Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015010.1 Kokia drynarioides strain JFW-HI SEQ_130054, 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: 114800
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 200 characters in sequence are not A, C, G, or T
Found at i:7093 original size:2 final size:2
Alignment explanation
Indices: 7086--7114 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
7076 TTTTCGATTT
7086 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
7115 TAATTTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:14051 original size:62 final size:62
Alignment explanation
Indices: 13954--14077 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
13944 CATGGCAATG
13954 AAAGGATGGGACAAAGCCAAGAAGTGCCCGTATTTGGTGAGGAGATCCACCACCACTAAGAT
1 AAAGGATGGGACAAAGCCAAGAAGTGCCCGTATTTGGTGAGGAGATCCACCACCACTAAGAT
14016 AAAGGATGGGACAAAGCCAAGAAGTGCCCGTATTTGGTGAGGAGATCCACCACCACTAAGAT
1 AAAGGATGGGACAAAGCCAAGAAGTGCCCGTATTTGGTGAGGAGATCCACCACCACTAAGAT
14078 CATATCCTTG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.16
Consensus pattern (62 bp):
AAAGGATGGGACAAAGCCAAGAAGTGCCCGTATTTGGTGAGGAGATCCACCACCACTAAGAT
Found at i:20454 original size:15 final size:15
Alignment explanation
Indices: 20420--20454 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
20410 ATTAAAATAT
*
20420 ATTTTTATTTTTTAA
1 ATTTTTATTTTTAAA
*
20435 TTTTTTATTTTTAAA
1 ATTTTTATTTTTAAA
20450 ATTTT
1 ATTTT
20455 AAAATCTTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
ATTTTTATTTTTAAA
Found at i:24074 original size:24 final size:24
Alignment explanation
Indices: 24030--24075 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
24020 TTTAGTTGTA
*
24030 TAATATATTTAACATTTATTAGCT
1 TAATATATTTAACATTGATTAGCT
* *
24054 TAATATATTTTATATTGATTAG
1 TAATATATTTAACATTGATTAG
24076 AATTAGTGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.52
Consensus pattern (24 bp):
TAATATATTTAACATTGATTAGCT
Found at i:31775 original size:18 final size:18
Alignment explanation
Indices: 31733--31781 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
31723 AAGCAACGAC
*
31733 ATAAATTTTATAA-TAAT
1 ATAAATTTTATAACAAAT
*
31750 -TAATATTTTTTAACAAAT
1 ATAA-ATTTTATAACAAAT
31768 ATAAATTTTATAAC
1 ATAAATTTTATAAC
31782 TATGTAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 3 0.12
17 8 0.31
18 12 0.46
19 3 0.12
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (18 bp):
ATAAATTTTATAACAAAT
Found at i:40930 original size:30 final size:29
Alignment explanation
Indices: 40884--41013 Score: 102
Period size: 30 Copynumber: 4.3 Consensus size: 29
40874 AAAAATTTGA
*
40884 TTTAA-CCTTCGAACTTTTCCATAATTACAT
1 TTTAACCCTT-GAACTTTT-CAAAATTACAT
* *
40914 TTTAGCCCTTGAACTTTTCAAAGACTACAT
1 TTTAACCCTTGAACTTTTCAAA-ATTACAT
* * *
40944 TTTAATCCTTAAACTTTTTCAAAATTTCAT
1 TTTAACCCTTGAAC-TTTTCAAAATTACAT
* * *
40974 TTTAACCCCT-AAGTTTTCTCAAAGTTACAT
1 TTTAACCCTTGAA-CTTT-TCAAAATTACAT
*
41004 TTTGACCCTT
1 TTTAACCCTT
41014 TTTTTAATCT
Statistics
Matches: 80, Mismatches: 15, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
29 8 0.10
30 60 0.75
31 12 0.15
ACGTcount: A:0.29, C:0.22, G:0.05, T:0.43
Consensus pattern (29 bp):
TTTAACCCTTGAACTTTTCAAAATTACAT
Found at i:45149 original size:11 final size:10
Alignment explanation
Indices: 45133--45187 Score: 58
Period size: 10 Copynumber: 5.3 Consensus size: 10
45123 TTCGATGAAG
45133 AAAAATAAATA
1 AAAAATAAA-A
45144 AAAAATAAAA
1 AAAAATAAAA
*
45154 AAAAGAGAAAA
1 AAAA-ATAAAA
*
45165 AAAAAGAAAA
1 AAAAATAAAA
45175 AAAGAA-AAAA
1 AAA-AATAAAA
45185 AAA
1 AAA
45188 GGAAAAAGAA
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
10 21 0.51
11 20 0.49
ACGTcount: A:0.87, C:0.00, G:0.07, T:0.05
Consensus pattern (10 bp):
AAAAATAAAA
Found at i:45156 original size:10 final size:10
Alignment explanation
Indices: 45133--45199 Score: 66
Period size: 11 Copynumber: 6.5 Consensus size: 10
45123 TTCGATGAAG
*
45133 AAAAATAAATA
1 AAAAAGAAA-A
*
45144 AAAAATAAAA
1 AAAAAGAAAA
45154 AAAAGAGAAAA
1 AAAA-AGAAAA
45165 AAAAAG--AA
1 AAAAAGAAAA
45173 AAAAAGAAAA
1 AAAAAGAAAA
45183 AAAAAGGAAAA
1 AAAAA-GAAAA
45194 AGAAAA
1 A-AAAA
45200 AGAGAGATCG
Statistics
Matches: 50, Mismatches: 1, Indels: 9
0.83 0.02 0.15
Matches are distributed among these distances:
8 8 0.16
10 14 0.28
11 24 0.48
12 4 0.08
ACGTcount: A:0.85, C:0.00, G:0.10, T:0.04
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:45164 original size:17 final size:15
Alignment explanation
Indices: 45130--45200 Score: 63
Period size: 17 Copynumber: 4.5 Consensus size: 15
45120 GATTTCGATG
45130 AAGAAAAATAAATAAAA
1 AAGAAAAA-AAA-AAAA
* * *
45147 AATAAAAAAAAGAGA
1 AAGAAAAAAAAAAAA
*
45162 AA-AAAAAAGAAAAA
1 AAGAAAAAAAAAAAA
45176 AAGAAAAAAAAAGGAAA
1 AAGAAAAAAAAA--AAA
45193 AAGAAAAA
1 AAGAAAAA
45201 GAGAGATCGA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
