Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007816.1 Hibiscus syriacus cultivar Beakdansim tig00110151_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: 3994936
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 14
Found at i:8679 original size:36 final size:36
Alignment explanation
Indices: 8575--8679 Score: 158
Period size: 36 Copynumber: 2.9 Consensus size: 36
8565 ATTTATAAGT
* * *
8575 TGGTGATAATATGGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
* *
8610 TGGTAATGATATAGACGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
8646 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
8680 AGATTGTATC
Statistics
Matches: 62, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
35 17 0.27
36 45 0.73
ACGTcount: A:0.30, C:0.05, G:0.35, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:12716 original size:23 final size:23
Alignment explanation
Indices: 12688--12741 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
12678 GTGATGGAAT
12688 ATGGTGATGATATAGGCGTGATA
1 ATGGTGATGATATAGGCGTGATA
12711 ATGGTGATGATATAGGCGTGATA
1 ATGGTGATGATATAGGCGTGATA
12734 ATGGTGAT
1 ATGGTGAT
12742 TGACAGATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.30, C:0.04, G:0.35, T:0.31
Consensus pattern (23 bp):
ATGGTGATGATATAGGCGTGATA
Found at i:14169 original size:24 final size:25
Alignment explanation
Indices: 14123--14177 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
14113 ATAGTTATGC
*
14123 CACTTGAAGTTCAAAAAGATGTG-T
1 CACTTGAAGTGCAAAAAGATGTGAT
* * *
14147 CACTTGAAGTGCCACAAGTTGTGAT
1 CACTTGAAGTGCAAAAAGATGTGAT
14172 CA-TTGA
1 CACTTGA
14178 GGCTCCAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (25 bp):
CACTTGAAGTGCAAAAAGATGTGAT
Found at i:18125 original size:17 final size:15
Alignment explanation
Indices: 18103--18159 Score: 60
Period size: 17 Copynumber: 3.5 Consensus size: 15
18093 AATTGGAGTG
18103 CAAAAAGAAAGAAAAGA
1 CAAAAAG-AAGAAAA-A
*
18120 CAAAAAGAAGAAAATT
1 CAAAAAGAAGAAAA-A
18136 CAGAAAAGAAGAAAAA
1 CA-AAAAGAAGAAAAA
*
18152 GAAAAAGA
1 CAAAAAGA
18160 TTTCAAAAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
15 6 0.17
16 10 0.29
17 19 0.54
ACGTcount: A:0.74, C:0.05, G:0.18, T:0.04
Consensus pattern (15 bp):
CAAAAAGAAGAAAAA
Found at i:18150 original size:26 final size:26
Alignment explanation
Indices: 18112--18175 Score: 80
Period size: 25 Copynumber: 2.5 Consensus size: 26
18102 GCAAAAAGAA
*
18112 AGAAAAGACAAAAAGAAGAAA-A-TTC
1 AGAAAAGAGAAAAAGAA-AAAGATTTC
18137 AGAAAAGAAGAAAAAGAAAAAGATTTC
1 AGAAAAG-AGAAAAAGAAAAAGATTTC
18164 A-AAAAGAGAAAA
1 AGAAAAGAGAAAA
18176 GCAAGCCAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
25 16 0.46
26 15 0.43
27 4 0.11
ACGTcount: A:0.70, C:0.05, G:0.17, T:0.08
Consensus pattern (26 bp):
AGAAAAGAGAAAAAGAAAAAGATTTC
Found at i:22657 original size:16 final size:16
Alignment explanation
Indices: 22636--22679 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
22626 TTGTGACCTT
22636 CCATGAATGATGCTGC
1 CCATGAATGATGCTGC
22652 CCATGAATGATGCTGC
1 CCATGAATGATGCTGC
22668 CCATGAA-GATGC
1 CCATGAATGATGC
22680 CTTTTCATCT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
15 5 0.18
16 23 0.82
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.23
Consensus pattern (16 bp):
CCATGAATGATGCTGC
Found at i:28570 original size:15 final size:16
Alignment explanation
Indices: 28542--28573 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
28532 TTCTGCCACC
28542 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
28558 TATGTTA-AATGCAAA
1 TATGTTAGAATGCAAA
28573 T
1 T
28574 GAGCTAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.44, C:0.06, G:0.16, T:0.34
Consensus pattern (16 bp):
TATGTTAGAATGCAAA
Found at i:35574 original size:23 final size:23
Alignment explanation
Indices: 35533--35576 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
35523 TTTCCTCCTC
*
35533 TTTGAGTGGTTTCAATTTCTTCT
1 TTTGAGTGCTTTCAATTTCTTCT
* *
35556 TTTGAGTGCTTTGATTTTCTT
1 TTTGAGTGCTTTCAATTTCTT
35577 TACTGGATTT
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:0.11, C:0.11, G:0.18, T:0.59
Consensus pattern (23 bp):
TTTGAGTGCTTTCAATTTCTTCT
Found at i:40797 original size:28 final size:26
Alignment explanation
Indices: 40744--40800 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 26
40734 TTCTTTTCTT
* *
40744 TTTCTTCTTTTGAGTGCTGGATTTTC
1 TTTCTTCTTTTGAGTGCTGCAATTTC
*
40770 TTTCTGTCTTTTGGAGTGCTTCAATTTC
1 TTTCT-TCTTTT-GAGTGCTGCAATTTC
40798 TTT
1 TTT
40801 TCTGATTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 5 0.19
27 6 0.23
28 15 0.58
ACGTcount: A:0.09, C:0.16, G:0.18, T:0.58
Consensus pattern (26 bp):
TTTCTTCTTTTGAGTGCTGCAATTTC
Found at i:43413 original size:47 final size:45
Alignment explanation
Indices: 43343--43468 Score: 164
Period size: 47 Copynumber: 2.8 Consensus size: 45
43333 TATAAAATCT
*
43343 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
43388 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCCTATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
43435 CTTGCCA-TTATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
43469 GCATGGTTAC
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
44 23 0.32
45 10 0.14
46 2 0.03
47 37 0.51
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:43627 original size:40 final size:40
Alignment explanation
Indices: 43573--43692 Score: 231
Period size: 40 Copynumber: 3.0 Consensus size: 40
43563 ACCGTAGTTC
43573 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
43613 TACATATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
43653 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
43693 ATAAACCTGC
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 78 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:46576 original size:13 final size:12
Alignment explanation
Indices: 46555--46622 Score: 61
Period size: 13 Copynumber: 5.5 Consensus size: 12
46545 TCTTCATTAT
46555 CATATTCCATCAC
1 CATA-TCCATCAC
46568 CATAGTCCATCAC
1 CATA-TCCATCAC
*
46581 CATTAT-CA-CGC
1 CA-TATCCATCAC
46592 CTATAT-CATCAC
1 C-ATATCCATCAC
46604 CATATTCCATCAC
1 CATA-TCCATCAC
46617 CATATC
1 CATATC
46623 ACGCCCATAT
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
11 11 0.23
12 9 0.19
13 25 0.53
14 2 0.04
ACGTcount: A:0.31, C:0.37, G:0.03, T:0.29
Consensus pattern (12 bp):
CATATCCATCAC
Found at i:46638 original size:35 final size:36
Alignment explanation
Indices: 46562--46640 Score: 124
Period size: 35 Copynumber: 2.2 Consensus size: 36
46552 TATCATATTC
*
46562 CATCACCATAGTCCATCACCATTATCACGCCTATAT
1 CATCACCATAGTCCATCACCATTATCACGCCCATAT
*
46598 CATCACCATATTCCATCACCA-TATCACGCCCATAT
1 CATCACCATAGTCCATCACCATTATCACGCCCATAT
*
46633 TATCACCA
1 CATCACCA
46641 ACTTATAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
35 20 0.50
36 20 0.50
ACGTcount: A:0.32, C:0.38, G:0.04, T:0.27
Consensus pattern (36 bp):
CATCACCATAGTCCATCACCATTATCACGCCCATAT
Found at i:51093 original size:13 final size:11
Alignment explanation
Indices: 51073--51138 Score: 62
Period size: 13 Copynumber: 5.5 Consensus size: 11
51063 TATCACGCAT
51073 ATATCATCACC
1 ATATCATCACC
51084 ATAGTCCATCACC
1 ATA-T-CATCACC
*
51097 ATTATCATGC-CT
1 A-TATCAT-CACC
51109 ATATCATCACC
1 ATATCATCACC
51120 ATATTCCATCACC
1 ATA-T-CATCACC
51133 ATATCA
1 ATATCA
51139 CGCCCATATT
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
10 1 0.02
11 15 0.33
12 8 0.17
13 20 0.43
14 2 0.04
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (11 bp):
ATATCATCACC
Found at i:51098 original size:36 final size:36
Alignment explanation
Indices: 51051--51155 Score: 158
Period size: 36 Copynumber: 2.9 Consensus size: 36
51041 GATACAATAT
*
51051 GTCCATCACCATTATCACGCATATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
51087 GTCCATCACCATTATCATGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
51123 TTCCATCACCA-TATCACGCCCATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
51156 ACTTATAAAT
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 19 0.30
