Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006316.1 Hibiscus syriacus cultivar Beakdansim tig00015091_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: 174431
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:7277 original size:29 final size:27
Alignment explanation
Indices: 7231--7308 Score: 90
Period size: 25 Copynumber: 2.9 Consensus size: 27
7221 GCGCTCTATA
7231 TGCACTC-AGAAGTGCCTCGTAGATAAATT
1 TGCACTCGA-AAGTGCCTCGTAGAT-AA-T
*
7260 TGCACTCGAAAGTTCCTCGTAG--AAT
1 TGCACTCGAAAGTGCCTCGTAGATAAT
*
7285 TACACTCGAAAGTGCCTCGTAGAT
1 TGCACTCGAAAGTGCCTCGTAGAT
7309 TTGCACCATA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
25 21 0.49
26 2 0.05
29 19 0.44
30 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (27 bp):
TGCACTCGAAAGTGCCTCGTAGATAAT
Found at i:11770 original size:114 final size:114
Alignment explanation
Indices: 11503--11995 Score: 435
Period size: 117 Copynumber: 4.3 Consensus size: 114
11493 GAATGAGCTC
* * *** * * *
11503 TTCTCATTATGAACTCCCTTTTGGAAGCATTGATCCACCTTCTTCTATGATTGATTT-AAGCAAA
1 TTCTCATTATGAACTCTC-TTTGAAAATGTTGATCCACCTCCTTCTGTGATGGATTTGAA-C-AA
* * ** * * *
11567 AAGATTGAACAAATTCTTCTCATTATAAAC-TCTT-TT-ATT-GTATGAGTTC
63 AAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTTCATTAG-ACGAGTTA
* *
11616 TTCTCATTATGAACTATCTTTTGAAAATGTTGATCCACCTCATTCTGTGATGGATTTGAACAAAA
1 TTCTCATTATGAACTCTC-TTTGAAAATGTTGATCCACCTCCTTCTGTGATGGATTTGAACAAAA
* * * * *
11681 GGTCAAACAAGTTATTCTCATTATGAACTTCTTCTTCTTTAGACGGGTTA
65 GGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTTCATTAGACGAGTTA
** *
11731 TTCTCATTATGAACTCTCACTGAAAATGTTGATCCACCTCCTTCTGTGATGGATTTGAAAAAAAG
1 TTCTCATTATGAACTCTCTTTGAAAATGTTGATCCACCTCCTTCTGTGATGGATTTGAACAAAAG
* * * * * *
11796 GTCGAACAAGCGCTTCTTATTTTGAACTTCTTTACCATCATTAGACTAGTTC
66 GTCGAACAAGCTCTTCTCATTATGAACTTC-TT--CTTCATTAGACGAGTTA
* * *
11848 TTATCATTATGAACTCTTTTTTGAAAATGTTGA-CCACCTCCTTCT-TCAATGGATTTGAACAAA
1 TTCTCATTATGAACTC-TCTTTGAAAATGTTGATCCACCTCCTTCTGT-GATGGATTTGAACAAA
* * * *
11911 ATGTCGAACAAGCTCTTCTCATTATGAACTTATTCTCCCCCATTAGACGAGTTC
64 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCT---TCATTAGACGAGTTA
* *
11965 TTCTCATTA-CAGACTCTTCATTGAAAATGTT
1 TTCTCATTATGA-ACTC-TCTTTGAAAATGTT
11996 TATGGGTCCG
Statistics
Matches: 312, Mismatches: 54, Indels: 24
0.80 0.14 0.06
Matches are distributed among these distances:
112 26 0.08
113 52 0.17
114 72 0.23
115 26 0.08
116 5 0.02
117 118 0.38
118 13 0.04
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (114 bp):
TTCTCATTATGAACTCTCTTTGAAAATGTTGATCCACCTCCTTCTGTGATGGATTTGAACAAAAG
GTCGAACAAGCTCTTCTCATTATGAACTTCTTCTTCATTAGACGAGTTA
Found at i:11903 original size:117 final size:117
Alignment explanation
Indices: 11610--11995 Score: 455
Period size: 117 Copynumber: 3.3 Consensus size: 117
11600 TTTATTGTAT
*
11610 GAGTTCTTCTCATTATGAACTATCTT--TTGAAAATGTTGATCCACCTCATTCTGTGATGGATTT
1 GAGTTCTTCTCATTATGAAC--TCTTCATTGAAAATGTTGATCCACCTCCTTCTGTGATGGATTT
* * * * *
11673 GAACAAAAGGTCAAACAAGTTATTCTCATTATGAACTTC-TT-CTTCTTTAGAC
64 GAACAAAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTTCCATCATTAGAC
* * *
11725 GGGTTATTCTCATTATGAACTC-TCACTGAAAATGTTGATCCACCTCCTTCTGTGATGGATTTGA
1 GAGTTCTTCTCATTATGAACTCTTCATTGAAAATGTTGATCCACCTCCTTCTGTGATGGATTTGA
* * * *
11789 AAAAAAGGTCGAACAAGCGCTTCTTATTTTGAACTTCTTTACCATCATTAGAC
66 ACAAAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTT-CCATCATTAGAC
* * ** *
11842 TAGTTCTTATCATTATGAACTCTTTTTTGAAAATGTTGA-CCACCTCCTTCT-TCAATGGATTTG
1 GAGTTCTTCTCATTATGAACTCTTCATTGAAAATGTTGATCCACCTCCTTCTGT-GATGGATTTG
* * **
11905 AACAAAATGTCGAACAAGCTCTTCTCATTATGAACTTATTCTCCCCCATTAGAC
65 AACAAAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTT-TCCATCATTAGAC
*
11959 GAGTTCTTCTCATTA-CAGACTCTTCATTGAAAATGTT
1 GAGTTCTTCTCATTATGA-ACTCTTCATTGAAAATGTT
11996 TATGGGTCCG
Statistics
Matches: 228, Mismatches: 34, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
112 1 0.00
113 2 0.01
114 67 0.29
115 20 0.09
116 2 0.01
117 122 0.54
118 14 0.06
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (117 bp):
GAGTTCTTCTCATTATGAACTCTTCATTGAAAATGTTGATCCACCTCCTTCTGTGATGGATTTGA
ACAAAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTTCCATCATTAGAC
Found at i:12363 original size:36 final size:36
Alignment explanation
Indices: 12338--12454 Score: 112
Period size: 36 Copynumber: 3.3 Consensus size: 36
12328 AGATAGTGTC
*
12338 TCGAGTGAGACAAAATTTCTTTCAAGAGAAACTATA
1 TCGAGTGAGACAAAATTTATTTCAAGAGAAACTATA
* * * * * * *
12374 TCAAGTGAGATAAACTTTTGTTTCTAGAG--AGTGTA
1 TCGAGTGAGACAAA-ATTTATTTCAAGAGAAACTATA
* * *
12409 TTGAGTGAGACAAAATATATTTCAAGAGAAACTATC
1 TCGAGTGAGACAAAATTTATTTCAAGAGAAACTATA
12445 TCGAGTGAGA
1 TCGAGTGAGA
12455 TGAAGTCTTT
Statistics
Matches: 60, Mismatches: 18, Indels: 6
0.71 0.21 0.07
Matches are distributed among these distances:
34 10 0.17
35 15 0.25
36 24 0.40
37 11 0.18
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (36 bp):
TCGAGTGAGACAAAATTTATTTCAAGAGAAACTATA
Found at i:31593 original size:3 final size:3
Alignment explanation