14 11 0.25
15 12 0.27
16 3 0.07
17 18 0.41
ACGTcount: A:0.85, C:0.00, G:0.11, T:0.04
Consensus pattern (15 bp):
AAGAAAAAAAAAAAA
Found at i:45164 original size:18 final size:18
Alignment explanation
Indices: 45130--45200 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 18
45120 GATTTCGATG
45130 AAGAAAAATAA-ATAAAAAA
1 AAGAAAAA-AAGA-AAAAAA
45149 TAA-AAAAAAGAGAAAAAAA
1 -AAGAAAAAA-AGAAAAAAA
45168 AAGAAAAAAAGAAAAAAA
1 AAGAAAAAAAGAAAAAAA
*
45186 AAG-GAAAAAGAAAAA
1 AAGAAAAAAAGAAAAA
45201 GAGAGATCGA
Statistics
Matches: 47, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
17 11 0.23
18 15 0.32
19 18 0.38
20 3 0.06
ACGTcount: A:0.85, C:0.00, G:0.11, T:0.04
Consensus pattern (18 bp):
AAGAAAAAAAGAAAAAAA
Found at i:45166 original size:20 final size:19
Alignment explanation
Indices: 45133--45194 Score: 72
Period size: 20 Copynumber: 3.2 Consensus size: 19
45123 TTCGATGAAG
*
45133 AAAAATAAATAAAAAATA-AA
1 AAAAAGAAA-AAAAAA-AGAA
45153 AAAAAGAGAAAAAAAAAGAA
1 AAAAAGA-AAAAAAAAAGAA
*
45173 AAAAAGAAAAAAAAAGGAA
1 AAAAAGAAAAAAAAAAGAA
45192 AAA
1 AAA
45195 GAAAAAGAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
19 15 0.39
20 21 0.55
21 2 0.05
ACGTcount: A:0.85, C:0.00, G:0.10, T:0.05
Consensus pattern (19 bp):
AAAAAGAAAAAAAAAAGAA
Found at i:45193 original size:8 final size:8
Alignment explanation
Indices: 45163--45200 Score: 51
Period size: 8 Copynumber: 4.6 Consensus size: 8
45153 AAAAAGAGAA
45163 AAAAAAAG
1 AAAAAAAG
45171 AAAAAAAG
1 AAAAAAAG
45179 AAAAAAA-
1 AAAAAAAG
45186 AAGGAAAAAG
1 AA--AAAAAG
45196 AAAAA
1 AAAAA
45201 GAGAGATCGA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
7 2 0.07
8 18 0.67
9 5 0.19
10 2 0.07
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:46162 original size:49 final size:49
Alignment explanation
Indices: 46109--46203 Score: 131
Period size: 49 Copynumber: 1.9 Consensus size: 49
46099 AGACAAATTT
* * *
46109 GGTACCAT-GAAGATATGA-AGGGAAAGGTTGAGGGCGCAACGGCGAACCC
1 GGTACCATAGAA-ACATGACAGGG-AAGATTGAGGCCGCAACGGCGAACCC
46158 GGTACCATAGAAACATGACAGGGAAGATTGAGGCCGCAACGGCGAA
1 GGTACCATAGAAACATGACAGGGAAGATTGAGGCCGCAACGGCGAA
46204 TCTTATACCC
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
49 34 0.83
50 7 0.17
ACGTcount: A:0.35, C:0.19, G:0.35, T:0.12
Consensus pattern (49 bp):
GGTACCATAGAAACATGACAGGGAAGATTGAGGCCGCAACGGCGAACCC
Found at i:46613 original size:43 final size:43
Alignment explanation
Indices: 46399--47404 Score: 759
Period size: 43 Copynumber: 23.1 Consensus size: 43
46389 AAACTGCAGT
* * * *
46399 CATTCCAATCTTTTACCCTTAGTCAAGAGGGGTAGATTGATGAC
1 CATTCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAG-C
* * **
46443 C-TTTCAATATTTTACTGCTAAGTCAAGAGGGGCAGATTGAAGCC
1 CATTCCAATCTTTTACCCCTAA-TCAAGAGGGGCAGATTGAAG-C
* * * *
46487 ACATTCCAATCTTTTACCCCCAAAATCAAGAGAGGTAGATTGAAGT
1 -CATTCCAATCTTTTA-CCCC-TAATCAAGAGGGGCAGATTGAAGC
* * * *
46533 CATCATCCAATCTCTTACCCTTAAATCAAGAGTGGTAGATTGAAGC
1 CAT--TCCAATCTTTTACCCCT-AATCAAGAGGGGCAGATTGAAGC
*** * * *
46579 CATTTTGATCTTTTACACTTAATCAAGAGGGGTAGATTGAAG-
1 CATTCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGC
* *
46621 -ATCCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAAAC
1 CATTCCAATCTTTTACCCCTAA-TCAAGAGGGGCAGATTGAAGC
* * * ** *
46664 CATTCCGACCTTTTACCCCTAATCAAGAGCGAAAGATTAAAG-
1 CATTCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGC
* ** *
46706 -ATTCTAATCTTTTACCTTTAAGTCAAGAGGGACAGATTGAA-C
1 CATTCCAATCTTTTACCCCTAA-TCAAGAGGGGCAGATTGAAGC
*
46748 CATTCCAATCTTTTACCCCTAATCAAGAAGGGCAGATTGAAG-
1 CATTCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGC
** * *
46790 -ATTTAAATCTTTTACCCCTAATCAAGAGGGACAAATTGAAG-
1 CATTCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGC
* * * * *
46831 -ATTACAATCTTTTACCCCT-ATCAAGAGGGACAAATTAAAAAC
1 CATTCCAATCTTTTACCCCTAATCAAGAGGGGCAGATT-GAAGC
* * * *
46873 C-TTCCAATCTTTTACCCCTAAGTCAAGAGGAGTAAATTAAAGCC
1 CATTCCAATCTTTTACCCCTAA-TCAAGAGGGGCAGATTGAAG-C
* * * * * *
46917 ACATTTCAATTTTTTACCCCTAAGTCAAAAGAGACAAATTGAAGC
1 -CATTCCAATCTTTTACCCCTAA-TCAAGAGGGGCAGATTGAAGC
* * * * *
46962 CATCATCAAATCTTTTACCCTTAAGTCAAGAGGAGCAAATTAAAGAC
1 CAT--TCCAATCTTTTACCCCTAA-TCAAGAGGGGCAGATTGAAG-C
*
47009 C-TTCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTAAAGAC
1 CATTCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAG-C
* * *
47052 C-TTCCAATCATTTACCCCTAAGTTAAGAGGGGCAAATTGAAGCC
1 CATTCCAATCTTTTACCCCTAA-TCAAGAGGGGCAGATTGAAG-C
* * * *
47096 ACATTCCAATCTTTTACCCTTAAGTCAAGAGGGGCAAACTAAAGC
1 -CATTCCAATCTTTTACCCCTAA-TCAAGAGGGGCAGATTGAAGC
* * * * *
47141 CGTTTCAATCTTTTACCCCTAATTAAGAGGGACAGATAGAAG-
1 CATTCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGC
** * * * *
47183 -ATTCCAATCTTTTACCTTTAATCGAGAGGGGTAGATTAAAAC
1 CATTCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGC
* * * * *
47225 TATTTCAATTTTTTA-CCCTAATCAAGAGGGGTAGATTGAAGAT