36 44 0.70
ACGTcount: A:0.31, C:0.35, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:53653 original size:17 final size:18
Alignment explanation
Indices: 53630--53693 Score: 67
Period size: 17 Copynumber: 3.4 Consensus size: 18
53620 TCATCTCTCA
*
53630 TCATTTTTTTTCTCTTTT
1 TCATTTTTTTTCTCGTTT
*
53648 TC-TTTTCTTTCTCGTTT
1 TCATTTTTTTTCTCGTTT
53665 TCATTTCTTTTCTTCTTCGTTT
1 TCA-TT-TTTT-TTC-TCGTTT
53687 TCATTTT
1 TCATTTT
53694 CATTTTATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
17 15 0.39
18 2 0.05
19 2 0.05
20 5 0.13
21 5 0.13
22 9 0.24
ACGTcount: A:0.05, C:0.20, G:0.03, T:0.72
Consensus pattern (18 bp):
TCATTTTTTTTCTCGTTT
Found at i:53672 original size:22 final size:22
Alignment explanation
Indices: 53646--53692 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 22
53636 TTTTTCTCTT
53646 TTTCTTTTCTT-TCTCGTTTTCA
1 TTTCTTTTCTTCT-TCGTTTTCA
53668 TTTCTTTTCTTCTTCGTTTTCA
1 TTTCTTTTCTTCTTCGTTTTCA
53690 TTT
1 TTT
53693 TCATTTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 23 0.96
23 1 0.04
ACGTcount: A:0.04, C:0.21, G:0.04, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTCTTCGTTTTCA
Found at i:53673 original size:28 final size:28
Alignment explanation
Indices: 53645--53698 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
53635 TTTTTTCTCT
*
53645 TTTTCTT-TTC-TTTCTCGTTTTCATTTC
1 TTTTCTTCTTCGTTT-TCATTTTCATTTC
53672 TTTTCTTCTTCGTTTTCATTTTCATTT
1 TTTTCTTCTTCGTTTTCATTTTCATTT
53699 TATATTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 7 0.29
28 14 0.58
29 3 0.12
ACGTcount: A:0.06, C:0.20, G:0.04, T:0.70
Consensus pattern (28 bp):
TTTTCTTCTTCGTTTTCATTTTCATTTC
Found at i:53711 original size:35 final size:33
Alignment explanation
Indices: 53634--53748 Score: 103
Period size: 34 Copynumber: 3.4 Consensus size: 33
53624 CTCTCATCAT
* *
53634 TTTTTTTCTCTTTTTC-TTTTCTTTCTCGTTTT-CA
1 TTTTTTT-TCTTCTTCGTTTTCTTT-TC-TTTTATA
*
53668 TTTCTTTTCTTCTTCGTTTTCATTTTCATTTTATA
1 TTTTTTTTCTTCTTCGTTTTC-TTTTC-TTTTATA
*
53703 TTTTTTTTCTTCTTCTGTTTT-TTTTCTTCTAT-
1 TTTTTTTTCTTCTTC-GTTTTCTTTTCTTTTATA
*
53735 TTTTTCTTCTTCTT
1 TTTTTTTTCTTCTT
53749 ATAATATATA
Statistics
Matches: 70, Mismatches: 7, Indels: 10
0.80 0.08 0.11
Matches are distributed among these distances:
32 13 0.19
33 12 0.17
34 22 0.31
35 18 0.26
36 5 0.07
ACGTcount: A:0.05, C:0.18, G:0.03, T:0.74
Consensus pattern (33 bp):
TTTTTTTTCTTCTTCGTTTTCTTTTCTTTTATA
Found at i:53723 original size:15 final size:15
Alignment explanation
Indices: 53705--53747 Score: 70
Period size: 14 Copynumber: 2.9 Consensus size: 15
53695 ATTTTATATT
*
53705 TTTTTTCTTCTTCTG
1 TTTTTTCTTCTTCTA
53720 TTTTTT-TTCTTCTA
1 TTTTTTCTTCTTCTA
53734 TTTTTTCTTCTTCT
1 TTTTTTCTTCTTCT
53748 TATAATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 13 0.50
15 13 0.50
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.77
Consensus pattern (15 bp):
TTTTTTCTTCTTCTA
Found at i:53723 original size:17 final size:17
Alignment explanation
Indices: 53672--53732 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 17
53662 TTTTCATTTC
53672 TTTTCTTCTTC-GTTTT
1 TTTTCTTCTTCTGTTTT
* *
53688 CATTTTCATT-TTATATTTT
1 --TTTTC-TTCTTCTGTTTT
53707 TTTTCTTCTTCTGTTTT
1 TTTTCTTCTTCTGTTTT
53724 TTTTCTTCT
1 TTTTCTTCT
53733 ATTTTTTCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
16 2 0.06
17 21 0.58
18 7 0.19
19 6 0.17
ACGTcount: A:0.07, C:0.16, G:0.03, T:0.74
Consensus pattern (17 bp):
TTTTCTTCTTCTGTTTT
Found at i:53739 original size:32 final size:34
Alignment explanation
Indices: 53667--53748 Score: 98
Period size: 35 Copynumber: 2.4 Consensus size: 34
53657 TCTCGTTTTC
* *
53667 ATTTCTTTTCTTCTTCGTTTTCATTTTCATTTTAT
1 ATTTTTTTTCTTCTTCGTTTT-ATTTTCATTCTAT
53702 ATTTTTTTTCTTCTTCTGTTTT-TTTTC-TTCTAT
1 ATTTTTTTTCTTCTTC-GTTTTATTTTCATTCTAT
*
53735 -TTTTTCTTCTTCTT
1 ATTTTTTTTCTTCTT
53749 ATAATATATA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
32 13 0.30
33 5 0.12
34 5 0.12
35 15 0.35
36 5 0.12
ACGTcount: A:0.07, C:0.17, G:0.02, T:0.73
Consensus pattern (34 bp):
ATTTTTTTTCTTCTTCGTTTTATTTTCATTCTAT
Found at i:56613 original size:47 final size:45
Alignment explanation
Indices: 56543--56669 Score: 157
Period size: 45 Copynumber: 2.8 Consensus size: 45
56533 TATAAAATCT
*
56543 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
56588 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTTCCTATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTA-TTTTACCAAAATA
* * *
56636 CTTGCCA-TTATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
56670 GCATGGTTAC
Statistics
Matches: 72, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
44 3 0.04
45 30 0.42
47 23 0.32
48 16 0.22
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:56829 original size:40 final size:40
Alignment explanation
Indices: 56774--56895 Score: 235
Period size: 40 Copynumber: 3.0 Consensus size: 40
56764 ACAGTAGTGC
56774 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
56814 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
56854 TACACATAAGGTCGTTCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
56894 TA
1 TA
56896 TAAACCTGCG
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
40 81 1.00
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:61953 original size:14 final size:14
Alignment explanation
Indices: 61928--61962 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
61918 GGAGTACAAA
61928 AAGAAG-AAAAAAG
1 AAGAAGAAAAAAAG
61941 AAGAAGAAAAAAAG
1 AAGAAGAAAAAAAG
*
61955 AAAAAGAA
1 AAGAAGAA
61963 GAACTTCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 6 0.30
14 14 0.70
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (14 bp):
AAGAAGAAAAAAAG
Found at i:62972 original size:127 final size:127
Alignment explanation
Indices: 62746--62988 Score: 477
Period size: 127 Copynumber: 1.9 Consensus size: 127
62736 CAAACAAGTC
62746 AACATTTCCTTTTCAATTGGGAAATACAAAGACCAAGTCCTTTGTGATGTCATTCCAATGAATGC
1 AACATTTCCTTTTCAATTGGGAAATACAAAGACCAAGTCCTTTGTGATGTCATTCCAATGAATGC
62811 GTGCCATATACTCCTAGGGAGGCCTTGGCAATTTGATAAGAAGGCTATTCATGATGTAGGAT
66 GTGCCATATACTCCTAGGGAGGCCTTGGCAATTTGATAAGAAGGCTATTCATGATGTAGGAT
*
62873 AACATTTCCTTTTCAATTGGGAAATACAAAGACCAAGTCCTTTGTGATGTCATTCTAATGAATGC
1 AACATTTCCTTTTCAATTGGGAAATACAAAGACCAAGTCCTTTGTGATGTCATTCCAATGAATGC
62938 GTGCCATATACTCCTAGGGAGGCCTTGGCAATTTGATAAGAAGGCTATTCA
66 GTGCCATATACTCCTAGGGAGGCCTTGGCAATTTGATAAGAAGGCTATTCA
62989 AGTTTCTGAA
Statistics
Matches: 115, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
127 115 1.00
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.31
Consensus pattern (127 bp):
AACATTTCCTTTTCAATTGGGAAATACAAAGACCAAGTCCTTTGTGATGTCATTCCAATGAATGC
GTGCCATATACTCCTAGGGAGGCCTTGGCAATTTGATAAGAAGGCTATTCATGATGTAGGAT
Found at i:73941 original size:16 final size:16
Alignment explanation
Indices: 73920--73952 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
73910 TAGTTAGCTC
73920 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
73936 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
73952 A
1 A
73953 GGTGGAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.42
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:76342 original size:79 final size:79
Alignment explanation
Indices: 76209--76355 Score: 240
Period size: 79 Copynumber: 1.9 Consensus size: 79
76199 GGGAAATGAT
*
76209 GCTTGGCCGAATAGGGAGAGAGCTCTTCATATTGGCGCCTAAATAAACCACATGCAAGGCACATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATATTGGCGCCTAAATAAACCACATGCAAGGCACATG
76274 GGGCTGTTCACATG
66 GGGCTGTTCACATG
* * * * *
76288 GCTTGGCCGAATAGGGATAGAACTCTTCATCTTGGCGCCTAAATGATCCTCATGCAAGGCACATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATATTGGCGCCTAAATAAACCACATGCAAGGCACATG
76353 GGG
66 GGG
76356 GCTGGTCATA
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
79 62 1.00
ACGTcount: A:0.27, C:0.23, G:0.28, T:0.22
Consensus pattern (79 bp):
GCTTGGCCGAATAGGGAGAGAACTCTTCATATTGGCGCCTAAATAAACCACATGCAAGGCACATG
GGGCTGTTCACATG