Indices: 31585--31615 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
31575 TGAATTATTT
31585 TAA TAA TAA TAA TAA TAA TAAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
31616 AAGTATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:32484 original size:23 final size:23
Alignment explanation
Indices: 32464--32523 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
32454 GATTCAGTGT
32464 TGACTGATTCAGCAAAACAGTAC
1 TGACTGATTCAGCAAAACAGTAC
32487 TGACTGATTCAGCAAAACAGTAC
1 TGACTGATTCAGCAAAACAGTAC
*
32510 TGAATGATTCAGCA
1 TGACTGATTCAGCA
32524 CATAAGTACA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.23
Consensus pattern (23 bp):
TGACTGATTCAGCAAAACAGTAC
Found at i:42687 original size:21 final size:21
Alignment explanation
Indices: 42649--42723 Score: 61
Period size: 21 Copynumber: 3.6 Consensus size: 21
42639 TTTTATTCGA
*
42649 TAAAT-ATTTTCTAAAATAATT
1 TAAATGATTTT-TATAATAATT
42670 TAAATGATTTTTATAAT-A-T
1 TAAATGATTTTTATAATAATT
*
42689 TAATTATGATTTTT-TTA-AATT
1 TAA--ATGATTTTTATAATAATT
42710 TATAATGATTTTTA
1 TA-AATGATTTTTA
42724 ATAGGTGAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
19 4 0.09
20 13 0.29
21 22 0.49
22 6 0.13
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (21 bp):
TAAATGATTTTTATAATAATT
Found at i:42717 original size:20 final size:20
Alignment explanation
Indices: 42666--42723 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
42656 TTTCTAAAAT
42666 AATTTA-AATGATTTTTATA
1 AATTTATAATGATTTTTATA
* * *
42685 ATATTAATTATGATTTTTTTA
1 A-ATTTATAATGATTTTTATA
42706 AATTTATAATGATTTTTA
1 AATTTATAATGATTTTTA
42724 ATAGGTGAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
19 1 0.03
20 18 0.58
21 12 0.39
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (20 bp):
AATTTATAATGATTTTTATA
Found at i:44892 original size:53 final size:53
Alignment explanation
Indices: 44834--44942 Score: 141
Period size: 53 Copynumber: 2.1 Consensus size: 53
44824 TCGCATCAGT
* * *
44834 ACTATGTGTGCA-CTCATAGTATTCATAATGAGTTTGTGAATTATC-ATTTCGAC
1 ACTATGTATGCATC-CATAGAATTCATAATAAGTTTGTGAATT-TCTATTTCGAC
* *
44887 ACTATGTATGCATCCATGGAATTCATAATAAGTTTGTGAATTTCTATTTCGGC
1 ACTATGTATGCATCCATAGAATTCATAATAAGTTTGTGAATTTCTATTTCGAC
44940 ACT
1 ACT
44943 TAGGTGCAAC
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
52 2 0.04
53 46 0.94
54 1 0.02
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (53 bp):
ACTATGTATGCATCCATAGAATTCATAATAAGTTTGTGAATTTCTATTTCGAC
Found at i:64374 original size:24 final size:24
Alignment explanation
Indices: 64347--64393 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
64337 TATGACATTA
64347 TACATAGATGTTTTATACATCATG
1 TACATAGATGTTTTATACATCATG
64371 TACATAGATGTTTTATACATCAT
1 TACATAGATGTTTTATACATCAT
64394 CAGGAAGACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.43
Consensus pattern (24 bp):
TACATAGATGTTTTATACATCATG
Found at i:64837 original size:61 final size:61
Alignment explanation
Indices: 64728--64842 Score: 142
Period size: 61 Copynumber: 1.9 Consensus size: 61
64718 GAAGGTGGAT
* * *
64728 ACGACCTTATGTATCATGTCTGGATTAACACTAGAGTGTAAACCTAGTGTAGGTGTTGGGC
1 ACGACCTTATGTATCATATCTGGATTAACACTAGAGCGTAAACCTAGTGCAGGTGTTGGGC
* * * * *
64789 ACGACCTTATGTGTCATATCTGGATTAGCAGTATG-GCGTAAGCTTAGTGCAGGT
1 ACGACCTTATGTATCATATCTGGATTAACACTA-GAGCGTAAACCTAGTGCAGGT
64843 TTAGCACTAC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
61 44 0.98
62 1 0.02
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (61 bp):
ACGACCTTATGTATCATATCTGGATTAACACTAGAGCGTAAACCTAGTGCAGGTGTTGGGC
Found at i:76786 original size:20 final size:22
Alignment explanation
Indices: 76736--76786 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
76726 TATAGCTTTC
*
76736 AAAATCCTAAAAATAAGGTAAA
1 AAAATCCTAAAAATAAAGTAAA
76758 AATAATCCT-AAAATAAAG-AAA
1 AA-AATCCTAAAAATAAAGTAAA
*
76779 TAAATCCT
1 AAAATCCT
76787 TATTAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 6 0.23
21 4 0.15
22 10 0.38
23 6 0.23
ACGTcount: A:0.61, C:0.12, G:0.06, T:0.22
Consensus pattern (22 bp):
AAAATCCTAAAAATAAAGTAAA
Found at i:77621 original size:53 final size:53
Alignment explanation
Indices: 77563--77665 Score: 154
Period size: 53 Copynumber: 1.9 Consensus size: 53
77553 GTACTTTCGG
* * *
77563 CACTATGTGTGCA-CTCATGGTATTCATAATGATTTTGTGAATTACCATTTTGA
1 CACTATGTGTGCATC-CATGGAATTCATAATAAGTTTGTGAATTACCATTTTGA
*
77616 CACTATGTGTGCATCCATGGAATTCATAATAAGTTTGTGAATTTCCATTT
1 CACTATGTGTGCATCCATGGAATTCATAATAAGTTTGTGAATTACCATTT
77666 CGGCACTTAG
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
53 44 0.98
54 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.41
Consensus pattern (53 bp):
CACTATGTGTGCATCCATGGAATTCATAATAAGTTTGTGAATTACCATTTTGA
Found at i:83269 original size:84 final size:84
Alignment explanation
Indices: 83158--83888 Score: 859
Period size: 84 Copynumber: 8.7 Consensus size: 84
83148 TTTAAGACAA
* * *
83158 CATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
83223 GCTCAGCTCCAAGGCACAT
66 GCTCAGCTCCAAGGCACAT
* * * *
83242 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATTTGTC-ACCAAAAGACCTTCGAGTTCGACTA