1 CATTCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAG-C
* * * * * *
47268 CTTTCCAATATTTTACCTCTAAGTCAAGAGGAGCAAATTGAAAAC
1 CATTCCAATCTTTTACCCCTAA-TCAAGAGGGGCAGATTG-AAGC
* * * *
47313 CTTTCCAATCTTTTACCCCTAAGTCAAGAGGAGCAAATTGAAAAC
1 CATTCCAATCTTTTACCCCTAA-TCAAGAGGGGCAGATTG-AAGC
* *
47358 CTTTCCAATCTTTTACCCCTAAGTCAAGAGGAGCAGATTGAAGC
1 CATTCCAATCTTTTACCCCTAA-TCAAGAGGGGCAGATTGAAGC
47402 CAT
1 CAT
47405 CTTCCTGGTC
Statistics
Matches: 782, Mismatches: 145, Indels: 70
0.78 0.15 0.07
Matches are distributed among these distances:
40 17 0.02
41 116 0.15
42 89 0.11
43 149 0.19
44 131 0.17
45 104 0.13
46 141 0.18
47 33 0.04
48 2 0.00
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.28
Consensus pattern (43 bp):
CATTCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGC
Found at i:46658 original size:85 final size:85
Alignment explanation
Indices: 46399--47400 Score: 766
Period size: 90 Copynumber: 11.5 Consensus size: 85
46389 AAACTGCAGT
* * * * * * **
46399 CATTCCAATCTTTTACCCTTAGTCAAGAGGGGTAGATTGATGACCTTTCAATATTTTACTGCTAA
1 CATTCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGA--TTCCAATCTTTTACCCCTAA
46464 GTCAAGAGGGGCAGATTGAAGCC
64 GTCAAGAGGGGCAGATTGAAG-C
* * * *
46487 ACATTCCAATCTTTTACCCCCAAAATCAAGAGAGGTAGATTGAAGTCATCATCCAATCTCTTACC
1 -CATTCCAATCTTTTA-CCCC-TAATCAAGAGGGGCAGATTGAAG--AT--TCCAATCTTTTACC
* * * *
46552 CTTAAATCAAGAGTGGTAGATTGAAGC
59 CCTAAGTCAAGAGGGGCAGATTGAAGC
*** * * * *
46579 CATTTTGATCTTTTACACTTAATCAAGAGGGGTAGATTGAAGATCCCAATCTTTTACCCCTAAGT
1 CATTCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGATTCCAATCTTTTACCCCTAAGT
*
46644 CAAGAGGGGCAGATTGAAAC
66 CAAGAGGGGCAGATTGAAGC
* * * ** * * **
46664 CATTCCGACCTTTTACCCCTAATCAAGAGCGAAAGATTAAAGATTCTAATCTTTTACCTTTAAGT
1 CATTCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGATTCCAATCTTTTACCCCTAAGT
*
46729 CAAGAGGGACAGATTGAA-C
66 CAAGAGGGGCAGATTGAAGC
* **
46748 CATTCCAATCTTTTACCCCTAATCAAGAAGGGCAGATTGAAGATTTAAATCTTTTACCCCTAA-T
1 CATTCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGATTCCAATCTTTTACCCCTAAGT
* *
46812 CAAGAGGGACAAATTGAAG-
66 CAAGAGGGGCAGATTGAAGC
* * * * *
46831 -ATTACAATCTTTTACCCCT-ATCAAGAGGGACAAATTAAAAACCTTCCAATCTTTTACCCCTAA
1 CATTCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGA--TTCCAATCTTTTACCCCTAA
* * * *
46894 GTCAAGAGGAGTAAATTAAAGCC
64 GTCAAGAGGGGCAGATTGAAG-C
* * * * * * *
46917 ACATTTCAATTTTTTACCCCTAAGTCAAAAGAGACAAATTGAAGCCATCATCAAATCTTTTACCC
1 -CATTCCAATCTTTTACCCCTAA-TCAAGAGGGGCAGATTGAAG--AT--TCCAATCTTTTACCC
* * * *
46982 TTAAGTCAAGAGGAGCAAATTAAAGAC
60 CTAAGTCAAGAGGGGCAGATTGAAG-C
* *
47009 C-TTCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTAAAGACCTTCCAATCATTTACCCCTAA
1 CATTCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGA--TTCCAATCTTTTACCCCTAA
* *
47073 GTTAAGAGGGGCAAATTGAAGCC
64 GTCAAGAGGGGCAGATTGAAG-C
* * * * * *
47096 ACATTCCAATCTTTTACCCTTAAGTCAAGAGGGGCAAACTAAAGCCGTTTCAATCTTTTACCCCT
1 -CATTCCAATCTTTTACCCCTAA-TCAAGAGGGGCAGATTGAAG--ATTCCAATCTTTTACCCCT
* * *
47161 AA-TTAAGAGGGACAGATAGAAG-
62 AAGTCAAGAGGGGCAGATTGAAGC
** * * * * * *
47183 -ATTCCAATCTTTTACCTTTAATCGAGAGGGGTAGATTAAAACTATTTCAATTTTTTA-CCCTAA
1 CATTCCAATCTTTTACCCCTAATCAAGAGGGGCAGATT-GAA-GATTCCAATCTTTTACCCCTAA
* *
47246 -TCAAGAGGGGTAGATTGAAGAT
64 GTCAAGAGGGGCAGATTGAAG-C
* * * * * *
47268 CTTTCCAATATTTTACCTCTAAGTCAAGAGGAGCAAATTGAAAACCTTTCCAATCTTTTACCCCT
1 CATTCCAATCTTTTACCCCTAA-TCAAGAGGGGCAGATTGAAGA---TTCCAATCTTTTACCCCT
* * *
47333 AAGTCAAGAGGAGCAAATTGAAAAC
62 AAGTCAAGAGGGGCAGATTG-AAGC
* *
47358 CTTTCCAATCTTTTACCCCTAAGTCAAGAGGAGCAGATTGAAG
1 CATTCCAATCTTTTACCCCTAA-TCAAGAGGGGCAGATTGAAG
47401 CCATCTTCCT
Statistics
Matches: 743, Mismatches: 131, Indels: 77
0.78 0.14 0.08
Matches are distributed among these distances:
81 17 0.02
82 18 0.02
83 58 0.08
84 93 0.13
85 127 0.17
86 20 0.03
87 50 0.07
88 29 0.04
89 95 0.13
90 129 0.17
91 35 0.05
92 40 0.05
93 32 0.04
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.28
Consensus pattern (85 bp):
CATTCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGATTCCAATCTTTTACCCCTAAGT
CAAGAGGGGCAGATTGAAGC
Found at i:47116 original size:133 final size:132
Alignment explanation
Indices: 46401--47388 Score: 712
Period size: 133 Copynumber: 7.6 Consensus size: 132
46391 ACTGCAGTCA
* * * * * * * * *
46401 TTCCAATCTTTTACCCTTAGTCAAGAGGGGTAGATTGATG-ACCTTTCAATATTTTACTGC-TAA
1 TTCCAATCTTTTACCCCTAATCAAGAGGGGCAAATTGAAGCACATTCCAATCTTTTAC-CCTTAA
* * * * * * * *
46464 GTCAAGAGGGGCAGATTGAAGCCACATTCCAATCTTTTACCCCCAAAATCAAGAGAGGTAGATTG
65 GTCAAGAGGGGCAAATTAAAG--ACCTTCCAATCTTTTA-CCCCTAAGTCAAGAGGGGCAGATTA
*
46529 AAGTCATC
127 AAG--ACC
* * * * * * *** *
46537 ATCCAATCTCTTACCCTTAAATCAAGAGTGGTAGATTGAAGC-CATTTTGATCTTTTACACTTAA
1 TTCCAATCTTTTACCCCT-AATCAAGAGGGGCAAATTGAAGCACATTCCAATCTTTTACCCTTAA
* * * * *