Found at i:79793 original size:23 final size:24
Alignment explanation
Indices: 79736--79795 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
79726 ACTTTTCTTT
*
79736 CTTTCTTTTTCTTCTTTTCGAGTG
1 CTTTCATTTTCTTCTTTTCGAGTG
*
79760 CTTTCAATTTCTTCTTTT-GAGTG
1 CTTTCATTTTCTTCTTTTCGAGTG
79783 CTGTT-ATTTTCTT
1 CT-TTCATTTTCTT
79796 TGCTGATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 14 0.44
24 18 0.56
ACGTcount: A:0.08, C:0.18, G:0.12, T:0.62
Consensus pattern (24 bp):
CTTTCATTTTCTTCTTTTCGAGTG
Found at i:80694 original size:79 final size:79
Alignment explanation
Indices: 80561--80706 Score: 238
Period size: 79 Copynumber: 1.8 Consensus size: 79
80551 GGGAAATGAT
* *
80561 GCTTGGCCGAATAGGGAGAGAGCTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGCACATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCACCTTGGCGCCTAAATAAACCACATGCAAGGCACATG
80626 GGGCTGTTCACATG
66 GGGCTGTTCACATG
* * * *
80640 GCTTGGCCGAATAGGGAGAGAACTCTTCACCTTGGCGCCTAAATGATCCTCATGCAAGGCATATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCACCTTGGCGCCTAAATAAACCACATGCAAGGCACATG
80705 GG
66 GG
80707 TGTTCTAGGA
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
79 61 1.00
ACGTcount: A:0.26, C:0.24, G:0.28, T:0.22
Consensus pattern (79 bp):
GCTTGGCCGAATAGGGAGAGAACTCTTCACCTTGGCGCCTAAATAAACCACATGCAAGGCACATG
GGGCTGTTCACATG
Found at i:82735 original size:27 final size:24
Alignment explanation
Indices: 82694--82752 Score: 82
Period size: 27 Copynumber: 2.3 Consensus size: 24
82684 CTATATTTTT
82694 CAAAAAAAAAAACAAAAAAAAAAGG
1 CAAAAAAAAAAACAAAAAAAAAA-G
*
82719 TAAAAAAAAAAGCACAAAAAAAAAAG
1 CAAAAAAAAAA--ACAAAAAAAAAAG
82745 CAAAAAAA
1 CAAAAAAA
82753 GCCAAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 10 0.33
26 8 0.27
27 12 0.40
ACGTcount: A:0.83, C:0.08, G:0.07, T:0.02
Consensus pattern (24 bp):
CAAAAAAAAAAACAAAAAAAAAAG
Found at i:82744 original size:14 final size:13
Alignment explanation
Indices: 82694--82752 Score: 77
Period size: 12 Copynumber: 4.6 Consensus size: 13
82684 CTATATTTTT
82694 CAAAAAAAAAA-A
1 CAAAAAAAAAAGA
*
82706 CAAAAAAAAAAGG
1 CAAAAAAAAAAGA
*
82719 TAAAAAAAAAAGCA
1 CAAAAAAAAAAG-A
82733 CAAAAAAAAAAG-
1 CAAAAAAAAAAGA
82745 CAAAAAAA
1 CAAAAAAA
82753 GCCAAAATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
12 19 0.46
13 11 0.27
14 11 0.27
ACGTcount: A:0.83, C:0.08, G:0.07, T:0.02
Consensus pattern (13 bp):
CAAAAAAAAAAGA
Found at i:90664 original size:16 final size:16
Alignment explanation
Indices: 90643--90675 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
90633 TAGTTAGCTC
90643 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
90659 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
90675 A
1 A
90676 GGTGGAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.42
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:96535 original size:17 final size:17
Alignment explanation
Indices: 96515--96564 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
96505 TTTAGGGAAG
96515 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
* *
96532 TAGTTCATTCATCAAAC
1 TAGTTCATTAATTAAAC
* *
96549 TAGTTCTTTTATTAAA
1 TAGTTCATTAATTAAA
96565 TTAAGTCTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.36, C:0.14, G:0.06, T:0.44
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:98068 original size:14 final size:15
Alignment explanation
Indices: 98049--98077 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
98039 GGAGTGTTTG
98049 GTGAGGTT-TTTTTT
1 GTGAGGTTATTTTTT
98063 GTGAGGTTATTTTTT
1 GTGAGGTTATTTTTT
98078 TATTACTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.10, C:0.00, G:0.28, T:0.62
Consensus pattern (15 bp):
GTGAGGTTATTTTTT
Found at i:101906 original size:24 final size:24
Alignment explanation
Indices: 101879--101926 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
101869 CGCTTCCATG
*
101879 ATGTCATCCTGTCTAGCTCCAAAT
1 ATGTCATCATGTCTAGCTCCAAAT
*
101903 ATGTGATCATGTCTAGCTCCAAAT
1 ATGTCATCATGTCTAGCTCCAAAT
101927 TTCTCCATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (24 bp):
ATGTCATCATGTCTAGCTCCAAAT
Found at i:103384 original size:23 final size:23
Alignment explanation
Indices: 103356--103476 Score: 74
Period size: 23 Copynumber: 5.1 Consensus size: 23
103346 ACAATTTGTC
*
103356 CATCACCATTATCA-CGCCTATAT
1 CATCACCATTATCATCACC-ATAT
*
103379 CATCACTA-TATTCCATCACCAT-T
1 CATCACCATTA-T-CATCACCATAT
*
103402 -ATCACGCCTATATCATCACCATATT
1 CATCAC-CAT-TATCATCACCATA-T
*
103427 CCATCACCATTATCA-CGCCTATAT
1 -CATCACCATTATCATCACC-ATAT
103451 CATCACCA-TAGTCCATCACCATAT
1 CATCACCATTA-T-CATCACCATAT
103475 CA
1 CA
103477 CGACTATATT
Statistics
Matches: 77, Mismatches: 7, Indels: 27
0.69 0.06 0.24
Matches are distributed among these distances:
22 9 0.12
23 27 0.35
24 17 0.22
25 17 0.22
26 2 0.03
27 5 0.06
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.30
Consensus pattern (23 bp):
CATCACCATTATCATCACCATAT
Found at i:103401 original size:36 final size:36
Alignment explanation
Indices: 103354--103493 Score: 237
Period size: 36 Copynumber: 3.9 Consensus size: 36
103344 ATACAATTTG
*
103354 TCCATCACCATTATCACGCCTATATCATCACTATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAT
103390 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAT
*
103426 TCCATCACCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAT
* *
103462 TCCATCACCA-TATCACGACTATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
103494 ACTTCTAAAT
Statistics
Matches: 100, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
35 20 0.20
36 80 0.80
ACGTcount: A:0.31, C:0.35, G:0.04, T:0.30
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAT
Found at i:103433 original size:13 final size:12
Alignment explanation
Indices: 103378--103474 Score: 53
Period size: 13 Copynumber: 8.0 Consensus size: 12
103368 CACGCCTATA
*
103378 TCATCACTATAT
1 TCATCACCATAT
103390 TCCATCACC--AT
1 T-CATCACCATAT
*
103401 T-ATCACGCCTAT
1 TCATCAC-CATAT
103413 ATCATCACCATAT
1 -TCATCACCATAT
103426 TCCATCACC--AT
1 T-CATCACCATAT
*
103437 T-ATCACGCCTAT
1 TCATCAC-CATAT
103449 ATCATCACCATAGT
1 -TCATCACCATA-T
*
103463 CCATCACCATAT
1 TCATCACCATAT
103475 CACGACTATA
Statistics
Matches: 68, Mismatches: 4, Indels: 26
0.69 0.04 0.27
Matches are distributed among these distances:
9 10 0.15
10 2 0.03
11 6 0.09
12 7 0.10
13 32 0.47
14 11 0.16
ACGTcount: A:0.31, C:0.35, G:0.03, T:0.31
Consensus pattern (12 bp):
TCATCACCATAT
Found at i:103955 original size:14 final size:16
Alignment explanation
Indices: 103931--103962 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
103921 TTGGAGTGCC
103931 AAAGAAAG-AAAAGAA
1 AAAGAAAGAAAAAGAA
103946 AAAG-AAGAAAAAGAA
1 AAAGAAAGAAAAAGAA
103961 AA
1 AA
103963 GTGAAGAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.19
15 13 0.81
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (16 bp):
AAAGAAAGAAAAAGAA
Found at i:104201 original size:15 final size:16
Alignment explanation
Indices: 104183--104216 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
104173 TCTTTCTACC
104183 CTAT-CATAACCATTT
1 CTATCCATAACCATTT
*
104198 CTATCCCTAACCATTT
1 CTATCCATAACCATTT
104214 CTA
1 CTA
104217 AACTGACGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.29, C:0.32, G:0.00, T:0.38
Consensus pattern (16 bp):
CTATCCATAACCATTT
Found at i:107542 original size:36 final size:36
Alignment explanation
Indices: 107490--107598 Score: 184
Period size: 36 Copynumber: 3.0 Consensus size: 36
107480 ATAAGATACA
107490 ATATGTCCATCACCATTATCACGCCTATATCATCACC
1 ATAT-TCCATCACCATTATCACGCCTATATCATCACC
107527 ATATTCCATCACCATTATCACGCCTATATCATCACC
1 ATATTCCATCACCATTATCACGCCTATATCATCACC
* *
107563 ATAGTCCATCACCA-TATCACGCCTATATTATCACC
1 ATATTCCATCACCATTATCACGCCTATATCATCACC
107598 A
1 A
107599 ACTACTAAAT
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
35 21 0.30
36 45 0.64
37 4 0.06
ACGTcount: A:0.31, C:0.35, G:0.05, T:0.29
Consensus pattern (36 bp):
ATATTCCATCACCATTATCACGCCTATATCATCACC
Found at i:112882 original size:90 final size:91