1 CATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGACTA
* *
83306 CGCTCAGCTCCTAGGCATAT
65 CGCTCAGCTCCAAGGCACAT
* * * * *
83326 CATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAA-CACAAGACCTTTGAGTTCAACTA
1 CATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTGCCAACCA-AAGACCTTCGAGTTCGACTA
* *
83390 TGCTCAGCT-CAACGACACAT
65 CGCTCAGCTCCAA-GGCACAT
* *
83410 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
83475 GCTCAGCTCCAAGGCACAT
66 GCTCAGCTCCAAGGCACAT
* * *
83494 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTC-ACCAAAAGACCTTCGAGTTCGACTA
1 CATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGACTA
* * *
83558 CACTCAGCTCCTAGGCATAT
65 CGCTCAGCTCCAAGGCACAT
* * * * * * *
83578 CATTTGCAACACAACTTAAGTCTAGAAGGGTTGTCTGCCAA-CACAAGACCTTTGAATTCAACTA
1 CATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTGCCAACCA-AAGACCTTCGAGTTCGACTA
83642 CGCTCAGCT-CAACGGCACAT
65 CGCTCAGCTCCAA-GGCACAT
* * ** *
83662 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCCCCGAGTTCGATTAC
1 CATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* * * *
83727 ACTCAGCTTCGAGGGCATAT
66 GCTCAGC-TCCAAGGCACAT
** * * ** * *
83747 CATTTATAGCATAACTCAAGGCTAGAAGGGTTATATG-TTACTAAAGGCCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
83811 GCTCAGCTCCAAGGCACAT
66 GCTCAGCTCCAAGGCACAT
* * *
83830 CATTTGCAGTATAGCTTAA-GTTGAGAAGGGTTATCTGCCAACCAAAGACC-TCTGAGTTC
1 CATTTGCAGCATAACTTAAGGCT-AGAAGGGTTATCTGCCAACCAAAGACCTTC-GAGTTC
83889 AATTACATTC
Statistics
Matches: 539, Mismatches: 92, Indels: 32
0.81 0.14 0.05
Matches are distributed among these distances:
82 2 0.00
83 50 0.09
84 439 0.81
85 47 0.09
86 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.25
Consensus pattern (84 bp):
CATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
GCTCAGCTCCAAGGCACAT
Found at i:83603 original size:252 final size:252
Alignment explanation
Indices: 83158--83890 Score: 1175
Period size: 252 Copynumber: 2.9 Consensus size: 252
83148 TTTAAGACAA
* *
83158 CATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
*
83223 GCTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATTTGTCACCAAAA
66 GCTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATATGTCACCAAAA
83288 GACCTTCGAGTTCGACTACGCTCAGCTCCTAGGCATATCATTTGCAGCACAACTTAAGTCTAGAA
131 GACCTTCGAGTTCGACTACGCTCAGCTCCTAGGCATATCATTTGCAGCACAACTTAAGTCTAGAA
*
83353 GGGTTGTCTGCCAACACAAGACCTTTGAGTTCAACTATGCTCAGCTCAACGACACAT
196 GGGTTGTCTGCCAACACAAGACCTTTGAGTTCAACTACGCTCAGCTCAACGACACAT
83410 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
*
83475 GCTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAA
66 GCTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATATGTCACCAAAA
* *
83540 GACCTTCGAGTTCGACTACACTCAGCTCCTAGGCATATCATTTGCAACACAACTTAAGTCTAGAA
131 GACCTTCGAGTTCGACTACGCTCAGCTCCTAGGCATATCATTTGCAGCACAACTTAAGTCTAGAA
* *
83605 GGGTTGTCTGCCAACACAAGACCTTTGAATTCAACTACGCTCAGCTCAACGGCACAT
196 GGGTTGTCTGCCAACACAAGACCTTTGAGTTCAACTACGCTCAGCTCAACGACACAT
** *
83662 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCCCCGAGTTCGATTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* * * * * * *
83727 ACTCAGCTTCGAGGGCATATCATTTATAGCATAACTCAAGGCTAGAAGGGTTATATGTTA-CTAA
66 GCTCAGC-TCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATATGTCACCAAA
* * * * * *
83791 AGGCCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGT-TGAG
130 AGACCTTCGAGTTCGACTACGCTCAGCTCCTAGGCATATCATTTGCAGCACAACTTAAGTCT-AG
* *
83855 AAGGGTTATCTGCCAAC-CAAAGACCTCTGAGTTCAA
194 AAGGGTTGTCTGCCAACAC-AAGACCTTTGAGTTCAA
83891 TTACATTCAG
Statistics
Matches: 448, Mismatches: 30, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
251 2 0.00
252 400 0.89
253 46 0.10
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (252 bp):
CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
GCTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATATGTCACCAAAA
GACCTTCGAGTTCGACTACGCTCAGCTCCTAGGCATATCATTTGCAGCACAACTTAAGTCTAGAA
GGGTTGTCTGCCAACACAAGACCTTTGAGTTCAACTACGCTCAGCTCAACGACACAT
Found at i:84449 original size:13 final size:13
Alignment explanation
Indices: 84431--84456 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
84421 TGTCCTATTT
84431 TTCGTTCCACGAA
1 TTCGTTCCACGAA
84444 TTCGTTCCACGAA
1 TTCGTTCCACGAA
84457 AAATGACAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.31, G:0.15, T:0.31
Consensus pattern (13 bp):
TTCGTTCCACGAA
Found at i:84835 original size:38 final size:37
Alignment explanation
Indices: 84747--85004 Score: 205
Period size: 39 Copynumber: 6.9 Consensus size: 37
84737 AATATTTGGG
* * *
84747 AAATATATAATATATAGCTTTTG-AAAGTATTTTTTGAAA
1 AAATATAT-TTATATAG-TTTTGAAAATTAGTTTTT-AAA
*
84786 ACATATA-TTATATAGTTTTGAAAATTAGTTTTTAAA
1 AAATATATTTATATAGTTTTGAAAATTAGTTTTTAAA
84822 AAATATATGTTATATAGTTTTGAAAATTAGTTTTTAAA
1 AAATATAT-TTATATAGTTTTGAAAATTAGTTTTTAAA
**
84860 AATATATATTATATATA-TATTTTTAAATTAGTTTTTAAA
1 AA-ATATATT-TATATAGT-TTTGAAAATTAGTTTTTAAA
* * *
84899 ATATTATATATTATCTAGTTTTGAAAATTA-TTCTTTTAA
1 A-AATATAT-TTATATAGTTTTGAAAATTAGTT-TTTAAA
*
84938 AAATATATACTATAT-GATTTTG--AATT--TTTTTAAA