46601 -TCAAGAGGGGTAGATTGAAGA--TCCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAA-
65 GTCAAGAGGGGCAAATTAAAGACCTTCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTAAAG
46662 ACC
130 ACC
* * * * * * *
46665 ATTCCGACCTTTTACCCCTAATCAAGA-GCGAAAGATT-AA--AGATTCTAATCTTTTACCTTTA
1 -TTCCAATCTTTTACCCCTAATCAAGAGGGGCAA-ATTGAAGCACATTCCAATCTTTTACCCTTA
* * * * *
46726 AGTCAAGAGGGACAGATT-GA-ACCATTCCAATCTTTTACCCCTAA-TCAAGAAGGGCAGATTGA
64 AGTCAAGAGGGGCAAATTAAAGACC-TTCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTAA
46788 AGA--
128 AGACC
** * * *
46791 TTTAAATCTTTTACCCCTAATCAAGAGGGACAAATTGAAG---ATTACAATCTTTTACCCCT-A-
1 TTCCAATCTTTTACCCCTAATCAAGAGGGGCAAATTGAAGCACATTCCAATCTTTTACCCTTAAG
* * * * *
46851 TCAAGAGGGACAAATTAAAAACCTTCCAATCTTTTACCCCTAAGTCAAGAGGAGTAAATTAAAGC
66 TCAAGAGGGGCAAATTAAAGACCTTCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTAAAG-
*
46916 CACA
130 -ACC
* * * * * *
46920 TTTCAATTTTTTACCCCTAAGTCAAAAGAGACAAATTGAAGC-CATCATCAAATCTTTTACCCTT
1 TTCCAATCTTTTACCCCTAA-TCAAGAGGGGCAAATTGAAGCACAT--TCCAATCTTTTACCCTT
*
46984 AAGTCAAGAGGAGCAAATTAAAGACCTTCCAATCTTTTACCCCTAA-TCAAGAGGGGCAGATTAA
63 AAGTCAAGAGGGGCAAATTAAAGACCTTCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTAA
47048 AGACC
128 AGACC
* *
47053 TTCCAATCATTTACCCCTAAGTTAAGAGGGGCAAATTGAAGCCACATTCCAATCTTTTACCCTTA
1 TTCCAATCTTTTACCCCTAA-TCAAGAGGGGCAAATTGAAG-CACATTCCAATCTTTTACCCTTA
* * * *
47118 AGTCAAGAGGGGCAAACTAAAG-CCGTTTCAATCTTTTACCCCTAA-TTAAGAGGGACAGA-TAG
64 AGTCAAGAGGGGCAAATTAAAGACC-TTCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTA-
47180 AAGA--
127 AAGACC
** * * * * * *
47184 TTCCAATCTTTTACCTTTAATCGAGAGGGGTAGATT-AA-AACTATTTCAATTTTTTACCC-TAA
1 TTCCAATCTTTTACCCCTAATCAAGAGGGGCAAATTGAAGCAC-ATTCCAATCTTTTACCCTTAA
* * * * * * * *
47246 -TCAAGAGGGGTAGATTGAAGATCTTTCCAATATTTTACCTCTAAGTCAAGAGGAGCAAATTGAA
65 GTCAAGAGGGGCAAATTAAAGA-CCTTCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATT-AA
47310 A-ACC
128 AGACC
* * * *
47314 TTTCCAATCTTTTACCCCTAAGTCAAGAGGAGCAAATTGAA-AACCTTTCCAATCTTTTACCCCT
1 -TTCCAATCTTTTACCCCTAA-TCAAGAGGGGCAAATTGAAGCA-CATTCCAATCTTTTACCCTT
47378 AAGTCAAGAGG
63 AAGTCAAGAGG
47389 AGCAGATTGA
Statistics
Matches: 694, Mismatches: 112, Indels: 93
0.77 0.12 0.10
Matches are distributed among these distances:
123 15 0.02
124 22 0.03
125 59 0.09
126 39 0.06
127 59 0.09
128 60 0.09
129 36 0.05
130 31 0.04
131 58 0.08
132 30 0.04
133 126 0.18
134 20 0.03
135 29 0.04
136 76 0.11
137 34 0.05
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (132 bp):
TTCCAATCTTTTACCCCTAATCAAGAGGGGCAAATTGAAGCACATTCCAATCTTTTACCCTTAAG
TCAAGAGGGGCAAATTAAAGACCTTCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTAAAGA
CC
Found at i:47727 original size:85 final size:85
Alignment explanation
Indices: 47575--47742 Score: 201
Period size: 85 Copynumber: 2.0 Consensus size: 85
47565 TCAAACCCCA
* * * * * * *
47575 TCTTCCTGATGAGATACAAAAAAGTGGGTCAAAGCAATAAAATGGTCATCTTCCTAATGAGATAC
1 TCTTCCTAATGAGATACAAAAAAGTGGATCAAAACAACAAAACGGTCATCTTCCTAATAAGAAAC
**
47640 AGAGAAGTGGACCAAATCCG
66 AGAGAAGAAGACCAAATCCG
* * * * * *
47660 TCTTCCTAATGAGATACAAAGAAGTGGATCAAAATAACGAAGCGGTCATCTTCTTGATAAGAAAC
1 TCTTCCTAATGAGATACAAAAAAGTGGATCAAAACAACAAAACGGTCATCTTCCTAATAAGAAAC
47725 AGAGAAGAAGACCAAATC
66 AGAGAAGAAGACCAAATC
47743 AATTAAGCGA
Statistics
Matches: 68, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
85 68 1.00
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.21
Consensus pattern (85 bp):
TCTTCCTAATGAGATACAAAAAAGTGGATCAAAACAACAAAACGGTCATCTTCCTAATAAGAAAC
AGAGAAGAAGACCAAATCCG
Found at i:49945 original size:30 final size:29
Alignment explanation
Indices: 49884--50023 Score: 92
Period size: 30 Copynumber: 4.7 Consensus size: 29
49874 ATCCTTAAAC
*
49884 TTTCCAAAAA-TCATATTTAAACGCTCAAAC-
1 TTTCCAAAAATTCAT-TTT-AAC-CTCGAACT
49914 TTTCCAAAAATTCGATTTTAACCTTCGAACT
1 TTTCCAAAAATTC-ATTTTAACC-TCGAACT
* *
49945 TTTCC-AAAATTACATTTTAGCCCCCGAACT
1 TTTCCAAAAATT-CATTTTA-ACCTCGAACT
* * * *
49975 TTTCC-AAAATTACATATCAATCTCTAAACT
1 TTTCCAAAAATT-CATTTTAACCTC-GAACT
50005 TTTCC-AAAATTACATTTTA
1 TTTCCAAAAATT-CATTTTA
50024 GCCCCTAAAC
Statistics
Matches: 92, Mismatches: 11, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
29 3 0.03
30 74 0.80
31 13 0.14
32 2 0.02
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.36
Consensus pattern (29 bp):
TTTCCAAAAATTCATTTTAACCTCGAACT
Found at i:49949 original size:31 final size:31
Alignment explanation
Indices: 49914--50110 Score: 133
Period size: 30 Copynumber: 6.6 Consensus size: 31
49904 ACGCTCAAAC
**
49914 TTTCCAAAAATT-CGATTTTAACCTTCGAACT
1 TTTCCAAAAATTAC-ATTTTAACCCCCGAACT
*
49945 TTTCC-AAAATTACATTTTAGCCCCCGAACT
1 TTTCCAAAAATTACATTTTAACCCCCGAACT
* * * * **
49975 TTTCC-AAAATTACATATCAATCTCTAAACT
1 TTTCCAAAAATTACATTTTAACCCCCGAACT
* **
50005 TTTCC-AAAATTACATTTTAGCCCCTAAAC-
1 TTTCCAAAAATTACATTTTAACCCCCGAACT