Alignment explanation
Indices: 112728--112909 Score: 267
Period size: 90 Copynumber: 2.0 Consensus size: 91
112718 TTCCTAGAAC
** *
112728 ACCCATGTGCCTTGCATATGACCAGCCCCCATGTTTCTTGCATGTGGATCATTTAGGCGCCAAGA
1 ACCCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATATGGATCATTTAGGCGCCAAGA
*
112793 TGAAGAGTTCTCTGCCTATTCGGCCA
66 TGAAGAGTTCTCTCCCTATTCGGCCA
** * * * *
112819 ACCCATGTGTTTTGCATGTGATCAG-CCCCATGTGCCTTGTATATGGTTCATTTAGGCGCCAAGA
1 ACCCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATATGGATCATTTAGGCGCCAAGA
112883 TGAAGAGTTCTCTCCCTATTCGGCCA
66 TGAAGAGTTCTCTCCCTATTCGGCCA
112909 A
1 A
112910 GCATCAACTA
Statistics
Matches: 81, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
90 60 0.74
91 21 0.26
ACGTcount: A:0.21, C:0.27, G:0.22, T:0.30
Consensus pattern (91 bp):
ACCCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATATGGATCATTTAGGCGCCAAGA
TGAAGAGTTCTCTCCCTATTCGGCCA
Found at i:117295 original size:15 final size:15
Alignment explanation
Indices: 117275--117304 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
117265 GCAACCTTGT
117275 TGTTTCCCGATCTAG
1 TGTTTCCCGATCTAG
117290 TGTTTCCCGATCTAG
1 TGTTTCCCGATCTAG
117305 GAGAGACACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.20, T:0.40
Consensus pattern (15 bp):
TGTTTCCCGATCTAG
Found at i:124475 original size:15 final size:15
Alignment explanation
Indices: 124455--124490 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
124445 GAAAGACCTA
124455 AAAGGAAATCTTATG
1 AAAGGAAATCTTATG
124470 AAAGGAAATCTTATG
1 AAAGGAAATCTTATG
124485 AAAGGA
1 AAAGGA
124491 TACCTAAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.50, C:0.06, G:0.22, T:0.22
Consensus pattern (15 bp):
AAAGGAAATCTTATG
Found at i:131075 original size:13 final size:13
Alignment explanation
Indices: 131057--131118 Score: 51
Period size: 13 Copynumber: 4.9 Consensus size: 13
131047 AGATACTATT
131057 TCCATCACCATAA
1 TCCATCACCATAA
* *
131070 TCCATCTTCCATTA
1 TCCATC-ACCATAA
131084 T-CA-CACC-TATA
1 TCCATCACCATA-A
*
131095 T-CATCACCATAG
1 TCCATCACCATAA
131107 TCCATCACCATA
1 TCCATCACCATA
131119 TCACGCCTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
10 1 0.03
11 6 0.15
12 6 0.15
13 20 0.51
14 6 0.15
ACGTcount: A:0.32, C:0.37, G:0.02, T:0.29
Consensus pattern (13 bp):
TCCATCACCATAA
Found at i:131128 original size:35 final size:37
Alignment explanation
Indices: 131059--131138 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
131049 ATACTATTTC
*
131059 CATCACCATAATCCATCTTCCATTATCACACCTATAT
1 CATCACCATAATCCATCTACCATTATCACACCTATAT
* *
131096 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACACCTATAT
131131 CATCACCA
1 CATCACCA
131139 AATTCTCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 21 0.52
36 3 0.08
37 16 0.40
ACGTcount: A:0.33, C:0.38, G:0.03, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACACCTATAT
Found at i:138195 original size:33 final size:33
Alignment explanation
Indices: 138153--138221 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
138143 GTTGATGAAT
*
138153 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
138186 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
138219 GAA
1 GAA
138222 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:147508 original size:35 final size:37
Alignment explanation
Indices: 147439--147518 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
147429 ATACTATTTC
*
147439 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
147476 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
147511 CATCACCA
1 CATCACCA
147519 AATTCTCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 22 0.54
36 3 0.07
37 16 0.39
ACGTcount: A:0.31, C:0.38, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:151557 original size:19 final size:20
Alignment explanation
Indices: 151533--151572 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
151523 TATCCTTTCT
151533 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
151552 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
151572 T
1 T
151573 ATTATTATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:151876 original size:21 final size:22
Alignment explanation
Indices: 151838--151887 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
151828 GAGTGCAAAA
151838 AGAAAGAAAATACAAAAAGAAG
1 AGAAAGAAAATACAAAAAGAAG
151860 AGAAA-AAAAT-CAGAAAAGAAG
1 AGAAAGAAAATACA-AAAAGAAG
151881 A-AAAGAA
1 AGAAAGAA
151888 GAAAAGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 5 0.19
21 16 0.62
22 5 0.19
ACGTcount: A:0.74, C:0.04, G:0.18, T:0.04
Consensus pattern (22 bp):
AGAAAGAAAATACAAAAAGAAG
Found at i:151882 original size:8 final size:8
Alignment explanation
Indices: 151871--151895 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
151861 GAAAAAAATC
151871 AGAAAAGA
1 AGAAAAGA
151879 AGAAAAGA
1 AGAAAAGA
151887 AGAAAAGA
1 AGAAAAGA
151895 A
1 A
151896 AAGAAAAAGA
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:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (8 bp):
AGAAAAGA
Found at i:151905 original size:16 final size:15
Alignment explanation
Indices: 151851--151905 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
151841 AAGAAAATAC
*
151851 AAAAAGAAGAGAAAA
1 AAAAAGAAAAGAAAA
*
151866 AAATCAGAAAAGAAGAA
1 AAA-AAGAAAAGAA-AA
*
151883 AAGAAGAAAAGAAAA
1 AAAAAGAAAAGAAAA
151898 GAAAAAGA
1 -AAAAAGA
151906 GAAGTTCAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
15 5 0.16
16 23 0.72
17 4 0.12
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (15 bp):
AAAAAGAAAAGAAAA
Found at i:154830 original size:23 final size:23
Alignment explanation
Indices: 154785--154830 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
154775 TTATACCTAT
*
154785 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
154808 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
154831 TATATTATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:156171 original size:19 final size:20
Alignment explanation
Indices: 156147--156186 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
156137 TATCCTTTCT
156147 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
156166 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
156186 T
1 T
156187 ATTATTATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:161516 original size:24 final size:23
Alignment explanation
Indices: 161467--161517 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
161457 AAAGTAAATC
**
161467 AAAGCACTCAAAAAAAGAAATTG
1 AAAGCACTCAAAAAAAGAAAAAG
* *
161490 AAAGCGCTCGAAAAAAGAAAAAAG
1 AAAGCACTCAAAAAAAG-AAAAAG
161514 AAAG
1 AAAG
161518 AAAGAAAAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.63, C:0.12, G:0.18, T:0.08
Consensus pattern (23 bp):
AAAGCACTCAAAAAAAGAAAAAG
Found at i:164284 original size:11 final size:13
Alignment explanation
Indices: 164252--164281 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
164242 TGGCCAAAGA
164252 TGAAAAGGTATGT
1 TGAAAAGGTATGT
164265 TGAAAAGGTATG-
1 TGAAAAGGTATGT
164277 TGAAA
1 TGAAA
164282 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:168316 original size:15 final size:16
Alignment explanation
Indices: 168289--168318 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
168279 AAACAACAAA
168289 AAAAACAAGAAAGAAG
1 AAAAACAAGAAAGAAG
168305 AAAAACAA-AAAGAA
1 AAAAACAAGAAAGAA
168319 AAGAAAGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.80, C:0.07, G:0.13, T:0.00
Consensus pattern (16 bp):
AAAAACAAGAAAGAAG
Found at i:171806 original size:35 final size:37
Alignment explanation
Indices: 171745--171815 Score: 119
Period size: 35 Copynumber: 2.0 Consensus size: 37
171735 ATAAGATACA
171745 ATATGTCCATCACCATTATCACGCCTATATCATCACT
1 ATATGTCCATCACCATTATCACGCCTATATCATCACT
*
171782 ATAT-TCCATCACCA-TATCACGCCTATATTATCAC
1 ATATGTCCATCACCATTATCACGCCTATATCATCAC
171816 CAACTTCTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
35 19 0.58
36 10 0.30
37 4 0.12
ACGTcount: A:0.31, C:0.32, G:0.04, T:0.32
