAAATTTGTATCTTTGATATTATAAATATATATTATGTGTTTCTTTTGCTT
66690 TC
1 TC
66692 TTATTTTCTA
Statistics
Matches: 53, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
52 42 0.79
53 11 0.21
ACGTcount: A:0.28, C:0.08, G:0.07, T:0.56
Consensus pattern (53 bp):
TCAAAATTTGTATCTTTGATATTATAAATATATATTATGTGTTTCTTTTGCTT
Found at i:76432 original size:21 final size:21
Alignment explanation
Indices: 76399--76439 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
76389 CTAAAGACAC
76399 AATACAAAGATAATATAAAAAT
1 AATACAAAGATAATA-AAAAAT
*
76421 AATA-AAATATAATAAAAAA
1 AATACAAAGATAATAAAAAA
76440 CATCTCACGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (21 bp):
AATACAAAGATAATAAAAAAT
Found at i:98749 original size:8 final size:8
Alignment explanation
Indices: 98736--98760 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
98726 CATGCTCATG
98736 TTCATGCA
1 TTCATGCA
98744 TTCATGCA
1 TTCATGCA
98752 TTCATGCA
1 TTCATGCA
98760 T
1 T
98761 AATACTATAG
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:0.24, C:0.24, G:0.12, T:0.40
Consensus pattern (8 bp):
TTCATGCA
Found at i:99363 original size:12 final size:12
Alignment explanation
Indices: 99346--99375 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
99336 TTACTCATTT
99346 ATCTCATCTTAA
1 ATCTCATCTTAA
99358 ATCTCATCTTAA
1 ATCTCATCTTAA
99370 ATCTCA
1 ATCTCA
99376 AAATCCTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.33, C:0.27, G:0.00, T:0.40
Consensus pattern (12 bp):
ATCTCATCTTAA
Found at i:100494 original size:15 final size:17
Alignment explanation
Indices: 100464--100495 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
100454 TTTGAACTCT
100464 TTCCTTTTATTTCATTA
1 TTCCTTTTATTTCATTA
100481 TTCC-TTTA-TTCATTA
1 TTCCTTTTATTTCATTA
100496 AAAAATCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 4 0.27
17 4 0.27
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.62
Consensus pattern (17 bp):
TTCCTTTTATTTCATTA
Done.