* *
50034 TTTCTC-AAAGTTACATTTTAACCCCC-AAAT
1 TTTC-CAAAAATTACATTTTAACCCCCGAACT
** * * *
50064 ACTCCTAAAATTACATTGTAACCCCCAAAC-
1 TTTCCAAAAATTACATTTTAACCCCCGAACT
*
50094 -TTCCCAAAATTACATTT
1 TTTCCAAAAATTACATTT
50111 CAGCCTTTAA
Statistics
Matches: 134, Mismatches: 27, Indels: 12
0.77 0.16 0.07
Matches are distributed among these distances:
29 21 0.16
30 105 0.78
31 8 0.06
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.35
Consensus pattern (31 bp):
TTTCCAAAAATTACATTTTAACCCCCGAACT
Found at i:50032 original size:30 final size:30
Alignment explanation
Indices: 49941--50170 Score: 182
Period size: 30 Copynumber: 7.7 Consensus size: 30
49931 TTAACCTTCG
**
49941 AACTTTTCCAAAATTACATTTTAGCCCCCG
1 AACTTTTCCAAAATTACATTTTAGCCCCTA
* * ** *
49971 AACTTTTCCAAAATTACATATCAATCTCTA
1 AACTTTTCCAAAATTACATTTTAGCCCCTA
50001 AACTTTTCCAAAATTACATTTTAGCCCCTA
1 AACTTTTCCAAAATTACATTTTAGCCCCTA
* * *
50031 AAC-TTTCTCAAAGTTACATTTTAACCCCCA
1 AACTTTTC-CAAAATTACATTTTAGCCCCTA
** * * *
50061 AA-TACTCCTAAAATTACATTGTAACCCCCA
1 AACTTTTCC-AAAATTACATTTTAGCCCCTA
* * **
50091 AAC-TTCCCAAAATTACATTTCAGCCTTTA
1 AACTTTTCCAAAATTACATTTTAGCCCCTA
*
50120 AAC-TTTCCTAAAATTACATTAT-GACCCCTA
1 AACTTTTCC-AAAATTACATTTTAG-CCCCTA
* * *
50150 AAGTTTTCCAAAGTTGCATTT
1 AACTTTTCCAAAATTACATTT
50171 GATCCTCGAA
Statistics
Matches: 156, Mismatches: 37, Indels: 14
0.75 0.18 0.07
Matches are distributed among these distances:
29 28 0.18
30 123 0.79
31 5 0.03
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (30 bp):
AACTTTTCCAAAATTACATTTTAGCCCCTA
Found at i:50147 original size:59 final size:59
Alignment explanation
Indices: 49909--50139 Score: 209
Period size: 60 Copynumber: 3.9 Consensus size: 59
49899 TTTAAACGCT
* * *
49909 CAAACTTTCCAAAAATT-CGATTTTAACCT-TCGAACTTTTCCAAAATTACATTTTAGCCCC
1 CAAACTTTCCCAAAATTAC-ATTTCAACCTCT-AAAC-TTTCCAAAATTACATTTTAGCCCC
* * * *
49969 CGAACTTTTCCAAAATTACATATCAATCTCTAAACTTTTCCAAAATTACATTTTAGCCCC
1 CAAACTTTCCCAAAATTACATTTCAACCTCTAAAC-TTTCCAAAATTACATTTTAGCCCC
* * * * * * * * *
50029 TAAACTTTCTCAAAGTTACATTTTAACCCCCAAA-TACTCCTAAAATTACATTGTAACCCC
1 CAAACTTTCCCAAAATTACATTTCAACCTCTAAACT-TTCC-AAAATTACATTTTAGCCCC
* *
50089 CAAAC-TTCCCAAAATTACATTTCAGCCTTTAAACTTTCCTAAAATTACATT
1 CAAACTTTCCCAAAATTACATTTCAACCTCTAAACTTTCC-AAAATTACATT
50140 ATGACCCCTA
Statistics
Matches: 137, Mismatches: 29, Indels: 11
0.77 0.16 0.06
Matches are distributed among these distances:
58 1 0.01
59 39 0.28
60 95 0.69
61 2 0.01
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.34
Consensus pattern (59 bp):
CAAACTTTCCCAAAATTACATTTCAACCTCTAAACTTTCCAAAATTACATTTTAGCCCC
Found at i:50150 original size:119 final size:120
Alignment explanation
Indices: 49950--50170 Score: 288
Period size: 119 Copynumber: 1.9 Consensus size: 120
49940 GAACTTTTCC
* * * * *
49950 AAAATTACATTTTAGCCCCCGAACTTTTCCAAAATTACATATCAATCTCTAAACTTTTCCAAAAT
1 AAAATTACATTGTAACCCCCAAACTTTCCCAAAATTACATATCAACCTCTAAACTTTTCCAAAAT
*
50015 TACATTTTAGCCCCTAAAC-TTTCTCAAAGTTACATTTTAACCCCCAAATACTCCT
66 TACATTTGAGCCCCTAAACTTTTC-CAAAGTTACATTTTAACCCCCAAATACTCCT
* * *
50070 AAAATTACATTGTAACCCCCAAAC-TTCCCAAAATTACATTTCAGCCTTTAAAC-TTTCCTAAAA
1 AAAATTACATTGTAACCCCCAAACTTTCCCAAAATTACATATCAACCTCTAAACTTTTCC-AAAA
* *
50133 TTACATTATGA-CCCCTAAAGTTTTCCAAAGTTGCATTT
65 TTACATT-TGAGCCCCTAAACTTTTCCAAAGTTACATTT
50171 GATCCTCGAA
Statistics
Matches: 87, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
118 5 0.06
119 55 0.63
120 27 0.31
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.34
Consensus pattern (120 bp):
AAAATTACATTGTAACCCCCAAACTTTCCCAAAATTACATATCAACCTCTAAACTTTTCCAAAAT
TACATTTGAGCCCCTAAACTTTTCCAAAGTTACATTTTAACCCCCAAATACTCCT
Found at i:52719 original size:19 final size:19
Alignment explanation
Indices: 52695--52732 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
52685 ATGATTAAAT
52695 TTGGTTGGGAATTCATTAA
1 TTGGTTGGGAATTCATTAA
52714 TTGGTTGGGAATTCATTAA
1 TTGGTTGGGAATTCATTAA
52733 CATCCATGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.05, G:0.26, T:0.42
Consensus pattern (19 bp):
TTGGTTGGGAATTCATTAA
Found at i:55023 original size:18 final size:18
Alignment explanation
Indices: 54991--55025 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
54981 AATTGATGTC
*
54991 GTTGTGGTTGCGGTTGTG
1 GTTGTGGTTGAGGTTGTG
*
55009 GTTGTGGTTTAGGTTGT
1 GTTGTGGTTGAGGTTGT
55026 TGAATCGACT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.03, C:0.03, G:0.46, T:0.49
Consensus pattern (18 bp):
GTTGTGGTTGAGGTTGTG
Found at i:56257 original size:18 final size:18
Alignment explanation
Indices: 56234--56270 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
56224 TCTTAAATTG
*
56234 TTTTATTTATAATATTAT
1 TTTTATTTATAAAATTAT
56252 TTTTATTTATAAAATTAT
1 TTTTATTTATAAAATTAT
56270 T
1 T
56271 GTTTTAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTATTTATAAAATTAT
Found at i:56601 original size:33 final size:31
Alignment explanation
Indices: 56563--56626 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
56553 GTTATAGATT
**
56563 TAACGAATGAGTGAAAAAAATATTAAATTTTAA
1 TAACG-AT-AGTGAAAAAAATAGAAAATTTTAA
**
56596 TAACGATAGTGACTAAAATAGAAAATTTTAA
1 TAACGATAGTGAAAAAAATAGAAAATTTTAA
56627 ACTTGAGTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 20 0.74
32 2 0.07
33 5 0.19
ACGTcount: A:0.53, C:0.05, G:0.12, T:0.30
Consensus pattern (31 bp):
TAACGATAGTGAAAAAAATAGAAAATTTTAA
Found at i:56764 original size:4 final size:4
Alignment explanation
Indices: 56755--56779 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
56745 TACATTTAAG
56755 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
56780 TGGTGACAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:58176 original size:59 final size:59
Alignment explanation
Indices: 58019--58210 Score: 206
Period size: 61 Copynumber: 3.2 Consensus size: 59
58009 TAATAAATTT
** ** * *
58019 AAGTACCAAATTGAATCTAAAAAAAAACTAAGGTACCAAATTTGGAAAGAATGTCAAGTTC
1 AAGTACCAAATTGGGTC-AAAAAAAAGTTAAGGTACCAAATTAGGAAA-AGTGTCAAGTTC
** * *
58080 GGGTACCAAATTGGGTCCAAAAAAAAGTTTAGATACCAAATTAGGAAAATGTGTCAAGTTC
1 AAGTACCAAATTGGGT-CAAAAAAAAGTTAAGGTACCAAATTAGGAAAA-GTGTCAAGTTC
* * *
58141 AAGTACCAAATTGGGTC-AAAAAAAGTTAAGGTACCAAATTAAGAAAAAGTATCAAGCTC
1 AAGTACCAAATTGGGTCAAAAAAAAGTTAAGGTACCAAATT-AGGAAAAGTGTCAAGTTC
*
58200 AAGTATCAAAT
1 AAGTACCAAAT
58211 GTTATATTAA
Statistics
Matches: 110, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
59 40 0.36
60 8 0.07
61 61 0.55
62 1 0.01
ACGTcount: A:0.47, C:0.13, G:0.17, T:0.23
Consensus pattern (59 bp):
AAGTACCAAATTGGGTCAAAAAAAAGTTAAGGTACCAAATTAGGAAAAGTGTCAAGTTC
Found at i:68280 original size:12 final size:11
Alignment explanation
Indices: 68256--68331 Score: 66
Period size: 12 Copynumber: 6.7 Consensus size: 11
68246 TTGTAATATA
*
68256 CATTTTATT-T
1 CATTTCATTCT
*
68266 CATTTCTATTTT
1 CATTTC-ATTCT
68278 CATTTCCATTCT
1 CATTT-CATTCT
*
68290 CATATCATTCT
1 CATTTCATTCT
68301 CATTTTCATTCT
1 CA-TTTCATTCT
*
68313 CACTTCAATT-T
1 CATTTC-ATTCT
68324 CATTTCAT
1 CATTTCAT
68332 ATTCAAATAA
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
10 7 0.13
11 20 0.36
12 27 0.49
13 1 0.02
ACGTcount: A:0.21, C:0.24, G:0.00, T:0.55
Consensus pattern (11 bp):
CATTTCATTCT
Found at i:68326 original size:23 final size:22
Alignment explanation
Indices: 68275--68329 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 22
68265 TCATTTCTAT
68275 TTTCATTTCCATTCTCATATCA
1 TTTCATTTCCATTCTCATATCA
*
68297 TTCTCATTTTCATTCTCACT-TCAA
1 TT-TCATTTCCATTCTCA-TATC-A
68321 TTTCATTTC
1 TTTCATTTC
68330 ATATTCAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 2 0.07
23 22 0.79
24 4 0.14
ACGTcount: A:0.20, C:0.27, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTCATTTCCATTCTCATATCA
Found at i:68336 original size:6 final size:5
Alignment explanation
Indices: 68256--68336 Score: 54
Period size: 5 Copynumber: 14.4 Consensus size: 5
68246 TTGTAATATA
* *
68256 CATTT TATTT CATTT CTATTTT CATTT CCATTCT CATAT CATTCT CATTTT
1 CATTT CATTT CATTT C-A-TTT CATTT -CATT-T CATTT CATT-T CA-TTT
*
68307 CATTCT CACTT CAATTT CATTT CATATT CA
1 CATT-T CATTT C-ATTT CATTT CAT-TT CA
68337 AATAATAAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 17
0.73 0.07 0.20
Matches are distributed among these distances:
5 27 0.44
6 27 0.44
7 7 0.11
ACGTcount: A:0.22, C:0.23, G:0.00, T:0.54
Consensus pattern (5 bp):
CATTT
Found at i:69132 original size:22 final size:21
Alignment explanation
Indices: 69107--69163 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 21
69097 TAATATATTT
*
69107 TATATTAATTCATAAAATAAAA
1 TATATTAATTAATAAAAT-AAA
* *
69129 TATATTATTTAATAATATAAA
1 TATATTAATTAATAAAATAAA
**
69150 TATAAAAATTAATA
1 TATATTAATTAATA
69164 TTTAATATGA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
21 14 0.48
22 15 0.52
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
TATATTAATTAATAAAATAAA
Found at i:69144 original size:29 final size:28
Alignment explanation
Indices: 69118--69170 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
69108 ATATTAATTC
69118 ATAAA-ATAAAATATATTATTTAATAAT
1 ATAAATATAAAATATATTATTTAATAAT
*
69145 ATAAATATAAAA-ATTAATATTTAATA
1 ATAAATATAAAATA-TATTATTTAATA
69171 TGAATAGATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 6 0.26
28 17 0.74
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (28 bp):
ATAAATATAAAATATATTATTTAATAAT
Found at i:81101 original size:14 final size:14
Alignment explanation
Indices: 81082--81109 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
81072 TGTTAATAGG
81082 GGGTTATTTTAGTT
1 GGGTTATTTTAGTT
81096 GGGTTATTTTAGTT
1 GGGTTATTTTAGTT
81110 TCCTTATTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.00, G:0.29, T:0.57
Consensus pattern (14 bp):