Consensus pattern (37 bp):
ATATGTCCATCACCATTATCACGCCTATATCATCACT
Found at i:173163 original size:24 final size:24
Alignment explanation
Indices: 173117--173168 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
173107 CCTTGGCACT
* * *
173117 TCAAGTGGCACATCTTTTTGAACA
1 TCAAGTGGCACAGCTGTTGGAACA
*
173141 TCAAGTGGCACAGCTGTTGGAACG
1 TCAAGTGGCACAGCTGTTGGAACA
173165 TCAA
1 TCAA
173169 AGGACATGTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (24 bp):
TCAAGTGGCACAGCTGTTGGAACA
Found at i:183645 original size:24 final size:24
Alignment explanation
Indices: 183591--183650 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
183581 ATCCCATTTC
* * *
183591 TTGGAACTTCAAGTGGCACATCTT
1 TTGGAACATCAAGTGGCACAGCTG
* *
183615 TTTGAACATCAAGTGGCATAGCTG
1 TTGGAACATCAAGTGGCACAGCTG
*
183639 TTGGAACGTCAA
1 TTGGAACATCAA
183651 AGGACATGTC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.30
Consensus pattern (24 bp):
TTGGAACATCAAGTGGCACAGCTG
Found at i:186363 original size:35 final size:35
Alignment explanation
Indices: 186317--186387 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
186307 TGATGTAAGG
186317 CGAATCTACACACTTTGGTGAGAAGAGTAGATAGC
1 CGAATCTACACACTTTGGTGAGAAGAGTAGATAGC
186352 CGAATCTACACACTTTGGTGAGAAGAGTAGATAGC
1 CGAATCTACACACTTTGGTGAGAAGAGTAGATAGC
186387 C
1 C
186388 TTATTGTGTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (35 bp):
CGAATCTACACACTTTGGTGAGAAGAGTAGATAGC
Found at i:191783 original size:19 final size:19
Alignment explanation
Indices: 191759--191807 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
191749 TCTTTTTGAA
191759 TTCTTTTTCTT-TTCTTTT
1 TTCTTTTTCTTCTTCTTTT
191777 CTTC-TTTTCTTCTTCTTTT
1 -TTCTTTTTCTTCTTCTTTT
191796 TGTCTTTTTCTT
1 T-TCTTTTTCTT
191808 ATTTTTGCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 8 0.30
19 12 0.44
20 7 0.26
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (19 bp):
TTCTTTTTCTTCTTCTTTT
Found at i:202647 original size:11 final size:11
Alignment explanation
Indices: 202633--202686 Score: 63
Period size: 12 Copynumber: 4.7 Consensus size: 11
202623 AAAACAAAAA
202633 CAAAAAAAAGG
1 CAAAAAAAAGG
202644 CAAAAAAAAAGG
1 C-AAAAAAAAGG
*
202656 TAAAAAAAAGG
1 CAAAAAAAAGG
*
202667 CACAAAAAAAAG
1 CA-AAAAAAAGG
*
202679 TAAAAAAA
1 CAAAAAAA
202687 GCCAAAATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
11 18 0.49
12 19 0.51
ACGTcount: A:0.76, C:0.07, G:0.13, T:0.04
Consensus pattern (11 bp):
CAAAAAAAAGG
Found at i:202660 original size:23 final size:23
Alignment explanation
Indices: 202634--202686 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
202624 AAACAAAAAC
202634 AAAAAAAAGGCA-AAAAAAAAGGT
1 AAAAAAAAGGCACAAAAAAAA-GT
202657 AAAAAAAAGGCACAAAAAAAAGT
1 AAAAAAAAGGCACAAAAAAAAGT
202680 AAAAAAA
1 AAAAAAA
202687 GCCAAAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 21 0.72
24 8 0.28
ACGTcount: A:0.77, C:0.06, G:0.13, T:0.04
Consensus pattern (23 bp):
AAAAAAAAGGCACAAAAAAAAGT
Found at i:202686 original size:12 final size:12
Alignment explanation
Indices: 202634--202678 Score: 65
Period size: 11 Copynumber: 3.8 Consensus size: 12
202624 AAACAAAAAC
202634 AAAAAAAAGGCA
1 AAAAAAAAGGCA
*
202646 AAAAAAAAGG-T
1 AAAAAAAAGGCA
202657 AAAAAAAAGGCA
1 AAAAAAAAGGCA
202669 CAAAAAAAAG
1 -AAAAAAAAG
202679 TAAAAAAAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 10 0.34
12 10 0.34
13 9 0.31
ACGTcount: A:0.76, C:0.07, G:0.16, T:0.02
Consensus pattern (12 bp):
AAAAAAAAGGCA
Found at i:212687 original size:36 final size:36
Alignment explanation
Indices: 212639--212743 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
212629 GATACAATCT
212639 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
212675 TTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
212711 GTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
212744 ACTTCTAAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 21 0.32
36 45 0.68
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:238857 original size:11 final size:12
Alignment explanation
Indices: 238838--238878 Score: 59
Period size: 11 Copynumber: 3.6 Consensus size: 12
238828 CAAAAGCAAC
238838 AAAAAGAAAAA-
1 AAAAAGAAAAAG
*
238849 AAGAAGAAAAAG
1 AAAAAGAAAAAG
238861 AAAAAG-AAAAG
1 AAAAAGAAAAAG
238872 AAAAAGA
1 AAAAAGA
238879 CTCCTACATC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
11 21 0.81
12 5 0.19
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAAG
Found at i:238858 original size:17 final size:17
Alignment explanation
Indices: 238838--238878 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
238828 CAAAAGCAAC
238838 AAAAAGAAAAA-AAGAAG
1 AAAAAGAAAAAGAA-AAG
238855 AAAAAGAAAAAGAAAAG
1 AAAAAGAAAAAGAAAAG
238872 AAAAAGA
1 AAAAAGA
238879 CTCCTACATC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 21 0.91
18 2 0.09
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAAGAAAAG
Found at i:238861 original size:6 final size:6
Alignment explanation
Indices: 238838--238878 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
238828 CAAAAGCAAC
*
238838 AAAAAG AAAAA- AAGAAG AAAAAG AAAAAG -AAAAG AAAAAG A
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG A
238879 CTCCTACATC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 9 0.29
6 22 0.71
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:239173 original size:17 final size:17
Alignment explanation
Indices: 239151--239183 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
239141 ATCCTACCCT
239151 TATACCATAACCATTTC
1 TATACCATAACCATTTC
*
239168 TATACCCTAACCATTT
1 TATACCATAACCATTT
239184 GTTTAAAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.36
Consensus pattern (17 bp):
TATACCATAACCATTTC
Found at i:241984 original size:28 final size:28
Alignment explanation
Indices: 241944--241997 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
241934 CTCACATTCA
*
241944 CATAACAGCATGTTCATCATTTGTTTTG
1 CATAACAACATGTTCATCATTTGTTTTG
241972 CATAACAACATGTTCATCATTTGTTT
1 CATAACAACATGTTCATCATTTGTTT
241998 AGTTAATTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.43
Consensus pattern (28 bp):
CATAACAACATGTTCATCATTTGTTTTG
Found at i:243745 original size:20 final size:20
Alignment explanation
Indices: 243720--243766 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
243710 TTTTCTTTTC
243720 TTTTTTTAATTTTCGGAATT
1 TTTTTTTAATTTTCGGAATT
243740 TTTTTTTAATTTTCGGAATT
1 TTTTTTTAATTTTCGGAATT
243760 TTTTTTT
1 TTTTTTT
243767 CAGGATGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.17, C:0.04, G:0.09, T:0.70
Consensus pattern (20 bp):
TTTTTTTAATTTTCGGAATT
Found at i:250792 original size:28 final size:28
Alignment explanation
Indices: 250752--250805 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
250742 TGAATTAACT
*
250752 AAACAAACGATGAACATGTTGTTATGCA
1 AAACAAACGATGAACATGCTGTTATGCA
*
250780 AAACAAATGATGAACATGCTGTTATG
1 AAACAAACGATGAACATGCTGTTATG
250806 TGAATGTGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.26
Consensus pattern (28 bp):
AAACAAACGATGAACATGCTGTTATGCA
Found at i:254178 original size:90 final size:91
Alignment explanation
Indices: 254024--254205 Score: 276
Period size: 90 Copynumber: 2.0 Consensus size: 91
254014 CCTAGAACAC
*
254024 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
*
254089 AAGAGTTCTCTCCCTATTCGGCCAAG
66 AAGAGCTCTCTCCCTATTCGGCCAAG
** * * * * *
254115 CCATGTGTTTTGCATGTGAACAG-CCCCATTTGCCTTGCATGTGGTTTATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
254179 AAGAGCTCTCTCCCTATTCGGCCAAG
66 AAGAGCTCTCTCCCTATTCGGCCAAG
254205 C
1 C
254206 ATCATTTCCC
Statistics
Matches: 82, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
90 63 0.77
91 19 0.23
ACGTcount: A:0.21, C:0.28, G:0.23, T:0.28
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
AAGAGCTCTCTCCCTATTCGGCCAAG
Found at i:255014 original size:23 final size:24
Alignment explanation
Indices: 254987--255040 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 24
254977 AAAAACAGCA
*
254987 AAGAAAATAAAAGCACTC-AACAG