1 AAATATAT-TTATATAG-TTTTGAAAATTAGTTTTTAAA
* * *
84972 AACATATA-TTGTATAGTTTTAAAAAAT-GTTTTT
1 AA-ATATATTTATATAGTTTTGAAAATTAGTTTTT
85005 TCATTTACTT
Statistics
Matches: 183, Mismatches: 20, Indels: 35
0.77 0.08 0.15
Matches are distributed among these distances:
33 8 0.04
34 8 0.04
35 10 0.05
36 23 0.13
37 18 0.10
38 51 0.28
39 62 0.34
40 3 0.02
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (37 bp):
AAATATATTTATATAGTTTTGAAAATTAGTTTTTAAA
Found at i:85027 original size:4 final size:4
Alignment explanation
Indices: 85007--85082 Score: 64
Period size: 4 Copynumber: 17.8 Consensus size: 4
84997 ATGTTTTTTC
* *
85007 ATTT ACTT ATCT ATTT ATTT ATTTT ATTTT ATTTT ATTT -TATT ATTT
1 ATTT ATTT ATTT ATTT ATTT A-TTT A-TTT A-TTT ATTT AT-TT ATTT
*
85054 ATTT ATCTT ATTT ATTAT TTTT ATTT ATT
1 ATTT AT-TT ATTT ATT-T ATTT ATTT ATT
85083 ATTAATTTCT
Statistics
Matches: 61, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
3 1 0.02
4 38 0.62
5 22 0.36
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:85034 original size:5 final size:5
Alignment explanation
Indices: 85020--85079 Score: 56
Period size: 5 Copynumber: 12.4 Consensus size: 5
85010 TACTTATCTA
*
85020 TTTA- TTTAT TTTAT TTTAT TTTAT TTTAT TATT-T ATTTAT CTTA- TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT T-TTAT -TTTAT TTTAT TTTAT
*
85069 TAT-T TTTAT TT
1 TTTAT TTTAT TT
85080 ATTATTAATT
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
4 10 0.22
5 32 0.70
6 4 0.09
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTAT
Found at i:85051 original size:13 final size:13
Alignment explanation
Indices: 85020--85085 Score: 50
Period size: 13 Copynumber: 5.1 Consensus size: 13
85010 TACTTATCTA
*
85020 TTTATTTATTTTAT
1 TTTATTT-TATTAT
85034 TTTATTTTATT-T
1 TTTATTTTATTAT
85046 TATTA-TTTATTTAT
1 T-TTATTTTA-TTAT
*
85060 CTTA-TTTATTAT
1 TTTATTTTATTAT
85072 TTT-TATTTATTAT
1 TTTAT-TTTATTAT
85085 T
1 T
85086 AATTTCTTGT
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
12 12 0.27
13 24 0.55
14 8 0.18
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTATTTTATTAT
Found at i:91570 original size:84 final size:84
Alignment explanation
Indices: 91429--92140 Score: 781
Period size: 84 Copynumber: 8.5 Consensus size: 84
91419 TTTAAGACAA
* * *
91429 CATTTACAGTATAACTTAAGTCAAGAAGGGTTATCTGCCAACC-AAAGGCCTTCGAGTTCGACTA
1 CATTTACAGCATAACTTAAGTCTAGAAGGGTTATCTGCC-ACCAAAAGACCTTCGAGTTCGACTA
91493 CGCTCAGCTCCAAGGCACAT
65 CGCTCAGCTCCAAGGCACAT
* * * *
91513 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATTTGTCACCAAAAGACCTTCGAGTTCGACTAC
1 CATTTACAGCATAACTTAAGTCTAGAAGGGTTATCTGCCACCAAAAGACCTTCGAGTTCGACTAC
* *
91578 GCTCAGCTCCTAGGCATAT
66 GCTCAGCTCCAAGGCACAT
* * * * * * * *
91597 CATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACACAAGACCTTTGAGTTCAACTAT
1 CATTTACAGCATAACTTAAGTCTAGAAGGGTTATCTGCCACCAAAAGACCTTCGAGTTCGACTAC
*
91662 GCTCAGCT-CAACGACACAT
66 GCTCAGCTCCAA-GGCACAT
* *
91681 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGACTA
1 CATTTACAGCATAACTTAAGTCTAGAAGGGTTATCTGCC-ACCAAAAGACCTTCGAGTTCGACTA
* *
91745 CACTCATCTCCAAGGCACAT
65 CGCTCAGCTCCAAGGCACAT
* * *
91765 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTAC
1 CATTTACAGCATAACTTAAGTCTAGAAGGGTTATCTGCCACCAAAAGACCTTCGAGTTCGACTAC
* * * *
91830 ACTCAACTCCTAGGCATAT
66 GCTCAGCTCCAAGGCACAT
* * * * * * * * *
91849 CATTTGCAACACAACTTAAGTCTAGAAGGGTTGTCTGCCAACACAAGACCTTTGAATTCAACTAC
1 CATTTACAGCATAACTTAAGTCTAGAAGGGTTATCTGCCACCAAAAGACCTTCGAGTTCGACTAC
91914 GCTCAGCT-CAACGGCACAT
66 GCTCAGCTCCAA-GGCACAT
* * * * ** *
91933 CATTTGCAGCATAACTTAAGTCGATAAGGGTTATCTGCCAACC-AAACACCCCCGAGTTCGATTA
1 CATTTACAGCATAACTTAAGTCTAGAAGGGTTATCTGCC-ACCAAAAGACCTTCGAGTTCGACTA
* * * *
91997 CACTCAGCTTCGAGGGCATAT
65 CGCTCAGC-TCCAAGGCACAT
* * * * ** *
92018 CATTTATAGCATAACTCAAGGCTAGAAGGGTTATATGTTA-CTAAAGACCTTCGAGTTCGACTAC
1 CATTTACAGCATAACTTAAGTCTAGAAGGGTTATCTGCCACCAAAAGACCTTCGAGTTCGACTAC
92082 GCTCAGCTCCAAGGCACAT
66 GCTCAGCTCCAAGGCACAT
* * *
92101 CATTTGCAGTATAGCTTAAGT-TGAGAAGGGTTATCTGCCA
1 CATTTACAGCATAACTTAAGTCT-AGAAGGGTTATCTGCCA
92141 ACCGAAGACC
Statistics
Matches: 514, Mismatches: 103, Indels: 23
0.80 0.16 0.04
Matches are distributed among these distances:
82 1 0.00
83 49 0.10
84 419 0.82
85 44 0.09
86 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (84 bp):
CATTTACAGCATAACTTAAGTCTAGAAGGGTTATCTGCCACCAAAAGACCTTCGAGTTCGACTAC
GCTCAGCTCCAAGGCACAT
Found at i:91730 original size:168 final size:168
Alignment explanation
Indices: 91429--92223 Score: 845
Period size: 168 Copynumber: 4.7 Consensus size: 168
91419 TTTAAGACAA
* * * *
91429 CATTTACAGTATAACTTAAGTCAAGAAGGGTTATCTGCCAACCAAAGGCCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* * *
91494 GCTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATTTGTC-ACCAAA
66 ACTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACC-AA
* *
91558 AGACCTTCGAGTTCGACTACGCTCAGCTCCTAGGCATAT
130 AGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
* * * *
91597 CATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAA-CACAAGACCTTTGAGTTCAACTA