GGGTTATTTTAGTT
Found at i:81190 original size:44 final size:44
Alignment explanation
Indices: 81127--81214 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
81117 TAGAAACTCT
*
81127 ATTCAATATATGACAAGCTATTAGAACAACTTCTCCCCAAAAAC
1 ATTCAATATATGACAAGCTACTAGAACAACTTCTCCCCAAAAAC
81171 ATTCAATATATGACAAGCTACTAGAACAACTTCTCCCCAAAAAC
1 ATTCAATATATGACAAGCTACTAGAACAACTTCTCCCCAAAAAC
81215 CTTGTCCAAG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.43, C:0.26, G:0.07, T:0.24
Consensus pattern (44 bp):
ATTCAATATATGACAAGCTACTAGAACAACTTCTCCCCAAAAAC
Found at i:88525 original size:29 final size:31
Alignment explanation
Indices: 88465--88534 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
88455 AAAATTAAAG
* *
88465 TTTCATATATATATTTAAACCACAATCAAAA
1 TTTCATGTATATAATTAAACCACAATCAAAA
* *
88496 TTTTATGTATATAATTACACCA-AATC-AAA
1 TTTCATGTATATAATTAAACCACAATCAAAA
88525 TTTCATGTAT
1 TTTCATGTAT
88535 CAAACTACGT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 12 0.35
30 4 0.12
31 18 0.53
ACGTcount: A:0.43, C:0.14, G:0.03, T:0.40
Consensus pattern (31 bp):
TTTCATGTATATAATTAAACCACAATCAAAA
Found at i:88828 original size:18 final size:18
Alignment explanation
Indices: 88805--88847 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
88795 AAATAGGTTT
88805 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
* *
88823 TTAATTGAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
88841 TTAATTA
1 TTAATTA
88848 CACCTTAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:89746 original size:29 final size:28
Alignment explanation
Indices: 89670--89746 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 28
89660 ATTGGATTTG
89670 AATTTTAAAATTTGAAAAGTAAAAAAACTA
1 AATTTT-AAATTT-AAAAGTAAAAAAACTA
** * *
89700 AATTTCTAAAAATAAAAGTATAATAACTA
1 AATTT-TAAATTTAAAAGTAAAAAAACTA
89729 AATTTTAAATTTACAAAG
1 AATTTTAAATTTA-AAAG
89747 AGTACAGTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
28 6 0.15
29 23 0.59
30 9 0.23
31 1 0.03
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.32
Consensus pattern (28 bp):
AATTTTAAATTTAAAAGTAAAAAAACTA
Found at i:90336 original size:6 final size:6
Alignment explanation
Indices: 90325--90402 Score: 65
Period size: 6 Copynumber: 13.5 Consensus size: 6
90315 ATTTGTTTAA
* * * *
90325 AAATTT AAATTT -ATTTT AAATTT AAATTT -ATTTT TAATTT ATATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
* *
90371 -AATTT AAGTTT AAATTT -ATTTT CAAATTT AAA
1 AAATTT AAATTT AAATTT AAATTT -AAATTT AAA
90403 ATTTCTAAAT
Statistics
Matches: 56, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
5 16 0.29
6 36 0.64
7 4 0.07
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (6 bp):
AAATTT
Found at i:90347 original size:17 final size:17
Alignment explanation
Indices: 90310--90402 Score: 114
Period size: 17 Copynumber: 5.4 Consensus size: 17
90300 AATTCATTTT
* *
90310 TTTAAATTTGTTTAAAAA
1 TTTAAATTTATTT-TAAA
90328 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
90345 TTTAAATTTATTTTTAA
1 TTTAAATTTATTTTAAA
* * *
90362 TTTATATTTAATTTAAG
1 TTTAAATTTATTTTAAA
90379 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTT-AAA
90397 TTTAAA
1 TTTAAA
90403 ATTTCTAAAT
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
17 44 0.69
18 20 0.31
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:90360 original size:12 final size:12
Alignment explanation
Indices: 90345--90400 Score: 62
Period size: 11 Copynumber: 4.8 Consensus size: 12
90335 TTATTTTAAA
90345 TTTAAATTTATT
1 TTTAAATTTATT
*
90357 TTT-AATTTATA
1 TTTAAATTTATT
**
90368 TTT-AATTTAAG
1 TTTAAATTTATT
90379 TTTAAATTTATT
1 TTTAAATTTATT
*
90391 TTCAAATTTA
1 TTTAAATTTA
90401 AAATTTCTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
11 19 0.51
12 18 0.49
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (12 bp):
TTTAAATTTATT
Found at i:92890 original size:21 final size:21
Alignment explanation
Indices: 92866--92916 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
92856 AACCAACCAA
*
92866 AGAAAACCAGCAACCTCTCTT
1 AGAAAACCAGCAACCACTCTT
* **
92887 AGAAAACTAGCAGTCACTCTT
1 AGAAAACCAGCAACCACTCTT
*
92908 GGAAAACCA
1 AGAAAACCA
92917 ACTGCCAAGA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.41, C:0.27, G:0.14, T:0.18
Consensus pattern (21 bp):
AGAAAACCAGCAACCACTCTT
Found at i:103970 original size:63 final size:63
Alignment explanation
Indices: 103871--103998 Score: 247
Period size: 63 Copynumber: 2.0 Consensus size: 63
103861 TACCTGCCCT
*
103871 TCACCATCATCAAATGTCACCGCCTGACCAGAACCCACCAAATTAATACTCTTTGCACCCTTA
1 TCACCATCATCAAATGTCACCGCCTGACCAGAACCCACCAAATTAATACTCTTTACACCCTTA
103934 TCACCATCATCAAATGTCACCGCCTGACCAGAACCCACCAAATTAATACTCTTTACACCCTTA
1 TCACCATCATCAAATGTCACCGCCTGACCAGAACCCACCAAATTAATACTCTTTACACCCTTA
103997 TC
1 TC
103999 CTTTTATCGG
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.32, C:0.37, G:0.07, T:0.24