1 AAGAAAATAAAAGCACTCGAAAAG
* *
255010 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
255034 AAGAAAA
1 AAGAAAA
255041 GAAAGAAAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 16 0.62
24 10 0.38
ACGTcount: A:0.61, C:0.13, G:0.17, T:0.09
Consensus pattern (24 bp):
AAGAAAATAAAAGCACTCGAAAAG
Found at i:258545 original size:90 final size:91
Alignment explanation
Indices: 258400--258572 Score: 249
Period size: 90 Copynumber: 1.9 Consensus size: 91
258390 CCCATGTTCC
* * *
258400 TTGCATATGACCAGCCCCCATATGCCTTGCATGAGGATCATTTAGGCGCCAAGATGAAGAGTTCT
1 TTGCATATGAACAGCCCCCATATGCCTTCCATGAGGATCATTTAGGCGCCAAGATGAAGAGCTCT
258465 CTCCCTATTCAGCCAAGCCATGTGTT
66 CTCCCTATTCAGCCAAGCCATGTGTT
* * * * *
258491 TTGCATGTGAACAG-CCCCATGTGCCTTCCATGTGGTTTATTTAGGCGCCAAGATGAAGAGCTCT
1 TTGCATATGAACAGCCCCCATATGCCTTCCATGAGGATCATTTAGGCGCCAAGATGAAGAGCTCT
**
258555 CTCCCTATTTGGCCAAGC
66 CTCCCTATTCAGCCAAGC
258573 ATCATTTCCC
Statistics
Matches: 72, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
90 60 0.83
91 12 0.17
ACGTcount: A:0.23, C:0.27, G:0.22, T:0.28
Consensus pattern (91 bp):
TTGCATATGAACAGCCCCCATATGCCTTCCATGAGGATCATTTAGGCGCCAAGATGAAGAGCTCT
CTCCCTATTCAGCCAAGCCATGTGTT
Found at i:262982 original size:21 final size:21
Alignment explanation
Indices: 262943--262982 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
262933 GCGATTATCT
* *
262943 AAAATCGCAACGCGGATTTCA
1 AAAATCGCAACACGAATTTCA
*
262964 AAAATCGCAATACGAATTT
1 AAAATCGCAACACGAATTT
262983 GTAAATCGCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.23
Consensus pattern (21 bp):
AAAATCGCAACACGAATTTCA
Found at i:262990 original size:20 final size:20
Alignment explanation
Indices: 262965--263013 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
262955 CGGATTTCAA
*
262965 AAATCGCAATACGAATTTGT
1 AAATCGCAATACGAATATGT
**
262985 AAATCGCAATGTGAATATGT
1 AAATCGCAATACGAATATGT
263005 AAATCGCAA
1 AAATCGCAA
263014 CGCGATAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (20 bp):
AAATCGCAATACGAATATGT
Found at i:263052 original size:61 final size:60
Alignment explanation
Indices: 263007--263170 Score: 231
Period size: 61 Copynumber: 2.7 Consensus size: 60
262997 GAATATGTAA
* * * *
263007 ATCGCAACGCGATAACACGTGATCGCAACGCGATTATGACTATCGCAACGCG-ATTCGGATT
1 ATCGCAACGCGATAATACGTGATCGCAACGCGATTCTGACTATCGCAACGAGAATT--GACT
* *
263068 ATCACAACGCGATAATACGTGATCGCAACGCGATTCTGACTATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATAATACGTGATCGCAACGCGATTCTGACTATCGCAACGAGAAT-TGACT
*
263129 ATCGCAACGCGATAATACGTGATCGCAACGTGATTCTGACTA
1 ATCGCAACGCGATAATACGTGATCGCAACGCGATTCTGACTA
263171 ACGCTTCACT
Statistics
Matches: 93, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
61 91 0.98
62 1 0.01
63 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (60 bp):
ATCGCAACGCGATAATACGTGATCGCAACGCGATTCTGACTATCGCAACGAGAATTGACT
Found at i:263053 original size:20 final size:20
Alignment explanation
Indices: 263028--263170 Score: 146
Period size: 20 Copynumber: 7.0 Consensus size: 20
263018 ATAACACGTG
*
263028 ATCGCAACGCGATTATGACT
1 ATCGCAACGCGATTCTGACT
* *
263048 ATCGCAACGCGATTCGGATT
1 ATCGCAACGCGATTCTGACT
* **
263068 ATCACAACGCGATAAT-ACGT
1 ATCGCAACGCGATTCTGAC-T
263088 GATCGCAACGCGATTCTGACT
1 -ATCGCAACGCGATTCTGACT
*
263109 ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
**
263129 ATCGCAACGCGATAAT-ACGT
1 ATCGCAACGCGATTCTGAC-T
*
263149 GATCGCAACGTGATTCTGACT
1 -ATCGCAACGCGATTCTGACT
263170 A
1 A
263171 ACGCTTCACT
Statistics
Matches: 99, Mismatches: 18, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
19 3 0.03
20 64 0.65
21 28 0.28
22 4 0.04
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:263154 original size:41 final size:41
Alignment explanation
Indices: 263007--263170 Score: 151
Period size: 41 Copynumber: 4.0 Consensus size: 41
262997 GAATATGTAA
*
263007 ATCGCAACGCGATAACACGTGATCGCAACGCGATTATGACT
1 ATCGCAACGCGATAATACGTGATCGCAACGCGATTATGACT
* * *
263048 ATCGCAACGCGAT--T-CGGATTATCACAACGCGATAAT-ACGT
1 ATCGCAACGCGATAATAC-G-TGATCGCAACGCGATTATGAC-T
** * *
263088 GATCGCAACGCGATTCTGAC-T-ATCGCAACGAGATTCTGACT
1 -ATCGCAACGCGATAAT-ACGTGATCGCAACGCGATTATGACT
* *
263129 ATCGCAACGCGATAATACGTGATCGCAACGTGATTCTGACT
1 ATCGCAACGCGATAATACGTGATCGCAACGCGATTATGACT
263170 A
1 A
263171 ACGCTTCACT
Statistics
Matches: 101, Mismatches: 11, Indels: 22
0.75 0.08 0.16
Matches are distributed among these distances:
38 1 0.01
39 5 0.05
40 31 0.31
41 59 0.58
42 3 0.03
43 1 0.01
45 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (41 bp):
ATCGCAACGCGATAATACGTGATCGCAACGCGATTATGACT
Found at i:264028 original size:24 final size:24
Alignment explanation
Indices: 263996--264049 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
263986 GTATTCGAAA
263996 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
264020 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
264044 TTTGAT
1 TTTGAT
264050 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:266320 original size:18 final size:18
Alignment explanation
Indices: 266297--266331 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
266287 AGCAAAAGGC
*
266297 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
266315 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
266332 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:266556 original size:20 final size:20
Alignment explanation
Indices: 266513--266560 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
266503 TTCATTTAAC
*
266513 TATCGCAACGCAAATATGAC
1 TATCGCAACGCAAATATGAA
** *
266533 TATCGCAACGTGAATTTGAA
1 TATCGCAACGCAAATATGAA
266553 TATCGCAA
1 TATCGCAA
266561 TGGGATAATC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.25
Consensus pattern (20 bp):
TATCGCAACGCAAATATGAA
Found at i:267757 original size:19 final size:21
Alignment explanation
Indices: 267733--267784 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
267723 CGGCCAAGAG
*
267733 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
267752 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
267773 CATGTATTTTCA
1 CATGTATTTTCA
267785 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:268540 original size:25 final size:25
Alignment explanation
Indices: 268506--268554 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
268496 ATTGGAGGAC
*
268506 AAAAAGAAGA-AAATTCAGAAAAGAA
1 AAAAAAAAGAGAAATTCA-AAAAGAA
*
268531 AAAAAAAAGAGAAGTTCAAAAAGA
1 AAAAAAAAGAGAAATTCAAAAAGA
268555 GAAAGCAAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.71, C:0.04, G:0.16, T:0.08
Consensus pattern (25 bp):
AAAAAAAAGAGAAATTCAAAAAGAA
Found at i:271837 original size:19 final size:21
Alignment explanation
Indices: 271813--271864 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
271803 CGGCCAAGAG
*
271813 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
271832 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
271853 CATGTATTTTCA
1 CATGTATTTTCA
271865 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:272529 original size:20 final size:20
Alignment explanation
Indices: 272504--272671 Score: 239
Period size: 20 Copynumber: 8.4 Consensus size: 20
272494 CAATGGGATA
* * *
272504 ATCGCAATGCAAAAATGACT
1 ATCGCAACGCGAATATGACT
*
272524 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAATATGACT
272544 ATCGCAACGCGAATATGACT
1 ATCGCAACGCGAATATGACT
*
272564 ATCACAACGCGAATATGACT
1 ATCGCAACGCGAATATGACT
*
272584 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATATGACT
*
272604 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATATGACT
272624 ATCGCAACGCGAA-ATGACT
1 ATCGCAACGCGAATATGACT
* *
272643 ATCGCAACGGGAATTTTGACT
1 ATCGCAACGCGAA-TATGACT
272664 ATCGCAAC
1 ATCGCAAC
272672 AAGAAAATCG
Statistics
Matches: 137, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
19 17 0.12
20 107 0.78
21 13 0.09
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGAATATGACT
Found at i:272856 original size:30 final size:30
Alignment explanation
Indices: 272822--272887 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