1 CATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGCCAACCA-AAGACCTTCGAGTTCGACTA
** * * * * *
91661 TGCTCAGCT-CAACGACACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCA
65 CACTCAGCTCCAA-GGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCA
* *
91725 AAGACCTTCGAGTTCGACTACACTCATCTCCAAGGCACAT
129 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
* * * *
91765 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTC-ACCAAAAGACCTTCGAGTTCGACTA
1 CATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGACTA
* * * * * * * * *
91829 CACTCAACTCCTAGGCATATCATTTGCAACACAACTTAAGTCTAGAAGGGTTGTCTGCCAA-CAC
65 CACTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCA-
* * *
91893 AAGACCTTTGAATTCAACTACGCTCAGCT-CAACGGCACAT
129 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACAT
* * * ** *
91933 CATTTGCAGCATAACTTAAGTCGATAAGGGTTATCTGCCAACCAAACACCCCCGAGTTCGATTAC
1 CATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* * * * * ** *
91998 ACTCAGCTTCGAGGGCATATCATTTATAGCATAACTCAAGGCTAGAAGGGTTATATG-TTACTAA
66 ACTCAGC-TCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAA
92062 AGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
130 AGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
* * * * *
92101 CATTTGCAGTATAGCTTAAGT-TGAGAAGGGTTATCTGCCAACCGAAGACC-TCTGAGTTCAATT
1 CATTTGCAGCATAACTTAAGTCT-AGAAGGGTTATCTGCCAACCAAAGACCTTC-GAGTTCGACT
* * * * * *
92164 ACATTCAGCT-CAGAGGCAAACCAAATTTACAGCATAGCTCAAGGCAAGAAGGGCTATCTG
64 ACACTCAGCTCCA-AGGCACATC--ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG
92224 TCAATAAAAT
Statistics
Matches: 521, Mismatches: 89, Indels: 33
0.81 0.14 0.05
Matches are distributed among these distances:
166 1 0.00
167 19 0.04
168 419 0.80
169 82 0.16
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (168 bp):
CATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
ACTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAA
GACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
Found at i:91884 original size:252 final size:252
Alignment explanation
Indices: 91429--92175 Score: 1131
Period size: 252 Copynumber: 3.0 Consensus size: 252
91419 TTTAAGACAA
* * * *
91429 CATTTACAGTATAACTTAAGTCAAGAAGGGTTATCTGCCAACCAAAGGCCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* *
91494 GCTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATTTGTCACCAAAA
66 ACTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATATGTCACCAAAA
91559 GACCTTCGAGTTCGACTACGCTCAGCTCCTAGGCATATCATTTGCAGCACAACTTAAGTCTAGAA
131 GACCTTCGAGTTCGACTACGCTCAGCTCCTAGGCATATCATTTGCAGCACAACTTAAGTCTAGAA
*
91624 GGGTTGTCTGCCAACACAAGACCTTTGAGTTCAACTATGCTCAGCTCAACGACACAT
196 GGGTTGTCTGCCAACACAAGACCTTTGAGTTCAACTACGCTCAGCTCAACGACACAT
91681 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* *
91746 ACTCATCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAA
66 ACTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATATGTCACCAAAA
* * *
91811 GACCTTCGAGTTCGACTACACTCAACTCCTAGGCATATCATTTGCAACACAACTTAAGTCTAGAA
131 GACCTTCGAGTTCGACTACGCTCAGCTCCTAGGCATATCATTTGCAGCACAACTTAAGTCTAGAA
* *
91876 GGGTTGTCTGCCAACACAAGACCTTTGAATTCAACTACGCTCAGCTCAACGGCACAT
196 GGGTTGTCTGCCAACACAAGACCTTTGAGTTCAACTACGCTCAGCTCAACGACACAT
* * ** *
91933 CATTTGCAGCATAACTTAAGTCGATAAGGGTTATCTGCCAACCAAACACCCCCGAGTTCGATTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* * * * * *
91998 ACTCAGCTTCGAGGGCATATCATTTATAGCATAACTCAAGGCTAGAAGGGTTATATGTTA-CTAA
66 ACTCAGC-TCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATATGTCACCAAA
* * * * *
92062 AGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGT-TGAG
130 AGACCTTCGAGTTCGACTACGCTCAGCTCCTAGGCATATCATTTGCAGCACAACTTAAGTCT-AG
* * * **
92126 AAGGGTTATCTGCCAAC-CGAAGACCTCTGAGTTCAATTACATTCAGCTCA
194 AAGGGTTGTCTGCCAACAC-AAGACCTTTGAGTTCAACTACGCTCAGCTCA
92176 GAGGCAAACC
Statistics
Matches: 452, Mismatches: 40, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
251 2 0.00
252 404 0.89
253 46 0.10
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (252 bp):
CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
ACTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATATGTCACCAAAA
GACCTTCGAGTTCGACTACGCTCAGCTCCTAGGCATATCATTTGCAGCACAACTTAAGTCTAGAA
GGGTTGTCTGCCAACACAAGACCTTTGAGTTCAACTACGCTCAGCTCAACGACACAT
Found at i:92720 original size:13 final size:13
Alignment explanation
Indices: 92702--92727 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
92692 TGTCCTATTT
92702 TTCGTTCCACGAA
1 TTCGTTCCACGAA
92715 TTCGTTCCACGAA
1 TTCGTTCCACGAA
92728 AAATGACAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.31, G:0.15, T:0.31
Consensus pattern (13 bp):
TTCGTTCCACGAA
Found at i:93023 original size:34 final size:35
Alignment explanation
Indices: 92868--93263 Score: 146
Period size: 38 Copynumber: 10.8 Consensus size: 35
92858 AAAAATATTT
* *
92868 TTTTG-AAA-TATATATTATATAGTTTTTTAAAACGT-
1 TTTTGAAAATTATATAATATATAG--TTTTGAAA-GTA
* **
92903 TTTTGAAAACTTATGTACAATATATAAGTTTT-AAAACA
1 TTTTGAAAA-TTA--TATAATATAT-AGTTTTGAAAGTA
* * *
92941 TTTTGAAAATTATTTATTATATAG-TTTGAAATTA
1 TTTTGAAAATTATATAATATATAGTTTTGAAAGTA