Consensus pattern (63 bp):
TCACCATCATCAAATGTCACCGCCTGACCAGAACCCACCAAATTAATACTCTTTACACCCTTA
Found at i:104401 original size:10 final size:9
Alignment explanation
Indices: 104374--104398 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
104364 TATAGATACC
104374 TTAAAAATA
1 TTAAAAATA
104383 TTAAAAATA
1 TTAAAAATA
104392 TTAAAAA
1 TTAAAAA
104399 ATAAAAGGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
TTAAAAATA
Found at i:104952 original size:20 final size:19
Alignment explanation
Indices: 104907--104962 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 19
104897 TTTTTTTATT
*
104907 ATTTATTTTTAAAATTT-TAA
1 ATTTA-TTTT-AAATTTAAAA
*
104927 ATTTATTTTTAATTTAAAA
1 ATTTATTTTAAATTTAAAA
104946 ATGTTATTTTAAATTTA
1 AT-TTATTTTAAATTTA
104963 TTTCTAATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
18 5 0.16
19 8 0.26
20 18 0.58
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (19 bp):
ATTTATTTTAAATTTAAAA
Found at i:104955 original size:31 final size:31
Alignment explanation
Indices: 104920--104986 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
104910 TATTTTTAAA
* *
104920 ATTTTAAATTTATTTTTAATTTAAAAATGTT
1 ATTTTAAATTTATTTCTAATTTAAAAATATT
104951 ATTTTAAATTTATTTCTAATTTAAAAATATT
1 ATTTTAAATTTATTTCTAATTTAAAAATATT
104982 ATTTT
1 ATTTT
104987 GGAAAAGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (31 bp):
ATTTTAAATTTATTTCTAATTTAAAAATATT
Found at i:105418 original size:29 final size:30
Alignment explanation
Indices: 105385--105443 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
105375 CTGTATATTT
* * *
105385 TAAATTATTTTCGTATTTAA-TTAAAAAAA
1 TAAATTATTTACATAATTAATTTAAAAAAA
105414 TAAATTATTTACATAATTAATTTAAAAAAA
1 TAAATTATTTACATAATTAATTTAAAAAAA
105444 GTTACTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (30 bp):
TAAATTATTTACATAATTAATTTAAAAAAA
Found at i:108456 original size:17 final size:19
Alignment explanation
Indices: 108428--108477 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
108418 AAGTCAGCGG
* *
108428 TCAATGGTCAAC-ATTCGA
1 TCAATAGTCAACGAGTCGA
*
108446 TCAA-AGTCAACGGGTCGA
1 TCAATAGTCAACGAGTCGA
108464 TCAATAGTCAACGA
1 TCAATAGTCAACGA
108478 TCAATCAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 6 0.23
18 12 0.46
19 8 0.31
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (19 bp):
TCAATAGTCAACGAGTCGA
Found at i:108484 original size:18 final size:18
Alignment explanation
Indices: 108445--108486 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
108435 TCAACATTCG
* *
108445 ATCAAAGTCAACGGGTCG
1 ATCAAAGTCAACGGATCA
108463 ATCAATAGTCAAC-GATCA
1 ATCAA-AGTCAACGGATCA
108481 ATCAAA
1 ATCAAA
108487 TTTAACGGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 1 0.05
18 13 0.62
19 7 0.33
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.19
Consensus pattern (18 bp):
ATCAAAGTCAACGGATCA
Found at i:108485 original size:36 final size:36
Alignment explanation
Indices: 108428--108496 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
108418 AAGTCAGCGG
* *
108428 TCAATGGTCAACATTCGATCAAAGTCAACGGGTCGA
1 TCAATAGTCAACATTCAATCAAAGTCAACGGGTCGA
* *
108464 TCAATAGTCAACGA-TCAATCAAATTTAACGGGT
1 TCAATAGTCAAC-ATTCAATCAAAGTCAACGGGT
108497 TGGTTCGGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
36 27 0.96
37 1 0.04
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (36 bp):
TCAATAGTCAACATTCAATCAAAGTCAACGGGTCGA
Found at i:109352 original size:30 final size:30
Alignment explanation
Indices: 109296--109361 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
109286 TTTTTCTATG
* *
109296 AATTAAACCCTAAACTTTACCAAAATTTCCA
1 AATTAAACCCTAAACTCTA-CAAAATTACCA
109327 AATTAAACCCTTAAACTCT-CAAAATTACCA
1 AATTAAACCC-TAAACTCTACAAAATTACCA
109357 AATTA
1 AATTA
109362 GTACCTAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
30 15 0.47
31 10 0.31
32 7 0.22
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (30 bp):
AATTAAACCCTAAACTCTACAAAATTACCA
Found at i:109796 original size:14 final size:15
Alignment explanation
Indices: 109777--109806 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
109767 CGGGAAGAAG
109777 AAGAAG-GAAGAAAA
1 AAGAAGAGAAGAAAA
109791 AAGAAGAGAAGAAAA
1 AAGAAGAGAAGAAAA
109806 A
1 A
109807 GAAAGAAACG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (15 bp):
AAGAAGAGAAGAAAA
Found at i:112566 original size:19 final size:22
Alignment explanation
Indices: 112532--112584 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 22
112522 CGCAATAATG
*
112532 TATTTTTAAATTTA-TTAT-TA
1 TATTTTTAAATATATTTATGTA
112552 TATTTTTAAA-ATATTTATGTA
1 TATTTTTAAATATATTTATGTA
*
112573 T-TTTTTATATAT
1 TATTTTTAAATAT
112585 TTCTTTGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 2 0.07
20 21 0.75
21 5 0.18
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
TATTTTTAAATATATTTATGTA
Done.