272812 TTAAGCAAGC
272822 ACAAATAAGAATTATTTACACATCAATTAA
1 ACAAATAAGAATTATTTACACATCAATTAA
*
272852 ACAAATAATAATTATTTACACATCAATTAA
1 ACAAATAAGAATTATTTACACATCAATTAA
*
272882 AAAAAT
1 ACAAAT
272888 CAAGTCTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.56, C:0.12, G:0.02, T:0.30
Consensus pattern (30 bp):
ACAAATAAGAATTATTTACACATCAATTAA
Found at i:274316 original size:21 final size:21
Alignment explanation
Indices: 274267--274365 Score: 81
Period size: 21 Copynumber: 4.7 Consensus size: 21
274257 TCTAGAATGT
*
274267 TGGGAGGGACCTCTTCAACGA
1 TGGGAGGGGCCTCTTCAACGA
** *
274288 TGACAGGGGCCTCTTCAACGG
1 TGGGAGGGGCCTCTTCAACGA
* * **
274309 TGGGAGGGGACTCTTGAGGGA
1 TGGGAGGGGCCTCTTCAACGA
** *
274330 TGATAGGGGCCTCTTGAACGA
1 TGGGAGGGGCCTCTTCAACGA
* *
274351 TAGGAGAGGCCTCTT
1 TGGGAGGGGCCTCTT
274366 GAATGATGAC
Statistics
Matches: 58, Mismatches: 20, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 58 1.00
ACGTcount: A:0.21, C:0.20, G:0.37, T:0.21
Consensus pattern (21 bp):
TGGGAGGGGCCTCTTCAACGA
Found at i:274332 original size:42 final size:42
Alignment explanation
Indices: 274269--274378 Score: 114
Period size: 42 Copynumber: 2.6 Consensus size: 42
274259 TAGAATGTTG
* * * *
274269 GGAG-GGACCTCTTCAACGATGACAGGGGCCTCTTCAACGGTG
1 GGAGAGGA-CTCTTGAAGGATGACAGGGGCCTCTTCAACGATA
* * * *
274311 GGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGATA
1 GGAGAGGACTCTTGAAGGATGACAGGGGCCTCTTCAACGATA
* *
274353 GGAGAGGCCTCTTGAATGATGACAGG
1 GGAGAGGACTCTTGAAGGATGACAGG
274379 TGAGTCGGGC
Statistics
Matches: 55, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
42 52 0.95
43 3 0.05
ACGTcount: A:0.24, C:0.19, G:0.37, T:0.20
Consensus pattern (42 bp):
GGAGAGGACTCTTGAAGGATGACAGGGGCCTCTTCAACGATA
Found at i:274881 original size:20 final size:20
Alignment explanation
Indices: 274856--274898 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
274846 ATAGTTTCTG
*
274856 AAACTTAAAATCGTAACACA
1 AAACTTAAAATCGCAACACA
274876 AAACTTAAAATCGCAACACA
1 AAACTTAAAATCGCAACACA
274896 AAA
1 AAA
274899 ATAATTATCG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.58, C:0.21, G:0.05, T:0.16
Consensus pattern (20 bp):
AAACTTAAAATCGCAACACA
Found at i:274927 original size:20 final size:20
Alignment explanation
Indices: 274904--274972 Score: 113
Period size: 20 Copynumber: 3.5 Consensus size: 20
274894 CAAAAATAAT
*
274904 TATCGCAACACGAATTTGAC
1 TATCGCAACGCGAATTTGAC
274924 TATCGCAACGCGAATTTGAC
1 TATCGCAACGCGAATTTGAC
*
274944 TATCGCAACGCGAA-ATGAC
1 TATCGCAACGCGAATTTGAC
274963 TATCGCAACG
1 TATCGCAACG
274973 AGAAAATCGC
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
19 14 0.30
20 33 0.70
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (20 bp):
TATCGCAACGCGAATTTGAC
Found at i:275026 original size:20 final size:20
Alignment explanation
Indices: 274997--275156 Score: 110
Period size: 20 Copynumber: 8.6 Consensus size: 20
274987 CGAAACTAAA
274997 TTCGCGTTGCGATAGTCATT
1 TTCGCGTTGCGATAGTCATT
*
275017 TTCGCATTGCGAT--T-A--
1 TTCGCGTTGCGATAGTCATT
* **
275032 -TCCCGTTGCGATAGTCAAA
1 TTCGCGTTGCGATAGTCATT
* *
275051 ATCACGTTGCGATAGTCATT
1 TTCGCGTTGCGATAGTCATT
275071 TTCGCGTTGCGATAGTCATT
1 TTCGCGTTGCGATAGTCATT
*
275091 TTCGCATTGCGAT--T-A--
1 TTCGCGTTGCGATAGTCATT
* * **
275106 -TCCCGTTGCGATAGTTAAA
1 TTCGCGTTGCGATAGTCATT
* *
275125 TTCGCGTTACGATAATCATT
1 TTCGCGTTGCGATAGTCATT
*
275145 TTCGTGTTGCGA
1 TTCGCGTTGCGA
275157 CTATTCTTCT
Statistics
Matches: 109, Mismatches: 19, Indels: 24
0.72 0.12 0.16
Matches are distributed among these distances:
14 20 0.18
16 2 0.02
17 4 0.04
18 2 0.02
20 81 0.74
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.37
Consensus pattern (20 bp):
TTCGCGTTGCGATAGTCATT
Found at i:275085 original size:74 final size:74
Alignment explanation
Indices: 274997--275156 Score: 266
Period size: 74 Copynumber: 2.2 Consensus size: 74
274987 CGAAACTAAA
*
274997 TTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCCCGTTGCGATAGTCAAAATCACGTTGCG
1 TTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCCCGTTGCGATAGTCAAAATCACGTTACG
*
275062 ATAGTCATT
66 ATAATCATT
* * *
275071 TTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCCCGTTGCGATAGTTAAATTCGCGTTACG
1 TTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCCCGTTGCGATAGTCAAAATCACGTTACG
275136 ATAATCATT
66 ATAATCATT
*
275145 TTCGTGTTGCGA
1 TTCGCGTTGCGA
275157 CTATTCTTCT
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
74 80 1.00
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.37
Consensus pattern (74 bp):
TTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCCCGTTGCGATAGTCAAAATCACGTTACG
ATAATCATT
Found at i:277137 original size:20 final size:20
Alignment explanation
Indices: 277114--277169 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
277104 TCTGAAACTT
277114 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
*
277134 AAAATTGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** *
277154 ATTATCGCAACGCGAA
1 AAAATCGCAACACGAA
277170 TTTGACTATC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.50, C:0.20, G:0.16, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:277218 original size:33 final size:34
Alignment explanation
Indices: 277160--277237 Score: 97
Period size: 33 Copynumber: 2.3 Consensus size: 34
277150 AATGATTATC
* *
277160 GCAACGCGAATTTGACTATCGCAACGAGATAATA
1 GCAACGCGAATATGACTATCACAACGAGATAATA
*
277194 GCAACGCGAA-ATGGCTATCACAACGAGATAA-A
1 GCAACGCGAATATGACTATCACAACGAGATAATA
*
277226 CGTAACGCGAAT
1 -GCAACGCGAAT
277238 TTTGTCATTG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
32 1 0.03
33 27 0.71
34 10 0.26
ACGTcount: A:0.40, C:0.22, G:0.22, T:0.17
Consensus pattern (34 bp):
GCAACGCGAATATGACTATCACAACGAGATAATA
Found at i:277608 original size:22 final size:22
Alignment explanation
Indices: 277580--277652 Score: 110
Period size: 22 Copynumber: 3.3 Consensus size: 22
277570 GATGCAGATA
*
277580 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCACCGGAGATGGG
* *
277602 GATGGATTTCACCGGAAATGGG
1 GACGGATTTCACCGGAGATGGG
*
277624 GACGGATTTCATCGGAGATGGG
1 GACGGATTTCACCGGAGATGGG
277646 GACGGAT
1 GACGGAT
277653 GTCGCTATAG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.23, C:0.15, G:0.41, T:0.21
Consensus pattern (22 bp):
GACGGATTTCACCGGAGATGGG
Found at i:277847 original size:20 final size:20
Alignment explanation
Indices: 277822--277927 Score: 99
Period size: 20 Copynumber: 5.2 Consensus size: 20
277812 TTATTGCAAC
*
277822 GCGATAGTCAAAATCTCGTT
1 GCGATAGTCAAAATCGCGTT
* *
277842 GCGATAGACAGAATCGCGTT
1 GCGATAGTCAAAATCGCGTT
* **
277862 ACGATCACGT-ATTATCGCGTT
1 GCGAT-A-GTCAAAATCGCGTT
277883 GCGATAGTTC-AAATCGCGTT
1 GCGATAG-TCAAAATCGCGTT
*
277903 GCGATAGTCAGAATCGCGTT
1 GCGATAGTCAAAATCGCGTT
*
277923 ACGAT
1 GCGAT
277928 CACGTGTTAC
Statistics
Matches: 69, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
19 3 0.04
20 51 0.74
21 14 0.20
22 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (20 bp):
GCGATAGTCAAAATCGCGTT
Found at i:277890 original size:61 final size:61
Alignment explanation
Indices: 277822--277948 Score: 202
Period size: 61 Copynumber: 2.1 Consensus size: 61
277812 TTATTGCAAC
* *
277822 GCGATAG-TCAAAATCTCGTTGCGATAGACAGAATCGCGTTACGATCACGTATTATCGCGTT
1 GCGATAGTTC-AAATCGCGTTGCGATAGACAGAATCGCGTTACGATCACGTATTACCGCGTT
* *
277883 GCGATAGTTCAAATCGCGTTGCGATAGTCAGAATCGCGTTACGATCACGTGTTACCGCGTT
1 GCGATAGTTCAAATCGCGTTGCGATAGACAGAATCGCGTTACGATCACGTATTACCGCGTT
277944 GCGAT
1 GCGAT
277949 TTACAATATT
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (61 bp):
GCGATAGTTCAAATCGCGTTGCGATAGACAGAATCGCGTTACGATCACGTATTACCGCGTT
Found at i:277979 original size:20 final size:21
Alignment explanation
Indices: 277942--277990 Score: 82
Period size: 20 Copynumber: 2.4 Consensus size: 21
277932 TGTTACCGCG
*
277942 TTGCGATTTACAATATTCGCA
1 TTGCGATTTACAATATTCACA
277963 TTGCGATTTAC-ATATTCACA
1 TTGCGATTTACAATATTCACA
277983 TTGCGATT
1 TTGCGATT
277991 ATCTAAAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (21 bp):