* *
92975 TTCTGAAAATTATATAATATATGAGTTTTTAAA-TA
1 TTTTGAAAATTATATAATATAT-AGTTTTGAAAGTA
*
93010 TTTTGGAAA-TATATAATATATAGCTTTTGAAAGTA
1 TTTTGAAAATTATATAATATATAG-TTTTGAAAGTA
* * * *
93045 TTTTTTGAAAA-CATATATTATGTAGTTTTGAAAATTA
1 --TTTTGAAAATTATATAATATATAGTTTTG-AAAGTA
* * ** *
93082 GTTTTTAAAAAATATATGTTATATAGTTTTGAAAATTA
1 --TTTTGAAAATTATATAATATATAGTTTTG-AAAGTA
* * * * *
93120 GTTTTTAAAAATATATATTATATATACATTTTTAAATTA
1 --TTTTGAAAAT-TATATAATATATA-GTTTTGAAAGTA
* * * *
93159 GTTTTTAAAAAATTATATATTATCTAGTTTTGAAAATTA
1 --TTTT-GAAAATTATATAATATATAGTTTTG-AAAGTA
* * * *
93198 TTCTTTTAAAAATATATACTATAT-GATTTTGAAAATTA
1 -T-TTTGAAAATTATATAATATATAG-TTTTG-AAAGTA
* * *
93236 TTTTTTAAAA-CATATAATGTATAGTTTT
1 -TTTTGAAAATTATATAATATATAGTTTT
93264 AAAAAAATGT
Statistics
Matches: 295, Mismatches: 43, Indels: 45
0.77 0.11 0.12
Matches are distributed among these distances:
33 5 0.02
34 44 0.15
35 25 0.08
36 27 0.09
37 46 0.16
38 82 0.28
39 46 0.16
40 18 0.06
41 2 0.01
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.48
Consensus pattern (35 bp):
TTTTGAAAATTATATAATATATAGTTTTGAAAGTA
Found at i:93109 original size:38 final size:38
Alignment explanation
Indices: 93016--93268 Score: 243
Period size: 38 Copynumber: 6.7 Consensus size: 38
93006 AATATTTTGG
* * **
93016 AAATATATAATATATAGCTTTTG-AAAGTA-TTTTTTGA
1 AAATATATATTATATAG-TTTTGAAAATTAGTTTTTAAA
* *
93053 AAACATATATTATGTAGTTTTGAAAATTAGTTTTTAAA
1 AAATATATATTATATAGTTTTGAAAATTAGTTTTTAAA
*
93091 AAATATATGTTATATAGTTTTGAAAATTAGTTTTT-AA
1 AAATATATATTATATAGTTTTGAAAATTAGTTTTTAAA
**
93128 AAATATATATTATATA-TACATTTTTAAATTAGTTTTTAAA
1 AAATATATATTATATAGT---TTTGAAAATTAGTTTTTAAA
* *
93168 AAATTATATATTATCTAGTTTTGAAAATTA-TTCTTTTAA
1 AAA-TATATATTATATAGTTTTGAAAATTAGTT-TTTAAA
* *
93207 AAATATATACTATAT-GATTTTGAAAATTATTTTTTAAA
1 AAATATATATTATATAG-TTTTGAAAATTAGTTTTTAAA
* * *
93245 ACATATA-A-TGTATAGTTTTAAAAA
1 AAATATATATTATATAGTTTTGAAAA
93269 AATGTTTTTT
Statistics
Matches: 182, Mismatches: 22, Indels: 25
0.79 0.10 0.11
Matches are distributed among these distances:
36 18 0.10
37 39 0.21
38 73 0.40
39 34 0.19
40 5 0.03
41 12 0.07
42 1 0.01
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.47
Consensus pattern (38 bp):
AAATATATATTATATAGTTTTGAAAATTAGTTTTTAAA
Found at i:93214 original size:77 final size:77
Alignment explanation
Indices: 93016--93268 Score: 247
Period size: 77 Copynumber: 3.3 Consensus size: 77
93006 AATATTTTGG
* * * * * *
93016 AAATATATAATATATAGCTTTTG-AAAGTATTTTTTGAAAACATATAT--TATGT-AGTTTTGAA
1 AAATATATATTATATAG-TTTTGAAAATTAGTTTTTAAAAATATATATACTATATCA-TTTTGAA
93077 AATTAGTTTTTAAA
64 AATTAGTTTTTAAA
* *
93091 AAATATATGTTATATAGTTTTGAAAATTAGTTTTTAAAAATATATATTA-TATATACATTTT-TA
1 AAATATATATTATATAGTTTTGAAAATTAGTTTTTAAAAATATATA-TACTATAT-CATTTTGAA
93154 AATTAGTTTTTAAA
64 AATTAGTTTTTAAA
* * *
93168 AAATTATATATTATCTAGTTTTGAAAATTA-TTCTTTTAAAA-ATATATACTATATGATTTTGAA
1 AAA-TATATATTATATAGTTTTGAAAATTAGTT-TTTAAAAATATATATACTATATCATTTTGAA
*
93231 AATTATTTTTTAAA
64 AATTAGTTTTTAAA
* * *
93245 ACATATA-A-TGTATAGTTTTAAAAA
1 AAATATATATTATATAGTTTTGAAAA
93269 AATGTTTTTT
Statistics
Matches: 151, Mismatches: 18, Indels: 19
0.80 0.10 0.10
Matches are distributed among these distances:
74 18 0.12
75 35 0.23
76 12 0.08
77 50 0.33
78 35 0.23
79 1 0.01
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.47
Consensus pattern (77 bp):
AAATATATATTATATAGTTTTGAAAATTAGTTTTTAAAAATATATATACTATATCATTTTGAAAA
TTAGTTTTTAAA
Found at i:93307 original size:5 final size:5
Alignment explanation
Indices: 93293--93322 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
93283 TACTTATCTA
93293 TTTA- TTTAT TTTAT TTTAT TTTAT TTTAT T
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT T
93323 ATTTATTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTAT
Found at i:93317 original size:15 final size:14
Alignment explanation
Indices: 93293--93342 Score: 61
Period size: 13 Copynumber: 3.7 Consensus size: 14
93283 TACTTATCTA
93293 TTTATTTATTTTAT
1 TTTATTTATTTTAT
93307 TTTATTTTATTTTA-
1 TTTA-TTTATTTTAT
93321 -TTATTTA-TTTAT
1 TTTATTTATTTTAT
*
93333 CTTATTTATT
1 TTTATTTATT
93343 ATTAATTTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
11 4 0.12
12 4 0.12
13 10 0.31
14 5 0.16
15 9 0.28
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTATTTATTTTAT
Found at i:93337 original size:5 final size:4
Alignment explanation
Indices: 93280--93342 Score: 56
Period size: 4 Copynumber: 14.8 Consensus size: 4
93270 ATGTTTTTTC
* *
93280 ATTT ACTT ATCT ATTT ATTT ATTTT ATTTT ATTTT ATTT -TATT ATTT
1 ATTT ATTT ATTT ATTT ATTT A-TTT A-TTT A-TTT ATTT AT-TT ATTT
93327 ATTT ATCTT ATTT ATT
1 ATTT AT-TT ATTT ATT
93343 ATTAATTTCT
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
3 1 0.02
4 31 0.61
5 19 0.37
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (4 bp):
ATTT
Found at i:135287 original size:18 final size:18
Alignment explanation
Indices: 135266--135324 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
135256 TATATATATA
135266 TATATGTTATGATGCTTG
1 TATATGTTATGATGCTTG
** * **
135284 TATATAATATAATTATATG
1 TATATGTTATGATGCT-TG
135303 -ATATGTTATGATGCTTG
1 TATATGTTATGATGCTTG
135320 TATAT
1 TATAT
135325 AAATACATTA
Statistics
Matches: 29, Mismatches: 10, Indels: 4
0.67 0.23 0.09
Matches are distributed among these distances:
17 2 0.07
18 25 0.86
19 2 0.07
ACGTcount: A:0.32, C:0.03, G:0.15, T:0.49
Consensus pattern (18 bp):
TATATGTTATGATGCTTG
Found at i:135289 original size:2 final size:2
Alignment explanation
Indices: 135203--135270 Score: 129
Period size: 2 Copynumber: 34.5 Consensus size: 2
135193 TTGAAACAAT
135203 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
135245 -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
135271 GTTATGATGC
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 64 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:135307 original size:36 final size:36
Alignment explanation
Indices: 135246--135336 Score: 132
Period size: 36 Copynumber: 2.5 Consensus size: 36
135236 ATATATATAA
*
135246 TATATATATATATATATATATATATGTTATGATGCTTG
1 TATATA-ATATACAT-TATATATATGTTATGATGCTTG
135284 TATATAATATA-ATTATATGATATGTTATGATGCTTG
1 TATATAATATACATTATAT-ATATGTTATGATGCTTG
135320 TATATAA-ATACATTATA
1 TATATAATATACATTATA
135337 CTTATAATAT
Statistics
Matches: 51, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
35 8 0.16
36 32 0.63
37 5 0.10
38 6 0.12
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (36 bp):
TATATAATATACATTATATATATGTTATGATGCTTG
Found at i:136637 original size:140 final size:136
Alignment explanation
Indices: 136297--136748 Score: 450
Period size: 136 Copynumber: 3.3 Consensus size: 136
136287 ATTAAACCTA
* * * * * *
136297 AAAATGTAGGCTCTAA-TATTAATCCAAAT-TATTTTTAATAAATTAATGAGTCGAATAATCAAA
1 AAAATGGAGGCTCTAATTATTAA-CCTAGTCAATTTTAAAT-AATTAATGAATCGAATAATCAAA
* * * *
136360 ATGGAACCTCGAGCATAAAAGCGAGTACCAAATTGAAAA-TTCTCATACATTAAAGGAATACAGT
64 ATGGAACCTCGAG-ATAAAAGCGAGGACCAAATTAAAAATTTC-CCTAAATTAAAGGAATA-AGT
*
136424 ATAAA--AACT
126 TTAAATTAACT
* ** ** * *
136433 AAAAGGGAGGCTCTAATTATTAACCTAACCAATTTTAACCAATTATTGAATCGAATAGTCAAAAT
1 AAAATGGAGGCTCTAATTATTAACCTAGTCAATTTTAAATAATTAATGAATCGAATAATCAAAAT
* ** * *
136498 GAAACCTCGAGTATAAAAATGAGGACCAAATAAAAAATTTCCCTAAATTAAAGGACTAAGTTTAA
66 GGAACCTCGAG-ATAAAAGCGAGGACCAAATTAAAAATTTCCCTAAATTAAAGGAATAAGTTT-A
136563 AATTAAGCAT
129 AATTAA-C-T
* * * * * *
136573 AAAATGGAGTCTCAAATTAGTAACCTAGTCAATTTTAAATAATTACTGATTCGAATAATTAAAAT
1 AAAATGGAGGCTCTAATTATTAACCTAGTCAATTTTAAATAATTAATGAATCGAATAATCAAAAT
* * *
136638 GGAACCTCGA-CTAAAAGCGATGACCAAATTAAAAATTAT-CCTAAATTAAAGGAATAATTTTGA
66 GGAACCTCGAGATAAAAGCGAGGACCAAATTAAAAATT-TCCCTAAATTAAAGGAATAAGTTT-A
136701 AATTAAACCT
129 AATT-AA-CT
136711 AAAATGGAGGCTCTAATTATTAACCTAGTCAATTTTAA
1 AAAATGGAGGCTCTAATTATTAACCTAGTCAATTTTAA
136749 CCAATTATTG
Statistics
Matches: 259, Mismatches: 47, Indels: 18
0.80 0.15 0.06
Matches are distributed among these distances:
135 4 0.02
136 87 0.34
137 15 0.06
138 85 0.33
139 5 0.02
140 63 0.24
ACGTcount: A:0.46, C:0.13, G:0.12, T:0.29
Consensus pattern (136 bp):
AAAATGGAGGCTCTAATTATTAACCTAGTCAATTTTAAATAATTAATGAATCGAATAATCAAAAT
GGAACCTCGAGATAAAAGCGAGGACCAAATTAAAAATTTCCCTAAATTAAAGGAATAAGTTTAAA
TTAACT
Found at i:136755 original size:138 final size:136
Alignment explanation
Indices: 136287--136761 Score: 476
Period size: 138 Copynumber: 3.4 Consensus size: 136
136277 GTCTAAAAAG
* * * * ** *
136287 ATTAAACCTAAAAATGTAGGCTCTAA-TATTAATCCAAATTATTTTTAATAAATTAATGAGTCGA
1 ATTAAACCT-AAAATGGAGGCTCTAATTATTAA-CCTAATCAATTTTAACCAATTAATGAATCGA
* * *
136351 ATAATCAAAATGGAACCTCGAGCATAAAAGCGAGTACCAAATTGAAAATTCTCATACATTAAAGG
64 ATAATCAAAATGGAACCTCGAGC-TAAAAGCGAG-ACCAAATTAAAAATT-TCCTAAATTAAAGG
*
136416 AATACAGTAT-A
126 AATA-AGTTTAA
* * *
136427 A--AAA-CTAAAAGGGAGGCTCTAATTATTAACCTAACCAATTTTAACCAATTATTGAATCGAAT
1 ATTAAACCTAAAATGGAGGCTCTAATTATTAACCTAATCAATTTTAACCAATTAATGAATCGAAT
* * * ** * *
136489 AGTCAAAATGAAACCTCGAGTATAAAAATGAGGACCAAATAAAAAATTTCCCTAAATTAAAGGAC
66 AATCAAAATGGAACCTCGAG-CTAAAAGCGA-GACCAAATTAAAAATTT-CCTAAATTAAAGGAA
136554 TAAGTTTAAA
128 TAAGTTT-AA
* * * * * * ** * *
136564 ATTAAGCATAAAATGGAGTCTCAAATTAGTAACCTAGTCAATTTTAAATAATTACTGATTCGAAT
1 ATTAAACCTAAAATGGAGGCTCTAATTATTAACCTAATCAATTTTAACCAATTAATGAATCGAAT
*
136629 AATTAAAATGGAACCTCGA-CTAAAAGCGATGACCAAATTAAAAATTATCCTAAATTAAAGGAAT
66 AATCAAAATGGAACCTCGAGCTAAAAGCGA-GACCAAATTAAAAATT-TCCTAAATTAAAGGAAT
*
136693 AATTTTGAA
129 AAGTTT-AA
* *
136702 ATTAAACCTAAAATGGAGGCTCTAATTATTAACCTAGTCAATTTTAACCAATTATTGAAT
1 ATTAAACCTAAAATGGAGGCTCTAATTATTAACCTAATCAATTTTAACCAATTAATGAAT
136762 GTTCATCTAA
Statistics
Matches: 272, Mismatches: 53, Indels: 22
0.78 0.15 0.06
Matches are distributed among these distances:
135 5 0.02
136 91 0.33
137 11 0.04
138 98 0.36
139 3 0.01
140 64 0.24
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (136 bp):
ATTAAACCTAAAATGGAGGCTCTAATTATTAACCTAATCAATTTTAACCAATTAATGAATCGAAT
AATCAAAATGGAACCTCGAGCTAAAAGCGAGACCAAATTAAAAATTTCCTAAATTAAAGGAATAA
GTTTAA
Found at i:138967 original size:30 final size:30
Alignment explanation
Indices: 138933--139008 Score: 136