TTGCGATTTACAATATTCACA
Found at i:278041 original size:20 final size:21
Alignment explanation
Indices: 277995--278043 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
277985 GCGATTATCT
*
277995 AAAATCGCAATGCGGATTTCA
1 AAAATCGCAATGCGGATGTCA
278016 AAAATCGCAATGC-GATGGTC-
1 AAAATCGCAATGCGGAT-GTCA
278036 AAAATCGC
1 AAAATCGC
278044 GTTGCGAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.20
Consensus pattern (21 bp):
AAAATCGCAATGCGGATGTCA
Found at i:305852 original size:16 final size:16
Alignment explanation
Indices: 305831--305863 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
305821 TTCTTCCACC
305831 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
305847 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
305863 T
1 T
305864 GAGCTAACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.33
Consensus pattern (16 bp):
TATGTTAGAATGCAAA
Found at i:312942 original size:33 final size:33
Alignment explanation
Indices: 312863--312966 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
312853 ATACAATCTG
* *
312863 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
312899 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
312932 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
312965 TC
1 TC
312967 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:315839 original size:23 final size:23
Alignment explanation
Indices: 315796--315840 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
315786 TGTCTTTAGA
*
315796 AGAACCAATGAACGTGACCTATG
1 AGAACCAATGAACATGACCTATG
*
315819 AGAATCCAATGATCATG-CCTAT
1 AGAA-CCAATGAACATGACCTAT
315841 TGGAGTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (23 bp):
AGAACCAATGAACATGACCTATG
Found at i:317413 original size:33 final size:33
Alignment explanation
Indices: 317334--317437 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
317324 ATACAATCTG
* *
317334 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
317370 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
317403 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
317436 TC
1 TC
317438 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:317818 original size:13 final size:13
Alignment explanation
Indices: 317796--317825 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
317786 ACTAAACACC
317796 TTTC-ACATACCT
1 TTTCAACATACCT
317808 TTTCAACATACCT
1 TTTCAACATACCT
317821 TTTCA
1 TTTCA
317826 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:328263 original size:19 final size:18
Alignment explanation
Indices: 328239--328288 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 18
328229 TCTTTTTGAA
328239 TTCTTTTTCTTTTCTTTT
1 TTCTTTTTCTTTTCTTTT
328257 CTTC-TTTTCTTCTTCTTTT
1 -TTCTTTTTCTT-TTCTTTT
328276 TGTCTTTTTCTTT
1 T-TCTTTTTCTTT
328289 ATTTTTGCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 8 0.29
19 13 0.46
20 7 0.25
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (18 bp):
TTCTTTTTCTTTTCTTTT
Found at i:330070 original size:24 final size:21
Alignment explanation
Indices: 330036--330078 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
330026 TGCACAAGAT
*
330036 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
330058 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
330079 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:331715 original size:19 final size:21
Alignment explanation
Indices: 331691--331742 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
331681 CGGCCAAGAG
*
331691 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
331710 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
*
331731 CTTGTATTTTCA
1 CATGTATTTTCA
331743 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 11 0.38
20 2 0.07
21 16 0.55
ACGTcount: A:0.33, C:0.13, G:0.06, T:0.48
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:332495 original size:8 final size:8
Alignment explanation
Indices: 332484--332508 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
332474 GAGAAAAATC
332484 AGAAAAGA
1 AGAAAAGA
332492 AGAAAAGA
1 AGAAAAGA
332500 AGAAAAGA
1 AGAAAAGA
332508 A
1 A
332509 AAGAAAAAGA
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:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (8 bp):
AGAAAAGA
Found at i:332518 original size:16 final size:16
Alignment explanation
Indices: 332467--332518 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
332457 TTGGAGTGCA
332467 AAAAGAAGAGAAAAATCAG
1 AAAAGAAGA-AAAAA--AG
*
332486 AAAAGAAGAAAAGAAG
1 AAAAGAAGAAAAAAAG
332502 AAAAGAA-AAGAAAAAG
1 AAAAGAAGAA-AAAAAG
332518 A
1 A
332519 GAAGTTCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
15 2 0.07
16 15 0.50
18 4 0.13
19 9 0.30
ACGTcount: A:0.75, C:0.02, G:0.21, T:0.02
Consensus pattern (16 bp):
AAAAGAAGAAAAAAAG
Found at i:334327 original size:19 final size:20
Alignment explanation
Indices: 334303--334353 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
334293 CGGCCAAGAG
* *
334303 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
334322 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
334342 CATGTATTTTCA
1 CATGTATTTTCA
334354 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:335079 original size:14 final size:13
Alignment explanation
Indices: 335062--335111 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
335052 GTGCAAAAAG
335062 AAAGAAAAAGACAA
1 AAAGAAAAAGA-AA
*
335076 AAAGAAGAAGAAA
1 AAAGAAAAAGAAA
335089 AGAAG-AAAAG--A
1 A-AAGAAAAAGAAA
335100 AAAGAAAAAGAA
1 AAAGAAAAAGAA
335112 TTCAAAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
10 3 0.10
11 7 0.23
13 7 0.23
14 13 0.43
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:335108 original size:19 final size:18
Alignment explanation
Indices: 335056--335111 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 18
335046 ATTGGAGTGC
335056 AAAAAG-AAAGAAAAAGA
1 AAAAAGAAAAGAAAAAGA
335073 CAAAAAGAAGAAG-AAAAGA
1 -AAAAAGAA-AAGAAAAAGA
335092 AGAAAAGAAAAGAAAAAGA
1 A-AAAAGAAAAGAAAAAGA
335111 A
1 A
335112 TTCAAAAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 10 0.29
19 21 0.62
20 3 0.09
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAAGA
Found at i:335109 original size:11 final size:11
Alignment explanation
Indices: 335056--335111 Score: 51
Period size: 11 Copynumber: 4.7 Consensus size: 11
335046 ATTGGAGTGC
335056 AAAAAG-AAAG
1 AAAAAGAAAAG
335066 AAAAAGACAAAAAG
1 AAAAAG---AAAAG
*
335080 AAGAAGAAAAG
1 AAAAAGAAAAG
335091 AAGAAAAGAAAAG
1 -A-AAAAGAAAAG
335104 AAAAAGAA
1 AAAAAGAA
335112 TTCAAAAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 6 0.16
11 12 0.32
12 2 0.05
13 9 0.24
14 9 0.24
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:338506 original size:18 final size:19
Alignment explanation
Indices: 338471--338517 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
338461 CGGCCAAGAG
*
338471 CATGTATCTTCAT-TAAAAT
1 CATGTAT-TTCATCAAAAAT
338490 CATGTATTTCATCAAAAAT
1 CATGTATTTCATCAAAAAT
338509 CATGTATTT
1 CATGTATTT
338518 TCAAAGGGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 5 0.19
19 21 0.81
ACGTcount: A:0.36, C:0.15, G:0.06, T:0.43
Consensus pattern (19 bp):
CATGTATTTCATCAAAAAT
Found at i:347555 original size:5 final size:5
Alignment explanation
Indices: 347540--347576 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
347530 AGTGCTGGAT
347540 TTTTC -TTTC TTTTC TTTTC -TTTC TTTTC TTTTTC TTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC -TTTTC TTT
347577 GACTTTGCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
4 8 0.28
5 16 0.55
6 5 0.17
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:347559 original size:14 final size:15
Alignment explanation
Indices: 347539--347576 Score: 69
Period size: 14 Copynumber: 2.6 Consensus size: 15
347529 GAGTGCTGGA
347539 TTTTTCTTTCTTTTC
1 TTTTTCTTTCTTTTC
347554 -TTTTCTTTCTTTTC
1 TTTTTCTTTCTTTTC
347568 TTTTTCTTT
1 TTTTTCTTT
347577 GACTTTGCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTTCTTTCTTTTC
Done.