Period size: 30 Copynumber: 2.6 Consensus size: 30
138923 GGTGGCCTTG
138933 ATGGAAGATGGTTGATGGTGTTGATATTGT
1 ATGGAAGATGGTTGATGGTGTTGATATTGT
*
138963 ATGGAAGATGGTTGATGGTGTTGATGTTGT
1 ATGGAAGATGGTTGATGGTGTTGATATTGT
138993 ATGGAAGATGG-TGATG
1 ATGGAAGATGGTTGATG
139009 ATAATGTATC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
29 5 0.11
30 40 0.89
ACGTcount: A:0.24, C:0.00, G:0.39, T:0.37
Consensus pattern (30 bp):
ATGGAAGATGGTTGATGGTGTTGATATTGT
Found at i:152331 original size:101 final size:100
Alignment explanation
Indices: 152155--152458 Score: 500
Period size: 101 Copynumber: 3.0 Consensus size: 100
152145 ACTTCAACTC
* * *
152155 TTTTTTTAAGCATACTTTAAGGGGAGTTAGCTCGTCACATTATCATCCCACACTCTAAGTGAAAG
1 TTTTTTT-AGCATACTTTAA-GGGAGTCAGCTCATCACACTATCATCCCACACTCTAAGTGAAAG
152220 GGAGCATACCTTCCACCCCCGAGCTAGTCAGGTAGAG
64 GGAGCATACCTTCCACCCCCGAGCTAGTCAGGTAGAG
*
152257 TTTTTTTAGCATACTTTAATGGGAGTCAGCTCATCACACTACCATCCCACACTCTAAGTGAAAGG
1 TTTTTTTAGCATACTTTAA-GGGAGTCAGCTCATCACACTATCATCCCACACTCTAAGTGAAAGG
* *
152322 GAGCATACCTTCCACCCCCGAGCTAGTCATGTAGAA
65 GAGCATACCTTCCACCCCCGAGCTAGTCAGGTAGAG
* * *
152358 TTTTTTTAGCATACTTTAAGGGGGTCAACTCATCACACTATCATCCCACACTCTAAGTGAAAAGG
1 TTTTTTTAGCATACTTTAAGGGAGTCAGCTCATCACACTATCATCCCACACTCTAAGTGAAAGGG
152423 AGCATACCTTCCACCCCCGAGCTAGTCAGGTAGAG
66 AGCATACCTTCCACCCCCGAGCTAGTCAGGTAGAG
152458 T
1 T
152459 CATCTTGTGA
Statistics
Matches: 189, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
100 76 0.40
101 106 0.56
102 7 0.04
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.27
Consensus pattern (100 bp):
TTTTTTTAGCATACTTTAAGGGAGTCAGCTCATCACACTATCATCCCACACTCTAAGTGAAAGGG
AGCATACCTTCCACCCCCGAGCTAGTCAGGTAGAG
Found at i:152894 original size:25 final size:25
Alignment explanation
Indices: 152863--152915 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
152853 CCATGACAAC
*
152863 AAATATTTCAACCAATTTTTATCAA
1 AAATATTTCAACCAATTATTATCAA
*
152888 AAATATTTCAACCTATTATTATCAA
1 AAATATTTCAACCAATTATTATCAA
152913 AAA
1 AAA
152916 AAAGAACTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (25 bp):
AAATATTTCAACCAATTATTATCAA
Found at i:158493 original size:15 final size:15
Alignment explanation
Indices: 158473--158501 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
158463 GACGAGGAAC
158473 TGCTAGTACCTCCAT
1 TGCTAGTACCTCCAT
158488 TGCTAGTACCTCCA
1 TGCTAGTACCTCCA
158502 CTGCAACACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.34, G:0.14, T:0.31
Consensus pattern (15 bp):
TGCTAGTACCTCCAT
Found at i:166654 original size:21 final size:21
Alignment explanation
Indices: 166629--166689 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
166619 AACTTTGGAA
166629 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
166650 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
166664 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
166685 AAATG
1 AAATG
166690 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:166735 original size:36 final size:36
Alignment explanation
Indices: 166621--166740 Score: 190
Period size: 35 Copynumber: 3.3 Consensus size: 36
166611 TGGCAACCAA
166621 CTTTGGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTT-GAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
166658 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
166693 CTTTGAAAAATGGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATGG-TTTTCAAAGTTTGGTAAATGTTT
*
166730 -GTTGAAAAATG
1 CTTTGAAAAATG
166741 ATAATGGGAT
Statistics
Matches: 79, Mismatches: 2, Indels: 5
0.92 0.02 0.06
Matches are distributed among these distances:
35 35 0.44
36 18 0.23
37 26 0.33
ACGTcount: A:0.30, C:0.05, G:0.22, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:169747 original size:23 final size:23
Alignment explanation
Indices: 169721--169795 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 23
169711 CACCACAGCT
169721 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
** * *
169744 CATATAATTGCGTCGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* * *
169767 CGTAGAATTGCACCGTAGTG-CA
1 CATATAATTGCACCGAAGTGCCA
169789 -ATATAAT
1 CATATAAT
169796 AATTTCCATA
Statistics
Matches: 40, Mismatches: 12, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
21 5 0.12
22 1 0.03
23 34 0.85
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:169979 original size:100 final size:102
Alignment explanation
Indices: 169805--170018 Score: 369
Period size: 100 Copynumber: 2.1 Consensus size: 102
169795 TAATTTCCAT
* *
169805 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
169870 GACTTCACACATGTTCCAAAGAATACATATGT-CCCG
66 GACTTCACACATGTTCCAAAGAATACATATATACCCG
*
169906 AAGGACCACATATCATT-CTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
169970 GACTTCACACATGTTCCAAAGAATACATATATATCCG
66 GACTTCACACATGTTCCAAAGAATACATATATACCCG
170007 AAGGACCACATA
1 AAGGACCACATA
170019 GACCCTCGAC
Statistics
Matches: 107, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
100 75 0.70
101 32 0.30
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (102 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATACCCG
Done.